Update dependency pysam to v0.23.0

[renovate]

This PR contains the following updates:

Package	Change	Age	Adoption	Passing	Confidence
pysam (changelog)	==0.22.0 -> ==0.23.0

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Release Notes

pysam-developers/pysam (pysam)

v0.23.0

Compare Source

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)

v0.22.1

Compare Source

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)

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