[med-svn] [bcftools] branch upstream updated (9a27f71 -> 202ee54)
Afif Elghraoui
afif-guest at moszumanska.debian.org
Tue Feb 2 08:04:42 UTC 2016
This is an automated email from the git hooks/post-receive script.
afif-guest pushed a change to branch upstream
in repository bcftools.
from 9a27f71 Imported Upstream version 1.2
new 202ee54 Imported Upstream version 1.3
The 1 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails. The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.
Summary of changes:
AUTHORS | 2 +
HMM.c | 81 +-
HMM.h | 57 +-
Makefile | 66 +-
bcftools.h | 8 +
call.h | 22 +-
ccall.c | 7 +-
consensus.c | 11 +-
convert.c | 106 +-
convert.h | 6 +
doc/bcftools.1 | 719 +++-
doc/bcftools.html | 493 ++-
doc/bcftools.txt | 463 ++-
filter.c | 187 +-
filter.h | 1 +
gvcf.c | 190 +-
gvcf.h | 41 +
main.c | 6 +-
mcall.c | 198 +-
peakfit.c | 599 +++
peakfit.h | 49 +
ploidy.c | 41 +-
ploidy.h | 14 +-
plot-vcfstats | 58 +-
plugins/color-chrs.c | 559 +++
plugins/color-chrs.mk | 2 +
plugins/color-chrs.pl | 528 +++
plugins/dosage.c | 2 +-
plugins/fill-tags.c | 262 ++
plugins/fixploidy.c | 7 +-
plugins/fixploidy.mk | 4 +-
plugins/impute-info.c | 163 +
plugins/mendelian.c | 248 ++
plugins/setGT.c | 223 ++
plugins/tag2tag.c | 36 +-
plugins/vcf2sex.c | 305 +-
plugins/vcf2sex.mk | 4 +-
polysomy.c | 646 +--
rbuf.h | 25 +-
test/annotate4.out | 2 +-
test/annotate5.out | 4 +-
test/{merge.3.out => annotate9.out} | 12 +-
test/{merge.3.a.vcf => annotate9.vcf} | 10 +-
test/annots9.tab | 5 +
test/{merge.3.b.vcf => annots9.vcf} | 10 +-
test/check.chk | 11 +-
test/check.vcf | 7 +-
test/{check.chk => check_merge.chk} | 57 +-
test/{consensus.fa => consensus.5.out} | 18 +-
test/consensus2.1.out | 10 +
test/consensus2.2.out | 12 +
test/consensus2.fa | 10 +
test/consensus2.vcf | 9 +
test/convert.gs.gt.gen | 2 +-
test/convert.gt.noHead.vcf | 36 +
test/convert.gt.vcf | 43 +
test/convert.gvcf.out | 726 ++--
test/convert.gvcf.vcf | 116 +-
test/{convert.hls.haps => convert.hls.gt.hap} | 3 +
test/{convert.hls.legend => convert.hls.gt.legend} | 3 +
...{convert.hls.samples => convert.hls.gt.samples} | 0
test/convert.hs.gt.hap | 35 +
...convert.gs.gt.samples => convert.hs.gt.samples} | 0
test/fill-tags.out | 40 +
test/filter.10.out | 11 +
test/{merge.3.a.vcf => filter.11.out} | 8 +-
test/filter.4.vcf | 10 +
test/filter.9.out | 1 +
test/gvcf.fa | 9 +
test/gvcf.fa.fai | 1 +
test/many.alleles.trim.out | 10 +
test/many.alleles.vcf | 7 +
test/merge.2.b.vcf | 2 +-
test/{annotate2.vcf => missing.vcf} | 1 +
test/mpileup.2.out | 27 +-
test/{mpileup.cAls.out => mpileup.X.out} | 17 +-
test/mpileup.X.vcf | 4127 ++++++++++++++++++++
test/mpileup.c.1.out | 43 +
test/mpileup.c.X.out | 43 +
test/mpileup.c.X.vcf | 4127 ++++++++++++++++++++
test/{mpileup.vcf => mpileup.c.vcf} | 0
test/mpileup.cAls.out | 7 +
test/mpileup.ped | 3 +
test/mpileup.ploidy | 4 +
test/mpileup.samples | 3 +
test/mpileup.tab | 7 +
test/mpileup.vcf | 14 +-
test/norm.fa | 2 +
test/norm.fa.fai | 1 +
test/{reheader.2.out => norm.merge.2.out} | 43 +-
test/{reheader.2.out => norm.merge.2.vcf} | 46 +-
test/norm.merge.3.out | 34 +
test/norm.merge.3.vcf | 37 +
test/norm.merge.out | 2 +-
test/norm.merge.strict.out | 2 +-
test/norm.merge.vcf | 2 +-
test/norm.out | 2 +-
test/{reheader.vcf => norm.setref.out} | 51 +-
test/{reheader.vcf => norm.setref.vcf} | 51 +-
test/norm.split.2.out | 107 +
test/norm.split.2.vcf | 85 +
test/{norm.out => norm.split.and.norm.out} | 33 +-
test/norm.split.out | 11 +-
test/norm.split.vcf | 6 +-
test/norm.vcf | 2 +-
test/query.18.out | 2 +
test/query.19.out | 3 +
test/query.20.out | 2 +
test/query.21.out | 3 +
test/query.22.out | 2 +
test/query.23.out | 3 +
test/stats.chk | 24 +-
test/test-rbuf.c | 2 +-
test/test.pl | 85 +-
test/view.9.out | 4 -
test/view.GL.vcf | 29 +
test/view.PL.vcf | 29 +
test/view.dropgenotypes.noheader.out | 5 +
test/view.dropgenotypes.out | 12 +
test/view.filter.annovar.1.out | 2 +
test/view.filter.annovar.2.out | 1 +
test/view.filter.annovar.3.out | 1 +
test/view.filter.annovar.vcf | 52 +
vcfannotate.c | 138 +-
vcfcall.c | 584 +--
vcfcnv.c | 826 +++-
vcfconcat.c | 132 +-
vcfconvert.c | 159 +-
vcffilter.c | 37 +-
vcfgtcheck.c | 32 +-
vcfindex.c | 8 +-
vcfisec.c | 73 +-
vcfmerge.c | 46 +-
vcfnorm.c | 931 ++---
vcfplugin.c | 124 +-
vcfquery.c | 15 +-
vcfroh.c | 101 +-
vcfstats.c | 180 +-
vcfview.c | 89 +-
vcmp.c | 14 +-
version.c | 8 +
141 files changed, 17589 insertions(+), 2788 deletions(-)
create mode 100644 gvcf.h
create mode 100644 peakfit.c
create mode 100644 peakfit.h
create mode 100644 plugins/color-chrs.c
create mode 100644 plugins/color-chrs.mk
create mode 100755 plugins/color-chrs.pl
create mode 100644 plugins/fill-tags.c
create mode 100644 plugins/impute-info.c
create mode 100644 plugins/mendelian.c
create mode 100644 plugins/setGT.c
copy test/{merge.3.out => annotate9.out} (72%)
copy test/{merge.3.a.vcf => annotate9.vcf} (74%)
create mode 100644 test/annots9.tab
copy test/{merge.3.b.vcf => annots9.vcf} (73%)
copy test/{check.chk => check_merge.chk} (62%)
copy test/{consensus.fa => consensus.5.out} (50%)
create mode 100644 test/consensus2.1.out
create mode 100644 test/consensus2.2.out
create mode 100644 test/consensus2.fa
create mode 100644 test/consensus2.vcf
create mode 100644 test/convert.gt.noHead.vcf
create mode 100644 test/convert.gt.vcf
copy test/{convert.hls.haps => convert.hls.gt.hap} (91%)
copy test/{convert.hls.legend => convert.hls.gt.legend} (87%)
copy test/{convert.hls.samples => convert.hls.gt.samples} (100%)
create mode 100644 test/convert.hs.gt.hap
copy test/{convert.gs.gt.samples => convert.hs.gt.samples} (100%)
create mode 100644 test/fill-tags.out
create mode 100644 test/filter.10.out
copy test/{merge.3.a.vcf => filter.11.out} (84%)
create mode 100644 test/filter.4.vcf
create mode 100644 test/filter.9.out
create mode 100644 test/gvcf.fa
create mode 100644 test/gvcf.fa.fai
create mode 100644 test/many.alleles.trim.out
create mode 100644 test/many.alleles.vcf
copy test/{annotate2.vcf => missing.vcf} (90%)
copy test/{mpileup.cAls.out => mpileup.X.out} (51%)
create mode 100644 test/mpileup.X.vcf
create mode 100644 test/mpileup.c.1.out
create mode 100644 test/mpileup.c.X.out
create mode 100644 test/mpileup.c.X.vcf
copy test/{mpileup.vcf => mpileup.c.vcf} (100%)
create mode 100644 test/mpileup.ped
create mode 100644 test/mpileup.ploidy
create mode 100644 test/mpileup.samples
copy test/{reheader.2.out => norm.merge.2.out} (56%)
copy test/{reheader.2.out => norm.merge.2.vcf} (56%)
create mode 100644 test/norm.merge.3.out
create mode 100644 test/norm.merge.3.vcf
copy test/{reheader.vcf => norm.setref.out} (59%)
copy test/{reheader.vcf => norm.setref.vcf} (59%)
create mode 100644 test/norm.split.2.out
create mode 100644 test/norm.split.2.vcf
copy test/{norm.out => norm.split.and.norm.out} (60%)
create mode 100644 test/query.18.out
create mode 100644 test/query.19.out
create mode 100644 test/query.20.out
create mode 100644 test/query.21.out
create mode 100644 test/query.22.out
create mode 100644 test/query.23.out
create mode 100644 test/view.GL.vcf
create mode 100644 test/view.PL.vcf
create mode 100644 test/view.dropgenotypes.noheader.out
create mode 100644 test/view.dropgenotypes.out
create mode 100644 test/view.filter.annovar.1.out
create mode 100644 test/view.filter.annovar.2.out
create mode 100644 test/view.filter.annovar.3.out
create mode 100644 test/view.filter.annovar.vcf
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