[med-svn] [htslib] annotated tag 1.5 created (now 9670193)

[Andreas Tille]

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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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