pysam-v0.17.0

Release 0.17.0

This release wraps htslib/samtools/bcftools version 1.13. Corresponding to new samtools commands, pysam.samtools now has additional functions ampliconclip, ampliconstats, fqimport, and version.

Bugs fixed:

• [#447] The maximum QNAME length is fully restored to 254
• [#506, #958, #1000] Don't crash the Python interpreter on pysam.bcftools.*() errors
• [#603] count_coverage: ignore reads that have no SEQ field
• [#928] Fix pysam.bcftools.mpileup() segmentation fault
• [#983] Add win32/*.[ch] to MANIFEST.in
• [#994] Raise exception in get_tid() if header could not be parsed
• [#995] Choose TBI/CSI in tabix_index() via both min_shift and csi
• [#996] AlignmentFile.fetch() now works with large chromosomes longer than 2²⁹ bases
• [#1019] Fix Sphinx documentation generation by avoiding Python 2 ur'string' syntax
• [#1035] Improved handling of file iteration errors
• [#1038] tabix_index() no longer leaks file descriptors
• [#1040] print(aligned_segment) now prints the correct TLEN value (it also now prints RNAME/RNEXT more clearly and prints POS/PNEXT 1-based)
• setup.py longer uses setup(use_2to3) for compatibility with setuptools >= v58.0.0

New facilities:

• [PR #963] Additional VCF classes are exposed to pysam programmers (thanks to @nh13)
• [#998, PR #1001] Add get/set_encoding_error_handler() to control UTF-8 conversion
• [PR #1012] Running python setup.py sdist now automatically runs cythonize (thanks to @marcelm)
• Running tests with pytest now automatically runs make to generate test data

Documentation improvements:

• [#726] Clarify get_forward_sequence/get_forward_qualities documentation
• [#865] Improved example
• [#968] get_index_statstics parameters
• [#986] Clarify VariantFile.fetch start/stop region parameters are 0-based and half-open.
• [#990] Corrected PileupColumn.get_query_sequences documentation
• [#999] Fix documentation for AlignmentFile.get_reference_length()
• [#1002] Document the default min_base_quality for pileup()

Notes and comments:

Apologies for the hiatus in releases. A big thank you to @jmarshall who has been doing a lot of the work of maintaining pysam in the last year. The delay in getting out releases has been entirely down to me. We have now automated the release process using Github actions. With less overhead, we should be able to release more timely again.

The priorities in the near future are to:

1. track htslib releases and release pysam in a timely manner.
2. remove python2 compatibility from pysam. This will simplify quite a bit of code within pysam.
3. review and triage the many open issues and pull requests. Many thanks to the whole community for submissions and apologies in the delay on acting on them.

The medium term priority is to review the pysam API in order to arrive at a 1.0 release with a consistent API.