v0.24.1

This minor pysam release wraps htslib/samtools/bcftools version 1.24.

It has been tested with Python versions 3.9 through 3.15 (RC2) 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 3.8 was v0.24.0.

Starting from v0.24.0 pysam wraps htslib 1.22 or later, which contains significant CRAM-related operational changes that are inherited by pysam: the default output CRAM version is now 3.1 rather than 3.0; CRAM reference data is no longer fetched from EBI's server by default.

Bugs fixed:

• Fixed type hints for VariantFile to re-allow file descriptors and file-like objects as “filenames” to be opened. (PR #1406, reported by @dpoznik)

• Fixed AlignedSegment.get_aligned_pairs() type hints so that omitted arguments also produce precise return types. (PR #1371, reported by @gshiba)

• Optimized AlignedSegment.query_sequence and AlignedSegment.query_alignment_sequence, resulting in an approximately 3× speed improvement. (PR #1411)

• Fixed tabix_compress() error handling, which now raises an exception when filename_in cannot be opened rather than treating it as an empty file.

• Reinstated S3 support in pre-built Linux wheels when used on Debian and Ubuntu, which was broken in v0.24.0 due to pysam's CA Certificate location workaround no longer being applied to S3 URLs. (PR #1420)

• Pre-built PyPI Linux wheels now load networking libraries dynamically at runtime when needed, rather than having copies of networking and security libraries bundled within the wheel. (PR #1420; #1097, #1276, reported by @MikeWazoWski123 and @shaze)

• Cython and C source files, which have been inadvertently present in binary wheels since v0.21.0, are now properly omitted again.

New functionality:

• New reverse_complement() and reverse_complement_inplace() functions. (PR #1411)

• VariantRecordSample now supports Number=P (VCF v4.4 or greater) and Number=LA, LR, LG, and M (VCF v4.5). (#1419, reported by @cjw85)

• Pre-built PyPI wheels are no longer built with C debugging symbols, which are largely unnecessary in a Python context. Due to this and the removal of most Linux bundled libraries and the inadvertently added source code, pre-built wheels are now much smaller, especially on Linux.

• Pysam's test suite has been overhauled to be natively pytest-based. It now uses tmp_path fixtures rather than its own ad hoc temporary file management and mostly no longer makes network requests.

Documentation improvements:

• Added new FastxRecord documentation. (PR #1245, thanks to @nh13)