[med-svn] [htslib] branch master updated (30646ba -> 9b683f1)
Andreas Tille
tille at debian.org
Mon Dec 11 13:58:51 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch master
in repository htslib.
from 30646ba Upload to unstable after verifying that bcftools does not need these htslib*.mk fragments
new 29f0445 Start using default Debian Med repository layout
new a7cd55f New upstream version 1.5
new 05e80df Update upstream source from tag 'upstream/1.5'
new a2ccfa8 Switch to default Debian Med repository layout
new 0b1efff New upstream version 1.6
new 57b2527 Update upstream source from tag 'upstream/1.6'
new 0876f84 New upstream version
new 86a38d1 Remove debian/patches/literal_version.patch since upstream stops running make to get the version number
new 02927ed Refresh patches
new ca55c40 Update symbols file
new 9b683f1 Upload to experimental
The 11 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails. The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.
Summary of changes:
.appveyor.yml | 43 +++
INSTALL | 6 +
Makefile | 66 +++--
NEWS | 37 ++-
bcf_sr_sort.c | 38 ++-
bcf_sr_sort.h | 6 +-
bgzf.c | 15 +
bgzip.c | 18 +-
configure.ac | 24 +-
cram/cram_codecs.c | 75 +++--
cram/cram_decode.c | 70 +++--
cram/cram_encode.c | 62 ++--
cram/cram_external.c | 3 +-
cram/cram_index.c | 6 +-
cram/cram_io.c | 107 ++++---
cram/cram_stats.c | 10 +-
cram/cram_structs.h | 3 +-
cram/mFILE.c | 3 +-
cram/mFILE.h | 5 +
cram/os.h | 24 +-
cram/sam_header.c | 6 +-
debian/README.source | 37 ---
debian/changelog | 10 +
debian/gbp.conf | 10 -
debian/libhts2.symbols | 9 +-
debian/patches/877670.patch | 4 +-
debian/patches/htslib-add-cram_to_bam.patch | 2 +-
debian/patches/literal_version.patch | 16 -
debian/patches/series | 1 -
errmod.c | 2 +
hfile.c | 27 +-
hfile_internal.h | 9 +-
hfile_libcurl.c | 433 +++++++++++++++++++++++-----
hfile_s3.c | 191 ++++++++----
hts.c | 121 +++++---
hts_internal.h | 2 +-
htslib/vcf_sweep.h => hts_os.c | 42 ++-
htsfile.1 | 2 +-
htslib/bgzf.h | 4 +
htslib/hfile.h | 4 +
htslib/hts.h | 5 +-
htslib/hts_defs.h | 18 ++
htslib/hts_endian.h | 6 +-
htslib/{vcf_sweep.h => hts_os.h} | 47 +--
htslib/knetfile.h | 2 +-
htslib/ksort.h | 8 +-
htslib/regidx.h | 10 +-
htslib/sam.h | 6 +-
htslib/vcfutils.h | 4 +-
knetfile.c | 4 +-
kstring.c | 2 +-
multipart.c | 31 +-
realn.c | 2 +-
regidx.c | 24 +-
sam.c | 27 +-
synced_bcf_reader.c | 4 +-
tabix.1 | 2 +-
tabix.c | 4 +-
test/compare_sam.pl | 2 +
test/hfile.c | 4 +-
test/sam.c | 2 +-
test/tabix/test-tabix.sh | 7 +-
test/test-bcf-sr.c | 12 +-
test/test-bcf-sr.pl | 6 +-
test/test-bcf-translate.c | 192 ++++++++++++
test/test-bcf-translate.out | 18 ++
test/test-regidx.c | 8 +-
test/test.pl | 92 ++++--
test/test_bgzf.c | 19 +-
test/test_view.c | 55 +++-
vcf.c | 43 +--
vcfutils.c | 2 +-
version.sh | 31 ++
win/rand.c | 98 +++++++
win/rand.h | 24 ++
75 files changed, 1691 insertions(+), 683 deletions(-)
create mode 100644 .appveyor.yml
delete mode 100644 debian/README.source
delete mode 100644 debian/patches/literal_version.patch
copy htslib/vcf_sweep.h => hts_os.c (61%)
copy htslib/{vcf_sweep.h => hts_os.h} (53%)
create mode 100644 test/test-bcf-translate.c
create mode 100644 test/test-bcf-translate.out
create mode 100755 version.sh
create mode 100644 win/rand.c
create mode 100644 win/rand.h
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