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Commits on Jun 16, 2025

• Remove obsolete source files and unnecessary includes

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  jmarshall

  committed
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• Simplify libctabix.pyx by using bgzf_getline() directly

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  jmarshall

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• Refactor htslib/kseq.h usage to avoid unused function warnings

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Commits on Jun 10, 2025

• Merge v0.23.3 release branch

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  committed
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• Bump version number to 0.23.3 and add release notes

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• Cherry-pick work-around for Cython 3.1.2 bug

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• Work around Cython 3.1.2 non-static internal function bug

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Commits on Jun 6, 2025

• Merge v0.23.2 release branch

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  committed
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• Bump version number to 0.23.2 and add release notes

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  committed
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Commits on Jun 5, 2025

• Move AlignedSegment cache fields to a new sub-object

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Commits on Jun 4, 2025

• Add FreeBSD CI workflow running on Cirrus CI

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Commits on Jun 3, 2025

• Take advantage of our minimum Python now being 3.8

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  committed
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Commits on Jun 2, 2025

• Reword ancient NEWS entry to try to avoid misparsing

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  jmarshall

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Commits on May 31, 2025

• Overhaul AlignmentFile error reporting

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Commits on May 29, 2025

• Overhaul VariantHeader and VariantFile error reporting

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• Add OSError_from_errno() utility function

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Commits on May 28, 2025

• Bump version number to 0.23.1 and add release notes

  jmarshall

  committed
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• Fix AlignedSegment.get_aligned_pairs() type hints (PR #1342)

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• Merge release workflow updates

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  committed
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Commits on May 27, 2025

• Probe for compiler flags required to compile C99 source code

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Commits on May 23, 2025

• Use Pythonesque pysam.CIGAR_OPS.CMATCH etc names in documentation

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  jmarshall

  committed
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• Improve AlignedSegment.cigarstring performance (PR #1295)

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Commits on May 22, 2025

• Enable musllinux wheel builds and update cibuildwheel

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  committed
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• Drop Python 3.6 and 3.7 wheels

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• Emulate samtools et al if these tools are not available

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Commits on May 21, 2025

• Merge AlignedSegment.query_qualities_str addition (PR #1341)

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Commits on May 15, 2025

• Improve AlignedSegment.query_sequence caching

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Commits on May 14, 2025

• Work around Cython 3.1.0 no longer copying enumerators as global names

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• Report Cython version and use f-strings throughout setup.py

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  committed
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Commits on May 12, 2025

• Add tests for query_sequence caching

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  committed
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Commits on May 11, 2025

• Add new AlignedSegment.query_qualities_str property and tests

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Commits on May 10, 2025

• Rewrite AlignedSegment.query_qualities and fix its caching

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  committed
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Commits on May 7, 2025

• Remove __set__ methods for read-only properties

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Commits on May 5, 2025

• Accept None/""/"*" as empty for cigarstring and query_sequence

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Commits on May 3, 2025

• Add tests for query_qualities

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  committed
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