[med-svn] [Git][med-team/libvcflib][upstream] New upstream version 1.0.15+dfsg

[Andreas Tille (@tille)]

Andreas Tille pushed to branch upstream at Debian Med / libvcflib


Commits:
bcc57ccb by Andreas Tille at 2026-10-22T16:01:22+02:00
New upstream version 1.0.15+dfsg
- - - - -


319 changed files:

- .github/workflows/ci_test.yml
- .gitignore
- CMakeLists.txt
- README.md
- RELEASE_NOTES.md
- + TODO.md
- VERSION
- doc/abba-baba.md
- doc/bFst.md
- doc/dumpContigsFromHeader.md
- doc/genotypeSummary.md
- doc/hapLrt.md
- doc/iHS.md
- doc/meltEHH.md
- doc/normalize-iHS.md
- doc/pFst.md
- doc/pVst.md
- doc/permuteGPAT++.md
- doc/permuteSmooth.md
- doc/plotHaps.md
- doc/popStats.md
- doc/segmentFst.md
- doc/segmentIhs.md
- doc/sequenceDiversity.md
- doc/smoother.md
- doc/vcf2dag.md
- doc/vcf2fasta.md
- doc/vcf2tsv.md
- doc/vcfaddinfo.md
- doc/vcfafpath.md
- doc/vcfallelicprimitives.md
- doc/vcfaltcount.md
- doc/vcfannotate.md
- doc/vcfannotategenotypes.md
- doc/vcfbreakmulti.md
- doc/vcfcat.md
- doc/vcfcheck.md
- doc/vcfclassify.md
- doc/vcfcleancomplex.md
- doc/vcfcombine.md
- doc/vcfcommonsamples.md
- doc/vcfcountalleles.md
- doc/vcfcreatemulti.md
- doc/vcfdistance.md
- doc/vcfecho.md
- doc/vcfentropy.md
- doc/vcfevenregions.md
- doc/vcffilter.md
- doc/vcffixup.md
- doc/vcfflatten.md
- doc/vcfgeno2alleles.md
- doc/vcfgeno2haplo.md
- doc/vcfgenosamplenames.md
- doc/vcfgenosummarize.md
- doc/vcfgenotypecompare.md
- doc/vcfgenotypes.md
- doc/vcfglbound.md
- doc/vcfglxgt.md
- doc/vcfhetcount.md
- doc/vcfhethomratio.md
- doc/vcfindex.md
- doc/vcfinfo2qual.md
- doc/vcfinfosummarize.md
- doc/vcfintersect.md
- doc/vcfkeepgeno.md
- doc/vcfkeepinfo.md
- doc/vcfkeepsamples.md
- doc/vcfld.md
- doc/vcfleftalign.md
- doc/vcflength.md
- doc/vcflib.md
- doc/vcfnullgenofields.md
- doc/vcfnumalt.md
- doc/vcfoverlay.md
- doc/vcfparsealts.md
- doc/vcfprimers.md
- doc/vcfqual2info.md
- doc/vcfrandom.md
- doc/vcfrandomsample.md
- doc/vcfremap.md
- doc/vcfremoveaberrantgenotypes.md
- doc/vcfremovesamples.md
- doc/vcfroc.md
- doc/vcfsample2info.md
- doc/vcfsamplediff.md
- doc/vcfsamplenames.md
- doc/vcfsitesummarize.md
- doc/vcfstats.md
- doc/vcfstreamsort.md
- doc/vcfuniq.md
- doc/vcfuniqalleles.md
- doc/vcfwave.md
- doc/wcFst.md
- guix.scm
- man/abba-baba.1
- man/bFst.1
- man/dumpContigsFromHeader.1
- man/genotypeSummary.1
- man/hapLrt.1
- man/iHS.1
- man/meltEHH.1
- man/normalize-iHS.1
- man/pFst.1
- man/pVst.1
- man/permuteGPAT++.1
- man/permuteSmooth.1
- man/plotHaps.1
- man/popStats.1
- man/segmentFst.1
- man/segmentIhs.1
- man/sequenceDiversity.1
- man/smoother.1
- man/vcf2dag.1
- man/vcf2fasta.1
- man/vcf2tsv.1
- man/vcfaddinfo.1
- man/vcfafpath.1
- man/vcfallelicprimitives.1
- man/vcfaltcount.1
- man/vcfannotate.1
- man/vcfannotategenotypes.1
- man/vcfbreakmulti.1
- man/vcfcat.1
- man/vcfcheck.1
- man/vcfclassify.1
- man/vcfcleancomplex.1
- man/vcfcombine.1
- man/vcfcommonsamples.1
- man/vcfcountalleles.1
- man/vcfcreatemulti.1
- man/vcfdistance.1
- man/vcfecho.1
- man/vcfentropy.1
- man/vcfevenregions.1
- man/vcffilter.1
- man/vcffixup.1
- man/vcfflatten.1
- man/vcfgeno2alleles.1
- man/vcfgeno2haplo.1
- man/vcfgenosamplenames.1
- man/vcfgenosummarize.1
- man/vcfgenotypecompare.1
- man/vcfgenotypes.1
- man/vcfglbound.1
- man/vcfglxgt.1
- man/vcfhetcount.1
- man/vcfhethomratio.1
- man/vcfindex.1
- man/vcfinfo2qual.1
- man/vcfinfosummarize.1
- man/vcfintersect.1
- man/vcfkeepgeno.1
- man/vcfkeepinfo.1
- man/vcfkeepsamples.1
- man/vcfld.1
- man/vcfleftalign.1
- man/vcflength.1
- man/vcflib.1
- man/vcfnullgenofields.1
- man/vcfnumalt.1
- man/vcfoverlay.1
- man/vcfparsealts.1
- man/vcfprimers.1
- man/vcfqual2info.1
- man/vcfrandom.1
- man/vcfrandomsample.1
- man/vcfremap.1
- man/vcfremoveaberrantgenotypes.1
- man/vcfremovesamples.1
- man/vcfroc.1
- man/vcfsample2info.1
- man/vcfsamplediff.1
- man/vcfsamplenames.1
- man/vcfsitesummarize.1
- man/vcfstats.1
- man/vcfstreamsort.1
- man/vcfuniq.1
- man/vcfuniqalleles.1
- man/vcfwave.1
- man/wcFst.1
- + samples/test_variant_drop.vcf
- src/BedReader.h
- src/LeftAlign.cpp
- src/LeftAlign.hpp
- src/Variant.cpp
- src/Variant.h
- src/abba-baba.cpp
- src/allele.cpp
- src/allele.hpp
- src/bFst.cpp
- − src/canonicalize.cpp
- − src/canonicalize.h
- src/cdflib.cpp
- src/cdflib.hpp
- src/cigar.cpp
- src/cigar.hpp
- src/dumpContigsFromHeader.cpp
- src/genotypeSummary.cpp
- src/gl-XPEHH.cpp
- src/gpatInfo.hpp
- src/hapLrt.cpp
- src/iHS.cpp
- + src/index.cpp
- + src/index.hpp
- src/join.h
- src/legacy.cpp
- src/legacy.h
- − src/makeUnique.h
- src/meltEHH.cpp
- src/mt19937ar.h
- src/multichoose.h
- src/normalize-iHS.cpp
- src/pFst.cpp
- src/pVst.cpp
- src/pdflib.cpp
- src/pdflib.hpp
- src/permuteGPAT++.cpp
- src/permuteGPATsmoother.cpp
- src/permuteRegions.cpp
- src/permuteSmooth.cpp
- + src/phase.cpp
- + src/phase.hpp
- src/plotHaps.cpp
- src/popStats.cpp
- src/rkmh.cpp
- src/rkmh.hpp
- src/rnglib.cpp
- src/rnglib.hpp
- src/segmentFst.cpp
- src/segmentIhs.cpp
- src/sequenceDiversity.cpp
- src/smoother.cpp
- src/split.h
- src/splitUniqStarts.cpp
- + src/stats.cpp
- + src/stats.hpp
- src/var.cpp
- src/var.hpp
- src/vcf-c-api.cpp
- src/vcf-c-api.h
- src/vcf-wfa.cpp
- src/vcf-wfa.h
- src/vcf2dag.cpp
- src/vcf2fasta.cpp
- src/vcf2tsv.cpp
- src/vcfToHap.cpp
- src/vcfaddinfo.cpp
- src/vcfafpath.cpp
- src/vcfallelicprimitives.cpp
- src/vcfannotate.cpp
- src/vcfannotategenotypes.cpp
- src/vcfbreakmulti.cpp
- src/vcfcheck.cpp
- src/vcfclassify.cpp
- src/vcfcleancomplex.cpp
- src/vcfcombine.cpp
- src/vcfcommonsamples.cpp
- src/vcfcreatemulti.cpp
- src/vcfdistance.cpp
- src/vcfentropy.cpp
- src/vcfevenregions.cpp
- src/vcffixup.cpp
- src/vcfflatten.cpp
- src/vcfgeno2alleles.cpp
- src/vcfgeno2haplo.cpp
- src/vcfgenosamplenames.cpp
- src/vcfgenosummarize.cpp
- src/vcfgenotypecompare.cpp
- src/vcfgenotypes.cpp
- src/vcfglbound.cpp
- src/vcfglxgt.cpp
- src/vcfhetcount.cpp
- src/vcfhethomratio.cpp
- src/vcfinfo2qual.cpp
- src/vcfinfosummarize.cpp
- src/vcfintersect.cpp
- src/vcfkeepgeno.cpp
- src/vcfkeepinfo.cpp
- src/vcfkeepsamples.cpp
- src/vcfld.cpp
- src/vcfleftalign.cpp
- src/vcfnull2ref.cpp
- src/vcfnullgenofields.cpp
- src/vcfnumalt.cpp
- src/vcfprimers.cpp
- src/vcfqual2info.cpp
- src/vcfrandom.cpp
- src/vcfrandomsample.cpp
- src/vcfremap.cpp
- src/vcfremoveaberrantgenotypes.cpp
- src/vcfremovesamples.cpp
- src/vcfsample2info.cpp
- src/vcfsamplediff.cpp
- src/vcfsamplenames.cpp
- src/vcfsamplestats.cpp
- src/vcfsitesummarize.cpp
- src/vcfsom.cpp
- src/vcfstats.cpp
- src/vcfstreamsort.cpp
- src/vcfuniq.cpp
- src/vcfuniqalleles.cpp
- src/vcfunphase.cpp
- src/vcfwave.cpp
- src/wcFst.cpp
- src/xpEHH.cpp
- src/zig/README.md
- src/zig/build.zig
- src/zig/compile.sh
- src/zig/samples.zig
- src/zig/vcf.zig
- test/data/regression/vcfwave_4.vcf
- test/data/regression/vcfwave_5.vcf
- + test/data/regression/vcfwave_6.vcf
- test/pytest/rtest.py
- test/pytest/vcfallelicprimitives.md
- test/pytest/vcfcreatemulti.md
- test/pytest/vcffilter.md
- test/pytest/vcfwave.md
- + vcflib.pc.in


The diff was not included because it is too large.


View it on GitLab: https://salsa.debian.org/med-team/libvcflib/-/commit/bcc57ccbfedab86310e5ab6855ec4a695c8e56bf

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