Bump pysam from 0.21.0 to 0.22.0

[dependabot[bot]]

Bumps pysam from 0.21.0 to 0.22.0.

Release notes

Sourced from pysam's releases.

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.

Changelog

Sourced from pysam's changelog.

Release 0.22.0

.. rubric:: 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 :meth:.AlignedSegment.fromstring (#1196, reported by DV Klopfenstein)

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

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

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

New functionality:

• Add optional :meth:HTSFile.seek(..., whence) <.HTSFile.seek> 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 :class:.FastxFile performance (PR #1227, thanks to Fabian Klötzl and Valentyn Bezshapkin)

... (truncated)

Commits

• 08de757 Bump version number to 0.22.0 and add release notes
• eac36ad Merge Cirrus CI-based release workflow revamp
• 21af5fa Build ARM Linux and macOS wheels natively on Cirrus CI
• 740d93e Clean libhts.a between wheels and simplify URL
• ed549e9 Add release dates to NEWS / release notes
• 9401189 Merge release workflow revamp and package metadata updates
• c16550a Update package description metadata
• 2926717 Use Trusted Publisher flow to upload to PyPI
• 7d1df29 Backport htslib/kseq.h parsing performance improvement (PR #1227)
• adf52b9 Clarify AlignedSegment.get_reference_positions() documentation
• Additional commits viewable in compare view

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Codecov Report

All modified and coverable lines are covered by tests :white_check_mark:

Project coverage is 88.07%. Comparing base (6e18045) to head (836bd57).

Additional details and impacted files

```diff @@ Coverage Diff @@ ## master #1057 +/- ## ======================================= Coverage 88.07% 88.07% ======================================= Files 29 29 Lines 7156 7156 ======================================= Hits 6303 6303 Misses 853 853 ```

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@dependabot rebase