Skip to content

Issues: samtools/htslib

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

136 Open 581 Closed
136 Open 581 Closed
Author
Filter by author
Loading
Label
Filter by label
Loading
Use alt + click/return to exclude labels
or ⇧ + click/return for logical OR
Projects
Filter by project
Loading
Milestones
Filter by milestone
Loading
Assignee
Filter by who’s assigned
Sort
Sort by
Newest Oldest Most commented Least commented Recently updated Least recently updated Best match
Most reactions
👍 👎 😄 🎉 😕 ❤️ 🚀 👀

Issues list

sam_read1 stuck after reaching end of the SAM file when using hts_tpool
#1855 opened Oct 30, 2024 by yangao07
1
@jkbonfield
HTSlib does not support VCF v4.4's explicit first phasing indicator
#1847 opened Oct 5, 2024 by jmarshall
@vasudeva8
The htscodecs version.h is not built unless its .git is present; no instructions to prepare a working tarball
#1846 opened Oct 3, 2024 by adamnovak
@daviesrob
1
VCF 4.4/4.5 specs: rlen should be computed rather than populated from END INFO field
#1820 opened Aug 12, 2024 by davmlaw
@vasudeva8
3
Google Cloud Storage hFILE not using multipart / resumable uploads or downloads for reliability
#1814 opened Jul 31, 2024 by pettyalex wishlist
@whitwham
1
No warning on messed up VCF
#1778 opened Apr 30, 2024 by pd3
todo: Improve --regions-overlap variant
#1746 opened Feb 9, 2024 by pd3
htslib in pysam.fetch on S3 Bucket
#1670 opened Sep 7, 2023 by StephanHolgerD
@whitwham
6
Index file downloads when using GCS file
#1615 opened May 3, 2023 by ggydush
1
bcftools view with region filter drops variants at POS=0 (telomeres)
#1571 opened Feb 24, 2023 by colin-nolan
1
@pd3
5
int overflow for big variant lines in vcf
#1539 opened Dec 16, 2022 by arnaldurgylfason
@daviesrob
4
bcf_hdr_remove leaves hash keys behind
#1533 opened Dec 6, 2022 by pd3
@pd3
10
tabix returns row from VCF file multiple times
#1470 opened Jul 11, 2022 by jwimberl
4
Extend vcf.h API to distinguish between the two indel types breaks-ABI
#1454 opened Jun 14, 2022 by pd3
1
Feature request: extend mpileup API
#1453 opened Jun 14, 2022 by pd3
3
Add support for bam/bai files in Azure blob storage
#1440 opened May 25, 2022 by smrgit
@whitwham
6
tabix: how to retain header for arbitrary file types?
#1434 opened May 11, 2022 by carbocation
@daviesrob
2
Random read error on google cloud.
#1424 opened Apr 21, 2022 by stefangroha
@whitwham
4
hts_log_error() extension for better error reporting
#1397 opened Feb 14, 2022 by lczech
@whitwham
5
[Documentation] Short examples?
#1368 opened Jan 1, 2022 by rubyFeedback wishlist
1
Feature request: Add option to tabix to interleave multiple bgzipped indexed files, without the need for external resorting.
#1338 opened Oct 4, 2021 by ghuls wishlist
12
Warning: shared-lib-calls-exit detected by a lint tool
#1315 opened Aug 8, 2021 by junaruga wishlist
1
Increase the mpileup default maximum depth
#1272 opened Apr 20, 2021 by valeriuo
@valeriuo
hts_str2dbl() (and hts_expr) can't parse hex by default on Illumos/OpenIndiana
#1251 opened Mar 9, 2021 by jmarshall
@daviesrob
HTSlib should fail on trailing INFO garbage
#1253 opened Mar 9, 2021 by yangyxt
3
ProTip! Add no:assignee to see everything that’s not assigned.