[med-svn] [Git][med-team/samtools][upstream] New upstream version 1.22.1

[Steffen Möller (@moeller)]

Steffen Möller pushed to branch upstream at Debian Med / samtools


Commits:
2425fa76 by Steffen Moeller at 2025-08-17T21:28:36+02:00
New upstream version 1.22.1
- - - - -


146 changed files:

- LICENSE
- Makefile
- NEWS.md
- README
- bam2depth.c
- + bam_checksum.c
- bam_consensus.c
- + bam_consensus_tab.h
- bam_fastq.c
- bam_index.c
- bam_markdup.c
- bam_mate.c
- bam_plcmd.c
- bam_reheader.c
- bam_sort.c
- bam_tview.c
- bamtk.c
- bedcov.c
- configure.ac
- consensus_pileup.c
- consensus_pileup.h
- doc/samtools-addreplacerg.1
- doc/samtools-ampliconclip.1
- doc/samtools-ampliconstats.1
- doc/samtools-bedcov.1
- doc/samtools-calmd.1
- doc/samtools-cat.1
- + doc/samtools-checksum.1
- doc/samtools-collate.1
- doc/samtools-consensus.1
- doc/samtools-coverage.1
- doc/samtools-cram-size.1
- doc/samtools-depad.1
- doc/samtools-depth.1
- doc/samtools-dict.1
- doc/samtools-faidx.1
- doc/samtools-fasta.1
- doc/samtools-fixmate.1
- doc/samtools-flags.1
- doc/samtools-flagstat.1
- doc/samtools-fqidx.1
- doc/samtools-head.1
- doc/samtools-idxstats.1
- doc/samtools-import.1
- doc/samtools-index.1
- doc/samtools-markdup.1
- doc/samtools-merge.1
- doc/samtools-mpileup.1
- doc/samtools-phase.1
- doc/samtools-quickcheck.1
- doc/samtools-reference.1
- doc/samtools-reheader.1
- doc/samtools-reset.1
- doc/samtools-rmdup.1
- doc/samtools-samples.1
- doc/samtools-sort.1
- doc/samtools-split.1
- doc/samtools-stats.1
- doc/samtools-targetcut.1
- doc/samtools-tview.1
- doc/samtools-view.1
- doc/samtools.1
- faidx.c
- misc/plot-bamstats
- misc/samtools_tab_completion → misc/samtools_tab_completion.bash
- + misc/samtools_tab_completion.fish
- misc/seq_cache_populate.pl
- misc/wgsim.1
- phase.c
- sam_view.c
- samtools.h
- stats.c
- + test/checksum/chk1.1.expected
- + test/checksum/chk1.3.expected
- + test/checksum/chk1.bam
- + test/checksum/chk2.1.expected
- + test/checksum/chk2.2.expected
- + test/checksum/chk2.3.expected
- + test/checksum/chk2.4.expected
- + test/checksum/chk2.cram
- test/consensus/consen1.sam
- + test/consensus/consen1b.sam
- + test/consensus/consen1c.fa
- + test/consensus/consen1c.fa.fai
- + test/consensus/consen1c.sam
- test/consensus/consensus.reg
- test/consensus/expected/19p.out
- test/consensus/expected/21p.out
- + test/consensus/expected/30.out
- + test/consensus/expected/30T.out
- + test/consensus/expected/31.out
- + test/consensus/expected/31T.out
- + test/consensus/expected/32.out
- + test/consensus/expected/32T.out
- + test/consensus/expected/40.out
- + test/consensus/expected/40T.out
- + test/consensus/expected/41.out
- + test/consensus/expected/41T.out
- + test/consensus/expected/42.out
- + test/consensus/expected/42T.out
- test/merge/test_trans_tbl_init.c
- test/mpileup/depth.reg
- + test/mpileup/expected/d7_nodup2.out
- test/mpileup/expected/mp_2018a.out
- test/mpileup/expected/mp_2018aa.out
- test/mpileup/mp_2018.fa
- test/mpileup/mp_2018.sam
- + test/mpileup/xx#depth5.sam
- test/sort/minimiser-basic.sam
- test/sort/minimiser-indexed-poly.sam
- test/sort/minimiser-indexed.sam
- test/stat/1.stats.expected
- test/stat/1.stats.large.expected
- test/stat/10.stats.expected
- test/stat/10_map_cigar.sam_s1_a_1.expected.bamstat
- test/stat/10_map_cigar.sam_s1_b_1.expected.bamstat
- test/stat/11.stats.expected
- test/stat/11.stats.g4.expected
- test/stat/12.2reads.nooverlap.expected
- test/stat/12.2reads.overlap.expected
- test/stat/12.3reads.nooverlap.expected
- test/stat/12.3reads.overlap.expected
- test/stat/13.barcodes.bc.ok.expected
- test/stat/13.barcodes.ox.ok.expected
- test/stat/14.rg.Sample.expected
- test/stat/14.rg.grp2.expected
- test/stat/14.rg.grp3.expected
- test/stat/14.rg.s1.expected
- test/stat/15.stats.expected
- test/stat/1_map_cigar.sam_s1_a_1.expected.bamstat
- test/stat/2.stats.expected
- test/stat/2.stats.large.expected
- test/stat/3.stats.expected
- test/stat/3.stats.large.expected
- test/stat/4.stats.expected
- test/stat/4.stats.large.expected
- test/stat/5.stats.expected
- test/stat/5.stats.large.expected
- test/stat/6.stats.expected
- test/stat/7.stats.expected
- test/stat/7.stats.large.expected
- test/stat/8.stats.expected
- test/stat/8.stats.large.expected
- test/stat/9.stats.expected
- test/test.pl
- version.sh


The diff was not included because it is too large.


View it on GitLab: https://salsa.debian.org/med-team/samtools/-/commit/2425fa7694d48bddc57b6e3803bd44316d8fee9d

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