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@AndreasHeger AndreasHeger released this 01 Apr 21:16
· 109 commits to master since this release
v0.21.0
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Release 0.21.0

This release wraps htslib/samtools/bcftools version 1.17.

Pysam is now compatible with Python 3.11. We have removed python 2.x
support. Pysam is tested with python versions 3.6 to 3.11.

  • [#1175] VariantHeader.new_record: set start/stop before alleles
  • [#1173] Add multiple build improvements in htscodecs on multi-arch macOS
  • [#1148] Ignore CIGAR-less reads in find_introns.
  • [#1172] Add new samtools cram-size and samtools reset commands
  • [#1169] Fix CRAM index-related crash when using the musl C standard library.
  • [#1168] Add a minimal pyproject.toml for PEP517.
  • [#1158] Fix type hints and add FastqProxy type hints.
  • [#1147] Py3.11 compatibility, get shared object suffix from EXT_SUFFIX.
  • [#1143] Add mypy symbols for samtools and bcftools.
  • [#1155] Fix pysam.index() when using recent samtools index options.
  • [#1151] Test suite py3.11 compatibility, work around failing test case.
  • [#1149] MacOS universal build compatibility.
  • [#1146] Fix build when CFLAGS/etc environment variables are set.

Big thanks to @jmarshall who again has done most of the heavy lifting for this release.

Contributors

jmarshall
Assets 2
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