[med-svn] [bcftools] branch master updated (dd74087 -> f857186)
Afif Elghraoui
afif-guest at moszumanska.debian.org
Tue Feb 2 08:04:41 UTC 2016
This is an automated email from the git hooks/post-receive script.
afif-guest pushed a change to branch master
in repository bcftools.
from dd74087 bcftools (1.2-2) unstable; urgency=medium
new 202ee54 Imported Upstream version 1.3
new 94ca8c0 Merge tag 'upstream/1.3'
new c84be00 Update patches
new 2dada45 Prepare new revision
new 4906458 Adjust pluginpath setting
new f857186 Add a TODO file documenting work remaining to be done
The 6 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 +
debian/TODO | 5 +
debian/changelog | 6 +
debian/patches/compiler-flags.patch | 38 +-
debian/patches/destdir.patch | 24 +-
debian/patches/external-libs.patch | 57 +-
debian/patches/improve-plugin-support.patch | 212 -
debian/patches/series | 1 -
debian/patches/spelling.patch | 28 +-
debian/patches/tests-pluginpath.patch | 2 +-
debian/rules | 2 +-
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 +
151 files changed, 17643 insertions(+), 3109 deletions(-)
create mode 100644 debian/TODO
delete mode 100644 debian/patches/improve-plugin-support.patch
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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