[med-svn] [htslib] 02/02: Merge branch 'debian/unstable' of ssh://anonscm.debian.org/git/debian-med/htslib into debian/unstable
Steffen Möller
moeller at moszumanska.debian.org
Thu Jul 20 10:42:32 UTC 2017
This is an automated email from the git hooks/post-receive script.
moeller pushed a commit to branch debian/unstable
in repository htslib.
commit 8ce1126f0fd7d4c8655f9c779440d56c91a1447c
Merge: 78d31d7 ada885d
Author: Steffen Moeller <moeller at debian.org>
Date: Thu Jul 20 12:41:54 2017 +0200
Merge branch 'debian/unstable' of ssh://anonscm.debian.org/git/debian-med/htslib into debian/unstable
.gitignore | 14 +
.travis.yml | 23 +-
INSTALL | 104 +-
Makefile | 256 +++--
NEWS | 124 +++
README.md | 5 +-
bcf_sr_sort.c | 647 ++++++++++++
bcf_sr_sort.h | 103 ++
bgzf.c | 1320 ++++++++++++++++++-------
bgzip.c | 39 +-
config.h.in | 38 -
config.mk.in | 56 +-
configure.ac | 252 ++++-
cram/cram_codecs.c | 204 +++-
cram/cram_codecs.h | 4 +
cram/cram_decode.c | 196 +++-
cram/cram_encode.c | 904 +++++++++--------
cram/cram_encode.h | 10 +
cram/cram_external.c | 16 +
cram/cram_index.c | 171 ++--
cram/cram_index.h | 4 +-
cram/cram_io.c | 629 ++++++------
cram/cram_io.h | 294 +++++-
cram/cram_samtools.c | 17 +-
cram/cram_samtools.h | 2 +-
cram/cram_stats.c | 266 +----
cram/cram_structs.h | 57 +-
cram/mFILE.c | 40 -
cram/open_trace_file.c | 1 -
cram/os.h | 96 +-
cram/pooled_alloc.h | 2 +
cram/rANS_byte.h | 18 +-
cram/rANS_static.c | 241 ++---
cram/sam_header.c | 5 +-
cram/string_alloc.c | 2 +-
cram/thread_pool.c | 757 --------------
cram/thread_pool.h | 218 ----
cram/vlen.c | 430 --------
cram/vlen.h | 48 -
cram/zfio.c | 183 ----
cram/zfio.h | 62 --
debian/changelog | 76 +-
debian/control | 10 +-
debian/htslib-test.install | 1 -
debian/libhts-dev.install | 1 +
debian/libhts1.lintian-overrides | 2 -
debian/libhts1.symbols | 639 ------------
debian/{libhts1.install => libhts2.install} | 0
debian/libhts2.lintian-overrides | 2 +
debian/patches/define_PATH_MAX.patch | 10 +-
debian/patches/fPIC.patch | 16 +
debian/patches/fix_pkg-config.patch | 18 +
debian/patches/htslib-add-cram_to_bam.patch | 28 +
debian/patches/series | 3 +
debian/rules | 12 +-
debian/tabix.install | 1 +
debian/tabix.manpages | 1 +
debian/tests/run-unit-test | 2 +-
errmod.c | 194 ++++
faidx.c | 455 +++++----
hfile.c | 283 ++++--
hfile_gcs.c | 137 +++
hfile_internal.h | 46 +-
hfile_irods.c | 259 -----
hfile_libcurl.c | 459 ++-------
hfile_s3.c | 400 ++++++++
hts.c | 696 ++++++++++---
hts_internal.h | 96 ++
htsfile.1 | 9 +-
htsfile.c | 191 ++--
htslib.mk | 31 +-
htslib.pc.in | 15 +-
htslib/bgzf.h | 106 +-
htslib/cram.h | 37 +-
htslib/faidx.h | 188 ++--
htslib/hfile.h | 190 ++--
htslib/hts.h | 200 +++-
htslib/hts_defs.h | 8 +-
htslib/hts_endian.h | 354 +++++++
htslib/hts_log.h | 93 ++
htslib/knetfile.h | 1 +
htslib/ksort.h | 3 +-
htslib/kstring.h | 99 +-
htslib/regidx.h | 2 +
htslib/sam.h | 184 +++-
htslib/synced_bcf_reader.h | 59 +-
htslib/tbx.h | 9 +-
htslib/thread_pool.h | 290 ++++++
htslib/vcf.h | 120 ++-
htslib/vcf_sweep.h | 5 +-
htslib/vcfutils.h | 14 +-
htslib_vars.mk | 9 +-
knetfile.c | 29 +-
kstring.c | 124 ++-
md5.c | 3 +-
multipart.c | 239 +++++
plugin.c | 10 +-
probaln.c | 285 ++++++
realn.c | 199 ++++
regidx.c | 32 +-
sam.c | 765 ++++++++++----
synced_bcf_reader.c | 291 +++---
tabix.1 | 14 +-
tabix.c | 50 +-
tbx.c | 89 +-
test/aux#aux_java.cram | Bin 3774 -> 0 bytes
test/auxf#values.sam | 4 +-
test/auxf#values_java.cram | Bin 0 -> 5152 bytes
test/bgziptest.txt | 1 +
test/bgziptest.txt.gz | Bin 0 -> 181 bytes
test/bgziptest.txt.gz.gzi | Bin 0 -> 88 bytes
test/compare_sam.pl | 22 +-
test/cross_validate.sh | 4 +-
test/formatmissing-out.vcf | 6 +
test/formatmissing.vcf | 6 +
test/hfile.c | 44 +-
test/hts_endian.c | 510 ++++++++++
test/md#1.sam | 12 +
test/md.fa | 3 +
test/md.fa.fai | 1 +
test/sam.c | 209 +++-
test/tabix/bed_file.Y.100200.out | 1 +
test/tabix/bed_file.bed | 39 +
test/tabix/gff_file.X.2934832.2935190.out | 4 +
test/tabix/gff_file.gff | 70 ++
test/tabix/large_chr.20.1.2147483647.out | 9 +
test/tabix/large_chr.vcf | 18 +
test/tabix/tabix.tst | 65 ++
test/tabix/test-tabix.sh | 182 ++++
test/tabix/vcf_file.1.3000151.out | 1 +
test/tabix/vcf_file.2.3199812.out | 1 +
test/tabix/vcf_file.vcf | 36 +
test/test-bcf-sr.c | 141 +++
test/test-bcf-sr.pl | 546 ++++++++++
test/test-logging.pl | 96 ++
test/test-regidx.c | 10 +-
test/test-vcf-api.c | 119 ++-
test/test.pl | 101 +-
test/test_bgzf.c | 789 +++++++++++++++
test/test_view.c | 21 +-
htslib/vcf_sweep.h => test/thrash_threads1.c | 56 +-
htslib/vcf_sweep.h => test/thrash_threads2.c | 54 +-
htslib/vcf_sweep.h => test/thrash_threads3.c | 59 +-
test/thrash_threads4.c | 68 ++
test/thrash_threads5.c | 66 ++
test/thrash_threads6.c | 108 ++
test/thread_pool.md | 58 ++
textutils.c | 379 +++++++
thread_pool.c | 1373 ++++++++++++++++++++++++++
thread_pool_internal.h | 165 ++++
vcf.c | 917 +++++++++++------
vcf_sweep.c | 4 +-
vcfutils.c | 244 ++++-
153 files changed, 15793 insertions(+), 6881 deletions(-)
diff --cc debian/changelog
index b96b95a,50b51aa..8cbe029
--- a/debian/changelog
+++ b/debian/changelog
@@@ -1,8 -1,76 +1,78 @@@
- htslib (1.3.2-3) UNRELEASED; urgency=medium
+ htslib (1.5-1) UNRELEASED; urgency=medium
- * [upstream/metadata] Added reference to OMICtools
+ * New upstream version
++ * [upstream/metadata] Added reference to OMICtools (Steffen Moeller)
+
+ -- Andreas Tille <tille at debian.org> Wed, 19 Jul 2017 21:53:39 +0200
+
+ htslib (1.4.1-5) unstable; urgency=medium
+
+ * Team upload
+ * Dereference symlinks to fix autopkgtest (Closes: #866137)
+
+ -- Graham Inggs <ginggs at debian.org> Wed, 19 Jul 2017 10:37:52 +0200
+
+ htslib (1.4.1-4) unstable; urgency=medium
+
+ * Team upload
+ * Fix FTBFS on s390x and sparc64, thanks Adrian Bunk (Closes: #865010)
+
+ -- Graham Inggs <ginggs at debian.org> Tue, 18 Jul 2017 00:49:30 +0200
+
+ htslib (1.4.1-3) unstable; urgency=medium
+
+ * Team upload.
+ * Fix FTBFS on i386. Thanks to Adrian Bunk for the patch.
+ Closes: #865012
+
+ -- Sascha Steinbiss <satta at debian.org> Mon, 17 Jul 2017 18:25:56 +0200
+
+ htslib (1.4.1-2) unstable; urgency=medium
+
+ * Create symlinks only for arch=indep target when target dir exists
+ Closes: #864979
+
+ -- Andreas Tille <tille at debian.org> Sun, 18 Jun 2017 14:19:22 +0200
+
+ htslib (1.4.1-1) unstable; urgency=medium
+
+ * New upstream version
+
+ -- Andreas Tille <tille at debian.org> Sun, 18 Jun 2017 00:17:35 +0200
+
+ htslib (1.4-3) experimental; urgency=medium
+
+ * add the cram_to_bam function to the public interface of htslib because
+ it is used by code in Sambamba
+
+ -- Andreas Tille <tille at debian.org> Thu, 04 May 2017 10:57:31 +0200
+
+ htslib (1.4-2) experimental; urgency=medium
+
+ * Include htsfile binary into tabix package since its used by manta
+ package
+
+ -- Andreas Tille <tille at debian.org> Tue, 02 May 2017 15:42:11 +0200
+
+ htslib (1.4-1) experimental; urgency=medium
+
+ * New upstream version
+ * Drop autoconf from Build-Depends
+ * Add libbz2-dev and liblzma-dev to Build-Depends
+ * Remove binary files from test results
+ * Remove symbols file
+ * Change library name to match soname
+
+ -- Andreas Tille <tille at debian.org> Tue, 21 Mar 2017 17:44:03 +0100
+
+ htslib (1.3.2-3) experimental; urgency=medium
+
+ * Install header files from cram dir in -dev package since these are
+ used in libseqlib
+ * Fix pkg-config
- -- Steffen Moeller <moeller at debian.org> Thu, 20 Jul 2017 12:39:46 +0200
+ -- Andreas Tille <tille at debian.org> Fri, 10 Feb 2017 08:46:29 +0100
++>>>>>>> ada885d3985096b9b32b19f087f5db1134f07cfd
htslib (1.3.2-2) unstable; urgency=medium
--
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