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Commits on Feb 5, 2025

• Update README.rst to reflect modern Bioconda practice

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  jmarshall

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• Remove obsolete build and maintenance scripts

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  jmarshall

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• Bump version number to 0.23.0 and add release notes

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Commits on Feb 4, 2025

• Fix wheels' bundled libcurl.so incompatibility with Debian [HACK]

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  jmarshall

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• Add fullstops in previous NEWS entries [formatting]

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Commits on Feb 3, 2025

• Update release workflows for Python 3.13, Ubuntu 24.04, etc

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Commits on Jan 21, 2025

• Update third-party web site URLs

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• Improve pysam.samtools.command() and pysam.bcftools.command() documentation

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Commits on Jan 20, 2025

• Update ci.yaml now that ubuntu-latest is Ubuntu 24.04

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  jmarshall

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• Update CIGAR_OPS and SAM_FLAGS type stub syntax

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  jmarshall

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• Merge PR #1294: New with_cigar argument for get_aligned_pairs()

  jmarshall

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• Use a function pointer to avoid repeated code

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  jmarshall

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• Refactor AlignedSegment.get_aligned_pairs() test cases

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Commits on Nov 24, 2024

• Use reference_name where available in str(AlignedSegment)

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  jmarshall

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Commits on Oct 30, 2024

• Consistently capitalise PyPI thus [minor]

  jmarshall

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• Clarify AlignmentFile.fetch() FAQ entry

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Commits on Oct 28, 2024

• Fix VCFRecord.qual and related type hints: QUAL in VCF may be float

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  jmarshall

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Commits on Oct 25, 2024

• Tests with_cigar in get_aligned_pair()

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  jmarshall

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• Add with_cigar option to AlignedSegment.get_aligned_pairs()

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  DrYak

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Commits on Oct 24, 2024

• Merge PR #1315: Fix typechecking for top-level samtools commands

  jmarshall

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• Use external pysam.CMATCH etc names in CIGAR documentation

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  jmarshall

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• Don't modify VariantHeader.new_record()'s mutable arguments

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Commits on Oct 22, 2024

• The bcftools head command does not support -o either

  jmarshall

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• Initialise subcommands directly instead of via _{SAM,BCF}TOOLS_DISPATCH

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  jmarshall

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• Set __all__ in both branches and to a literal value

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  jmarshall

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• Install mypy on direct CI jobs to run new tests

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Commits on Oct 20, 2024

• Add tests that check type hints by invoking mypy via its API

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  jmarshall

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Commits on Oct 17, 2024

• Fix AlignmentHeader.get_reference_length() type hint (PR #1313)

  msto

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Commits on Oct 11, 2024

• Fix AlignedSegment's pack_tags()'s exceptions

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  jmarshall

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Commits on Oct 10, 2024

• Add AlignedSegment.__repr__ displaying the most useful fields (PR #1267)

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• Apply 2014's s/getMessages/get_messages/ renaming to the docs (PR #1261)

  

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• Add HTSFile.flush() for flushing output streams

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  jmarshall

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Commits on Oct 9, 2024

• Fix type hint for IteratorColumn's __iter__ (PR #1296)

  

  mshunjan

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  jmarshall

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• Merge PR #1310: Update imports to htslib/samtools/bcftools 1.21

  jmarshall

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• Add config.{guess,sub} to sdist manifest

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