[med-svn] [bcftools] 01/02: Merge tag 'debian/1.3.1-1' into ubuntu/trusty-backports
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 commit to branch ubuntu/trusty-backports
in repository bcftools.
commit 133771c34a6884da0131d8e63d94d7126df52f83
Merge: 1f6973f f9a9e80
Author: Andreas Tille <tille at debian.org>
Date: Thu Jun 30 15:52:32 2016 +0200
Merge tag 'debian/1.3.1-1' into ubuntu/trusty-backports
tagging package bcftools version debian/1.3.1-1
Makefile | 8 +-
bcftools.h | 3 +-
consensus.c | 2 +-
debian/TODO | 6 -
debian/changelog | 26 ++
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 | 2 +-
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/annotate10.out | 18 +
test/annotate10.vcf | 17 +
test/annots10.tab | 4 +
test/concat.1.a.vcf | 2 -
test/concat.1.b.vcf | 2 -
test/fill-tags.2.out | 49 +++
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/{norm.merge.strict.out => reheader.3.out} | 43 +--
test/{norm.merge.strict.out => reheader.4.out} | 43 +--
test/reheader.empty.hdr | 7 +
test/reheader.empty.out | 8 +
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, 1760 insertions(+), 317 deletions(-)
diff --cc debian/changelog
index 7fdebdc,90e2f7b..07d1c68
--- a/debian/changelog
+++ b/debian/changelog
@@@ -1,11 -1,29 +1,37 @@@
+ bcftools (1.3.1-1) unstable; urgency=medium
+
+ * Imported Upstream version 1.3.1
+ * Remove backported patches
+ * Refresh remaining patches
+ * Bump htslib minimum dependency
+ * Bump Standards-Version to 3.9.8
+ * Add a manpage for the color-chrs command
+
+ -- Afif Elghraoui <afif at debian.org> Mon, 25 Apr 2016 22:24:50 -0700
+
+ bcftools (1.3-3) unstable; urgency=medium
+
+ * Backport upstream patch to fix build on arm64, armel, and ppc64el
+ (Closes: #812268)
+
+ -- Afif Elghraoui <afif at debian.org> Thu, 31 Mar 2016 00:57:18 -0700
+
+ bcftools (1.3-2) unstable; urgency=medium
+
+ * Backport upstream patch to be able to build plugin with GSL2
+ * Bump Standards-Version
+ * Use encrypted protocols for VCS URLs
+
+ -- Afif Elghraoui <afif at ghraoui.name> Sun, 21 Feb 2016 16:35:44 -0800
+
+bcftools (1.3-1~ubuntu14.04~ppa1) trusty; urgency=medium
+
+ * Rebuild for Debian Med PPA
+ * Some tests are failing for whatever reason - ignore this for the intended
+ purpose.
+
+ -- Andreas Tille <tille at debian.org> Thu, 30 Jun 2016 14:52:05 +0200
+
bcftools (1.3-1) unstable; urgency=medium
* New upstream release (Closes: #813465)
--
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