All pull requests

Pull requests

• fix: reuse already loaded index in pileup instead of reloading per call

  #1423·kokhlo opened Oct 6, 2026·

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• fix: stop samtools wrappers from blocking forever on stdin

  #1422·kokhlo opened Sep 29, 2026·

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• Enable libdeflate in Linux wheels

  #1421·DylanCosto opened Sep 29, 2026·

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• Honor explicit output paths in samtools and bcftools dispatch

  #1417·AtomicGlance opened Aug 29, 2026·

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• Fix PileupColumn use-after-free once its iterator is exhausted or unreferenced

  #1416·nh13 opened Aug 22, 2026Contributor·

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• MinGW support

  #1400·theAeon opened Mar 24, 2026·

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• Consolidate aux tag value decoding in get_tag and get_tags

  #1391·nh13 opened Mar 2, 2026Contributor·1 task·

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• Extract shared helpers for reference_name and next_reference_name

  #1390·nh13 opened Mar 2, 2026Contributor·1 task·

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• Use bam_set_qname in query_name setter

  #1389·nh13 opened Mar 2, 2026Contributor·1 task·

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• Accumulate insertion count during CIGAR loop in build_alignment_sequence

  #1387·nh13 opened Mar 2, 2026Contributor·1 task·

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• Fix TypeError in modified_bases_forward when query_sequence is None

  #1381·nh13 opened Mar 2, 2026Contributor·1 task·

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• Add missing NULL guard in PileupColumn.get_query_qualities

  #1380·nh13 opened Mar 2, 2026Contributor·1 task·

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• Fix silent truncation in IteratorRowAllRefs on I/O errors

  #1379·gileshall opened Feb 12, 2026·

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• Adding option to ignore non-existing references.

  #1374·blaiseli opened Jan 19, 2026·

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• AlignedSegment.set_tag(): validate Hex values for tag type 'H'

  #1366·bentyeh opened Nov 8, 2025·

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• Support value_type of 'B' in get_tag_typecode()

  #1365·bentyeh opened Nov 8, 2025·

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• feat: add IteratorColumnRecords, a lazy pileup iterator over AlignedSegments

  #1353·nh13 opened Jul 4, 2025Contributor·

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• Add bespoke classes for accessing SEQ and QUAL

  #1347·jmarshall opened Jun 10, 2025Member·

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• Avoid string escaping for str(SamtoolsError)

  #1345·Fan-iX opened Jun 4, 2025·

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• Add support for filtering rows by flags

  #1337·althonos opened Apr 27, 2025Contributor·

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• Speed up bcf genotype count

  #1281·astaric opened Apr 22, 2024·

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• MinGW version of pysam

  #1274·teepean opened Mar 28, 2024·

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• Automatically translate VariantRecord on write

  #1270·kkchau opened Feb 26, 2024·

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• Update handling of INFO/END when writing records in VCF

  #1201·rickymagner opened Jun 29, 2023·

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• Added support for persisting IndexedReads index to disk

  #1037·Prakash2403 opened Aug 26, 2021·

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