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.