[med-svn] [Git][med-team/bcftools][master] 5 commits: New upstream version

Sun Aug 17 21:46:09 BST 2025

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

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1ceb304e by Steffen Moeller at 2025-08-17T20:55:22+02:00
New upstream version 1.22
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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
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f7b45e31 by Steffen Moeller at 2025-08-17T20:55:39+02:00
Standards-Version: 4.7.2 (routine-update)

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7f818e8a by Steffen Moeller at 2025-08-17T22:44:31+02:00
New upstream versionn 1.22.

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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

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View it on GitLab: https://salsa.debian.org/med-team/bcftools/-/compare/97185075bb2916a200ba662d1a5feb8b5778ae0b...7f818e8a29a900c7a15a0855695e5158b5b0f8f6
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