[med-svn] [htslib] 01/02: Merge tag '1.5' into debian/unstable

[Andreas Tille]

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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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