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Pull requests: samtools/samtools

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Pull requests list

feat: Add --move-umi-to-tag option to samtools markdup to extract UMI from QNAME and add to RX tag.
#2316 opened Mar 19, 2026 by matthdsm Loading…
@whitwham
9
Authoritative FASTQ import options
#2310 opened Feb 16, 2026 by dkj • Draft
FASTQ import name consistency check
#2309 opened Feb 15, 2026 by dkj • Draft
Add support for single-end FASTQ imports with CASAVA tags for BC auxtag
#2308 opened Feb 14, 2026 by dkj Loading…
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! Updated in the last three days: updated:>2026-03-31.