Skip to content

Pull requests: samtools/samtools

New pull request New
21 Open 875 Closed
21 Open 875 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
Reviews
Filter by reviews
No reviews Review required Approved review Changes requested
Assignee
Filter by who’s assigned
Assigned to nobody Loading
Sort
Sort by
Newest Oldest Most commented Least commented Recently updated Least recently updated Best match
Most reactions
👍 👎 😄 🎉 😕 ❤️ 🚀 👀

Pull requests list

Add a --regions-file BED-FILE option to samtools consensus
#2295 opened Jan 13, 2026 by jkbonfield Loading…
1
Input validation on some numeric command-line values
#2292 opened Dec 31, 2025 by StephenTannerAtTempus Loading…
@whitwham
Use canonical calloc arguments order for parsed_opts_t allocation
#2289 opened Dec 9, 2025 by bentyeh Loading…
@whitwham
1
Ignore hard clips in template coordinate sort
#2287 opened Nov 25, 2025 by nh13 • Draft
@whitwham
2
Adding badges for usegalaxy.org and usegalaxy.eu
#2275 opened Oct 14, 2025 by nekrut Loading…
@whitwham
3
Merge alignments into existing BAM/CRAM/SAM
#1979 opened Feb 1, 2024 by mp15 • Draft
6
sample name for samtools stats
#1864 opened Jun 27, 2023 by lindenb Loading…
@daviesrob
1
Add samtools head -e EXPR header filtering option [DRAFT; requires htslib#1351]
#1537 opened Nov 2, 2021 by jmarshall • Draft
@whitwham
8
Mpileup maxcnt tweak.
#1269 opened Jun 15, 2020 by jkbonfield Loading…
Make more functions static.
#1192 opened Feb 12, 2020 by jkbonfield Loading…
2
Proposal: Dynamic Read filtering using dlopen/dclose
#1016 opened Mar 1, 2019 by lindenb Loading…
Small samtools stats speed up, ~5%.
#893 opened Jul 11, 2018 by jkbonfield Loading…
1
Add view -X flag to drop all aux tags
#871 opened Jun 14, 2018 by EvanTheB Loading…
5
Add fastaref subcommand.
#748 opened Dec 4, 2017 by ThomasHickman Loading…
38
Make dist and distcheck targets
#682 opened May 15, 2017 by jkbonfield Loading…
3
option -v to filter out reads in given regions.
#669 opened Apr 23, 2017 by jyh1 Loading…
6
Fix how stats handles Supp reads on alternate haplotypes bug D1: Difficult enhancement P1: Urgent
#469 opened Sep 18, 2015 by mp15 Loading…
3
add option -t for turning off translation; add option -p and -i for samtools merge
#369 opened Mar 25, 2015 by ionzhangj8 Loading… wishlist
7
Adds tests for and fixes handling of corrupted and truncated BAMs
#363 opened Mar 15, 2015 by jrandall Loading…
2
samtools merge to trace transformations applied to @RG IDs
#264 opened Aug 8, 2014 by SamStudio8 Loading…
2
Removes all randomness from samtools merge
#223 opened May 29, 2014 by jrandall Loading…
@jrandall
ProTip! Mix and match filters to narrow down what you’re looking for.