Release notes

Release 0.22.1

24 April 2024

Bugfix release, which still wraps htslib/samtools/bcftools 1.18.

Bugs fixed:

  • Preserve all header field tags defined in the SAM specification (notably TP) in AlignmentHeader.from_dict() and AlignmentHeader.to_dict() (#1237, PR #1238, thanks to Tim Fennell and Nils Homer)

  • Adjust HTSlib’s Makefile so that make distclean no longer tries to rebuild the htscodecs configury (PR #1247, reported by Nicola Soranzo)

  • Reinstate S3 support in pre-built Linux wheels: support for this protocol was inadvertently omitted from the pre-built 0.22.0 wheels on Linux (#1249, #1277, etc varying circumstances; likely it is this that was reported by Mathew Baines, Benjamin Sargsyan, et al)

  • Add missing AlignedSegment.is_mapped etc properties to type stubs (PR #1273, thanks to Matt Stone)

  • Fix off-by-one NamedTupleProxy, asBed, etc array bounds check (#1279, reported by Dan Bolser)

  • Make pysam’s klib headers compatible with C++ (reported by Martin Grigorov)

Release 0.22.0

5 October 2023

This pysam release wraps htslib/samtools/bcftools 1.18 (PR #1208).

It has been tested with Python versions 3.6 through 3.12, and wheels are available via PyPI for all of those Python versions. Python versions 3.6 and 3.7 are end-of-life; particularly if you use pysam with either of these versions, please vote in the version survey at issue #1230.

The final pysam release that supported Python 2.7 was v0.20.0.

Bugs fixed:

  • Remove Cython from runtime dependencies (PR #1186, thanks to Nicola Soranzo, also reported by Arya Massarat in PR #1194)

  • Miscellaneous dependency improvements (PR #1216, #1217, PR #1218, PR #1219, thanks to Martin Larralde and Arthur Vigil)

  • Suppress spurious “Could not retrieve index file” message when opening an AlignmentFile (#939, #1214, reported by ChengYong Tham and Sebastian Röner)

  • Propagate SAM parsing errors encounted in AlignedSegment.fromstring() (#1196, reported by DV Klopfenstein)

  • Accept invalid MD:A tagged fields produced by HTSeq instead of crashing in AlignedSegment.get_aligned_pairs(with_seq=True) (#1226, reported by Isaac Vock)

  • Fix multiarch macOS CI builds by removing brewed liblzma (#1205, reported by Till Hartmann)

  • Fix VariantRecordSample.alleles type hint (#1179, reported by David Seifert)

New functionality:

  • Add optional HTSFile.seek(..., whence) parameter and clarify which functions use libc.SEEK_SET vs io.SEEK_SET (#1185, requested by luyulin)

  • File handling improvements in samtools & bcftools commands (should improve #1193 and #1195, reported by Rob Bierman and Sam Chorlton)

  • Improve FastxFile performance (PR #1227, thanks to Fabian Klötzl and Valentyn Bezshapkin)

  • Improve the accuracy of type hints for AlignmentFile iteration (#1184, PR #1189, reported by @PikalaxALT)

Documentation improvements:

A message from pysam’s founder, Andreas Heger:

As many of you will have noticed, John Marshall has been effectively maintaining pysam and supporting users over the last few years. I, Andreas, am very grateful for the countless hours he has contributed. Unfortunately, I will not be able to contribute much in the near and intermediate future. To keep pysam going, John has kindly agreed to continue maintaining and supporting pysam as the principal developer of pysam. I am very happy to know that pysam is in good hands and want to thank again John and the wider pysam community for their suggestions, bug reports, code contributions and general support.

Thank you Andreas for all your work over the years and the solid foundations that pysam enjoys and the useful functionality it provides.

Release 0.21.0

2 April 2023

This release wraps htslib/samtools/bcftools version 1.17.

Pysam is now compatible with Python 3.11. We have removed Python 2.x support. Pysam is tested with Python versions 3.6 to 3.11.

  • [#1175] VariantHeader.new_record: set start/stop before alleles

  • [#1173] Add multiple build improvements in htscodecs on multi-arch macOS

  • [#1148] Ignore CIGAR-less reads in find_introns.

  • [#1172] Add new samtools cram-size and samtools reset commands

  • [#1169] Fix CRAM index-related crash when using the musl C standard library.

  • [#1168] Add a minimal pyproject.toml for PEP517.

  • [#1158] Fix type hints and add FastqProxy type hints.

  • [#1147] Py3.11 compatibility, get shared object suffix from EXT_SUFFIX.

  • [#1143] Add mypy symbols for samtools and bcftools.

  • [#1155] Fix pysam.index() when using recent samtools index options.

  • [#1151] Test suite py3.11 compatibility, work around failing test case.

  • [#1149] MacOS universal build compatibility.

  • [#1146] Fix build when CFLAGS/etc environment variables are set.

Release 0.20.0

29 October 2022

This release wraps htslib/bcftools version 1.16 and samtools version 1.16.1.

  • [#1113] Full compatibility with setuptools v62.1.0’s build directory name changes

  • [#1121] Build-time symbol check portability improved

  • [#1122] Fix setting sample genotype using .alleles property

  • [#1128] Fix test suite failure when using a libdeflate-enabled samtools

Many additional type hints have been provided by the community, thanks!

Release 0.19.1

27 May 2022

This release wraps htslib/samtools/bcftools version 1.15.1.

  • [#1104] add an add_samples() method to quickly add multiple samples to VCF.

Release 0.19.0

30 March 2022

This release wraps htslib/samtools/bcftools version 1.15.

  • [#1085] Improve getopt()/getopt_long() resetting when running samtools/bcftools commands

  • [#1078] Support BAM_CPAD in get_aligned_pairs

  • [#1063] Run flake8 and fix some linting issues

  • [#1088] Add AlignedSegment is_mapped/mate_is_mapped/is_forward/mate_is_forward properties

  • Write an absent AlignedSegment.qual as all-bytes-0xff

  • Fix BGZFile.read() behaviour near or at EOF

  • First API for the htslib modified bases interface

Release 0.18.0

17 November 2021

This release wraps htslib/samtools/bcftools version 1.14.

  • [#1048] and [#1060], clarify documentation of index statistics with CRAM files

  • Prevent “retval may be used uninitialised” warning.

  • Add new “samples” subcommand to pysam/samtools.py

  • Introduce TupleProxyIterator iterator object class

Release 0.17.0

30 September 2021

This release wraps htslib/samtools/bcftools version 1.13. Corresponding to new samtools commands, pysam.samtools now has additional functions ampliconclip, ampliconstats, fqimport, and version.

Bugs fixed:

  • [#447] The maximum QNAME length is fully restored to 254

  • [#506, #958, #1000] Don’t crash the Python interpreter on pysam.bcftools.*() errors

  • [#603] count_coverage: ignore reads that have no SEQ field

  • [#928] Fix pysam.bcftools.mpileup() segmentation fault

  • [#983] Add win32/*.[ch] to MANIFEST.in

  • [#994] Raise exception in get_tid() if header could not be parsed

  • [#995] Choose TBI/CSI in tabix_index() via both min_shift and csi

  • [#996] AlignmentFile.fetch() now works with large chromosomes longer than 229 bases

  • [#1019] Fix Sphinx documentation generation by avoiding Python 2 ur'string' syntax

  • [#1035] Improved handling of file iteration errors

  • [#1038] tabix_index() no longer leaks file descriptors

  • [#1040] print(aligned_segment) now prints the correct TLEN value (it also now prints RNAME/RNEXT more clearly and prints POS/PNEXT 1-based)

  • setup.py longer uses setup(use_2to3) for compatibility with setuptools >= v58.0.0

New facilities:

  • [PR #963] Additional VCF classes are exposed to pysam programmers

  • [#998, PR #1001] Add get/set_encoding_error_handler() to control UTF-8 conversion

  • [PR #1012] Running python setup.py sdist now automatically runs cythonize

  • Running tests with pytest now automatically runs make to generate test data

Documentation improvements:

  • [#726] Clarify get_forward_sequence/get_forward_qualities documentation

  • [#865] Improved example

  • [#968] get_index_statstics parameters

  • [#986] Clarify VariantFile.fetch start/stop region parameters are 0-based and half-open.

  • [#990] Corrected PileupColumn.get_query_sequences documentation

  • [#999] Fix documentation for AlignmentFile.get_reference_length()

  • [#1002] Document the default min_base_quality for pileup()

Release 0.16.0

8 June 2020

This release wraps htslib/bcftools version 1.10.2 and samtools version 1.10. The following bugs reported against pysam are fixed due to this:

  • [#447] Writing out QNAME longer than 251 characters corrupts BAM

  • [#640, #734, #843] Setting VariantRecord pos or stop raises error

  • [#738, #919] FastxFile truncates concatenated plain gzip compressed files

Additional bugfixes:

  • [#840] Pileup doesn’t work on python3 when index_filename is used

  • [#886] FastqProxy raises ValueError when instantiated from python

  • [#904] VariantFile.fetch() throws ValueError on files with no records

  • [#909] Fix incorrect quoting in VariantFile contig records

  • [#915, #916] Implement pileup() for unindexed files and/or SAM files

Backwards incompatible changes:

  • The samtools import command was removed in samtools 1.10, so pysam no longer exports a samimport function. Use pysam.view() instead.

Release 0.15.4

Bugfix release. Principal reason for release is to update cython version in order to fix pip install pysam with python 3.8.

  • [#879] Fix add_meta function in libcbcf.pyx, so meta-information lines in header added with this function have double-quoting rules in accordance to rules specified in VCF4.2 and VCF4.3 specifications

  • [#863] Force arg to bytes to support non-ASCII encoding

  • [#875] Bump minimum Cython version

  • [#868] Prevent segfault on Python 2.7 AlignedSegment.compare(other=None)

  • [#867] Fix wheel building on TravisCI

  • [#863] Force arg to bytes to support non-ASCII encoding

  • [#799] disambiguate interpretation of bcf_read return code

  • [#841] Fix silent truncation of FASTQ with bad q strings

  • [#846] Prevent segmentation fault on ID, when handling malformed records

  • [#829] Run configure with the correct CC/CFLAGS/LDFLAGS env vars

Release 0.15.3

Bugfix release.

  • [#824] allow reading of UTF-8 encoded text in VCF/BCF files.

  • [#780] close all filehandles before opening new ones in pysam_dispatch

  • [#773] do not cache VariantRecord.id to avoid memory leak

  • [#781] default of multiple_iterators=True is changed to False for CRAM files.

  • [#825] fix collections.abc import

  • [#825] use bcf_hdr_format instead of bcf_hdr_fmt_text, fix memcpy bug when setting FORMAT fields.

  • [#804] Use HTSlib’s kstring_t, which reallocates and enlarges its memory as needed, rather than a fixed-size char buffer.

  • [#814] Build wheels and upload them to PyPI

  • [#755] Allow passing flags and arguments to index methods

  • [#763] Strip 0 in header check

  • [#761] Test Tabix index contents, not the compression

Release 0.15.2

Bugfix release.

  • [#746] catch pileup itorator out-of-scope segfaults

  • [#747] fix faixd fetch with region

  • [#748] increase max_pos to (1<<31)-1

  • [#645] Add missing macOS stub files in MANIFEST.in, @SoapZA

  • [#737] Fix bug in get_aligned_pairs, @bkohrn

Release 0.15.1

Bugfix release.

  • [#716] raise ValueError if tid is out of range when writing

  • [#697] release version using cython 0.28.5 for python 3.7 compatibility

Release 0.15.0

This release wraps htslib/samtools/bcftools version 1.9.

  • [#673] permit dash in chromosome name of region string

  • [#656] Support text when opening a SAM file for writing

  • [#658] return None in get_forward_sequence if sequence not in record

  • [#683] allow lower case bases in MD tags

  • Ensure that = and X CIGAR ops are treated the same as M

Release 0.14.1

This is mostly a bugfix release, though bcftools has now also been upgraded to 1.7.0.

  • [#621] Add a warning to count_coverage when an alignment has an empty QUAL field

  • [#635] Speed-up of AlignedSegment.find_intro()

  • treat border case of all bases in pileup column below quality score

  • [#634] Fix access to pileup reference_sequence

Release 0.14.0

This release wraps htslib/samtools versions 1.7.0.

  • SAM/BAM/CRAM headers are now managed by a separate AlignmentHeader class.

  • AlignmentFile.header.as_dict() returns an ordered dictionary.

  • Use “stop” instead of “end” to ensure consistency to VariantFile. The end designations have been kept for backwards compatibility.

  • [#611] and [#293] CRAM repeated fetch now works, each iterator reloads index if multiple_iterators=True

  • [#608] pysam now wraps htslib 1.7 and samtools 1.7.

  • [#580] reference_name and next_reference_name can now be set to “*” (will be converted to None to indicate an unmapped location)

  • [#302] providing no coordinate to count_coverage will not count from start/end of contig.

  • [#325] @SQ records will be automatically added to header if they are absent from text section of header.

  • [#529] add get_forward_sequence() and get_forward_qualities() methods

  • [#577] add from_string() and to_dict()/from_dict() methods to AlignedSegment. Rename tostring() to to_string() throughout for consistency

  • [#589] return None from build_alignment_sequence if no MD tag is set

  • [#528] add PileupColumn.__len__ method

Backwards incompatible changes:

  • AlignmentFile.header now returns an AlignmentHeader object. Use AlignmentFile.header.to_dict() to get the dictionary as previously. Most dictionary accessor methods (keys(), values(), __getitem__, …) have been implemented to ensure some level of backwards compatibility when only reading.

    The rationale for this change is to have consistency between AlignmentFile and VariantFile.

  • AlignmentFile and FastaFile now raise IOError instead of OSError

Medium term we plan to have a 1.0 release. The pysam interface has grown over the years and the API is cluttered with deprecated names (Samfile, getrname(), gettid(), …). To work towards this, the next release (0.15.0) will yield DeprecationWarnings for any parts of the API that are considered obsolete and will not be in 1.0. Once 1.0 has been reached, we will use semantic versioning.

Release 0.13.0

This release wraps htslib/samtools/bcftools versions 1.6.0 and contains a series of bugfixes.

  • [#544] reading header from remote TabixFiles now works.

  • [#531] add missing tag types H and A. A python float will now be added as ‘f’ type instead of ‘d’ type.

  • [#543] use FastaFile instead of Fastafile in pileup.

  • [#546] set is_modified flag in setAttribute so updated attributes are output.

  • [#537] allow tabix index files to be created in a custom location.

  • [#530] add get_index_statistics() method

Release 0.12.0.1

Bugfix release to solve compilation issue due to missinge bcftools/config.h file.

Release 0.12.0

This release wraps htslib/samtools/bcftools versions 1.5.0 and contains a series of bugfixes.

  • [#473] A new FastxRecord class that can be instantiated from class and modified in-place. Replaces PersistentFastqProxy.

  • [#521] In AligmentFile, Simplify file detection logic and allow remote index files

    • Removed attempts to guess data and index file names; this is magic left to htslib.

    • Removed file existence check prior to opening files with htslib

    • Better error checking after opening files that raise the appropriate error (IOError for when errno is set, ValueError otherwise for backward compatibility).

    • Report IO errors when loading an index by name.

    • Allow remote indices (tested using S3 signed URLs).

    • Document filepath_index and make it an alias for index_filename.

    • Added a require_index parameter to AlignmentFile

  • [#526] handle unset ref when creating new records

  • [#513] fix bcf_translate to skip deleted FORMAT fields to avoid segfaults

  • [#516] expose IO errors via IOError exceptions

  • [#487] add tabix line_skip, remove ‘pileup’ preset

  • add FastxRecord, replaces PersistentFastqProxy (still present for backwards compatibility)

  • [#496] upgrade to htslib/samtools/bcftools versions 1.5

  • add start/stop to AlignmentFile.fetch() to be consistent with VariantFile.fetch(). “end” is kept for backwards compatibility.

  • [#512] add get_index_statistics() method to AlignmentFile.

Upcoming changes:

In the next release we are plannig to separate the header information from AlignmentFile into a separate class AlignmentHeader. This layout is similar to VariantFile/VariantHeader. With this change we will ensure that an AlignedSegment record will be linked to a header so that chromosome names can be automatically translated from the numeric representation. As a consequence, the way new AlignedSegment records are created will need to change as the constructor requires a header:

header = pysam.AlignmentHeader(
    reference_names=["chr1", "chr2"],
    reference_lengths=[1000, 1000])

read = pysam.AlignedSegment(header)

This will affect all code that instantiates AlignedSegment objects directly. We have not yet merged to allow users to provide feed-back. The pull-request is here: https://github.com/pysam-developers/pysam/pull/518 Please comment on github.

Release 0.11.2.2

Bugfix release to address two issues:

  • Changes in 0.11.2.1 broke the GTF/GFF3 parser. Corrected and more tests have been added.

  • [#479] Correct VariantRecord edge cases described in issue

Release 0.11.2.1

Release to fix release tar-ball containing 0.11.1 pre-compiled C-files.

Release 0.11.2

This release wraps htslib/samtools/bcfools versions 1.4.1 in response to a security fix in these libraries. Additionally the following issues have been fixed:

  • [#452] add GFF3 support for tabix parsers

  • [#461] Multiple fixes related to VariantRecordInfo and handling of INFO/END

  • [#447] limit query name to 251 characters (only partially addresses issue)

VariantFile and related object fixes

  • Restore VariantFile.__dealloc__

  • Correct handling of bcf_str_missing in bcf_array_to_object and bcf_object_to_array

  • Added update() and pop() methods to some dict-like proxy objects

  • scalar INFO entries could not be set again after being deleted

  • VariantRecordInfo.__delitem__ now allows unset flags to be deleted without raising a KeyError

  • Multiple other fixes for VariantRecordInfo methods

  • INFO/END is now accessible only via VariantRecord.stop and VariantRecord.rlen. Even if present behind the scenes, it is no longer accessible via VariantRecordInfo.

  • Add argument to issue a warning instead of an exception if input appears to be truncated

Other features and fixes:

  • Make AlignmentFile __dealloc__ and close more stringent

  • Add argument AlignmentFile to issue a warning instead of an exception if input appears to be truncated

Release 0.11.1

Bugfix release

  • [#440] add deprecated ‘always’ option to infer_query_length for backwards compatibility.

Release 0.11.0

This release wraps the latest versions of htslib/samtools/bcftools and implements a few bugfixes.

  • [#413] Wrap HTSlib/Samtools/BCFtools 1.4

  • [#422] Fix missing pysam.sort.usage() message

  • [#411] Fix BGZfile initialization bug

  • [#412] Add seek support for BGZFile

  • [#395] Make BGZfile iterable

  • [#433] Correct getQueryEnd

  • [#419] Export SAM enums such as pysam.CMATCH

  • [#415] Fix access by tid in AlignmentFile.fetch()

  • [#405] Writing SAM now outputs a header by default.

  • [#332] split infer_query_length(always) into infer_query_length and infer_read_length

Release 0.10.0

This release implements further functionality in the VariantFile API and includes several bugfixes:

  • treat special case -c option in samtools view outputs to stdout even if -o given, fixes #315

  • permit reading BAM files with CSI index, closes #370

  • raise Error if query name exceeds maximum length, fixes #373

  • new method to compute hash value for AlignedSegment

  • AlignmentFile, VariantFile and TabixFile all inherit from HTSFile

  • Avoid segfault by detecting out of range reference_id and next_reference in AlignedSegment.tostring

  • Issue #355: Implement streams using file descriptors for VariantFile

  • upgrade to htslib 1.3.2

  • fix compilation with musl libc

  • Issue #316, #360: Rename all Cython modules to have lib as a prefix

  • Issue #332, hardclipped bases in cigar included by pysam.AlignedSegment.infer_query_length()

  • Added support for Python 3.6 filename encoding protocol

  • Issue #371, fix incorrect parsing of scalar INFO and FORMAT fields in VariantRecord

  • Issue #331, fix failure in VariantFile.reset() method

  • Issue #314, add VariantHeader.new_record(), VariantFile.new_record() and VariantRecord.copy() methods to create new VariantRecord objects

  • Added VariantRecordFilter.add() method to allow setting new VariantRecord filters

  • Preliminary (potentially unsafe) support for removing and altering header metadata

  • Many minor fixes and improvements to VariantFile and related objects

Please note that all internal cython extensions now have a lib prefix to facilitate linking against pysam extension modules. Any user cython extensions using cimport to import pysam definitions will need changes, for example:

cimport pysam.csamtools

will become:

cimport pysam.libcsamtools

Release 0.9.1

This is a bugfix release addressing some installation problems in pysam 0.9.0, in particular:

  • patch included htslib to work with older libcurl versions, fixes #262.

  • do not require cython for python 3 install, fixes #260

  • FastaFile does not accept filepath_index any more, see #270

  • add AlignedSegment.get_cigar_stats method.

  • py3 bugfix in VariantFile.subset_samples, fixes #272

  • add missing sysconfig import, fixes #278

  • do not redirect stdout, but instead write to a separately created file. This should resolve issues when pysam is used in notebooks or other environments that redirect stdout.

  • wrap htslib-1.3.1, samtools-1.3.1 and bcftools-1.3.1

  • use bgzf throughout instead of gzip

  • allow specifying a fasta reference for CRAM file when opening for both read and write, fixes #280

Release 0.9.0

Overview

The 0.9.0 release upgrades htslib to htslib 1.3 and numerous other enhancements and bugfixes. See below for a detailed list.

Htslib 1.3 comes with additional capabilities for remote file access which depend on the presence of optional system libraries. As a consequence, the installation script setup.py has become more complex. For an overview, see Installing pysam. We have tested installation on linux and OS X, but could not capture all variations. It is possible that a 0.9.1 release might follow soon addressing installation issues.

The VariantFile class provides access to vcf and bcf formatted files. The class is certainly usable and interface is reaching completion, but the API and the functionality is subject to change.

Detailed release notes

  • upgrade to htslib 1.3

  • python 3 compatibility tested throughout.

  • added a first set of bcftools commands in the pysam.bcftools submodule.

  • samtools commands are now in the pysam.samtools module. For backwards compatibility they are still imported into the pysam namespace.

  • samtools/bcftools return stdout as a single (byte) string. As output can be binary (VCF.gz, BAM) this is necessary to ensure py2/py3 compatibility. To replicate the previous behaviour in py2.7, use:

    pysam.samtools.view(self.filename).splitlines(True)

  • get_tags() returns the tag type as a character, not an integer (#214)

  • TabixFile now raises ValueError on indices created by tabix <1.0 (#206)

  • improve OSX installation and develop mode

  • FastxIterator now handles empty sequences (#204)

  • TabixFile.isremote is not TabixFile.is_remote in line with AlignmentFile

  • AlignmentFile.count() has extra optional argument read_callback

  • setup.py has been changed to:

    • install a single builtin htslib library. Previously, each pysam module contained its own version. This reduces compilation time and code bloat.

    • run configure for the builtin htslib library in order to detect optional libraries such as libcurl. Configure behaviour can be controlled by setting the environment variable HTSLIB_CONFIGURE_OPTIONS.

  • get_reference_sequence() now returns the reference sequence and not something looking like it. This bug had effects on get_aligned_pairs(with_seq=True), see #225. If you have relied on on get_aligned_pairs(with_seq=True) in pysam-0.8.4, please check your results.

  • improved autodetection of file formats in AlignmentFile and VariantFile.

Release 0.8.4

This release contains numerous bugfixes and a first implementation of a pythonic interface to VCF/BCF files. Note that this code is still incomplete and preliminary, but does offer a nearly complete immutable Pythonic interface to VCF/BCF metadata and data with reading and writing capability.

Potential isses when upgrading from v0.8.3:

  • binary tags are now returned as python arrays

  • renamed several methods for pep8 compatibility, old names still retained for backwards compatibility, but should be considered deprecated.

    • gettid() is now get_tid()

    • getrname() is now get_reference_name()

    • parseRegion() is now parse_region()

  • some methods have changed for pep8 compatibility without the old names being present:

    • fromQualityString() is now qualitystring_to_array()

    • toQualityString() is now qualities_to_qualitystring()

  • faidx now returns strings and not binary strings in py3.

  • The cython components have been broken up into smaller files with more specific content. This will affect users using the cython interfaces.

Edited list of commit log changes:

  • fixes AlignmentFile.check_index to return True

  • add RG/PM header tag - closes #179

  • add with_seq option to get_aligned_pairs

  • use char * inside reconsituteReferenceSequence

  • add soft clipping for get_reference_sequence

  • add get_reference_sequence

  • queryEnd now computes length from cigar string if no sequence present, closes #176

  • tolerate missing space at end of gtf files, closes #162

  • do not raise Error when receiving output on stderr

  • add docu about fetching without index, closes #170

  • FastaFile and FastxFile now return strings in python3, closes #173

  • py3 compat: relative -> absolute imports.

  • add reference_name and next_reference_name attributes to AlignedSegment

  • add function signatures to cvcf cython. Added note about other VCF code.

  • add context manager functions to FastaFile

  • add reference_name and next_reference_name attributes to AlignedSegment

  • PileupColumn also gets a reference_name attribute.

  • add context manager functions to FastaFile

  • TabixFile.header for remote files raises AttributeError, fixes #157

  • add context manager interface to TabixFile, closes #165

  • change ctypedef enum to typedef enum for cython 0.23

  • add function signatures to cvcf cython, also added note about other VCF code

  • remove exception for custom upper-case header record tags.

  • rename VALID_HEADER_FIELDS to KNOWN_HEADER_FIELDS

  • fix header record tag parsing for custom tags.

  • use cython.str in count_coverage, fixes #141

  • avoid maketrans (issues with python3)

  • refactoring: AlignedSegment now in separate module

  • do not execute remote tests if URL not available

  • fix the unmapped count, incl reads with no SQ group

  • add raw output to tags

  • added write access for binary tags

  • bugfix in call to resize

  • implemented writing of binary tags from arrays

  • implemented convert_binary_tag to use arrays

  • add special cases for reads that are unmapped or whose mates are unmapped.

  • rename TabProxies to ctabixproxies

  • remove underscores from utility functions

  • move utility methods into cutils

  • remove callback argument to fetch - closes #128

  • avoid calling close in dealloc

  • add unit tests for File object opening

  • change AlignmentFile.open to filepath_or_object

  • implement copy.copy, close #65

  • add chaching of array attributes in AlignedSegment, closes #121

  • add export of Fastafile

  • remove superfluous pysam_dispatch

  • use persist option in FastqFile

  • get_tag: expose tag type if requested with with_value_type

  • fix to allow reading vcf record info via tabix-based vcf reader

  • add pFastqProxy and pFastqFile objects to make it possible to work with multiple fastq records per file handle, unlike FastqProxy/FastqFile.

  • release GIL around htslib IO operations

  • More work on read/write support, API improvements

  • add phased property on VariantRecordSample

  • add mutable properties to VariantRecord

  • BCF fixes and start of read/write support

  • VariantHeaderRecord objects now act like mappings for attributes.

  • add VariantHeader.alts dict from alt ID->Record.

  • Bug fix to strong representation of structured header records.

  • VariantHeader is now mutable

Release 0.8.3

  • samtools command now accept the “catch_stdout” option.

  • get_aligned_pairs now works for soft-clipped reads.

  • query_position is now None when a PileupRead is not aligned to a particular position.

  • AlignedSegments are now comparable and hashable.

Release 0.8.2.1

  • Installation bugfix release.

Release 0.8.2

  • Pysam now wraps htslib 1.2.1 and samtools version 1.2.

  • Added CRAM file support to pysam.

  • New alignment info interface.

    • opt() and setTag are deprecated, use get_tag() and set_tag() instead.

    • added has_tag()

    • tags is deprecated, use get_tags() and set_tags() instead.

  • FastqFile is now FastxFile to reflect that the latter permits iteration over both fastq- and fasta-formatted files.

  • A Cython wrapper for htslib VCF/BCF reader/writer. The wrapper provides a nearly complete Pythonic interface to VCF/BCF metadata with reading and writing capability. However, the interface is still incomplete and preliminary and lacks capability to mutate the resulting data.

Release 0.8.1

  • Pysam now wraps htslib and samtools versions 1.1.

  • Bugfixes, most notable:

    • issue #43: uncompressed BAM output

    • issue #42: skip tests requiring network if none available

    • issue #19: multiple iterators can now be made to work on the same tabix file

    • issue #24: All strings returned from/passed to the pysam API are now unicode in python 3

    • issue #5: type guessing for lists of integers fixed

  • API changes for consistency. The old API is still present, but deprecated. In particular:

    • Tabixfile -> TabixFile

    • Fastafile -> FastaFile

    • Fastqfile -> FastqFile

    • Samfile -> AlignmentFile

    • AlignedRead -> AlignedSegment

      • qname -> query_name

      • tid -> reference_id

      • pos -> reference_start

      • mapq -> mapping_quality

      • rnext -> next_reference_id

      • pnext -> next_reference_start

      • cigar -> cigartuples

      • cigarstring -> cigarstring

      • tlen -> template_length

      • seq -> query_sequence

      • qual -> query_qualities, now returns array

      • qqual -> query_alignment_qualities, now returns array

      • tags -> tags

      • alen -> reference_length, reference is always “alignment”, so removed

      • aend -> reference_end

      • rlen -> query_length

      • query -> query_alignment_sequence

      • qstart -> query_alignment_start

      • qend -> query_alignment_end

      • qlen -> query_alignment_length

      • mrnm -> next_reference_id

      • mpos -> next_reference_start

      • rname -> reference_id

      • isize -> template_length

      • blocks -> get_blocks()

      • aligned_pairs -> get_aligned_pairs()

      • inferred_length -> infer_query_length()

      • positions -> get_reference_positions()

      • overlap() -> get_overlap()

    • All strings are now passed to or received from the pysam API as strings, no more bytes.

Other changes:

  • AlignmentFile.fetch(reopen) option is now multiple_iterators. The default changed to not reopen a file unless requested by the user.

  • FastaFile.getReferenceLength is now FastaFile.get_reference_length

Backwards incompatible changes

  • Empty cigarstring now returns None (instead of ‘’)

  • Empty cigar now returns None (instead of [])

  • When using the extension classes in cython modules, AlignedRead needs to be substituted with AlignedSegment.

  • fancy_str() has been removed

  • qual, qqual now return arrays

Release 0.8.0

  • Disabled features

    • IteratorColumn.setMask() disabled as htslib does not implement this functionality?

  • Not implemented yet:

    • reading SAM files without header

Tabix files between version 0.7.8 and 0.8.0 are not compatible and need to be re-indexed.

While version 0.7.8 and 0.8.0 should be mostly compatible, there are some notable exceptions:

  • tabix iterators will fail if there are comments in the middle or the end of a file.

  • tabix raises always ValueError for invalid intervals. Previously, different types of errors were raised (KeyError, IndexError, ValueError) depending on the type of invalid intervals (missing chromosome, out-of-range, malformatted interval).

Release 0.7.8

  • added AlignedRead.setTag method

  • added AlignedRead.blocks

  • unsetting CIGAR strings is now possible

  • empty CIGAR string returns empty list

  • added reopen flag to Samfile.fetch()

  • various bugfixes

Release 0.7.7

  • added Fastafile.references, .nreferences and .lengths

  • tabix_iterator now uses kseq.h for python 2.7

Release 0.7.6

  • added inferred_length property

  • issue 122: MACOSX getline missing, now it works?

  • seq and qual can be set None

  • added Fastqfile

Release 0.7.5

  • switch to samtools 0.1.19

  • issue 122: MACOSX getline missing

  • issue 130: clean up tempfiles

  • various other bugfixes

Release 0.7.4

  • further bugfixes to setup.py and package layout

Release 0.7.3

  • further bugfixes to setup.py

  • upgraded distribute_setup.py to 0.6.34

Release 0.7.2

  • bugfix in installer - failed when cython not present

  • changed installation locations of shared libraries

Release 0.7.1

  • bugfix: missing PP tag PG records in header

  • added pre-built .c files to distribution

Release 0.7

  • switch to tabix 0.2.6

  • added cigarstring field

  • python3 compatibility

  • added B tag handling

  • added check_sq and check_header options to Samfile.__init__

  • added lazy GTF parsing to tabix

  • reworked support for VCF format parsing

  • bugfixes

Release 0.6

  • switch to samtools 0.1.18

  • various bugfixes

  • removed references to deprecated ‘samtools pileup’ functionality

  • AlignedRead.tags now returns an empty list if there are no tags.

  • added pnext, rnext and tlen

Release 0.5

  • switch to samtools 0.1.16 and tabix 0.2.5

  • improved tabix parsing, added vcf support

  • re-organized code to permit linking against pysam

  • various bugfixes

  • added Samfile.positions and Samfile.overlap

Release 0.4

  • switch to samtools 0.1.12a and tabix 0.2.3

  • added snp and indel calling.

  • switch from pyrex to cython

  • changed handling of samtools stderr

  • various bugfixes

  • added Samfile.count and Samfile.mate

  • deprecated AlignedRead.rname, added AlignedRead.tid

Release 0.3

  • switch to samtools 0.1.8

  • added support for tabix files

  • numerous bugfixes including

  • permit simultaneous iterators on the same file

  • working access to remote files