[med-svn] [bwa] branch upstream updated (41430b9 -> 11ce18b)

[Andreas Tille]

This is an automated email from the git hooks/post-receive script.

tille pushed a change to branch upstream
in repository bwa.

      from  41430b9   Imported Upstream version 0.7.12
       new  11ce18b   Imported Upstream version 0.7.13

The 1 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.


Summary of changes:
 .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(-)
 create mode 100644 .gitignore
 create mode 100644 .travis.yml
 create mode 100644 maxk.c
 create mode 100644 rle.c
 create mode 100644 rle.h
 create mode 100644 rope.c
 create mode 100644 rope.h

-- 
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