Commits

Commits on Nov 24, 2023

Fix a couple minor samtools view memory problems.
jkbonfield
committed
4c5285f

Commits on Nov 14, 2023

Fix various --write-index issues

daviesrob
authored and
whitwham
committed
528e1b2
Add tests for split by string aux tag functionality

daviesrob
authored and
whitwham
committed
050362f
Add a -M option to limit the number of split files made

daviesrob
authored and
whitwham
committed
7f829ec
Allow `-d RG` to make new files from alignment RG tag values

daviesrob
authored and
whitwham
committed
d3cec4b
Refactor some names as we now split on tags other than RG

daviesrob
authored and
whitwham
committed
41e1543
Add -d TAG option, which allows read split by custom aux tags.

authored and
whitwham
committed
57de9c2

Commits on Oct 31, 2023

updated cat to support multiple non-seekable streams

vasudeva8
authored and
jkbonfield
committed
9a59467
Add plot of read lengths ("RL") from samtools stats output.

erboone
authored and
jkbonfield
committed
7cce918

Commits on Oct 25, 2023

treats empty barcode as no barcode - avoids issues with realloc

Vasudeva Easwara Sarma
authored and
whitwham
committed
04d53eb

Commits on Oct 13, 2023

Remove -5 option from samtools consensus.

jkbonfield
authored and
whitwham
committed
147ac2f

Commits on Sep 20, 2023

Use the spec-defined PL values in man page example

jmarshall
authored and
jkbonfield
committed
379f1a6

Commits on Sep 15, 2023

mpileup manual updated with samples

vasudeva8
authored and
jkbonfield
committed
007d83e

Commits on Sep 8, 2023

Minor layout changes and added const modifier.
whitwham
committed
38e4517
new option --plot-depth for samtools coverage

lindenb
authored and
whitwham
committed
5d67a96

Commits on Aug 31, 2023

Check fclose(stdout) at the end of main()

jmarshall
authored and
jkbonfield
committed
ae19296

Commits on Aug 22, 2023

Add the order of filtering to the man page. (#1907)
whitwham
authored
117549f

Commits on Aug 15, 2023

Add hclen SAM filter documentation.

jkbonfield
authored and
daviesrob
committed
ed3b05f

Commits on Aug 14, 2023

Bug fix samtools sort --write-index sort mode checks.
jkbonfield
committed
ef78409
Add samtools sort -N / samtools merge -N option.
jkbonfield
committed
3aa4778
Add view -N/-R ^FILE for FILE negation. (#1896)
jkbonfield
authored
88bb16a

Commits on Jul 25, 2023

Merge version number bump and NEWS file from master
daviesrob
committed
fc5524a
Release 1.18
daviesrob
committed
554bb90

Commits on Jul 21, 2023

News Updates for Summer 2023. (PR #1878)

whitwham
and
jkbonfield
authored
8f2ab89

Commits on Jul 20, 2023

Summer 2023 copyright update.
whitwham
committed
ba5f1b2
Document samtools consensus --qual-calibration

jkbonfield
authored and
whitwham
committed
03d7d15

Commits on Jul 19, 2023

Unmap reads where there are no aligned bases left.

whitwham
authored and
daviesrob
committed
28da63c
Add missing Makefile dependencies

jmarshall
authored and
jkbonfield
committed
086414c
Cast off_t values to type expected by format directive [minor]

jmarshall
authored and
jkbonfield
committed
fba4baf
Rename test output file so it is ignored and cleaned

jmarshall
authored and
jkbonfield
committed
1832d07

Commits on Jul 13, 2023

whatis entry for samtools-fasta and samtools-fastq

emollier
authored and
whitwham
committed
46242e7
fix various typos caught by lintian parsers

emollier
authored and
whitwham
committed
28c5243
Be consistent with rounding of "average length" in samtools stats.

jkbonfield
authored and
whitwham
committed
d014a04

Commits on Jul 5, 2023

Fix a minor memory leak. (#1875)
whitwham
authored
e116b0a

Commits on Jul 3, 2023

Documentation formatting etc fixes [minor]

jmarshall
authored and
jkbonfield
committed
cc18465