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Pull requests: samtools/htslib

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29 Open 1,157 Closed
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Pull requests list

Fix bugs foudn in the revised header parsing code
#1953 opened Sep 12, 2025 by daviesrob Loading…
Recognise the tabix comment character (-c) when reading records.
#1952 opened Sep 11, 2025 by jkbonfield Loading…
1
Correct TLEN assignment in CRAM decode
#1951 opened Sep 8, 2025 by jkbonfield Loading…
1
@whitwham
1
Fix compilation failure on MacOS X 10.9 (and likely other very old platforms)
#1945 opened Aug 14, 2025 by daviesrob Loading…
1
1
converting bcf 1st phase data as in v44
#1938 opened Jul 22, 2025 by vasudeva8 Loading…
@daviesrob
17
ISA-L compression support evaluation.
#1908 opened Apr 29, 2025 by rhpvorderman • Draft
2
Add support for VCFv4.4 / VCFv4.5 Number= fields
#1874 opened Jan 16, 2025 by daviesrob Loading…
@vasudeva8
3
Add VCF/BCF support for POS=0 coordinate
#1573 opened Mar 1, 2023 by pd3 Loading…
1
5
Proposal to add hts_log callback function and hts_log_set_logger()
#1414 opened Mar 23, 2022 by jmarshall • Draft
@daviesrob
2
Progress and Cancelation for Indexing
#1379 opened Jan 12, 2022 by BickfordA Loading…
11
Iteration over SAM header lines and header expression filtering
#1351 opened Nov 2, 2021 by jmarshall • Draft
@whitwham
2
Improve cross-compilation support [once autoconf 2.70 is widespread]
#1199 opened Jan 4, 2021 by jmarshall • 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 Loading…
4
Speed up of VCF parsing / writing with FORMAT fields.
#1081 opened May 28, 2020 by jkbonfield Loading…
4
Add method sam_open_write
#1055 opened Apr 6, 2020 by valeriuo Loading…
14
Fixes involving CRAM and header API for long references.
#976 opened Nov 15, 2019 by jkbonfield 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 Loading…
12
Provide more informative error message when encountering unexpected n…
#689 opened Apr 22, 2018 by cinquin Loading…
2
Add hts_open_cb() interface which allows callback function used as data source
#647 opened Jan 10, 2018 by 38 Loading…
12
Abstract ref_to_m5 from cram_io
#589 opened Sep 8, 2017 by ThomasHickman Loading…
@jkbonfield
37
Added "make dist" and "make distcheck" targets.
#533 opened May 15, 2017 by jkbonfield Loading…
Add a flexible array member to the bam1_t struct to facilitate a BAM … breaks-ABI
#393 opened Jun 21, 2016 by nathanweeks Loading…
1
IAM role support enhancement
#362 opened Mar 28, 2016 by jpiper Loading…
6
ProTip! Updated in the last three days: updated:>2025-09-10.