All pull requests

Pull requests

• Miscellaneous CRAM encoder fixes

  #2141·jkbonfield opened Nov 10, 2026Contributor·

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• Do size check correctly in cram_extract_block()

  #2139·daviesrob opened Nov 9, 2026Member·

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• annot-tsv: fix column index bounds checks to prevent heap overflow

  #2138·Lukecele opened Nov 7, 2026·

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  1

• News update since last release

  #2136·vasudeva8 opened Nov 6, 2026Contributor·

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• Better checking of function return values in HTSlib

  #2135·daviesrob opened Nov 5, 2026Member·

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• Validate min_shift and depth when loading a CSI index

  #2127·madib06ops opened Oct 31, 2026Contributor·

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  6

• Reject negative GT alleles in bcf_trim_alleles and bcf_remove_allele_set

  #2125·madib06ops opened Oct 29, 2026Contributor·

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  1

  

• Fix 32-bit overflow in skip_aux() B-array length check

  #2122·madib06ops opened Oct 28, 2026Contributor·

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  4

  

• Further reduce CRAM decode memory (threads)

  #2111·jkbonfield opened Oct 19, 2026Contributor·

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• OSS-Fuzz: Add new fuzzer targets fai processing

  #2039·arthurscchan opened Jun 19, 2026·

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  3

  

• 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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  15

  

• 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