[med-svn] [htslib] 01/04: Merge branch 'master' into debian/unstable

[Charles Plessy]

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

plessy pushed a commit to branch debian/unstable
in repository htslib.

commit cc559b80e8063cfaa457fccdaf954e4eda5ef132
Merge: 53af783 f2af2ad
Author: Charles Plessy <plessy at debian.org>
Date:   Sat Aug 16 18:20:52 2014 +0900

    Merge branch 'master' into debian/unstable

 .gitattributes             |    4 +
 .gitignore                 |    4 +
 INSTALL                    |   25 +
 LICENSE                    |   69 ++
 Makefile                   |   97 +-
 README                     |    5 +
 README.md                  |   25 +-
 bgzf.c                     | 1080 +++++++++---------
 bgzip.c                    |  284 +++++
 cram/cram_codecs.c         |    5 +-
 cram/cram_decode.c         |   62 +-
 cram/cram_index.c          |  160 ++-
 cram/cram_index.h          |    2 +-
 cram/cram_io.c             |  134 ++-
 cram/cram_io.h             |   15 +-
 cram/cram_structs.h        |    4 +-
 cram/mFILE.c               |   71 +-
 cram/mFILE.h               |    1 +
 cram/open_trace_file.c     |  131 +--
 cram/sam_header.c          |    4 +-
 cram/sam_header.h          |    8 +-
 faidx.5                    |   23 +
 faidx.c                    |  548 +++++-----
 hfile.c                    |   98 +-
 hfile_internal.h           |   23 +-
 hfile_net.c                |   25 +-
 hts.c                      | 1943 ++++++++++++++++++---------------
 htslib.mk                  |   44 +-
 htslib.pc.in               |   10 +
 htslib/bgzf.h              |  411 +++----
 htslib/faidx.h             |  124 ++-
 hfile.h => htslib/hfile.h  |   34 +-
 htslib/hts.h               |  218 ++--
 htslib/hts_defs.h          |   47 +
 htslib/kfunc.h             |   30 +-
 htslib/khash_str2int.h     |   36 +-
 htslib/klist.h             |    4 +-
 htslib/knetfile.h          |   26 +
 htslib/kstdint.h           |   64 --
 htslib/kstring.h           |   19 +-
 htslib/razf.h              |  134 ---
 htslib/sam.h               |  337 ++++--
 htslib/synced_bcf_reader.h |  152 ++-
 htslib/tbx.h               |   67 +-
 htslib/vcf.h               |  619 +++++++----
 htslib/vcf_sweep.h         |   28 +-
 htslib/vcfutils.h          |   60 +-
 htslib_vars.mk             |   23 +-
 kfunc.c                    |   26 +
 knetfile.c                 |   17 +-
 kstring.c                  |   25 +
 razf.c                     |  856 ---------------
 sam.5                      |   23 +
 sam.c                      | 2327 +++++++++++++++++++++------------------
 synced_bcf_reader.c        |  539 ++++-----
 tabix.1                    |  155 +++
 tabix.c                    |  399 +++++++
 tbx.c                      |  418 +++----
 test/compare_sam.pl        |  100 +-
 test/fieldarith.c          |   60 +-
 test/hfile.c               |   45 +-
 test/sam.c                 |  143 +++
 test/test-vcf-api.c        |  113 +-
 test/test-vcf-api.out      |   12 +-
 test/test-vcf-sweep.c      |   41 +-
 test/test.pl               |   44 +-
 test/test_view.c           |  239 ++--
 test/test_view.pl          |   32 +-
 vcf.5                      |   24 +
 vcf.c                      | 2595 +++++++++++++++++++++++++++++---------------
 vcf_sweep.c                |   24 +
 vcfutils.c                 |  736 ++++++++-----
 72 files changed, 9852 insertions(+), 6478 deletions(-)

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