[med-svn] [bwa] 03/04: Merge tag 'upstream/0.7.12'

[Andreas Tille]

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tille pushed a commit to branch master
in repository bwa.

commit a13c75225905861a18adf7665ec4d2fb3bc0b220
Merge: 013d1b5 41430b9
Author: Andreas Tille <tille at debian.org>
Date:   Tue Jan 27 08:47:34 2015 +0100

    Merge tag 'upstream/0.7.12'
    
    Upstream version 0.7.12

 Makefile                 |  10 +-
 NEWS.md                  |  72 +++++
 README-alt.md            | 178 ++++++++++++
 README.md                |  72 +++--
 bntseq.c                 |  48 +++-
 bntseq.h                 |   1 +
 bwa-helper.js            | 706 -----------------------------------------------
 bwa.1                    |  58 +++-
 bwa.c                    | 146 +++++++++-
 bwa.h                    |  16 +-
 bwakit/README.md         | 115 ++++++++
 bwakit/bwa-postalt.js    | 524 +++++++++++++++++++++++++++++++++++
 bwakit/run-HLA           |  20 ++
 bwakit/run-bwamem        | 186 +++++++++++++
 bwakit/run-gen-ref       |  39 +++
 bwakit/typeHLA-selctg.js |  62 +++++
 bwakit/typeHLA.js        | 496 +++++++++++++++++++++++++++++++++
 bwakit/typeHLA.sh        |  49 ++++
 bwamem.c                 | 159 ++++++++---
 bwamem.h                 |  15 +-
 bwamem_extra.c           |  68 +++--
 bwamem_pair.c            | 102 ++++---
 bwashm.c                 | 213 ++++++++++++++
 bwt.c                    |  42 ++-
 bwt.h                    |   4 +-
 bwt_gen.c                |   9 +-
 bwtindex.c               |  18 +-
 example.c                |  12 +-
 fastmap.c                | 251 ++++++++++++-----
 kseq.h                   |  18 +-
 kthread.c                | 104 ++++++-
 main.c                   |   8 +-
 utils.c                  |  11 +
 utils.h                  |   2 +-
 34 files changed, 2846 insertions(+), 988 deletions(-)

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