Andreas Tille pushed to branch upstream at Debian Med / bcftools
Commits: 2db306a6 by Andreas Tille at 2026-09-16T09:56:16+02:00 New upstream version 1.24 - - - - - 298 changed files: - + CONTRIBUTING.md - HMM.c - HMM.h - Makefile - NEWS - abuf.c - bam2bcf.c - bam2bcf.h - bam2bcf_iaux.c - bam2bcf_indel.c - bam_sample.c - bcftools.h - bin.c - ccall.c - config.mk.in - configure.ac - consensus.c - convert.c - csq.c - dist.c - doc/bcftools.1 - doc/bcftools.html - doc/bcftools.txt - filter.c - gff.c - hex.h - m4/hts_prog_cc_warnings.m4 - main.c - mcall.c - misc/roh-viz - misc/vrfs-variances - mpileup.c - mpileup2/mpileup.c - ploidy.c - plugins/add-variantkey.c - plugins/af-dist.c - plugins/check-sparsity.c - plugins/fill-tags.c - plugins/fixploidy.c - plugins/fixref.c - plugins/guess-ploidy.c - plugins/gvcfz.c - plugins/mendelian2.c - plugins/missing2ref.c - plugins/prune.c - plugins/scatter.c - plugins/setGT.c - plugins/split-vep.c - plugins/split.c - plugins/tag2tag.c - plugins/trio-dnm2.c → plugins/trio-dnm3.c - plugins/trio-switch-rate.c - plugins/vcf2table.c - plugins/vrfs.c - rbuf.h - read_consensus.c - regidx.c - reheader.c - smpl_ilist.c - str_finder.c - tabix.c - + test/annotate.AR.1.out - + test/annotate.AR.2.out - + test/annotate.AR.tab - + test/annotate.AR.vcf - + test/annotate.int.1.out - + test/annotate.int.dst.vcf - + test/annotate.int.src.vcf - + test/annotate.pipes.1.out - + test/annotate.pipes.2.out - + test/annotate.pipes.tab - + test/annotate.pipes.vcf - + test/annotate.rename.1.out - + test/annotate.rename.2.out - + test/annotate.rename.vcf - test/annotate29.out - + test/annotate36.1.out - + test/annotate36.vcf - test/annotate8.out - + test/annots36.bed - test/atomize.split.1.0.out - test/atomize.split.1.1.out - + test/consensus.overlaps.2.fa - + test/convert.gvcf.2.out - + test/convert.gvcf.2.vcf - test/convert.gvcf.out - test/convert.gvcf.vcf - test/csq.1.out - + test/csq.greedy.1.1.out - + test/csq.greedy.1.2.out - + test/csq.greedy.1.3.out - + test/csq.greedy.1.4.out - + test/csq.greedy.1.fa - + test/csq.greedy.1.gff - + test/csq.greedy.1.vcf - + test/csq.greedy.2.1.out - + test/csq.greedy.2.2.out - + test/csq.greedy.2.3.out - + test/csq.greedy.2.4.out - + test/csq.greedy.2.fa - + test/csq.greedy.2.gff - + test/csq.greedy.2.vcf - + test/csq.ismpl.1.out - + test/csq.ismpl.fa - + test/csq.ismpl.gff - + test/csq.ismpl.vcf - + test/csq.oob-codon.fa - + test/csq.oob-codon.gff - + test/csq.oob-codon.out - + test/csq.oob-codon.vcf - + test/csq.splice.issue-2543.1.out - + test/csq.splice.issue-2543.fa - + test/csq.splice.issue-2543.gff - + test/csq.splice.issue-2543.vcf - + test/csq.vcf.ascii-art.txt - + test/csq/ENST00000000001/ENST00000000001.fa - + test/csq/ENST00000000001/ENST00000000001.fa.fai - + test/csq/ENST00000000001/ENST00000000001.gff - + test/csq/ENST00000000001/test.1.cmd - + test/csq/ENST00000000001/test.1.cmd.out - + test/csq/ENST00000000001/test.2.cmd - + test/csq/ENST00000000001/test.2.cmd.out - + test/csq/ENST00000000001/test.vcf - test/csq/ENST00000263103-INS/insertions.txt - test/csq/ENST00000263103-INS/insertions.vcf - + test/csq/ENST00000428061/ENST00000428061.fa - + test/csq/ENST00000428061/ENST00000428061.fa.fai - + test/csq/ENST00000428061/ENST00000428061.gff - + test/csq/ENST00000428061/ascii-art.txt - + test/csq/ENST00000428061/failed-assert.vcf - test/fill-tags-AN0.out - test/fill-tags-hemi.1.out - test/fill-tags-hemi.2.out - test/fill-tags-hwe.out - + test/fill-tags-rw.vcf - test/fill-tags.5.out - + test/fill-tags.MAC-MAF.1.out - + test/fill-tags.MAC-MAF.vcf - + test/fill-tags.func.1.out - + test/filter.mac.1.out - + test/filter.mac.vcf - + test/fmissing.1.out - + test/fmissing.2.out - + test/fmissing.txt - + test/fmissing.vcf - test/gtcheck.2.out - test/gtcheck.5.1.out - + test/gtcheck.gvcf.1.out - + test/gtcheck.gvcf.2.out - + test/gtcheck.gvcf.a.vcf - + test/gtcheck.gvcf.b.vcf - test/mendelian.1.out - test/mendelian.3.out - test/mendelian.4.out - test/mendelian.6.out - test/mendelian.8.out - + test/mendelian.9.out - + test/mendelian.ped - test/merge.LPL.3.out - + test/merge.exact.1.out - + test/merge.exact.2.out - + test/merge.exact.a.vcf - + test/merge.exact.b.vcf - test/norm.2.out - test/norm.2.vcf - + test/norm.check-ref.1.out - + test/norm.check-ref.fa - + test/norm.check-ref.vcf - + test/norm.dup-end.1.out - + test/norm.dup-end.2.out - + test/norm.dup-end.3.out - + test/norm.dup-end.fa - + test/norm.dup-end.vcf - + test/norm.filter.1.out - + test/norm.filter.2.out - + test/norm.filter.txt - + test/norm.filter.vcf - + test/norm.iupac.2.1.out - + test/norm.iupac.2.fa - + test/norm.iupac.2.vcf - test/norm.setref.out - + test/norm.split.1.out - test/norm.vcf - test/query.func.1.2.out - test/query.func.1.3.out - test/roh.1.1.out - test/roh.1.2.out - test/roh.1.3.out - test/roh.1.4.out - + test/smpl-count.1.out - + test/smpl-count.2.out - + test/smpl-count.3.out - + test/smpl-count.vcf - + test/split-vep.11.1.out - + test/split-vep.11.2.out - + test/split-vep.11.vcf - + test/split-vep.12.1.out - + test/split-vep.12.4.out - + test/split-vep.12.vcf - test/split-vep.filter.1.out - test/split-vep.filter.2.out - + test/split-vep.icase.1.1.out - + test/split-vep.icase.1.severity - + test/split-vep.icase.1.vcf - + test/stats-smpl-order.chk - + test/stats-smpl-order.vcf - test/test-regidx.c - test/test.pl - test/trio-dnm/trio-dnm.1.out - test/trio-dnm/trio-dnm.11.1.out - test/trio-dnm/trio-dnm.11.2.out - + test/trio-dnm/trio-dnm.12.1.out - + test/trio-dnm/trio-dnm.12.vcf - test/trio-dnm/trio-dnm.8.1.out - test/trio-dnm/trio-dnm.9.1.out - + test/trio-dnm3.1.out - + test/trio-dnm3/create-dnm-test - + test/trio-dnm3/dnm01.vcf - + test/trio-dnm3/dnm06.vcf - + test/trio-dnm3/dnm07.vcf - + test/trio-dnm3/dnm09.vcf - + test/trio-dnm3/dnm10.vcf - + test/trio-dnm3/dnm11.vcf - + test/trio-dnm3/dnm12.vcf - + test/trio-dnm3/dnm13.vcf - + test/trio-dnm3/dnm14.vcf - + test/trio-dnm3/dnm15.vcf - + test/trio-dnm3/dnm16.vcf - + test/trio-dnm3/dnm17.vcf - + test/trio-dnm3/dnm18.vcf - + test/trio-dnm3/dnm19.vcf - + test/trio-dnm3/dnm20.vcf - + test/trio-dnm3/dnm21.vcf - + test/trio-dnm3/dnm22.vcf - + test/trio-dnm3/dnm23.vcf - + test/trio-dnm3/dnm24.vcf - + test/trio-dnm3/dnm25.vcf - + test/trio-dnm3/dnm26.vcf - + test/trio-dnm3/dnm27.vcf - + test/trio-dnm3/dnm28.vcf - + test/trio-dnm3/dnm29.vcf - + test/trio-dnm3/dnm30.vcf - + test/trio-dnm3/dnm31.vcf - + test/trio-dnm3/dnm32.vcf - + test/trio-dnm3/dnm33.vcf - + test/trio-dnm3/dnm34.vcf - + test/trio-dnm3/dnm35.vcf - + test/trio-dnm3/dnm36.vcf - + test/trio-dnm3/dnm37.vcf - + test/trio-dnm3/dnm38.vcf - + test/trio-dnm3/dnm39.vcf - + test/trio-dnm3/dnm40.vcf - + test/trio-dnm3/dnm41.vcf - + test/trio-dnm3/dnm42.vcf - + test/trio-dnm3/dnm43.vcf - + test/trio-dnm3/dnm44.vcf - + test/trio-dnm3/dnm45.vcf - + test/trio-dnm3/dnm46.vcf - + test/trio-dnm3/dnm47.vcf - + test/trio-dnm3/dnm48.vcf - + test/trio-dnm3/dnm49.vcf - + test/trio-dnm3/dnm50.vcf - + test/trio-dnm3/dnm51.vcf - + test/trio-dnm3/dnm52.vcf - + test/trio-dnm3/dnm53.vcf - + test/trio-dnm3/dnm54.vcf - + test/trio-dnm3/test.sh - + test/view.types.1.out - + test/view.types.2.out - + test/view.types.3.out - + test/view.types.4.out - + test/view.types.5.out - + test/view.types.6.out - + test/view.types.7.out - + test/view.types.vcf - test/view.vectors.C.out - tsv2vcf.c - tsv2vcf.h - variantkey.h - vcfannotate.c - vcfbuf.c - vcfcall.c - vcfcnv.c - vcfconcat.c - vcfconvert.c - vcffilter.c - vcfgtcheck.c - vcfisec.c - vcfmerge.c - vcfnorm.c - vcfplugin.c - vcfquery.c - vcfroh.c - vcfstats.c - vcfview.c - vcmp.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/-/commit/2db306a6a016d34cd170ebaf154d144e456b1f3d -- View it on GitLab: https://salsa.debian.org/med-team/bcftools/-/commit/2db306a6a016d34cd170ebaf154d144e456b1f3d 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
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