Andreas Tille pushed to branch upstream at Debian Med / samtools
Commits: 816f54ad by Andreas Tille at 2026-09-16T15:12:20+02:00 New upstream version 1.24 - - - - - 161 changed files: - + CONTRIBUTING.md - LICENSE - Makefile - NEWS.md - README - amplicon_stats.c - bam.c - bam.h - bam_addrprg.c - bam_ampliconclip.c - bam_checksum.c - bam_consensus.c - bam_fastq.c - bam_import.c - bam_index.c - bam_markdup.c - bam_mate.c - bam_md.c - bam_plcmd.c - bam_sort.c - bam_split.c - bam_tview.c - bamtk.c - bedcov.c - bedidx.c - bedidx.h - configure.ac - coverage.c - cram_size.c - dict.c - 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 - m4/hts_prog_cc_warnings.m4 - misc/md5fa.c - misc/plot-bamstats - + misc/seq_cache_populate.py - misc/wgsim.1 - padding.c - reset.c - sam_opts.c - sam_opts.h - sam_utils.h - sam_view.c - stats.c - + test/bam2fq/21.fq.expected - + test/bam2fq/22.fq.expected - + test/bam2fq/23.fq.expected - + test/bam2fq/24.fq.expected - + test/bam2fq/UMI.fq.expected - + test/checksum/chk1.4.expected - + test/checksum/chk1.5.expected - + test/checksum/chk1.6.expected - + test/checksum/chk1.7.expected - + test/checksum/chk1.8.expected - test/checksum/chk2.2.expected - test/checksum/chk2.4.expected - + test/consensus/consen4.bed - + test/consensus/consen4.sam - test/consensus/consensus.reg - test/consensus/expected/14q.out → test/consensus/expected/14q1.out - + test/consensus/expected/14q2.out - test/consensus/expected/16q.out - + test/consensus/expected/bf1.out - + test/consensus/expected/bf2.out - + test/consensus/expected/bp1.out - + test/consensus/expected/bp2.out - + test/coverage/1.expected - + test/coverage/2.expected - + test/coverage/3.expected - + test/coverage/4.expected - + test/coverage/5.expected - + test/dat/bam2fq.sc.sam - + test/dat/sample.sam - + test/fixmate/9_supplementary_mc.sam - + test/fixmate/9_supplementary_mc.sam.expected - test/import/1.expected.sam - test/import/2.expected.sam - + test/import/3.expected.sam - test/import/4.expected-XZ,XA,AA.sam - test/import/4.expected.sam - test/import/5-BC.expected.sam - test/import/5-OX.expected.sam - + test/import/UMI-OX.expected.sam - + test/import/UMI.expected.sam - + test/markdup/19_move_umi_to_tag.expected.sam - + test/markdup/19_move_umi_to_tag.sam - + test/markdup/20_move_umi_in_middle.expected.sam - + test/markdup/20_move_umi_in_middle.sam - + test/markdup/21_move_umi_custom_sep.expected.sam - + test/markdup/21_move_umi_custom_sep.sam - test/merge/tag.pg.merge.expected.sam - test/merge/tag.pg.n.merge.expected.sam - test/merge/test_bam_translate.c - + test/reset/cram.expected - test/sort/tag.as.sort.expected.sam - test/sort/tag.fi.sort.expected.sam - test/sort/tag.rg.n.sort.expected.sam - test/sort/tag.rg.sort.expected.sam - + test/sort/template-coordinate-hardclip.sort.expected.sam - + test/sort/template-coordinate-hardclip.sort.sam - + test/sort/template-coordinate-supplementary.expected.sam - + test/sort/template-coordinate-supplementary.sam - + test/sort/template-coordinate.cell-barcode.sort.expected.sam - + test/sort/template-coordinate.cell-barcode.sort.sam - + test/split/split.expected_d_nn_sorted.-1.sam - + test/split/split.expected_d_nn_sorted.-2.sam - + test/split/split.expected_d_nn_sorted.1.sam - + test/split/split.expected_d_nn_sorted.2.sam - + test/split/split.expected_d_nn_sorted.unk.sam - test/split/test_count_rg.c - test/split/test_expand_format_string.c - test/split/test_filter_header_rg.c - test/split/test_parse_args.c - + test/stat/16.stats.expected - + test/stat/17.stats.expected - + test/stat/18.stats.expected - + test/stat/19.stats.expected - − test/stat/test.fa.fai - + test/stat/test1.fa - 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/816f54adcf5ae599506f03a083a97b032965761e -- View it on GitLab: https://salsa.debian.org/med-team/samtools/-/commit/816f54adcf5ae599506f03a083a97b032965761e You're receiving this email because of your account on salsa.debian.org. Manage all notifications: https://salsa.debian.org/-/profile/notifications | Help: https://salsa.debian.org/help
_______________________________________________ debian-med-commit mailing list [email protected] https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
