[med-svn] samtools 01/07: Merge tag '1.2' into debian/unstable

[Charles Plessy]

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

commit a5f28a0f7a32c48ea7241913cec87fce0de35ab3
Merge: 6ce5671 255f97d
Author: Charles Plessy <plessy at debian.org>
Date:   Mon Jun 15 21:23:53 2015 +0900

    Merge tag '1.2' into debian/unstable
    
    Bug fix release

 INSTALL                          |   2 +-
 Makefile                         |  11 +-
 NEWS                             |  16 ++
 README                           |  23 ++
 bam.h                            |   2 +-
 bam2bcf_indel.c                  |  40 ++--
 bam2depth.c                      |  16 +-
 bam_mate.c                       |   3 +-
 bam_md.c                         |   1 -
 bam_plcmd.c                      |  45 +++-
 bam_sort.c                       |  61 +++--
 bam_stat.c                       |  40 +++-
 bamtk.c                          |   6 +-
 errmod.c                         |   7 +-
 kaln.c                           | 486 ---------------------------------------
 kaln.h                           |  67 ------
 misc/ace2sam.c                   |   2 +-
 misc/plot-bamstats               |   2 +-
 misc/seq_cache_populate.pl       |   5 +
 padding.c                        |   2 +-
 sam.c                            |   8 +-
 sam.h                            |   3 +-
 sam_view.c                       |  27 ++-
 samtools.1                       |  36 +--
 stats.c                          |  21 +-
 test/merge/test_rtrans_build.c   |   4 +-
 test/merge/test_trans_tbl_init.c |   2 +-
 test/mpileup/expected/9.out      |  20 +-
 test/mpileup/regression.sh       | 125 +++++-----
 test/stat/1.stats.expected       |   2 +-
 test/stat/2.stats.expected       |   2 +-
 test/stat/3.stats.expected       |   2 +-
 test/stat/4.stats.expected       |   2 +-
 test/stat/5.stats.expected       |   2 +-
 test/stat/6.stats.expected       |   2 +-
 test/test.pl                     |  41 +++-
 36 files changed, 374 insertions(+), 762 deletions(-)

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