[med-svn] [htslib] 01/02: Merge tag 'debian/1.3-1' into debian/jessie-backports
Charles Plessy
plessy at moszumanska.debian.org
Mon Feb 8 06:12:28 UTC 2016
This is an automated email from the git hooks/post-receive script.
plessy pushed a commit to annotated tag debian/1.3-1_bpo8+1
in repository htslib.
commit e030698015c663e5e6222778182bf85ca545587f
Merge: 0fcfccf 6c3a0f5
Author: Charles Plessy <plessy at debian.org>
Date: Mon Feb 8 12:42:21 2016 +0900
Merge tag 'debian/1.3-1' into debian/jessie-backports
htslib Debian release 1.3-1
Conflicts:
debian/changelog
.gitignore | 4 +
INSTALL | 23 +
Makefile | 224 +++++----
NEWS | 24 +
bgzf.c | 33 +-
bgzip.c | 75 +--
config.h.in | 27 +
config.mk.in | 53 +-
configure.ac | 99 ++++
cram/cram.h | 12 +-
cram/cram_codecs.c | 385 +++++++++------
cram/cram_codecs.h | 35 +-
cram/cram_decode.c | 608 ++++++++++++++++++-----
cram/cram_encode.c | 92 ++--
cram/cram_external.c | 377 ++++++++++++++
cram/cram_index.c | 103 ++--
cram/cram_index.h | 9 +-
cram/cram_io.c | 599 ++++++++++++++++++-----
cram/cram_io.h | 85 +++-
cram/cram_samtools.c | 2 +
cram/cram_samtools.h | 8 +
cram/cram_stats.c | 4 +-
cram/cram_structs.h | 37 +-
cram/files.c | 4 +-
cram/mFILE.c | 78 ++-
cram/mFILE.h | 1 +
cram/md5.h | 54 --
cram/open_trace_file.c | 93 +++-
cram/open_trace_file.h | 10 +
cram/pooled_alloc.c | 28 +-
cram/pooled_alloc.h | 8 +
cram/rANS_static.c | 67 ++-
cram/rANS_static.h | 7 +
cram/sam_header.c | 124 +++--
cram/sam_header.h | 35 +-
cram/string_alloc.c | 2 +
cram/string_alloc.h | 7 +-
cram/thread_pool.c | 2 +
cram/thread_pool.h | 8 +
cram/vlen.c | 4 +-
cram/zfio.c | 4 +-
cram/zfio.h | 8 +
debian/README.source | 34 ++
debian/changelog | 20 +
debian/control | 22 +-
debian/copyright | 4 +-
debian/libhts1.lintian-overrides | 2 +-
debian/libhts1.symbols | 97 +++-
debian/patches/define_PATH_MAX.patch | 23 +
debian/patches/series | 1 +
debian/source/options | 1 +
faidx.5 | 9 +-
faidx.c | 85 ++--
hfile.c | 257 ++++++++--
hfile_internal.h | 75 ++-
hfile_irods.c | 72 +--
hfile_libcurl.c | 919 +++++++++++++++++++++++++++++++++++
hfile_net.c | 15 +-
hts.c | 672 +++++++++++++++++++------
hts_internal.h | 69 +++
htsfile.1 | 8 +-
htsfile.c | 114 ++++-
htslib.mk | 27 +-
htslib/bgzf.h | 26 +-
htslib/cram.h | 492 +++++++++++++++++++
htslib/faidx.h | 12 +-
htslib/hfile.h | 5 +-
htslib/hts.h | 245 ++++++++--
htslib/hts_defs.h | 35 +-
htslib/kbitset.h | 160 ++++++
htslib/kfunc.h | 8 +
htslib/khash.h | 10 +-
htslib/klist.h | 36 +-
htslib/kstring.h | 9 +-
htslib/regidx.h | 7 +
htslib/sam.h | 70 ++-
htslib/synced_bcf_reader.h | 15 +-
htslib/tbx.h | 12 +-
htslib/vcf.h | 74 ++-
htslib/vcf_sweep.h | 8 +
htslib/vcfutils.h | 26 +-
htslib_vars.mk | 16 +-
kstring.c | 20 +
cram/md5.c => md5.c | 241 ++++++---
plugin.c | 171 +++++++
regidx.c | 10 +-
sam.c | 303 +++++++++---
synced_bcf_reader.c | 49 +-
tabix.1 | 5 +-
tabix.c | 39 +-
tbx.c | 25 +-
test/c1#noseq.sam | 10 +
test/c1#pad2.sam | 2 +-
test/c1#pad3.sam | 2 +-
test/c1#unknown.sam | 9 +
test/c2#pad.sam | 26 +
test/c2.fa | 2 +
test/c2.fa.fai | 1 +
test/ce#1.sam | 2 +-
test/ce#2.sam | 2 +-
test/ce#5.sam | 10 +-
test/ce#5b.sam | 10 +-
test/ce#large_seq.sam | 2 +-
test/ce#supp.sam | 6 +
test/ce#tag_depadded.sam | 2 +-
test/ce#tag_padded.sam | 2 +-
test/ce#unmap1.sam | 14 +-
test/ce#unmap2.sam | 14 +-
test/compare_sam.pl | 24 +-
test/cross_validate.sh | 126 +++++
test/faidx.fa | 17 +
test/sam.c | 33 +-
test/test-vcf-hdr-in.vcf | 25 +
test/test-vcf-hdr.out | 16 +
test/test.pl | 27 +-
test/test_view.c | 149 ++----
test/test_view.pl | 22 +
test/xx#tlen.sam | 34 ++
test/xx#tlen2.sam | 36 ++
vcf.c | 321 +++++++++---
vcf_sweep.c | 3 +-
vcfutils.c | 50 +-
122 files changed, 7491 insertions(+), 1625 deletions(-)
diff --cc debian/changelog
index 08fb683,d40ff69..1720357
--- a/debian/changelog
+++ b/debian/changelog
@@@ -1,10 -1,23 +1,30 @@@
+ htslib (1.3-1) unstable; urgency=medium
+
+ * Team upload
+ * New upstream version
+ * Ignore metadata files different between git and tarball
+
+ -- Sascha Steinbiss <sascha at steinbiss.name> Sat, 30 Jan 2016 12:16:06 +0000
+
+ htslib (1.2.1-2) unstable; urgency=medium
+
+ * Team upload
+ * Enable build on hurd-i386
+ Closes: #793512
+ * More verbose description vor -dev and -test package
+ * Fix lintian override
+ * Verified Mayhem bug report which is solved in this version
+ Closes: #716376
+
+ -- Andreas Tille <tille at debian.org> Wed, 09 Dec 2015 17:00:47 +0100
+
+htslib (1.2.1-1~bpo8+1) jessie-backports; urgency=medium
+
+ * Team upload.
+ * Rebuild for jessie-backports.
+
+ -- Afif Elghraoui <afif at ghraoui.name> Mon, 28 Sep 2015 18:43:33 -0700
+
htslib (1.2.1-1) unstable; urgency=medium
0662716 Merge tag '1.2.1' into debian/unstable
--
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