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)
Bugfix release, which still wraps htslib/samtools/bcftools 1.18.
Bugs fixed:
Preserve all header field tags defined in the SAM specification (notably TP)
in :meth:.AlignmentHeader.from_dict and :meth:.AlignmentHeader.to_dict
(#1237, PR #1238, thanks to Tim Fennell and Nils Homer)
Adjust HTSlib's Makefile so that make distclean no longer tries to
rebuild the htscodecs configury (PR #1247, reported by Nicola Soranzo)
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 Baines, Benjamin Sargsyan, et al)
Add missing :attr:.AlignedSegment.is_mapped etc properties to type stubs
(PR #1273, thanks to Matt Stone)
Fix off-by-one NamedTupleProxy, :class:.asBed, etc array bounds check
(#1279, reported by Dan Bolser)
Make pysam's klib headers compatible with C++ (reported by Martin Grigorov)
Commits
36a0304 Bump version number to 0.22.1 and add release notes
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Bumps pysam from 0.22.0 to 0.22.1.
Release notes
Sourced from pysam's releases.
Changelog
Sourced from pysam's changelog.
Commits
36a0304Bump version number to 0.22.1 and add release notes5754de3Merge release workflow updates75654b6Update Cirrus CI workflow8ab5287Remove hts_probe_cc.sh and don't try to run it from Makefilea6b21fdInstall openssl-devel/etc package as well as curl-devel3e145c8Increase release build verbosityb163e9eUse absolute imports rather than relativee61ac20Backport htslib/htslib/*.h C++ casts addition2f00e84Update up/download-artifact actions to v4da80f5eRun release build_sdist job only onceDependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting
@dependabot rebase.Dependabot commands and options
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