[med-svn] [bwa] 04/04: Merge tag 'upstream/0.7.9a'

[Andreas Tille]

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tille pushed a commit to branch master
in repository bwa.

commit 2db920b60a8b73b11673907dba0ffe908874864d
Merge: 06b333e 30f8d35
Author: Andreas Tille <tille at debian.org>
Date:   Fri Jun 6 21:55:37 2014 +0200

    Merge tag 'upstream/0.7.9a'
    
    Upstream version 0.7.9a

 Makefile        |  10 +-
 NEWS => NEWS.md | 186 ++++++++++-----
 README.md       | 136 +++++++++--
 bntseq.c        |  36 +++
 bntseq.h        |   3 +
 bwa-helper.js   | 706 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 bwa.1           |  14 +-
 bwa.c           |  65 +-----
 bwa.h           |   2 -
 bwamem.c        | 618 ++++++++++++++++++++++++++++---------------------
 bwamem.h        |  18 +-
 bwamem_extra.c  | 147 ++++++++++++
 bwamem_pair.c   |  66 ++++--
 bwape.c         |   1 +
 bwase.c         |   2 +-
 bwt_lite.c      |   4 +-
 bwtaln.c        |   4 +-
 fastmap.c       | 114 ++++++---
 kbtree.h        |   2 +-
 ksw.c           | 116 ++++++----
 main.c          |   2 +-
 21 files changed, 1744 insertions(+), 508 deletions(-)

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