Steffen Möller pushed to branch master at Debian Med / bcftools
Commits: 6794df34 by Steffen Moeller at 2025-08-17T20:55:21+02:00 New upstream version - - - - - 1ceb304e by Steffen Moeller at 2025-08-17T20:55:22+02:00 New upstream version 1.22 - - - - - fedfece5 by Steffen Moeller at 2025-08-17T20:55:38+02:00 Update upstream source from tag 'upstream/1.22' Update to upstream version '1.22' with Debian dir 35b370725616b4f49177db6a798325ce3febb447 - - - - - f7b45e31 by Steffen Moeller at 2025-08-17T20:55:39+02:00 Standards-Version: 4.7.2 (routine-update) - - - - - 7f818e8a by Steffen Moeller at 2025-08-17T22:44:31+02:00 New upstream versionn 1.22. - - - - - 207 changed files: - AUTHORS - Makefile - NEWS - bcftools.h - consensus.c - convert.c - csq.c - debian/changelog - debian/control - debian/patches/2to3.patch - debian/patches/skip_new_test_failing_on_32bit.patch - doc/bcftools.1 - doc/bcftools.html - doc/bcftools.txt - filter.c - gff.c - gff.h - main.c - + misc/gencode-tables - misc/plot-vcfstats - + misc/roh-viz - + misc/vrfs-variances - mpileup.c - + mpileup2/mpileup.c - + mpileup2/mpileup.h - mpileup_bench/get_data.sh - ploidy.c - ploidy.h - plugins/check-sparsity.c - plugins/contrast.c - plugins/fill-tags.c - plugins/guess-ploidy.c - plugins/gvcfz.c - plugins/indel-stats.c - plugins/isecGT.c - plugins/mendelian2.c - plugins/parental-origin.c - plugins/prune.c - plugins/remove-overlaps.c - plugins/scatter.c - plugins/setGT.c - plugins/smpl-stats.c - plugins/split-vep.c - plugins/split.c - plugins/trio-dnm2.c - plugins/trio-stats.c - plugins/variant-distance.c - + plugins/vcf2table.c - + plugins/vrfs.c - + plugins/vrfs.mk - polysomy.c - read_consensus.c - regidx.c - regidx.h - reheader.c - smpl_ilist.c - test/annotate19.1.out - test/annotate19.2.out - test/annotate19.3.out - test/annotate19.4.out - test/annotate19.5.out - test/annotate19.6.out - test/annotate19.7.out - + test/annotate35.1.out - + test/annotate35.2.out - + test/annotate35.vcf - + test/annots35.tab - + test/annots35.vcf - + test/call-ploidy.1.1.out - + test/call-ploidy.1.ped - + test/call-ploidy.1.txt - + test/call-ploidy.1.vcf - + test/concat.6.out - + test/consensus.20.a.txt - + test/consensus.20.b.txt - + test/consensus.gvcf-missing.1.out - + test/consensus.gvcf-missing.1.vcf - + test/consensus.gvcf-missing.fa - + test/csq.yychr.fa - + test/csq.yychr.gff - + test/csq.yychr.out - + test/csq.yychr.vcf - + test/csq/ENSCAFT00000047742/ENSCAFT00000047742.fa - + test/csq/ENSCAFT00000047742/ENSCAFT00000047742.fa.fai - + test/csq/ENSCAFT00000047742/ENSCAFT00000047742.gff - + test/csq/ENSCAFT00000047742/test.txt - + test/csq/ENSCAFT00000047742/test.vcf - + test/csq/ENST00000368801.2/alt-gencode.1.cmd - + test/csq/ENST00000368801.2/alt-gencode.1.cmd.out - + test/csq/ENST00000368801.2/alt-gencode.2.cmd - + test/csq/ENST00000368801.2/alt-gencode.2.cmd.out - + test/csq/ENST00000368801.2/alt-gencode.vcf - + test/fill-tags-AD.5.out - + test/fisher.1.out - + test/fisher.2.out - + test/fisher.3.out - + test/fisher.4.out - + test/fisher.5.out - + test/fisher.6.out - + test/fisher.vcf - + test/isec.match-id.1.1.vcf - + test/isec.match-id.1.2.vcf - + test/isec.match-id.1.out - + test/isec.match-id.2.out - + test/merge.12.1.out - + test/merge.12.a.vcf - + test/merge.12.b.vcf - test/merge.2.both.out - test/merge.2.none.out - test/merge.abc.2.out - test/merge.abc.3.out - test/merge.abc.out - + test/merge.broken-gvcf.1.out - + test/merge.broken-gvcf.a.vcf - + test/merge.broken-gvcf.b.vcf - test/merge.gvcf.2.1.out - test/merge.gvcf.2.2.out - test/merge.gvcf.2.out - + test/merge.multiallelics.1.1.out - + test/merge.multiallelics.1.a.vcf - + test/merge.multiallelics.1.b.vcf - + test/merge.phased.1.1.out - + test/merge.phased.1.a.vcf - + test/merge.phased.1.b.vcf - + test/merge.symbolic.1.1.out - + test/merge.symbolic.1.a.vcf - + test/merge.symbolic.1.b.vcf - + test/mpileup/iupac.1.out - + test/mpileup/iupac.bam - + test/mpileup/iupac.bam.bai - + test/mpileup/iupac.fa - + test/mpileup/iupac.fa.fai - + test/mpileup/mpileup.12.out - test/norm.2.out - test/norm.3.2.out - test/norm.3.out - + test/norm.6.1.out - + test/norm.6.vcf - + test/norm.breakend.1.1.out - + test/norm.breakend.1.fa - + test/norm.breakend.1.vcf - test/norm.iupac.out - test/norm.rmdup.3.1.out - test/norm.rmdup.3.2.out - test/norm.rmdup.3.vcf - test/prune.1.1.out - test/prune.2.1.out - + test/prune.3.1.out - + test/prune.3.2.out - + test/prune.3.3.out - + test/prune.3.vcf - + test/query.3.1.out - + test/query.3.2.out - + test/query.3.3.out - + test/query.3.vcf - + test/query.filter.14.1.out - + test/query.filter.14.2.out - + test/query.filter.14.3.out - + test/query.filter.14.vcf - + test/query.filter.15.1.out - + test/query.filter.15.2.out - + test/query.filter.15.vcf - + test/query.func.1.1.out - + test/query.func.1.2.out - + test/query.func.1.3.out - + test/query.func.1.4.out - + test/query.func.1.vcf - + test/samples.1.out - + test/samples.2.out - + test/samples.vcf - + test/setGT.2.1.out - + test/setGT.3.7.out - + test/split-vep.1.1.out - + test/split-vep.13.1.out - + test/split-vep.2.1.out - + test/split-vep.3.1.out - + test/split-vep.7.1.out - test/test.pl - test/trio-dnm/trio-dnm.11.1.out - test/trio-dnm/trio-dnm.11.2.out - test/trio-dnm/trio-dnm.11.vcf - + test/vcf2table.1.out - + test/vcf2table.2.out - + test/vrfs.1.1.out - + test/vrfs.sites.txt - vcfannotate.c - vcfbuf.c - vcfbuf.h - vcfcall.c - vcfcnv.c - vcfconcat.c - vcfconvert.c - vcffilter.c - vcfgtcheck.c - vcfhead.c - vcfindex.c - vcfisec.c - vcfmerge.c - vcfnorm.c - vcfplugin.c - vcfquery.c - vcfroh.c - vcfsort.c - vcfstats.c - vcfview.c - version.c - version.sh The diff was not included because it is too large. View it on GitLab: https://salsa.debian.org/med-team/bcftools/-/compare/97185075bb2916a200ba662d1a5feb8b5778ae0b...7f818e8a29a900c7a15a0855695e5158b5b0f8f6 -- View it on GitLab: https://salsa.debian.org/med-team/bcftools/-/compare/97185075bb2916a200ba662d1a5feb8b5778ae0b...7f818e8a29a900c7a15a0855695e5158b5b0f8f6 You're receiving this email because of your account on salsa.debian.org.
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