[med-svn] samtools 25/26: Merge branch 'develop' into debian/unstable

[Charles Plessy]

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

commit f96482fc6a8d69541736b9dc66a3326e5478470d
Merge: c930cbb 85f1c53
Author: Charles Plessy <plessy at debian.org>
Date:   Tue Dec 10 18:17:50 2013 +0900

    Merge branch 'develop' into debian/unstable

 INSTALL                |   3 +
 Makefile               |   5 +-
 bam2bcf.c              |  50 +--
 bam2bcf.h              |   2 +-
 bam2bcf_indel.c        |   2 +-
 bam2depth.c            |  30 +-
 bam_flags.c            |  43 +++
 bam_index.c            |   4 +-
 bam_lpileup.c          |   2 +-
 bam_md.c               |   2 +-
 bam_plcmd.c            |  95 ++---
 bam_sort.c             |   4 +-
 bamshuf.c              |   6 +-
 bamtk.c                |   5 +-
 bedcov.c               |  19 +-
 cut_target.c           |  27 +-
 errmod.c               |   1 -
 faidx.c                |   2 +-
 khash_utils.h          |  81 ----
 kprobaln.c             |   4 +-
 misc/plot-bamstats     |   2 +-
 phase.c                |  29 +-
 sam_header.c           |   2 +-
 sample.c               |   2 +-
 samtools.h             |   9 +
 stats.c                |  38 +-
 test/dat/mpileup.out.2 | 976 ++++++++++++++++++++++++-------------------------
 test/dat/mpileup.out.3 |  11 +
 test/test.pl           |  94 ++++-
 29 files changed, 841 insertions(+), 709 deletions(-)

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