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Pull requests: samtools/htslib

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35 Open 1,205 Closed
35 Open 1,205 Closed
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Pull requests list

Parallel cram2bam
#2015 opened May 20, 2026 by jkbonfield Contributor Loading…
Remove a signed overflow bug in bgzf_read_small.
#2013 opened May 20, 2026 by jkbonfield Contributor Loading…
hfile_s3: fix s3_seek returning wrong offset on cache-hit
#2012 opened May 18, 2026 by NickEdwards7502 Loading…
bcf_sr_set_regions: opt-in fastpath for dense single-base BEDs (samtools/bcftools#2557)
#2011 opened May 16, 2026 by carstenerickson Loading…
Add missing ref_cache/misc.o dependency line
#2010 opened May 15, 2026 by daviesrob Member Loading…
Long chr region
#2009 opened May 14, 2026 by jkbonfield Contributor • Draft
Make faidx work with very long (>4 Gbyte!) lines
#2008 opened May 12, 2026 by daviesrob Member Loading…
1
@jkbonfield
5
Improve "not defined in the header" messages
#2007 opened May 12, 2026 by daviesrob Member Loading…
@pd3
Add opt-in planned parser for VCF FORMAT fields
#2005 opened May 8, 2026 by jhl-oai Loading…
5
fix(performance): Use bounded HTTP Range requests for indexed BAM queries
#1998 opened Apr 14, 2026 by TechIsCool Loading…
@daviesrob
3
Add multi-region iterator support for tabix
#1997 opened Apr 6, 2026 by HeyangQin Loading…
4 tasks done
1
1
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…
4
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
ProTip! Exclude everything labeled bug with -label:bug.