[med-svn] [htslib] 01/01: Merge tag '1.2.1' into debian/unstable

[Charles Plessy]

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

commit 0662716ffdbffe1d3606a8182a0ce33f4edd81c0
Merge: 9750123 26229a3
Author: Charles Plessy <plessy at riken.jp>
Date:   Mon May 25 11:44:54 2015 +0900

    Merge tag '1.2.1' into debian/unstable
    
    HTSlib patch release 1.2.1, reinstated hts_file_type()

 .gitignore                            |   10 +-
 INSTALL                               |   88 +-
 Makefile                              |  103 +-
 NEWS                                  |   50 +
 README.md                             |   16 +
 bgzf.c                                |   13 +-
 bgzip.c                               |    2 +-
 config.h                              |    3 -
 config.mk.in                          |   72 ++
 configure.ac                          |   93 ++
 cram/cram.h                           |    9 +-
 cram/cram_codecs.c                    |  230 ++--
 cram/cram_codecs.h                    |   22 +-
 cram/cram_decode.c                    | 1339 ++++++++++++++++------
 cram/cram_encode.c                    | 1994 ++++++++++++++++++++-------------
 cram/cram_index.c                     |   82 +-
 cram/cram_io.c                        | 1382 ++++++++++++++++-------
 cram/cram_io.h                        |   98 +-
 cram/cram_samtools.c                  |    5 +-
 cram/cram_stats.c                     |  123 +-
 cram/cram_structs.h                   |  329 +++---
 cram/os.h                             |    2 +
 cram/rANS_byte.h                      |  336 ++++++
 cram/rANS_static.c                    |  841 ++++++++++++++
 cram/rANS_static.h                    |   44 +
 cram/sam_header.c                     |    8 +-
 cram/sam_header.h                     |    8 -
 cram/thread_pool.c                    |  178 ++-
 cram/thread_pool.h                    |   15 +-
 cram/vlen.c                           |    2 +-
 faidx.c                               |   36 +-
 hfile.c                               |   23 +-
 hfile_internal.h                      |    3 +-
 hfile_irods.c                         |  243 ++++
 hts.c                                 |  531 +++++++--
 htsfile.1                             |   71 ++
 htsfile.c                             |  168 +++
 htslib.mk                             |    7 +-
 htslib/faidx.h                        |    2 +-
 htslib/hfile.h                        |   10 +-
 htslib/hts.h                          |  146 ++-
 htslib/khash.h                        |    8 +-
 htslib/kseq.h                         |   10 +-
 htslib/regidx.h                       |   13 +-
 htslib/sam.h                          |    2 +-
 htslib/synced_bcf_reader.h            |   15 +-
 htslib/vcf.h                          |   15 +-
 htslib_vars.mk                        |    2 +-
 knetfile.c                            |   11 +-
 regidx.c                              |   18 +-
 sam.c                                 |  134 ++-
 synced_bcf_reader.c                   |   82 +-
 tabix.1                               |  121 +-
 tabix.c                               |  268 +++--
 tbx.c                                 |    5 +
 test/{aux#aux.sam => auxf#values.sam} |    0
 test/{aux.fa => auxf.fa}              |    0
 test/{aux.fa.fai => auxf.fa.fai}      |    0
 test/hfile.c                          |    4 +-
 test/sam.c                            |   52 +-
 test/test-vcf-api.c                   |   57 +-
 test/test_view.c                      |   92 +-
 vcf.c                                 |  207 ++--
 vcfutils.c                            |   63 +-
 64 files changed, 7514 insertions(+), 2402 deletions(-)

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