[med-svn] [bwa] 01/02: Merge branch 'master' into debian/jessie-backports

[Andreas Tille]

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tille pushed a commit to branch debian/jessie-backports
in repository bwa.

commit 55dcc11f94f1042ee912b2e50a6d8141f4c97489
Merge: 7ae8f2e b67632f
Author: Andreas Tille <tille at debian.org>
Date:   Mon Mar 14 13:54:42 2016 +0100

    Merge branch 'master' into debian/jessie-backports

 .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 ++++++++-----
 debian/changelog          |  13 ++
 debian/control            |  31 ++++-
 debian/libbwa-dev.install |   9 ++
 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 +-
 29 files changed, 912 insertions(+), 119 deletions(-)

diff --cc debian/changelog
index eb9b8f1,5308ff7..9c5aff7
--- a/debian/changelog
+++ b/debian/changelog
@@@ -1,9 -1,16 +1,22 @@@
+ bwa (0.7.13-1) unstable; urgency=medium
+ 
+   * New upstream version
+   * cme fix dpkg-control
+ 
+  -- Andreas Tille <tille at debian.org>  Mon, 14 Mar 2016 13:44:35 +0100
+ 
+ bwa (0.7.12-5) unstable; urgency=medium
+ 
+   * Make a libbwa-dev package for `salmon`.
+ 
+  -- Michael R. Crusoe <crusoe at ucdavis.edu>  Sun, 27 Sep 2015 17:16:04 -0700
+ 
 +bwa (0.7.12-4~bpo8+1) jessie-backports; urgency=medium
 +
 +  * Backport to Jessie
 +
 + -- Andreas Tille <tille at debian.org>  Wed, 15 Jul 2015 09:36:43 +0200
 +
  bwa (0.7.12-4) unstable; urgency=medium
  
    * Check exact number of arguments of bwtupdate

-- 
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