[med-svn] [htslib] 01/03: Merge tag '1.3' into debian/unstable
Charles Plessy
plessy at moszumanska.debian.org
Thu Dec 24 04:22:11 UTC 2015
This is an automated email from the git hooks/post-receive script.
plessy pushed a commit to branch debian/unstable
in repository htslib.
commit 68e6f6c1b6dd413a13f61eb8ca174a503da8e394
Merge: e6d7e9d 87141ea
Author: Charles Plessy <plessy at riken.jp>
Date: Thu Dec 24 13:14:35 2015 +0900
Merge tag '1.3' into debian/unstable
HTSlib release 1.3, plugins, libcurl, CRAM v3.0, bug fixes
* Files can now be accessed via HTTPS and Amazon S3 in addition to HTTP
and FTP, when HTSlib is configured to use libcurl for network file access
rather than the included basic knetfile networking.
* HTSlib can be built to use remote access hFILE backends (such as iRODS
and libcurl) via a plugin mechanism. This allows other backends to be
easily added and facilitates building tools that use HTSlib, as they
don't need to be linked with the backends' various required libraries.
* fai_build() and samtools faidx now accept initial whitespace in ">"
headers (e.g., "> chr1 description" is taken to refer to "chr1").
* tabix --only-header works again (was broken in 1.2.x; #249).
* HTSlib's configure script and Makefile now fully support the standard
convention of allowing CC/CPPFLAGS/CFLAGS/LDFLAGS/LIBS to be overridden
as needed. Previously the Makefile listened to $(LDLIBS) instead; if you
were overriding that, you should now override LIBS rather than LDLIBS.
* Fixed bugs #168, #172, #176, #197, #206, #225, #245, #265, #295, and #296.
.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 +
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 ++-
113 files changed, 7303 insertions(+), 1609 deletions(-)
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/htslib.git
More information about the debian-med-commit
mailing list