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 -- View it on GitLab: https://salsa.debian.org/med-team/samtools/-/commit/2425fa7694d48bddc57b6e3803bd44316d8fee9d You're receiving this email because of your account on salsa.debian.org.
_______________________________________________ debian-med-commit mailing list [email protected] https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
