[med-svn] [htslib] branch debian/unstable updated (7b16102 -> ada885d)

[Andreas Tille]

This is an automated email from the git hooks/post-receive script.

tille pushed a change to branch debian/unstable
in repository htslib.

      from  7b16102   Dereference symlinks to fix autopkgtest
      adds  7771288   Merge version number bump and NEWS file from master
      adds  6163114   First draft of a new logging mechanism.
      adds  e1848ae   Added helper macros log_error, log_error, etc.
      adds  ddcc3ab   Switched to new logging functions in bgzf.c. NOTE suspicious buggy bracket placements on lines 1716 and 1752 (before edit) changed.
      adds  c54f23c   Added tests for logging.
      adds  c6d03a1   Adapted to gcc/unix environment.
      adds  08c16ef   Moved the declaration of hts_log & co to the public API. Appended the hts_ prefix to the log_<level> macros. Switched to standard C99 __VA_ARGS__ instead of ##__VA_ARGS__. Added HTS_FORMAT checking to the hts_log function. Changed the initialization of hts_verbose to use the literal HTS_LOG_INFO instead of magic number 3. Centralized newline handling to the hts_log function. Re-purposed the test-logging.pl script to test for message consistency.
      adds  0d3d32f   Restored the default log level (3) but now interpreted as HTS_LOG_WARNING. Added HTS_LOG_TRACE log level.
      adds  ea59199   Adjusted log levels in bgzf.c.
      adds  49fe80f   Added trace log level to get_severity_tag.
      adds  0cad436   Add htslib/hts_log.h to htslib_vars.mk and htslib.mk
      adds  0664276   Adjusted log levels for a few messages
      adds  e66ab04   Make hts_log() preserve errno.
      adds  3e85cce   Merge logging mechanism (PR #499)
      adds  a58cd85   Bug fix to CRAM index creation (reported by Brent Pedersen).
      adds  499245e   Added a PTHREAD_MUTEX_RECURSIVE check.
      adds  a7df765   Fix buffer overrun in vcf_format.
      adds  4051805   Also added Number= checking for INFO headers.
      adds  15b2f21   Remove read-past-buffer when printing error message.
      adds  c4deecd   Additional argument protection in sam_hdr_write and bcf_hdr_write.
      adds  31650a4   Prevent out of bounds read on BAM_CIGAR_STR by extending to 16 bytes
      adds  d8e5ec4   Fix clang warning
      adds  54bfd95   Fix length calculation in bam_read1 and possible memory leak
      adds  f613867   Limit subexp and gamma decoders to integer cram_external_type
      adds  df51916   Additional error checking for invalid CRAM ref_id.
      adds  389c4f3   Replaced fprintf(stderr, ...) calls with hts_log_<level> calls. Fixed a few cases of irregular indentation in the process. Made the logging test script ignore multi-line messages.
      adds  1189660   Replaced fprintf(stderr, ...) calls with hts_log_<level> calls.
      adds  dc45f18   Cosmetic improvements to the error messages.
      adds  403353f   Fixed format string errors.
      adds  fe2627f   Merge Logging improvements 2 (PR #543) into develop
      adds  a0fe63f   Use BGZF* in cram_index_build() instead of zfp*
      adds  5b9361d   Removed the (>20 year old!) unnecessary vlen.[ch] code.
      adds  979571b   Allow out to be NULL in cram_huffman_decode_char()
      adds  7fd21f5   Adds HTS_OPT_BLOCK_SIZE support for SAM/BAM/CRAM.
      adds  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.
      adds  f0fc3ee   Replaced fprintf(stderr, ...) calls with hts_log_<level> calls.
      adds  03c4be2   Replaced fprintf(stderr, ...) calls with hts_log_<level> calls.
      adds  3c0302d   Use htslib_hts_log_h definition from htslib_vars.mk
      adds  f1b95e1   Merge branch 'pr551' into pr551_merge
      adds  b28aa8d   Remove autom4te.cache during `make distclean`
      adds  3872861   Updated NEWS file for Solstice release.
      adds  fba943d   Stop threaded bgzf_read_block from using stale values at EOF
      adds  49fdfbd   Relase 1.5: Solstice
       new  ffd8e11   Merge tag '1.5' into debian/unstable
       new  ada885d   New upstream version

The 2 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.


Summary of changes:
 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 --------
 debian/changelog     |   6 +
 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 +++++-----
 37 files changed, 827 insertions(+), 1320 deletions(-)
 delete mode 100644 cram/vlen.c
 delete mode 100644 cram/vlen.h
 delete mode 100644 cram/zfio.c
 delete mode 100644 cram/zfio.h
 create mode 100644 htslib/hts_log.h
 create mode 100755 test/test-logging.pl

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