[med-svn] [bcftools] branch ubuntu/trusty-backports updated (1f6973f -> 72a3526)
Andreas Tille
tille at debian.org
Thu Jun 30 14:06:40 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch ubuntu/trusty-backports
in repository bcftools.
from 1f6973f Some tests are failing for whatever reason - ignore this for the intended purpose.
adds a0f5384 Backport upstream patch to be able to build plugin with GSL2
adds 0c497fa Bump Standards-Version
adds 9f2857a Use encrypted protocols for VCS URLs
adds 3e13cc4 bcftools (1.3-2) unstable; urgency=medium
adds 692a80b Update email address and bump copyright year
adds 4558479 Backport upstream patch to fix build on arm64, armel, and ppc64el
adds 45ff8ed Update changelog
adds c7f7f8b Imported Upstream version 1.3.1
adds d3ea0f8 Merge tag 'upstream/1.3.1'
adds d35e058 Remove backported patches
adds 9d2f206 Refresh remaining patches
adds ab357e2 Bump htslib minimum dependency
adds 13c1a3b Bump Standards-Version to 3.9.8
adds 8b2259e Add a manpage for the color-chrs command
adds f9a9e80 releasing package bcftools version 1.3.1-1
new 133771c Merge tag 'debian/1.3.1-1' into ubuntu/trusty-backports
new 72a3526 Rebuild for Debian Med PPA, Build-Depends: s/libgsl-dev/libgsl0-dev/, Tests are working fine now
The 2 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:
Makefile | 8 +-
bcftools.h | 3 +-
consensus.c | 2 +-
debian/TODO | 6 -
debian/changelog | 34 +++
debian/control | 12 +-
debian/copyright | 2 +-
debian/man/color-chrs.pl.1 | 19 ++
debian/patches/series | 1 -
debian/patches/tests-pluginpath.patch | 2 +-
debian/rules | 5 +-
doc/bcftools.1 | 96 ++++++-
doc/bcftools.html | 101 +++++--
doc/bcftools.txt | 87 ++++--
khash_str2str.h | 19 +-
main.c | 4 +-
peakfit.c | 6 +
ploidy.c | 30 +-
plot-vcfstats | 6 +-
plugins/GTisec.c | 470 ++++++++++++++++++++++++++++++++
plugins/GTisec.mk | 2 +
plugins/color-chrs.c | 2 +-
plugins/fill-tags.c | 46 +++-
plugins/impute-info.c | 10 +-
plugins/mendelian.c | 2 +-
plugins/tag2tag.c | 4 +-
plugins/vcf2sex.c | 11 +-
polysomy.c | 3 +-
reheader.c | 62 +++--
test/annotate10.hdr | 3 +
test/{annots2.vcf => annotate10.out} | 3 +-
test/{annots2.vcf => annotate10.vcf} | 12 +-
test/annots10.tab | 4 +
test/concat.1.a.vcf | 2 -
test/concat.1.b.vcf | 2 -
test/{view.vcf => fill-tags.2.out} | 33 ++-
test/norm.fa | 2 +
test/norm.fa.fai | 1 +
test/norm.merge.out | 2 +-
test/norm.merge.strict.out | 2 +-
test/norm.merge.vcf | 4 +-
test/norm.telomere.out | 5 +
test/norm.telomere.vcf | 4 +
test/{reheader.2.out => reheader.3.out} | 2 +-
test/{reheader.2.out => reheader.4.out} | 2 +-
test/{empty.vcf => reheader.empty.hdr} | 1 +
test/{empty.vcf => reheader.empty.out} | 2 +
test/reheader.samples3 | 2 +
test/reheader.samples4 | 1 +
test/test.pl | 96 ++++---
test/view.GTisec.H.out | 20 ++
test/view.GTisec.Hm.out | 25 ++
test/view.GTisec.Hmv.out | 25 ++
test/view.GTisec.Hv.out | 20 ++
test/view.GTisec.m.out | 20 ++
test/view.GTisec.mv.out | 20 ++
test/view.GTisec.out | 15 +
test/view.GTisec.v.out | 15 +
test/view.filter.annovar.vcf | 1 +
vcfannotate.c | 212 +++++++++++---
vcfcall.c | 43 ++-
vcfconcat.c | 139 +++++++++-
vcfconvert.c | 18 +-
vcffilter.c | 8 +-
vcfindex.c | 3 +-
vcfisec.c | 12 +-
vcfmerge.c | 10 +-
vcfnorm.c | 20 +-
vcfplugin.c | 41 +--
vcfroh.c | 43 ++-
vcfview.c | 8 +-
71 files changed, 1654 insertions(+), 304 deletions(-)
delete mode 100644 debian/TODO
create mode 100644 debian/man/color-chrs.pl.1
create mode 100644 plugins/GTisec.c
create mode 100644 plugins/GTisec.mk
create mode 100644 test/annotate10.hdr
copy test/{annots2.vcf => annotate10.out} (91%)
copy test/{annots2.vcf => annotate10.vcf} (67%)
create mode 100644 test/annots10.tab
copy test/{view.vcf => fill-tags.2.out} (69%)
create mode 100644 test/norm.telomere.out
create mode 100644 test/norm.telomere.vcf
copy test/{reheader.2.out => reheader.3.out} (98%)
copy test/{reheader.2.out => reheader.4.out} (98%)
copy test/{empty.vcf => reheader.empty.hdr} (87%)
copy test/{empty.vcf => reheader.empty.out} (72%)
create mode 100644 test/reheader.samples3
create mode 100644 test/reheader.samples4
create mode 100644 test/view.GTisec.H.out
create mode 100644 test/view.GTisec.Hm.out
create mode 100644 test/view.GTisec.Hmv.out
create mode 100644 test/view.GTisec.Hv.out
create mode 100644 test/view.GTisec.m.out
create mode 100644 test/view.GTisec.mv.out
create mode 100644 test/view.GTisec.out
create mode 100644 test/view.GTisec.v.out
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