[med-svn] [bcftools] 01/03: Merge branch 'master' into debian/jessie-backports
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 commit to branch debian/jessie-backports
in repository bcftools.
commit ffa2e495bbbfbf4ba677e01194e3162eaf59e682
Merge: 2a949c3 dd78c28
Author: Afif Elghraoui <afif at ghraoui.name>
Date: Tue Feb 9 22:09:56 2016 -0800
Merge branch 'master' into debian/jessie-backports
Conflicts:
debian/control
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 | 6 +
debian/changelog | 11 +
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 | 16 +-
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.2.b.vcf => annotate9.out} | 15 +-
test/{merge.2.b.vcf => annotate9.vcf} | 14 +-
test/annots9.tab | 5 +
test/{merge.2.b.vcf => annots9.vcf} | 14 +-
test/check.chk | 11 +-
test/check.vcf | 7 +-
test/{check.chk => check_merge.chk} | 57 +-
test/consensus.5.out | 20 +
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.gt.hap | 35 +
test/convert.hls.gt.legend | 36 +
test/convert.hls.gt.samples | 11 +
test/convert.hs.gt.hap | 35 +
test/convert.hs.gt.samples | 12 +
test/fill-tags.out | 40 +
test/filter.10.out | 11 +
test/{merge.2.b.vcf => filter.11.out} | 12 +-
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/{annotate5.out => missing.vcf} | 11 +-
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/norm.merge.2.out | 38 +
test/norm.merge.2.vcf | 41 +
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/norm.setref.out | 45 +
test/norm.setref.vcf | 45 +
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 +
153 files changed, 17854 insertions(+), 3014 deletions(-)
diff --cc debian/changelog
index 88d9ac6,7381425..351b703
--- a/debian/changelog
+++ b/debian/changelog
@@@ -1,10 -1,14 +1,21 @@@
+ bcftools (1.3-1) unstable; urgency=medium
+
+ * New upstream release (Closes: #813465)
+ * Disable building with libgsl until build issue with GSL2 is addressed
+ * Update d/TODO to indicate GSL issue forwarded
+ * Simplify d/rules as a result of improvements to build system
+ * Update htslib minimum dependency
+ * Add libhts-dev dependency for CI tests
+
+ -- Afif Elghraoui <afif at ghraoui.name> Wed, 03 Feb 2016 23:44:03 -0800
+
+bcftools (1.2-2~bpo8+1) jessie-backports; urgency=medium
+
+ * Adjust libgsl dependency for Stable.
+ * Rebuild for jessie-backports.
+
+ -- Afif Elghraoui <afif at ghraoui.name> Thu, 28 Jan 2016 23:02:03 -0800
+
bcftools (1.2-2) unstable; urgency=medium
* Fix autopkgtest dependencies
diff --cc debian/control
index 057cb64,7ae260c..93f6eed
--- a/debian/control
+++ b/debian/control
@@@ -7,8 -7,8 +7,8 @@@ Uploaders
Build-Depends:
debhelper (>= 9),
zlib1g-dev,
- libhts-dev (>= 1.2.1),
+ libhts-dev (>= 1.3),
-# libgsl-dev,
+ libgsl0-dev,
# Test-Depends:
tabix,
libio-pty-perl
--
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