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Pull requests: samtools/htslib

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33 Open 1,247 Closed
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Pull requests list

Update build badge, remove .cirrus.yml, spelling corrections
#2071 opened Aug 18, 2026 by jmarshall Member Loading…
Protect against high memory usage in malformed CRAM files.
#2070 opened Aug 17, 2026 by jkbonfield Contributor Loading…
Apply CURL_CA_BUNDLE environment variable in the S3 backend too
#2069 opened Aug 14, 2026 by jmarshall Member Loading…
Remove an infinite loop in bam_mods_at_qpos().
#2068 opened Aug 13, 2026 by jkbonfield Contributor Loading…
@daviesrob
Add S3 integration tests
#2067 opened Aug 13, 2026 by PeterDowdy Contributor Loading…
@whitwham
2
OSS-Fuzz: Add new fuzzer targets fai processing
#2039 opened Jun 19, 2026 by arthurscchan Loading…
@daviesrob
1
change to have hts wide depth filtering
#2016 opened May 21, 2026 by vasudeva8 Contributor Loading…
@jkbonfield
21
Long chr region
#2009 opened May 14, 2026 by jkbonfield Contributor • Draft
fix(performance): Use bounded HTTP Range requests for indexed BAM queries
#1998 opened Apr 14, 2026 by TechIsCool Loading…
@daviesrob
3
Add API functions to parse and format SEQ and QUAL fields
#1974 opened Nov 26, 2025 by jmarshall Member Loading…
@daviesrob
4
hts wide maxdepth limit check
#1965 opened Oct 30, 2025 by vasudeva8 Contributor • Draft
1
@whitwham
ISA-L compression support evaluation.
#1908 opened Apr 29, 2025 by rhpvorderman Contributor • Draft
2
Add VCF/BCF support for POS=0 coordinate
#1573 opened Mar 1, 2023 by pd3 Member Loading…
1
5
Proposal to add hts_log callback function and hts_log_set_logger()
#1414 opened Mar 23, 2022 by jmarshall Member • Draft
@daviesrob
2
Progress and Cancelation for Indexing
#1379 opened Jan 12, 2022 by BickfordA Contributor Loading…
11
Iteration over SAM header lines and header expression filtering
#1351 opened Nov 2, 2021 by jmarshall Member • Draft
@whitwham
2
Improve cross-compilation support [once autoconf 2.70 is widespread]
#1199 opened Jan 4, 2021 by jmarshall Member • Draft
2
improve compatibility for c++
#1191 opened Dec 11, 2020 by s-wakaba Loading…
6
Update to the depth filtering for mpileup.
#1084 opened Jun 15, 2020 by jkbonfield Contributor Loading…
5
Speed up of VCF parsing / writing with FORMAT fields.
#1081 opened May 28, 2020 by jkbonfield Contributor Loading…
4
Add method sam_open_write
#1055 opened Apr 6, 2020 by valeriuo Contributor Loading…
14
Fixes involving CRAM and header API for long references.
#976 opened Nov 15, 2019 by jkbonfield Contributor Loading…
2
sam_format1 : replace if/then with switch/case
#704 opened May 24, 2018 by lindenb Loading…
1
Add mmap hfile backend
#690 opened Apr 23, 2018 by ThomasHickman Contributor Loading…
12
Provide more informative error message when encountering unexpected n…
#689 opened Apr 22, 2018 by cinquin Contributor Loading…
2
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