[med-svn] [bcftools] 01/02: Merge tag 'debian/1.3.1-1' into debian/jessie-backports
Afif Elghraoui
afif at moszumanska.debian.org
Thu May 12 03:43:54 UTC 2016
This is an automated email from the git hooks/post-receive script.
afif pushed a commit to branch debian/jessie-backports
in repository bcftools.
commit 133abec90de076d41683422bbb5c39e5d8b59819
Merge: ee606b6 f9a9e80
Author: Afif Elghraoui <afif at ghraoui.name>
Date: Wed May 11 20:09:59 2016 -0700
Merge tag 'debian/1.3.1-1' into debian/jessie-backports
tagging package bcftools version debian/1.3.1-1
Conflicts:
debian/control
Makefile | 8 +-
bcftools.h | 3 +-
consensus.c | 2 +-
debian/changelog | 26 ++
debian/control | 10 +-
debian/copyright | 2 +-
debian/man/color-chrs.pl.1 | 19 +
debian/patches/series | 1 -
debian/patches/tests-pluginpath.patch | 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 +-
69 files changed, 1758 insertions(+), 309 deletions(-)
diff --cc debian/changelog
index ce8df15,90e2f7b..135c071
--- a/debian/changelog
+++ b/debian/changelog
@@@ -1,10 -1,29 +1,36 @@@
+ 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~bpo8+1) jessie-backports; urgency=medium
+
+ * Rebuild for jessie-backports.
+ * Re-enable building with GSL since there is no API problem here.
+
+ -- Afif Elghraoui <afif at ghraoui.name> Tue, 09 Feb 2016 22:12:24 -0800
+
bcftools (1.3-1) unstable; urgency=medium
* New upstream release (Closes: #813465)
diff --cc debian/control
index 93f6eed,c8f518e..a8abcfc
--- a/debian/control
+++ b/debian/control
@@@ -7,8 -7,8 +7,8 @@@ Uploaders
Build-Depends:
debhelper (>= 9),
zlib1g-dev,
- libhts-dev (>= 1.3),
+ libhts-dev (>= 1.3.1),
- libgsl-dev,
+ libgsl0-dev,
# Test-Depends:
tabix,
libio-pty-perl
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/bcftools.git
More information about the debian-med-commit
mailing list