All pull requests

Pull requests

• Describe Ma, Aq, and An molecular annotation tags

  samsam-tags
  #862·cademirch opened Aug 4, 2026·

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  1

• Fix for #860 - Modify URL so that it is actually invalid.

  vcf
  #861·markwoon opened Jul 25, 2026·

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• Further clarify ITF-8 and LTF-8 encodings

  cram
  #858·jkbonfield opened Jul 7, 2026Contributor·

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  1

  5

• Vcf/gvcf example fix

  vcf
  #853·d-cameron opened Feb 24, 2026Contributor·

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  1

  4

• Clarify GQ

  vcf
  #852·d-cameron opened Feb 24, 2026Contributor·

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  1

  1

• Clarified INFO END deprecation status

  vcf
  #844·d-cameron opened Sep 9, 2025Contributor·

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  5

• Minor CRAM notation suggestion: Use IEC-style MiB notation for powers of two, rather than MB

  cram
  #841·jmarshall opened Aug 12, 2025Member·

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  5

• Add succinct description of refget sequence collection in metadata

  vcf
  #832·tcezard opened Jun 18, 2025Contributor·

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  2

• Remove refget from hts-specs

  refget
  #830·andrewyatz opened Jun 2, 2025Contributor·

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• feat: add proof of concept solution for #814

  samsam-tags
  #815·yfarjoun opened Feb 17, 2025Contributor·

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• feat: add tags related to optical duplicates.

  samsam-tags
  #813·yfarjoun opened Feb 16, 2025Contributor·

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  7

• Add encryptionScheme parameter to htsget

  htsget
  #808·brainstorm opened Feb 3, 2025Contributor·

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  16

• Copy the tag type text from SAM spec to SAMtags (PR #804)

  samsam-tags
  #804·jkbonfield opened Jan 7, 2025Contributor·

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  1

  5

• Explicitly permit eg N+m in MM tag (PR#799)

  samsam-tags
  #799·jkbonfield opened Oct 28, 2024Contributor·

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  1

  4

• fix discrepancy of empty bed files

  bed
  #775·kloetzl opened Jun 28, 2024Contributor·

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  5

• Add SAM recommendation of MAPQ=0 for unmapped reads

  sam
  #753·jkbonfield opened Jan 29, 2024Contributor·

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  1

  8

  

• Adding AEAD support as new encryption method

  crypt4gh
  #736·silverdaz opened Jul 22, 2023·

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  5

• Allow for UTF-8 field values in header regular expression

  sam
  #726·jmarshall opened May 12, 2023Member·

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  1

  11

• Fix typos (refget)

  refget
  #700·jkbonfield opened Feb 2, 2023Contributor·

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• Remove "top strand" phrase from MM tag description.

  samsam-tags
  #668·jkbonfield opened Aug 31, 2022Contributor·

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  1

  1

  

• Define optional HTTP 426 response for requests for index files

  htsget
  #665·jmarshall opened Aug 3, 2022Member·

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• Clarify MI for identifying source molecule strand

  samsam-tags
  #633·nh13 opened Mar 2, 2022Member·

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  15

  

• Clarification of empty vector representation

  vcf
  #617·pd3 opened Dec 16, 2021Member·

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  3

  

• Phred scale clarifications

  samvcf
  #579·jkbonfield opened Jun 16, 2021Contributor·

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  1

  19

• strawman attempt at adding array of booleans

  vcf
  #537·yfarjoun opened Dec 17, 2020Contributor·2 tasks·

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  2