samtools/htslib

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C library for high-throughput sequencing data formats

Stars: 950
Forks: 475
Open beginner issues: 0
Indexed issues: 139
Avg merge: 3d 13h
Merged PRs (30d): 11

Dominant language: C
License: No license data
Last GitHub push: Sep 17, 2026
Latest indexed: Sep 20, 2026
Contributing guide: Contributing guide
Code of conduct: No code of conduct
Beginner labels: No beginner labels indexed

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139 open issues indexed

[Bug]hts_getline() aborts on a bzip2-compressed input: hts_detect_format() classifies BZh-prefixed data as bzip2_compression, but the line reader only handles no_compression/gzip/bgzf and hits default: abort() (CWE-617) Open

Difficulty 3/5 1-2 days Newbie friendliness 74/100

samtools/htslib#2091 · Opened Sep 15, 2026
[Bug]Signed integer overflow in bcf_get_version() on the VCF header path: the version string ##fileformat=VCFv4.<huge> drives ver += tmp * 1000 past LONG_MAX (UBSan trap @ vcf.c:186, CWE-190) Open

Difficulty 3/5 1-2 days Newbie friendliness 76/100

samtools/htslib#2088 · 2 comments · Opened Sep 15, 2026
CI testing for signed-off-by commits Open

samtools/htslib#2014 · 1 assignee · Opened May 20, 2026
Suggestion: populate INFO name in warning "INFO tag id=146" Open

samtools/htslib#1996 · 4 comments · 1 assignee · Opened Feb 20, 2026
tabix performance Open

samtools/htslib#1949 · 1 comment · 1 assignee · Opened Sep 2, 2025
hts_idx_t file query API Open

samtools/htslib#1902 · 4 comments · 1 assignee · Opened Apr 2, 2025
Add option to disable periodic `hflush` during multithreaded writes? Open

samtools/htslib#1869 · 1 comment · 1 assignee · Opened Jan 2, 2025
`bcftools consensous` fails to write to GCP Open

samtools/htslib#1865 · 1 comment · 1 assignee · Opened Nov 11, 2024
Google Cloud Storage hFILE not using multipart / resumable uploads or downloads for reliability Open

samtools/htslib#1814 · 4 comments · 1 assignee · Opened Jul 31, 2024
Linking against Intel ISAL for faster deflate operations Open

samtools/htslib#1780 · 9 comments · 1 assignee · Opened May 6, 2024
No warning on messed up VCF Open

Difficulty 3/5 1-2 days Newbie friendliness 38/100

samtools/htslib#1778 · Opened Apr 30, 2024
todo: Improve `--regions-overlap variant` Open

Difficulty 5/5 Over a week Newbie friendliness 35/100

samtools/htslib#1746 · Opened Feb 9, 2024
Index file downloads when using GCS file Open

Difficulty 4/5 3-5 days Newbie friendliness 38/100

samtools/htslib#1615 · 1 comment · Opened May 3, 2023
`bcftools view` with region filter drops variants at POS=0 (telomeres) Open

samtools/htslib#1571 · 5 comments · 1 assignee · Opened Feb 24, 2023
int overflow for big variant lines in vcf Open

samtools/htslib#1539 · 4 comments · 1 assignee · Opened Dec 16, 2022
bcf_hdr_remove leaves hash keys behind Open

samtools/htslib#1533 · 10 comments · 1 assignee · Opened Dec 6, 2022
tabix returns row from VCF file multiple times Open

Difficulty 4/5 3-5 days Newbie friendliness 38/100

samtools/htslib#1470 · 4 comments · Opened Jul 11, 2022
Extend vcf.h API to distinguish between the two indel types Open

breaks-ABI

Difficulty 3/5 1-2 days Newbie friendliness 35/100

samtools/htslib#1454 · 1 comment · Opened Jun 14, 2022
Feature request: extend mpileup API Open

Difficulty 5/5 Over a week Newbie friendliness 30/100

samtools/htslib#1453 · 3 comments · Opened Jun 14, 2022
Add support for bam/bai files in Azure blob storage Open

samtools/htslib#1440 · 6 comments · 1 assignee · Opened May 25, 2022
tabix: how to retain header for arbitrary file types? Open

samtools/htslib#1434 · 2 comments · 1 assignee · Opened May 11, 2022
Random read error on google cloud. Open

samtools/htslib#1424 · 4 comments · 1 assignee · Opened Apr 21, 2022
hts_log_error() extension for better error reporting Open

samtools/htslib#1397 · 5 comments · 1 assignee · Opened Feb 14, 2022
[Documentation] Short examples? Open

Difficulty 2/5 1-3 hours Newbie friendliness 45/100

samtools/htslib#1368 · 1 comment · 3 reactions · Opened Jan 1, 2022
Feature request: Add option to tabix to interleave multiple bgzipped indexed files, without the need for external resorting. Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

samtools/htslib#1338 · 12 comments · 2 reactions · Opened Oct 4, 2021
Warning: shared-lib-calls-exit detected by a lint tool Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

samtools/htslib#1315 · 1 comment · Opened Aug 8, 2021
Increase the mpileup default maximum depth Open

samtools/htslib#1272 · 1 assignee · Opened Apr 20, 2021
hts_str2dbl() (and hts_expr) can't parse hex by default on Illumos/OpenIndiana Open

samtools/htslib#1251 · 1 assignee · Opened Mar 9, 2021
HTSlib should fail on trailing INFO garbage Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

samtools/htslib#1253 · 3 comments · Opened Mar 9, 2021
Trouble building htslib-1.11.tar.bz2 Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

samtools/htslib#1243 · 5 comments · Opened Feb 26, 2021
bgzf_useek and bgzidx_t scope Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

samtools/htslib#1239 · Opened Feb 19, 2021
Skip to last record using tabix Open

samtools/htslib#1231 · 2 comments · 1 assignee · Opened Feb 13, 2021
bcf_hdr_parse_line() validation of INFO/FORMAT/etc keys and IDs Open

samtools/htslib#1218 · 1 assignee · Opened Feb 2, 2021
Allow empty file in `bcf_sr_set_regions` Open

Difficulty 3/5 1-2 days Newbie friendliness 42/100

samtools/htslib#1183 · 1 comment · Opened Dec 1, 2020
Wish list - automatic merging and/or concatenation. Open

Difficulty 5/5 Over a week Newbie friendliness 20/100

samtools/htslib#1174 · Opened Nov 3, 2020
CRAM incorrectly reporting success after malloc failure on read using threads Open

Difficulty 4/5 3-5 days Newbie friendliness 45/100

samtools/htslib#1122 · Opened Aug 18, 2020
Phasing of first genotype Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

samtools/htslib#1113 · 5 comments · Opened Jul 28, 2020
Multiple strings in FORMAT fields Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

samtools/htslib#1111 · 2 comments · Opened Jul 24, 2020
a patch to fix some broken 'wbu' case Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

samtools/htslib#1101 · 5 comments · Opened Jul 10, 2020
bcf_hdr_parse_line() and bcf_hrec_add_key() in vcf.c do not check for INFO and FORMAT keys matching VCF specifications Open

samtools/htslib#1065 · 1 comment · 1 assignee · Opened May 13, 2020
tabix randomly and silently dropping records retrieved from GCS bucket Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

samtools/htslib#1037 · 25 comments · Opened Mar 3, 2020
GCE implementation does not support user pays buckets Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

samtools/htslib#993 · 5 comments · Opened Nov 28, 2019
make -j race condition on "make install install-htslib" Open

Difficulty 3/5 1-2 days Newbie friendliness 45/100

samtools/htslib#991 · Opened Nov 26, 2019
Issues with long ref and ref-skips Open

Difficulty 4/5 3-5 days Newbie friendliness 42/100

samtools/htslib#971 · 3 comments · Opened Nov 14, 2019
Potential for lzma dependency avoidance. Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 25/100

samtools/htslib#937 · 2 comments · Opened Sep 25, 2019
hts_idx_set_meta Open

Difficulty 3/5 1-2 days Newbie friendliness 42/100

samtools/htslib#936 · 8 comments · Opened Sep 24, 2019
synced_bcf_reader needs to better handle running out of file descriptors Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

samtools/htslib#886 · Opened Jun 25, 2019
For consideration: replace cram rANS with htscodecs Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

samtools/htslib#875 · 2 comments · Opened May 24, 2019
Expose hFILE_backend and hfile_init to allow custom hFILE implementations Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

samtools/htslib#849 · 1 comment · Opened Apr 4, 2019
max_unpack BCF_UN_STR SIGSEGV, other strange behavior Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

samtools/htslib#848 · 5 comments · Opened Apr 3, 2019

samtools/htslib

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