[med-svn] [bcftools] branch debian/jessie-backports updated (2a949c3 -> ee606b6)
Afif Elghraoui
afif-guest at moszumanska.debian.org
Wed Feb 10 07:27:48 UTC 2016
This is an automated email from the git hooks/post-receive script.
afif-guest pushed a change to branch debian/jessie-backports
in repository bcftools.
from 2a949c3 bcftools (1.2-2~bpo8+1) jessie-backports; urgency=medium
adds 202ee54 Imported Upstream version 1.3
adds 94ca8c0 Merge tag 'upstream/1.3'
adds c84be00 Update patches
adds 2dada45 Prepare new revision
adds 4906458 Adjust pluginpath setting
adds f857186 Add a TODO file documenting work remaining to be done
adds 3397444 Simplify d/rules as a result of improvements to build system
adds 88e070d Update htslib minimum dependency
adds 75f6179 Disable building with libgsl until build issue with GSL2 is addressed
adds e71887b Update d/TODO to indicate GSL issue forwarded
adds b0f27fd Add libhts-dev dependency for autopkgtest runs
adds dd78c28 bcftools (1.3-1) unstable; urgency=medium
new ffa2e49 Merge branch 'master' into debian/jessie-backports
new f66f261 Re-enable building with GSL
new ee606b6 bcftools (1.3-1~bpo8+1) jessie-backports; urgency=medium
The 3 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/changelog | 18 +
debian/control | 2 +-
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 | 14 +-
debian/tests/control | 1 +
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 +
152 files changed, 17653 insertions(+), 3121 deletions(-)
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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