[med-svn] [htslib] annotated tag debian/1.5-1 created (now 7b06444)

[Matthias Klumpp]

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ximion-guest pushed a change to annotated tag debian/1.5-1
in repository htslib.

        at  7b06444   (tag)
   tagging  f45af8db9a5ba46f89d6bf24d5193cf9c4aaeddb (commit)
  replaces  debian/1.4.1-5
 tagged by  Matthias Klumpp
        on  Thu Aug 3 23:08:12 2017 -0400

- Log -----------------------------------------------------------------
htslib Debian release 1.5-1

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.

Andreas Tille (7):
      Merge tag '1.5' into debian/unstable
      New upstream version
      Standards-Version: 4.0.0 (no changes needed)
      do not parse d/changelog explicitly
      Refresh patches
      hardening=+all
      install htslib*.mk files that are used in bcftools

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*

Matthias Klumpp (3):
      libhts-dev: Depend on missing liblzma-dev
      Wrap and sort
      Finalize changelog for 1.5-1

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

Steffen Moeller (2):
      Added ref to OMICtools
      Merge branch 'debian/unstable' of ssh://anonscm.debian.org/git/debian-med/htslib into debian/unstable

Valeriu Ohan (1):
      Relase 1.5: Solstice

jenniferliddle (1):
      Merge version number bump and NEWS file from master

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