All pull requests

Pull requests

• Warn when FORMAT is "." but the sample columns are not

  #2112·musharna opened Oct 20, 2026·

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  1

• Further reduce CRAM decode memory (threads)

  #2111·jkbonfield opened Oct 19, 2026Contributor·

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• Autumn news 2026

  #2101·whitwham opened Oct 7, 2026Member·

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  11

• OSS-Fuzz: Add new fuzzer targets fai processing

  #2039·arthurscchan opened Jun 19, 2026·

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  2

  

• change to have hts wide depth filtering

  #2016·vasudeva8 opened May 21, 2026Contributor·

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  37

  

• Long chr region

  #2009·jkbonfield opened May 14, 2026Contributor·

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• fix(performance): Use bounded HTTP Range requests for indexed BAM queries

  #1998·TechIsCool opened Apr 14, 2026·

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  3

  

• Add API functions to parse and format SEQ and QUAL fields

  #1974·jmarshall opened Nov 26, 2025Member·

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  4

  

• hts wide maxdepth limit check

  #1965·vasudeva8 opened Oct 30, 2025Contributor·

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  1

  

• ISA-L (de)compression support for BGZF blocks

  #1908·rhpvorderman opened Apr 29, 2025Contributor·

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  3

• Add VCF/BCF support for POS=0 coordinate

  #1573·pd3 opened Mar 1, 2023Member·

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  1

  5

• Proposal to add hts_log callback function and hts_log_set_logger()

  #1414·jmarshall opened Mar 23, 2022Member·

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  2

  

• Progress and Cancelation for Indexing

  #1379·BickfordA opened Jan 12, 2022Contributor·

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  11

• Iteration over SAM header lines and header expression filtering

  #1351·jmarshall opened Nov 2, 2021Member·

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  2

  

• Improve cross-compilation support [once autoconf 2.70 is widespread]

  #1199·jmarshall opened Jan 4, 2021Member·

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  2

• improve compatibility for c++

  #1191·s-wakaba opened Dec 11, 2020·

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  6

• Update to the depth filtering for mpileup.

  #1084·jkbonfield opened Jun 15, 2020Contributor·

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  5

• Speed up of VCF parsing / writing with FORMAT fields.

  #1081·jkbonfield opened May 28, 2020Contributor·

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  4

• Add method sam_open_write

  #1055·valeriuo opened Apr 6, 2020Contributor·

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  14

• Fixes involving CRAM and header API for long references.

  #976·jkbonfield opened Nov 15, 2019Contributor·

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  2

• sam_format1 : replace if/then with switch/case

  #704·lindenb opened May 24, 2018·

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  1

• Add mmap hfile backend

  #690·ThomasHickman opened Apr 23, 2018Contributor·

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  12

• Provide more informative error message when encountering unexpected n…

  #689·cinquin opened Apr 22, 2018Contributor·

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  2

• Add hts_open_cb() interface which allows callback function used as data source

  #647·38 opened Jan 10, 2018·

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  12

• Abstract ref_to_m5 from cram_io

  #589·ThomasHickman opened Sep 8, 2017Contributor·

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  37