[med-svn] [htslib] 01/03: Merge branch 'master' into debian/jessie-backports
Andreas Tille
tille at debian.org
Tue Mar 21 18:40:51 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch debian/jessie-backports
in repository htslib.
commit adc8ffc6ddb7d5e3b240570f92ce474583378ed5
Merge: 83fbdd9 879855b
Author: Andreas Tille <tille at debian.org>
Date: Tue Mar 21 19:30:10 2017 +0100
Merge branch 'master' into debian/jessie-backports
.gitignore | 13 +
.travis.yml | 23 +-
INSTALL | 104 +-
Makefile | 247 +++--
NEWS | 102 +-
README.md | 5 +-
bcf_sr_sort.c | 645 ++++++++++++
bcf_sr_sort.h | 103 ++
bgzf.c | 1250 +++++++++++++++++------
bgzip.c | 38 +-
config.h.in | 38 -
config.mk.in | 56 +-
configure.ac | 243 ++++-
cram/cram_codecs.c | 180 +++-
cram/cram_codecs.h | 4 +
cram/cram_decode.c | 182 +++-
cram/cram_encode.c | 904 +++++++++--------
cram/cram_encode.h | 10 +
cram/cram_external.c | 16 +
cram/cram_index.c | 134 +--
cram/cram_index.h | 4 +-
cram/cram_io.c | 335 +++++--
cram/cram_io.h | 79 +-
cram/cram_samtools.c | 17 +-
cram/cram_samtools.h | 2 +-
cram/cram_stats.c | 266 +----
cram/cram_structs.h | 57 +-
cram/open_trace_file.c | 1 -
cram/os.h | 96 +-
cram/pooled_alloc.h | 2 +
cram/rANS_byte.h | 14 +
cram/rANS_static.c | 200 ++--
cram/sam_header.c | 5 +-
cram/string_alloc.c | 2 +-
cram/thread_pool.c | 757 --------------
cram/thread_pool.h | 218 ----
cram/vlen.h | 2 +
cram/zfio.c | 41 +-
errmod.c | 194 ++++
faidx.c | 334 ++++---
hfile.c | 248 ++++-
hfile_gcs.c | 137 +++
hfile_internal.h | 25 +-
hfile_irods.c | 259 -----
hfile_libcurl.c | 459 ++-------
hfile_s3.c | 400 ++++++++
hts.c | 582 ++++++++---
hts_internal.h | 96 ++
htsfile.1 | 9 +-
htsfile.c | 191 ++--
htslib.mk | 24 +-
htslib.pc.in | 15 +-
htslib/bgzf.h | 106 +-
htslib/cram.h | 37 +-
htslib/faidx.h | 188 ++--
htslib/hfile.h | 190 ++--
htslib/hts.h | 194 +++-
htslib/hts_defs.h | 8 +-
htslib/hts_endian.h | 354 +++++++
htslib/knetfile.h | 1 +
htslib/ksort.h | 3 +-
htslib/kstring.h | 99 +-
htslib/regidx.h | 2 +
htslib/sam.h | 178 +++-
htslib/synced_bcf_reader.h | 59 +-
htslib/tbx.h | 9 +-
htslib/thread_pool.h | 290 ++++++
htslib/vcf.h | 108 +-
htslib/vcf_sweep.h | 5 +-
htslib/vcfutils.h | 14 +-
htslib_vars.mk | 6 +-
knetfile.c | 6 +-
kstring.c | 124 ++-
md5.c | 3 +-
multipart.c | 242 +++++
plugin.c | 34 +-
probaln.c | 285 ++++++
realn.c | 199 ++++
regidx.c | 15 +-
sam.c | 623 ++++++++----
synced_bcf_reader.c | 242 ++---
tabix.1 | 14 +-
tabix.c | 48 +-
tbx.c | 88 +-
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-regidx.c | 10 +-
test/test.pl | 89 +-
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 | 1376 ++++++++++++++++++++++++++
thread_pool_internal.h | 165 +++
vcf.c | 596 ++++++++---
vcf_sweep.c | 4 +-
vcfutils.c | 218 +++-
130 files changed, 14375 insertions(+), 4818 deletions(-)
--
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