Import bcftools_1.3.1.orig.tar.gz
authorAfif Elghraoui <afif@debian.org>
Tue, 26 Apr 2016 05:24:50 +0000 (06:24 +0100)
committerAfif Elghraoui <afif@debian.org>
Tue, 26 Apr 2016 05:24:50 +0000 (06:24 +0100)
commitb47afd5fb976f3864e498c8e9a97e5f83b41eff8
tree23dd139dff1252938df1eb3feafa59ac802e8fc8
Import bcftools_1.3.1.orig.tar.gz

[dgit import orig bcftools_1.3.1.orig.tar.gz]
382 files changed:
AUTHORS [new file with mode: 0644]
HMM.c [new file with mode: 0644]
HMM.h [new file with mode: 0644]
INSTALL [new file with mode: 0644]
LICENSE [new file with mode: 0644]
Makefile [new file with mode: 0644]
README [new file with mode: 0644]
bcftools.h [new file with mode: 0644]
call.h [new file with mode: 0644]
ccall.c [new file with mode: 0644]
consensus.c [new file with mode: 0644]
convert.c [new file with mode: 0644]
convert.h [new file with mode: 0644]
doc/bcftools.1 [new file with mode: 0644]
doc/bcftools.html [new file with mode: 0644]
doc/bcftools.txt [new file with mode: 0644]
doc/docbook-xsl.css [new file with mode: 0644]
em.c [new file with mode: 0644]
filter.c [new file with mode: 0644]
filter.h [new file with mode: 0644]
gvcf.c [new file with mode: 0644]
gvcf.h [new file with mode: 0644]
khash_str2str.h [new file with mode: 0644]
kmin.c [new file with mode: 0644]
kmin.h [new file with mode: 0644]
main.c [new file with mode: 0644]
mcall.c [new file with mode: 0644]
peakfit.c [new file with mode: 0644]
peakfit.h [new file with mode: 0644]
ploidy.c [new file with mode: 0644]
ploidy.h [new file with mode: 0644]
plot-vcfstats [new file with mode: 0755]
plugins/GTisec.c [new file with mode: 0644]
plugins/GTisec.mk [new file with mode: 0644]
plugins/color-chrs.c [new file with mode: 0644]
plugins/color-chrs.mk [new file with mode: 0644]
plugins/color-chrs.pl [new file with mode: 0755]
plugins/counts.c [new file with mode: 0644]
plugins/dosage.c [new file with mode: 0644]
plugins/fill-AN-AC.c [new file with mode: 0644]
plugins/fill-tags.c [new file with mode: 0644]
plugins/fixploidy.c [new file with mode: 0644]
plugins/fixploidy.mk [new file with mode: 0644]
plugins/frameshifts.c [new file with mode: 0644]
plugins/impute-info.c [new file with mode: 0644]
plugins/mendelian.c [new file with mode: 0644]
plugins/missing2ref.c [new file with mode: 0644]
plugins/setGT.c [new file with mode: 0644]
plugins/tag2tag.c [new file with mode: 0644]
plugins/vcf2sex.c [new file with mode: 0644]
plugins/vcf2sex.mk [new file with mode: 0644]
polysomy.c [new file with mode: 0644]
prob1.c [new file with mode: 0644]
prob1.h [new file with mode: 0644]
rbuf.h [new file with mode: 0644]
reheader.c [new file with mode: 0644]
tabix.c [new file with mode: 0644]
test/23andme.fa [new file with mode: 0644]
test/23andme.fa.fai [new file with mode: 0644]
test/annotate.hdr [new file with mode: 0644]
test/annotate.out [new file with mode: 0644]
test/annotate.tab [new file with mode: 0644]
test/annotate.vcf [new file with mode: 0644]
test/annotate10.hdr [new file with mode: 0644]
test/annotate10.out [new file with mode: 0644]
test/annotate10.vcf [new file with mode: 0644]
test/annotate2.out [new file with mode: 0644]
test/annotate2.tab [new file with mode: 0644]
test/annotate2.vcf [new file with mode: 0644]
test/annotate3.out [new file with mode: 0644]
test/annotate3.vcf [new file with mode: 0644]
test/annotate4.hdr [new file with mode: 0644]
test/annotate4.out [new file with mode: 0644]
test/annotate4.vcf [new file with mode: 0644]
test/annotate5.out [new file with mode: 0644]
test/annotate6.out [new file with mode: 0644]
test/annotate7.out [new file with mode: 0644]
test/annotate8.out [new file with mode: 0644]
test/annotate9.out [new file with mode: 0644]
test/annotate9.vcf [new file with mode: 0644]
test/annots.vcf [new file with mode: 0644]
test/annots10.tab [new file with mode: 0644]
test/annots2.vcf [new file with mode: 0644]
test/annots4.tab [new file with mode: 0644]
test/annots4.vcf [new file with mode: 0644]
test/annots9.tab [new file with mode: 0644]
test/annots9.vcf [new file with mode: 0644]
test/check.chk [new file with mode: 0644]
test/check.gs.chrom.gen [new file with mode: 0644]
test/check.gs.chrom.samples [new file with mode: 0644]
test/check.gs.vcfids.gen [new file with mode: 0644]
test/check.gs.vcfids.samples [new file with mode: 0644]
test/check.gs.vcfids_chrom.gen [new file with mode: 0644]
test/check.gs.vcfids_chrom.samples [new file with mode: 0644]
test/check.vcf [new file with mode: 0644]
test/check_merge.chk [new file with mode: 0644]
test/concat.1.a.vcf [new file with mode: 0644]
test/concat.1.b.vcf [new file with mode: 0644]
test/concat.1.bcf.out [new file with mode: 0644]
test/concat.1.vcf.out [new file with mode: 0644]
test/concat.2.a.vcf [new file with mode: 0644]
test/concat.2.b.vcf [new file with mode: 0644]
test/concat.2.bcf.out [new file with mode: 0644]
test/concat.2.vcf.out [new file with mode: 0644]
test/concat.3.0.vcf [new file with mode: 0644]
test/concat.3.a.vcf [new file with mode: 0644]
test/concat.3.b.vcf [new file with mode: 0644]
test/concat.3.bcf.out [new file with mode: 0644]
test/concat.3.c.vcf [new file with mode: 0644]
test/concat.3.d.vcf [new file with mode: 0644]
test/concat.3.e.vcf [new file with mode: 0644]
test/concat.3.f.vcf [new file with mode: 0644]
test/concat.3.vcf.out [new file with mode: 0644]
test/concat.4.bcf.out [new file with mode: 0644]
test/concat.4.vcf.out [new file with mode: 0644]
test/consensus.1.chain [new file with mode: 0644]
test/consensus.1.out [new file with mode: 0644]
test/consensus.2.chain [new file with mode: 0644]
test/consensus.2.out [new file with mode: 0644]
test/consensus.3.chain [new file with mode: 0644]
test/consensus.3.out [new file with mode: 0644]
test/consensus.4.chain [new file with mode: 0644]
test/consensus.4.out [new file with mode: 0644]
test/consensus.5.out [new file with mode: 0644]
test/consensus.fa [new file with mode: 0644]
test/consensus.tab [new file with mode: 0644]
test/consensus.vcf [new file with mode: 0644]
test/consensus2.1.out [new file with mode: 0644]
test/consensus2.2.out [new file with mode: 0644]
test/consensus2.fa [new file with mode: 0644]
test/consensus2.vcf [new file with mode: 0644]
test/convert.23andme [new file with mode: 0644]
test/convert.23andme.vcf [new file with mode: 0644]
test/convert.gs.gt.gen [new file with mode: 0644]
test/convert.gs.gt.samples [new file with mode: 0644]
test/convert.gs.pl.gen [new file with mode: 0644]
test/convert.gs.pl.samples [new file with mode: 0644]
test/convert.gt.noHead.vcf [new file with mode: 0644]
test/convert.gt.vcf [new file with mode: 0644]
test/convert.gvcf.out [new file with mode: 0644]
test/convert.gvcf.vcf [new file with mode: 0644]
test/convert.hls.gt.hap [new file with mode: 0644]
test/convert.hls.gt.legend [new file with mode: 0644]
test/convert.hls.gt.samples [new file with mode: 0644]
test/convert.hls.haps [new file with mode: 0644]
test/convert.hls.legend [new file with mode: 0644]
test/convert.hls.samples [new file with mode: 0644]
test/convert.hs.gt.hap [new file with mode: 0644]
test/convert.hs.gt.samples [new file with mode: 0644]
test/convert.hs.hap [new file with mode: 0644]
test/convert.hs.sample [new file with mode: 0644]
test/convert.vcf [new file with mode: 0644]
test/dosage.out [new file with mode: 0644]
test/empty.idx.out [new file with mode: 0644]
test/empty.idx_count.out [new file with mode: 0644]
test/empty.vcf [new file with mode: 0644]
test/ex1.gtf.gz [new file with mode: 0644]
test/ex2.vcf [new file with mode: 0644]
test/ex3.sam [new file with mode: 0644]
test/fill-AN-AC.out [new file with mode: 0644]
test/fill-tags.2.out [new file with mode: 0644]
test/fill-tags.out [new file with mode: 0644]
test/filter.1.out [new file with mode: 0644]
test/filter.1.vcf [new file with mode: 0644]
test/filter.10.out [new file with mode: 0644]
test/filter.11.out [new file with mode: 0644]
test/filter.2.out [new file with mode: 0644]
test/filter.2.vcf [new file with mode: 0644]
test/filter.3.out [new file with mode: 0644]
test/filter.3.vcf [new file with mode: 0644]
test/filter.4.out [new file with mode: 0644]
test/filter.4.vcf [new file with mode: 0644]
test/filter.5.out [new file with mode: 0644]
test/filter.6.out [new file with mode: 0644]
test/filter.7.out [new file with mode: 0644]
test/filter.8.out [new file with mode: 0644]
test/filter.9.out [new file with mode: 0644]
test/fixploidy.out [new file with mode: 0644]
test/fixploidy.ploidy [new file with mode: 0644]
test/fixploidy.samples [new file with mode: 0644]
test/fixploidy.vcf [new file with mode: 0644]
test/gvcf.fa [new file with mode: 0644]
test/gvcf.fa.fai [new file with mode: 0644]
test/idx.out [new file with mode: 0644]
test/idx.vcf [new file with mode: 0644]
test/idx_count.out [new file with mode: 0644]
test/isec.a.vcf [new file with mode: 0644]
test/isec.ab.C.out [new file with mode: 0644]
test/isec.ab.any.out [new file with mode: 0644]
test/isec.ab.both.out [new file with mode: 0644]
test/isec.ab.flt.out [new file with mode: 0644]
test/isec.ab.out [new file with mode: 0644]
test/isec.b.vcf [new file with mode: 0644]
test/isec.tab [new file with mode: 0644]
test/isec.tab.out [new file with mode: 0644]
test/large_chrom.20.1.2147483647.out [new file with mode: 0644]
test/large_chrom_csi_limit.20.1.2147483647.out [new file with mode: 0644]
test/large_chrom_csi_limit.vcf [new file with mode: 0644]
test/large_chrom_tbi_limit.20.1.536870912.out [new file with mode: 0644]
test/large_chrom_tbi_limit.vcf [new file with mode: 0644]
test/many.alleles.trim.out [new file with mode: 0644]
test/many.alleles.vcf [new file with mode: 0644]
test/merge.2.a.vcf [new file with mode: 0644]
test/merge.2.all.out [new file with mode: 0644]
test/merge.2.b.vcf [new file with mode: 0644]
test/merge.2.both.out [new file with mode: 0644]
test/merge.2.none.out [new file with mode: 0644]
test/merge.3.a.vcf [new file with mode: 0644]
test/merge.3.b.vcf [new file with mode: 0644]
test/merge.3.out [new file with mode: 0644]
test/merge.4.a.vcf [new file with mode: 0644]
test/merge.4.b.vcf [new file with mode: 0644]
test/merge.4.out [new file with mode: 0644]
test/merge.a.chk [new file with mode: 0644]
test/merge.a.vcf [new file with mode: 0644]
test/merge.abc.out [new file with mode: 0644]
test/merge.b.vcf [new file with mode: 0644]
test/merge.c.vcf [new file with mode: 0644]
test/missing.vcf [new file with mode: 0644]
test/missing2ref.out [new file with mode: 0644]
test/mpileup.1.out [new file with mode: 0644]
test/mpileup.2.out [new file with mode: 0644]
test/mpileup.X.out [new file with mode: 0644]
test/mpileup.X.vcf [new file with mode: 0644]
test/mpileup.c.1.out [new file with mode: 0644]
test/mpileup.c.X.out [new file with mode: 0644]
test/mpileup.c.X.vcf [new file with mode: 0644]
test/mpileup.c.vcf [new file with mode: 0644]
test/mpileup.cAls.out [new file with mode: 0644]
test/mpileup.ped [new file with mode: 0644]
test/mpileup.ploidy [new file with mode: 0644]
test/mpileup.samples [new file with mode: 0644]
test/mpileup.tab [new file with mode: 0644]
test/mpileup.vcf [new file with mode: 0644]
test/norm.fa [new file with mode: 0644]
test/norm.fa.fai [new file with mode: 0644]
test/norm.merge.2.out [new file with mode: 0644]
test/norm.merge.2.vcf [new file with mode: 0644]
test/norm.merge.3.out [new file with mode: 0644]
test/norm.merge.3.vcf [new file with mode: 0644]
test/norm.merge.out [new file with mode: 0644]
test/norm.merge.strict.out [new file with mode: 0644]
test/norm.merge.vcf [new file with mode: 0644]
test/norm.out [new file with mode: 0644]
test/norm.setref.out [new file with mode: 0644]
test/norm.setref.vcf [new file with mode: 0644]
test/norm.split.2.out [new file with mode: 0644]
test/norm.split.2.vcf [new file with mode: 0644]
test/norm.split.and.norm.out [new file with mode: 0644]
test/norm.split.out [new file with mode: 0644]
test/norm.split.vcf [new file with mode: 0644]
test/norm.telomere.out [new file with mode: 0644]
test/norm.telomere.vcf [new file with mode: 0644]
test/norm.vcf [new file with mode: 0644]
test/plugin-missing2ref.out.vcf [new file with mode: 0644]
test/plugin-missing2ref.vcf [new file with mode: 0644]
test/plugin1.vcf [new file with mode: 0644]
test/query.10.out [new file with mode: 0644]
test/query.11.out [new file with mode: 0644]
test/query.12.out [new file with mode: 0644]
test/query.13.out [new file with mode: 0644]
test/query.14.out [new file with mode: 0644]
test/query.15.out [new file with mode: 0644]
test/query.16.out [new file with mode: 0644]
test/query.17.out [new file with mode: 0644]
test/query.18.out [new file with mode: 0644]
test/query.19.out [new file with mode: 0644]
test/query.2.out [new file with mode: 0644]
test/query.2.vcf [new file with mode: 0644]
test/query.20.out [new file with mode: 0644]
test/query.21.out [new file with mode: 0644]
test/query.22.out [new file with mode: 0644]
test/query.23.out [new file with mode: 0644]
test/query.3.out [new file with mode: 0644]
test/query.4.out [new file with mode: 0644]
test/query.5.out [new file with mode: 0644]
test/query.6.out [new file with mode: 0644]
test/query.7.out [new file with mode: 0644]
test/query.8.out [new file with mode: 0644]
test/query.9.out [new file with mode: 0644]
test/query.filter.vcf [new file with mode: 0644]
test/query.out [new file with mode: 0644]
test/query.vcf [new file with mode: 0644]
test/regions.out [new file with mode: 0644]
test/regions.tab [new file with mode: 0644]
test/regions.vcf [new file with mode: 0644]
test/reheader.1.out [new file with mode: 0644]
test/reheader.1.out.bcf [new file with mode: 0644]
test/reheader.2.out [new file with mode: 0644]
test/reheader.3.out [new file with mode: 0644]
test/reheader.4.out [new file with mode: 0644]
test/reheader.empty.hdr [new file with mode: 0644]
test/reheader.empty.out [new file with mode: 0644]
test/reheader.hdr [new file with mode: 0644]
test/reheader.samples [new file with mode: 0644]
test/reheader.samples2 [new file with mode: 0644]
test/reheader.samples3 [new file with mode: 0644]
test/reheader.samples4 [new file with mode: 0644]
test/reheader.vcf [new file with mode: 0644]
test/stats.a.vcf [new file with mode: 0644]
test/stats.b.vcf [new file with mode: 0644]
test/stats.chk [new file with mode: 0644]
test/tabix.1.3000151.out [new file with mode: 0644]
test/tabix.2.3199812.out [new file with mode: 0644]
test/test-rbuf.c [new file with mode: 0644]
test/test.pl [new file with mode: 0755]
test/vcf2sex.out [new file with mode: 0644]
test/vcf2sex.vcf [new file with mode: 0644]
test/view.1.out [new file with mode: 0644]
test/view.10.out [new file with mode: 0644]
test/view.2.out [new file with mode: 0644]
test/view.3.out [new file with mode: 0644]
test/view.4.out [new file with mode: 0644]
test/view.5.out [new file with mode: 0644]
test/view.6.out [new file with mode: 0644]
test/view.7.out [new file with mode: 0644]
test/view.8.out [new file with mode: 0644]
test/view.9.out [new file with mode: 0644]
test/view.GL.vcf [new file with mode: 0644]
test/view.GTisec.H.out [new file with mode: 0644]
test/view.GTisec.Hm.out [new file with mode: 0644]
test/view.GTisec.Hmv.out [new file with mode: 0644]
test/view.GTisec.Hv.out [new file with mode: 0644]
test/view.GTisec.m.out [new file with mode: 0644]
test/view.GTisec.mv.out [new file with mode: 0644]
test/view.GTisec.out [new file with mode: 0644]
test/view.GTisec.v.out [new file with mode: 0644]
test/view.PL.vcf [new file with mode: 0644]
test/view.chrs.out [new file with mode: 0644]
test/view.chrs.tab [new file with mode: 0644]
test/view.chrs.vcf [new file with mode: 0644]
test/view.dropgenotypes.noheader.out [new file with mode: 0644]
test/view.dropgenotypes.out [new file with mode: 0644]
test/view.exclude.out [new file with mode: 0644]
test/view.filter.1.out [new file with mode: 0644]
test/view.filter.10.out [new file with mode: 0644]
test/view.filter.11.out [new file with mode: 0644]
test/view.filter.2.out [new file with mode: 0644]
test/view.filter.3.out [new file with mode: 0644]
test/view.filter.4.out [new file with mode: 0644]
test/view.filter.5.out [new file with mode: 0644]
test/view.filter.6.out [new file with mode: 0644]
test/view.filter.7.out [new file with mode: 0644]
test/view.filter.8.out [new file with mode: 0644]
test/view.filter.9.out [new file with mode: 0644]
test/view.filter.annovar.1.out [new file with mode: 0644]
test/view.filter.annovar.2.out [new file with mode: 0644]
test/view.filter.annovar.3.out [new file with mode: 0644]
test/view.filter.annovar.vcf [new file with mode: 0644]
test/view.filter.vcf [new file with mode: 0644]
test/view.minmaxac.1.out [new file with mode: 0644]
test/view.minmaxac.2.out [new file with mode: 0644]
test/view.minmaxac.vcf [new file with mode: 0644]
test/view.omitgenotypes.out [new file with mode: 0644]
test/view.omitgenotypes.vcf [new file with mode: 0644]
test/view.vcf [new file with mode: 0644]
test/view.vectors.A.out [new file with mode: 0644]
test/view.vectors.B.out [new file with mode: 0644]
test/view.vectors.vcf [new file with mode: 0644]
tsv2vcf.c [new file with mode: 0644]
tsv2vcf.h [new file with mode: 0644]
vcfannotate.c [new file with mode: 0644]
vcfcall.c [new file with mode: 0644]
vcfcnv.c [new file with mode: 0644]
vcfconcat.c [new file with mode: 0644]
vcfconvert.c [new file with mode: 0644]
vcffilter.c [new file with mode: 0644]
vcfgtcheck.c [new file with mode: 0644]
vcfindex.c [new file with mode: 0644]
vcfisec.c [new file with mode: 0644]
vcfmerge.c [new file with mode: 0644]
vcfnorm.c [new file with mode: 0644]
vcfplugin.c [new file with mode: 0644]
vcfquery.c [new file with mode: 0644]
vcfroh.c [new file with mode: 0644]
vcfsom.c [new file with mode: 0644]
vcfstats.c [new file with mode: 0644]
vcfutils.pl [new file with mode: 0755]
vcfview.c [new file with mode: 0644]
vcmp.c [new file with mode: 0644]
vcmp.h [new file with mode: 0644]
version.c [new file with mode: 0644]