[med-svn] [bwa] 02/05: Merge tag 'upstream/0.7.13'

[Andreas Tille]

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tille pushed a commit to branch master
in repository bwa.

commit f3a990b6ad6abbe5086377689578ae7268868f7c
Merge: 502ebba 11ce18b
Author: Andreas Tille <tille at debian.org>
Date:   Mon Mar 14 13:42:48 2016 +0100

    Merge tag 'upstream/0.7.13'
    
    Upstream version 0.7.13

 .gitignore            |   7 ++
 .travis.yml           |   5 +
 Makefile              |  15 ++-
 NEWS.md               |  29 +++++
 README-alt.md         |   2 +-
 bwa.1                 |   7 +-
 bwa.h                 |   7 ++
 bwakit/README.md      |   2 +-
 bwakit/bwa-postalt.js |   2 +-
 bwakit/run-gen-ref    |   2 +-
 bwamem.c              |  19 +--
 bwamem.h              |   2 -
 bwamem_extra.c        |  25 ----
 bwape.c               |   2 +-
 bwase.c               |   1 +
 bwtindex.c            |  91 ++++++++++-----
 fastmap.c             |  22 +---
 kthread.c             |  19 +--
 main.c                |   4 +-
 maxk.c                |  67 +++++++++++
 qualfa2fq.pl          |   2 +-
 rle.c                 | 191 ++++++++++++++++++++++++++++++
 rle.h                 |  77 ++++++++++++
 rope.c                | 318 ++++++++++++++++++++++++++++++++++++++++++++++++++
 rope.h                |  58 +++++++++
 xa2multi.pl           |   2 +-
 26 files changed, 864 insertions(+), 114 deletions(-)

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