[med-svn] [htslib] annotated tag 1.5 created (now 9670193)
Andreas Tille
tille at debian.org
Wed Jul 19 19:54:28 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a change to annotated tag 1.5
in repository htslib.
at 9670193 (tag)
tagging 49fdfbda20acbd73303df3c7fef84f2d972c5f8d (commit)
replaces 1.4.1
tagged by Valeriu Ohan
on Tue Jun 20 14:48:47 2017 +0100
- Log -----------------------------------------------------------------
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.
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Anders Kaplan (16):
First draft of a new logging mechanism.
Added helper macros log_error, log_error, etc.
Switched to new logging functions in bgzf.c. NOTE suspicious buggy bracket placements on lines 1716 and 1752 (before edit) changed.
Added tests for logging.
Adapted to gcc/unix environment.
Moved the declaration of hts_log & co to the public API.
Restored the default log level (3) but now interpreted as HTS_LOG_WARNING.
Adjusted log levels in bgzf.c.
Added trace log level to get_severity_tag.
Replaced fprintf(stderr, ...) calls with hts_log_<level> calls.
Replaced fprintf(stderr, ...) calls with hts_log_<level> calls.
Cosmetic improvements to the error messages.
Fixed format string errors.
Added dependency from knetfile.c to hts_log.h, with some cascading. Added missing dependencies to the Makefile, including the missing definition of htslib_hts_h.
Replaced fprintf(stderr, ...) calls with hts_log_<level> calls.
Replaced fprintf(stderr, ...) calls with hts_log_<level> calls.
James Bonfield (10):
Bug fix to CRAM index creation (reported by Brent Pedersen).
Added a PTHREAD_MUTEX_RECURSIVE check.
Fix buffer overrun in vcf_format.
Also added Number= checking for INFO headers.
Remove read-past-buffer when printing error message.
Additional argument protection in sam_hdr_write and bcf_hdr_write.
Additional error checking for invalid CRAM ref_id.
Removed the (>20 year old!) unnecessary vlen.[ch] code.
Adds HTS_OPT_BLOCK_SIZE support for SAM/BAM/CRAM.
Updated NEWS file for Solstice release.
John Marshall (1):
Use BGZF* in cram_index_build() instead of zfp*
Rob Davies (14):
Add htslib/hts_log.h to htslib_vars.mk and htslib.mk
Adjusted log levels for a few messages
Make hts_log() preserve errno.
Merge logging mechanism (PR #499)
Prevent out of bounds read on BAM_CIGAR_STR by extending to 16 bytes
Fix clang warning
Fix length calculation in bam_read1 and possible memory leak
Limit subexp and gamma decoders to integer cram_external_type
Merge Logging improvements 2 (PR #543) into develop
Allow out to be NULL in cram_huffman_decode_char()
Use htslib_hts_log_h definition from htslib_vars.mk
Merge branch 'pr551' into pr551_merge
Remove autom4te.cache during `make distclean`
Stop threaded bgzf_read_block from using stale values at EOF
Valeriu Ohan (1):
Relase 1.5: Solstice
jenniferliddle (1):
Merge version number bump and NEWS file from master
-----------------------------------------------------------------------
This annotated tag includes the following new commits:
new 8d201be Added dependency from knetfile.c to hts_log.h, with some cascading. Added missing dependencies to the Makefile, including the missing definition of htslib_hts_h.
new f0fc3ee Replaced fprintf(stderr, ...) calls with hts_log_<level> calls.
new 03c4be2 Replaced fprintf(stderr, ...) calls with hts_log_<level> calls.
new 7fd21f5 Adds HTS_OPT_BLOCK_SIZE support for SAM/BAM/CRAM.
new 3c0302d Use htslib_hts_log_h definition from htslib_vars.mk
new f1b95e1 Merge branch 'pr551' into pr551_merge
new b28aa8d Remove autom4te.cache during `make distclean`
new 3872861 Updated NEWS file for Solstice release.
new fba943d Stop threaded bgzf_read_block from using stale values at EOF
new 49fdfbd Relase 1.5: Solstice
The 10 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.
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