pysam - v0.23.2

This is a bugfix release, still wrapping htslib/samtools/bcftools 1.21.

It has been tested with Python versions 3.8 through 3.13, and wheels are available via PyPI for all of those Python versions. Wheels are built for macOS and Linux (manylinux_2_28 and musllinux_1_2) on both ARM and x86-64.

The final pysam release that supported Python 3.6 and 3.7 was v0.23.0.

Bugs fixed:

Pysam 0.23.1 inadvertently broke binary compatibility for Cython projects by changing the size of AlignedSegment. That class has been restored to its previous size, so v0.23.2 restores binary compatibility with Cython projects previously compiled against v0.23.0 and earlier. (This bug does not affect pure Python projects using pysam.)
Improved I/O exception messages in AlignmentFile and VariantFile, and ensured that error codes returned by all HTSlib function invocations result in an exception being raised.

- Cython
Published by jmarshall 9 months ago

pysam - v0.23.1

This is a bugfix release, still wrapping htslib/samtools/bcftools 1.21.

It has been tested with Python versions 3.8 through 3.13, and wheels are available via PyPI for all of those Python versions. Wheels are built for macOS and Linux (manylinux_2_28 and musllinux_1_2) on both ARM and x86-64.

The final pysam release that supported Python 3.6 and 3.7 was v0.23.0.

Bugs fixed:

Worked around Cython 3.1.0 behaviour change so that pysam.CMATCH etc remain as synonyms for pysam.CIGAR_OPS.CMATCH etc. Note that a future release will remove these synonyms to comply with Cython's new convention. (#1339, PR #1340, reported by @Adamtaranto, @andyb3, et al)
The Python interpreter no longer exits abruptly on x86-64 Linux when pysam.bcftools.*() commands terminate with error messages. (#1333, #1335, reported by @3ng7n33r and @Ben-Habermeyer)
Fixed AlignedSegment.get_aligned_pairs() type hint, which now has overloaded hints reflecting the different tuples returned. (PR #1342, thanks to @gshiba)
Corrected “invalid type for record” exception message. (PR #1334, thanks to @gtamazian)
Fixed TabixIterator error handling. (#1328, reported by @Fan-iX)
Fixed bugs in the caching of AlignedSegment.query_sequence and AlignedSegment.query_qualities values.
Pysam once again builds on CentOS 7, as it now works around limitations in that obsolete platform's obsolete GCC 4.8.x system compiler. (#1327, reported by @mfasold)

New functionality:

New AlignedSegment.query_qualities_str property enables accessing the QUAL field as an ASCII-encoded base quality string. The existing AlignedSegment.query_qualities property can now take an array or such a string when setting the value. (PR #1324, PR #1341, requested by @nh13)
Improved AlignedSegment.cigarstring performance. (PR #1295, thanks to @limwz01)
Wheels are now built for musllinux in addition to manylinux and macOS. (Requested by @nh13)

- Cython
Published by jmarshall 9 months ago

pysam - v0.23.0

This pysam release wraps htslib/samtools/bcftools 1.21 (PR #1310).

It has been tested with Python versions 3.6 through 3.13, and wheels are available via PyPI for all of those Python versions. Python versions 3.6 through 3.8 are end-of-life; particularly if you use pysam with one of these versions, please vote in the version survey at issue #1230.

This is expected to be the last release supporting Python 3.6 and 3.7.

Bugs fixed:

Fix pysam.samtools.command(save_stdout=filename) redirection of output to a file. (#677, reported by @haowenz and analysed by @yhoogstrate)
Reinstate HTTPS/S3/GCS support in pre-built Linux wheels when used on Debian and Ubuntu: these wheels now work around the discrepancy between Red Hat and Debian CA Certificate file locations. (#1257, #1268, reported by @daisieh and @litaifang)
Calling VariantHeader.new_record() repeatedly with the same samples object now sets GT correctly every time. (#1308, reported by @awgymer)
Correct the exception produced when AlignedSegment.set_tags() is used with an invalid value type. (#1233, PR #1235, reported by @weishwu and @marcus1487)
Numerous type hinting corrections. (#1298, #1316, PR #1296, PR #1306, PR #1313, PR #1315, thanks to @vepain, @awgymer, @mshunjan, and @msto)
The undocumented pysam.samtools.import_() alias for invoking samtools import has been removed; use pysam.samtools.fqimport() instead.
Corrections to several test data files to account for HTSlib 1.20 and later's improved validity checking. (#1291, reported by @SoapGentoo; etc)

New functionality:

AlignedSegment.get_aligned_pairs() now optionally returns the associated CIGAR operator in each position tuple. (#1292, PR #1294, thanks to @LaraFuhrmann and @DrYak)
New AlignmentFile.flush() and VariantFile.flush() methods for flushing buffered output to streams. (#1299, requested by @blex-max)
Improved str() for AlignedSegment now displays reference sequence names when they are available and uses #N only when necessary. (#1318, requested by @creaturemoon)
Implement repr() for AlignedSegment so that it displays the most useful fields. (PR #1267, thanks to @marcelm)
Pysam's tests can now be run in parallel. (#1284, reported by @yurivict)

Documentation improvements:

More complete documentation of invoking SAMtools and BCFtools subcommands via Pysam. (#1096, #1241, PR #1261, PR #1275, #1323, et al, reported by @sbslee, @robertwhbaldwin, @mbhall88, @indraniel, and @shokrofont)
Use the Pysam names for CIGAR operators rather than internal C names. (#1255, reported by @notestaff)
Mention AlignmentFile.fetch("*") in the FAQ entry on fetching unmapped reads. (#424, reported by @bw2)

- Cython
Published by jmarshall about 1 year ago

pysam - v0.22.1

This bug fix release 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 @tfenne and @nh13)
Adjust HTSlib's Makefile so that make distclean no longer tries to rebuild the htscodecs configury (PR #1247, reported by @nsoranzo)
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-B-SDGS, @BenjaminSargsyan, et al)
Add missing AlignedSegment.is_mapped etc properties to type stubs (PR #1273, thanks to @msto)
Fix off-by-one NamedTupleProxy, asBed, etc array bounds check (#1279, reported by @dbolser)
Make pysam's klib headers compatible with C++ (reported by @martin-g)

- Cython
Published by jmarshall almost 2 years ago

pysam - v0.22.0

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 #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 @nsoranzo, also reported by @aryarm in PR #1194)
Miscellaneous dependency improvements (PR #1216, #1217, PR #1218, PR #1219, thanks to @althonos and @ahvigil)
Suppress spurious “Could not retrieve index file” message when opening an AlignmentFile (#939, #1214, reported by @cytham and @sroener)
Propagate SAM parsing errors encounted in AlignedSegment.fromstring() (#1196, reported by @dvklopfenstein)
Accept invalid MD:A tagged fields produced by HTSeq instead of crashing in get_aligned_pairs(with_seq=True) (#1226, reported by @isaacvock)
Fix multiarch macOS CI builds by removing brewed liblzma (#1205, reported by @tedil)
Fix VariantRecordSample.alleles type hint (#1179, reported by @SoapGentoo)

New functionality:

Add optional HTSFile.seek(..., whence) parameter and clarify which functions use libc.SEEK_SET vs io.SEEK_SET (#1185, requested by @ylluX)
File handling improvements in samtools & bcftools commands (should improve #1193 and #1195, reported by @biermanr and @schorlton)
Improve FastxFile performance (PR #1227, thanks to @kloetzl and @valentynbez)
Improve the accuracy of type hints for AlignmentFile iteration (#1184, PR #1189, reported by @PikalaxALT)

Documentation improvements:

Clarify that AlignedSegment.get_aligned_pairs() results are 0-based (#1180, reported by @semenko)
Clarify AlignedSegment.get_reference_positions() documentation (#836, #838, reported by @weir12 and @NickSto)
Clarify that installation via pip usually uses a wheel, and that configuring the build via $HTSLIB_CONFIGURE_OPTIONS etc only applies when installing from an sdist (#1086, reported by @aiqc)

A message from pysam's founder, @AndreasHeger:

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.

- Cython
Published by jmarshall over 2 years ago

pysam - pysam-v0.21.0

Release 0.21.0

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.

Big thanks to @jmarshall who again has done most of the heavy lifting for this release.

- Cython
Published by AndreasHeger almost 3 years ago

pysam - pysam-v0.20.0

Release 0.20.0

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!

This will be the last release with python2.7 support.

- Cython
Published by AndreasHeger over 3 years ago

pysam - pysam-v0.19.1

Release 0.19.1

This release wraps htslib/samtools/bcftools version 1.15.1.

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

Wheels are now built using manylinux224

- Cython
Published by AndreasHeger over 3 years ago

pysam - pysam-v0.19.0

Release 0.19.0

This release wraps htslib/samtools/bcftools version 1.15.

[#1085] Improve getopt()/getopt_long() resetting when running samtools/bcftools commands
[#1078] Support BAMCPAD in getaligned_pairs
[#1063] Run flake8 and fix some linting issues
[#1088] Add AlignedSegment ismapped/mateismapped/isforward/mateisforward 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 interfac

- Cython
Published by AndreasHeger almost 4 years ago

pysam - pysam-v0.18.0

Release 0.18.0

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

- Cython
Published by AndreasHeger over 4 years ago

pysam - pysam-v0.17.0

Release 0.17.0

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 (thanks to @nh13)
[#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 (thanks to @marcelm)
Running tests with pytest now automatically runs make to generate test data

Documentation improvements:

[#726] Clarify getforwardsequence/getforwardqualities 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 minbasequality for pileup()

Notes and comments:

Apologies for the hiatus in releases. A big thank you to @jmarshall who has been doing a lot of the work of maintaining pysam in the last year. The delay in getting out releases has been entirely down to me. We have now automated the release process using Github actions. With less overhead, we should be able to release more timely again.

The priorities in the near future are to: 1. track htslib releases and release pysam in a timely manner. 2. remove python2 compatibility from pysam. This will simplify quite a bit of code within pysam. 3. review and triage the many open issues and pull requests. Many thanks to the whole community for submissions and apologies in the delay on acting on them.

The medium term priority is to review the pysam API in order to arrive at a 1.0 release with a consistent API.

- Cython
Published by AndreasHeger over 4 years ago

pysam - pysam-v0.16.0.1

Release is identical to v0.16.0.

This release was made to be able re-upload fixed wheels of v0.16.0 to pypi.

- Cython
Published by AndreasHeger over 5 years ago

pysam - pysam-v0.16.0

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.

Many thanks to @jmarshall who has done most of the heavy lifting.

- Cython
Published by AndreasHeger over 5 years ago

pysam - pysam-v0.15.4

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 va

- Cython
Published by AndreasHeger about 6 years ago

pysam - pysam-v0.15.3

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 bcfhdrformat instead of bcfhdrfmt_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

- Cython
Published by AndreasHeger over 6 years ago

pysam - pysam-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 getalignedpairs, @bkohrn

- Cython
Published by AndreasHeger about 7 years ago

pysam - pysam-0.15.1

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

- Cython
Published by AndreasHeger over 7 years ago

pysam - pysam-0.15.0.1

This release is the same as v0.15.0 release on pypi, I was not aware that v0.15.0 had been release on github.

Release notes:

Release 0.15.0.1

This release wraps htslib/samtools/bcftools version 1.9.0.

[#673] permit dash in chromosome name of region string
[#656] Support text when opening a SAM file for writing
[#658] return None in getforwardsequence 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

- Cython
Published by AndreasHeger over 7 years ago

pysam - 0.15.0

This release wraps htslib (and friends) versions 1.9.

- Cython
Published by kyleabeauchamp over 7 years ago

pysam - pysam-0.14.1

Release 0.14.1

This is predominantly 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

- Cython
Published by AndreasHeger almost 8 years ago

pysam - pysam-0.14

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] referencename and nextreference_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 getforwardsequence() and getforwardqualities() methods
[#577] add fromstring() and todict()/fromdict() methods to
AlignedSegment. Rename tostring() to tostring() throughout for consistency
[#589] return None from buildalignmentsequence if no MD tag is set
[#528] add PileupColumn.len method

Backwards incompatible changes:

AlignmentFile.header now returns an AlignmentHeader object. Use AlignmentFile.header.todict() 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.

- Cython
Published by AndreasHeger about 8 years ago

pysam - pysam-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 getindexstatistics() method

- Cython
Published by AndreasHeger over 8 years ago

pysam - pysam-0.12.0.1

Bugfix release resolving an issue with a missing config.h file in bcftools.

- Cython
Published by AndreasHeger over 8 years ago

pysam - pysam-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 filepathindex and make it an alias for indexfilename.
- 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.

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.

- Cython
Published by AndreasHeger over 8 years ago

pysam - pysam-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

- Cython
Published by AndreasHeger over 8 years ago

pysam - pysam-0.11.2

This release wraps htslib/samtools/bcfools versions 1.4.1 in response to a security fix in these libraries. Additionaly 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 bcfstrmissing in bcfarraytoobject and bcfobjecttoarray
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

- Cython
Published by AndreasHeger almost 9 years ago

pysam - pysam-0.11.1

Bugfix release to improve backwards compatibility:

[#440] add deprecated 'always' option to inferquerylength for backwards compatibility.

- Cython
Published by AndreasHeger almost 9 years ago

pysam - pysam-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 inferquerylength(always) into inferquerylength and inferreadlength

- Cython
Published by AndreasHeger almost 9 years ago

pysam - pysam-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 referenceid and nextreference 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.inferquerylength() - 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.newrecord(), VariantFile.newrecord() 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. Any user cython extensions using cimport to import pysam definitions will need changes.

- Cython
Published by AndreasHeger about 9 years ago

pysam - pysam-0.9.1.4

This release is (almost) identical to 0.9.1 but aims to improve installation by querying htslib configuration directly.

Many thanks @jmarshall

This release also fixes a bug when parsing tags following CL tags in SAM/BAM headers.