[med-svn] [htslib] 01/02: Merge tag '1.5' into debian/unstable
Andreas Tille
tille at debian.org
Wed Jul 19 19:54:42 UTC 2017
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tille pushed a commit to branch debian/unstable
in repository htslib.
commit ffd8e1101c57a95a87239189c5cb12652a890c71
Merge: 7b16102 49fdfbd
Author: Andreas Tille <tille at debian.org>
Date: Wed Jul 19 21:52:19 2017 +0200
Merge tag '1.5' into debian/unstable
Noteworthy changes in release 1.5 (21st June 2017)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
* Added a new logging API: hts_log(), along with hts_log_error(),
hts_log_warn() etc. convenience macros. Thanks go to Anders Kaplan
for the implementation. (#499, #543, #551)
* Added a new file I/O option "block_size" (HTS_OPT_BLOCK_SIZE) to
alter the hFILE buffer size.
* Fixed various bugs, including compilation issues samtools/bcftools#610,
samtools/bcftools#611 and robustness to corrupted data #537, #538,
#541, #546, #548, #549, #554.
Makefile | 17 +-
NEWS | 15 ++
bgzf.c | 165 ++++++--------------
configure.ac | 4 +
cram/cram_codecs.c | 29 ++--
cram/cram_decode.c | 10 +-
cram/cram_index.c | 39 +++--
cram/cram_io.c | 18 +--
cram/cram_io.h | 6 +
cram/mFILE.c | 40 -----
cram/vlen.c | 430 ---------------------------------------------------
cram/vlen.h | 50 ------
cram/zfio.c | 154 ------------------
cram/zfio.h | 62 --------
faidx.c | 106 +++++--------
hfile.c | 39 ++++-
hfile_internal.h | 21 +++
hts.c | 159 ++++++++++++++-----
htsfile.1 | 2 +-
htslib.mk | 7 +-
htslib/hts.h | 6 +-
htslib/hts_log.h | 93 +++++++++++
htslib/sam.h | 6 +-
htslib/vcf.h | 2 +-
htslib_vars.mk | 3 +-
knetfile.c | 25 +--
multipart.c | 11 +-
regidx.c | 16 +-
sam.c | 114 ++++++--------
synced_bcf_reader.c | 46 +++---
tabix.1 | 2 +-
tbx.c | 11 +-
test/test-logging.pl | 96 ++++++++++++
test/test.pl | 12 ++
vcf.c | 245 +++++++++++++++--------------
vcfutils.c | 80 +++++-----
36 files changed, 821 insertions(+), 1320 deletions(-)
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