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)