Commits

History for

Commits on Nov 14, 2023

Add tests for split by string aux tag functionality

daviesrob
authored and
whitwham
committed
050362f

Commits on Aug 14, 2023

Add samtools sort -N / samtools merge -N option.
jkbonfield
committed
3aa4778

Commits on Jul 19, 2023

Unmap reads where there are no aligned bases left.

whitwham
authored and
daviesrob
committed
28da63c
Rename test output file so it is ignored and cleaned

jmarshall
authored and
jkbonfield
committed
1832d07

Commits on Jun 29, 2023

Add samtools fastq -d TAG:value check

jkbonfield
authored and
whitwham
committed
89ed96b

Commits on Apr 17, 2023

Commits on Apr 3, 2023

Add sort minimiser tests

jkbonfield
authored and
whitwham
committed
c75edb0

Commits on Feb 10, 2023

General consensus code tidyup
jkbonfield
committed
77f10f1

Commits on Feb 2, 2023

Improvements to samtools consensus for platforms with higher indel error rates.
jkbonfield
committed
4a4eeb4

Commits on Jan 24, 2023

Update copyright for winter release.

whitwham
authored and
daviesrob
committed
75a7806

Commits on Jan 20, 2023

Make test/regression.sh report diffs when failing
jkbonfield
committed
50aa8cd
Improve samtools cram_size subcommand.
jkbonfield
committed
23dec7b

Commits on Jan 13, 2023

reset functionality base

vasudeva8
authored and
jkbonfield
committed
b40bda2
update to show line nr

vasudeva8
authored and
jkbonfield
committed
437fea0

Commits on Dec 16, 2022

Fix view -X command line parsing.

jkbonfield
authored and
daviesrob
committed
11f9bdc

Commits on Nov 7, 2022

Fixes needed to accommodate samtools/htslib#1522
jkbonfield
committed
a48c76b

Commits on Oct 25, 2022

Changed the default UMI barcode regex. (#1735)
whitwham
authored
8007960

Commits on Oct 10, 2022

Allow ampliconstats bed file to use fewer refs than the input file

daviesrob
authored and
whitwham
committed
0863cb4

Commits on Sep 30, 2022

Stop reads wrongly being removed in hard clip mode. (PR #1722)
whitwham
authored
15f42a9

Commits on Sep 27, 2022

Use POSIX `grep`

SoapGentoo
authored and
whitwham
committed
64cbfb6

Commits on Sep 22, 2022

Adds --incl-flags and --require-flags to the samtools depth command.

jkbonfield
authored and
whitwham
committed
33b293b
Add depth --excl-flags synonym for -G.

jkbonfield
authored and
whitwham
committed
7f977bf

Commits on Sep 16, 2022

Fix stats breakage on long deletions when given a reference

daviesrob
authored and
whitwham
committed
ede7603
Update bam sanitizer to use the new aux tag iterator.

jkbonfield
authored and
whitwham
committed
97dfc67
Add a bam_sanitize function to fixmate and view.

jkbonfield
authored and
whitwham
committed
4f2301f

Commits on Aug 26, 2022

Also add a --min-BQ option to samtools consensus.

jkbonfield
authored and
daviesrob
committed
5627e9d
Make consensus -m simple use a more usual definition of min_depth.

jkbonfield
authored and
daviesrob
committed
537667d

Commits on Aug 24, 2022

Added tests and documentation.

whitwham
authored and
daviesrob
committed
629fb5e

Commits on Aug 23, 2022

add mapq histogram to samtools stats (PR #1684)
lindenb
authored
0ec8128

Commits on Aug 16, 2022

Add reference and head to the list of known usage/tty failures on MINGW

jkbonfield
authored and
daviesrob
committed
434242e

Commits on Aug 10, 2022

Ensure test output files are ignored and cleaned
jmarshall
committed
9082f4c

Commits on Aug 1, 2022

Summer 2022 copyright corrections.

whitwham
authored and
daviesrob
committed
c9c1722

Commits on Jul 28, 2022