[med-svn] [htslib] branch master updated (979571b -> cc55632)

[Andreas Tille]

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

tille pushed a change to branch master
in repository htslib.

      from  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  9156a41   Merge version number bump and NEWS file from master
       new  2739558   Trivial fix for reading empty cram indices.
       new  6999a09   Adaptations to Windows line endings and binary/text files: -stop git from converting line endings on the reference fasta files. -make the test scripts handle CRLF line endings, too. Perl should take care of it, according to the docs, but it doesn't.
       new  75d9f0d   Further Windows/Mingw/MSYS improvements.
       new  da5c0c7   Fixes #531 from PR suggestions.
       new  5c15581   Replaced fprintf(stderr, ...) calls with hts_log_<level> calls.
       new  ab66ccd   Replaced fprintf(stderr, ...) calls with hts_log_<level> calls.
       new  fc05969   Replaced commented-out debugging code with #ifdef equivalent.
       new  68cd7e5   Minor reformatting.
       new  cc55632   Replaced the CRAM-specific verbosity flag with the regular log level setting.

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.


Summary of changes:
 .appveyor.yml                    |  43 ++++++++++++++
 .gitattributes                   |   5 ++
 .gitignore                       |   2 +
 INSTALL                          |   6 ++
 Makefile                         |  32 +++++++++--
 NEWS                             |  17 +++++-
 bcf_sr_sort.c                    |  20 ++++++-
 bgzf.c                           |  13 ++++-
 bgzip.c                          |  18 +++++-
 configure.ac                     |  22 ++++++--
 cram/cram_codecs.c               |  28 +++++-----
 cram/cram_decode.c               |  70 +++++++++++------------
 cram/cram_encode.c               |  62 ++++++++------------
 cram/cram_external.c             |   3 +-
 cram/cram_index.c                |   6 +-
 cram/cram_io.c                   |  97 +++++++++++++++-----------------
 cram/cram_io.h                   |   6 ++
 cram/cram_stats.c                |  10 +++-
 cram/cram_structs.h              |   3 +-
 cram/mFILE.c                     |   3 +-
 cram/mFILE.h                     |   5 ++
 cram/os.h                        |  24 ++------
 cram/sam_header.c                |   6 +-
 errmod.c                         |   2 +
 faidx.c                          |  19 +++----
 hfile.c                          |  58 +++++++++++++++++--
 hfile_internal.h                 |  21 +++++++
 hfile_libcurl.c                  |   4 +-
 hts.c                            |  42 ++++++++++++--
 htslib/vcf_sweep.h => hts_os.c   |  37 ++++--------
 htsfile.1                        |   2 +-
 htslib/bgzf.h                    |   3 +
 htslib/hfile.h                   |   4 ++
 htslib/hts.h                     |   3 +-
 htslib/hts_defs.h                |  12 ++++
 htslib/hts_log.h                 |   2 +
 htslib/{vcf_sweep.h => hts_os.h} |  39 ++++++-------
 htslib/vcf.h                     |   2 +-
 knetfile.c                       |  25 +++++----
 realn.c                          |   2 +-
 regidx.c                         |  16 +++---
 sam.c                            |  16 +++---
 synced_bcf_reader.c              |  46 ++++++++-------
 tabix.1                          |   2 +-
 tabix.c                          |   2 +-
 tbx.c                            |   5 +-
 test/compare_sam.pl              |   2 +
 test/hfile.c                     |   4 +-
 test/sam.c                       |   2 +-
 test/tabix/test-tabix.sh         |   7 ++-
 test/test-bcf-sr.pl              |   6 +-
 test/test.pl                     |  84 +++++++++++++++++++---------
 test/test_bgzf.c                 |  15 ++---
 test/test_view.c                 |  55 ++++++++++++------
 vcf.c                            | 118 ++++++++++++++++++++-------------------
 vcfutils.c                       |  10 ++--
 win/rand.c                       |  98 ++++++++++++++++++++++++++++++++
 win/rand.h                       |  23 ++++++++
 58 files changed, 855 insertions(+), 434 deletions(-)
 create mode 100644 .appveyor.yml
 copy htslib/vcf_sweep.h => hts_os.c (64%)
 copy htslib/{vcf_sweep.h => hts_os.h} (64%)
 create mode 100644 win/rand.c
 create mode 100644 win/rand.h

-- 
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/htslib.git