[med-svn] [bwa] branch master updated (19d6988 -> 2db920b)

[Andreas Tille]

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

tille pushed a change to branch master
in repository bwa.

      from  19d6988   New upstream version
       new  e82a700   Update contact info
       new  06b333e   New upstream version
       new  30f8d35   Imported Upstream version 0.7.9a
       new  2db920b   Merge tag 'upstream/0.7.9a'

The 4 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:
 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 +-
 debian/changelog |   7 +
 debian/copyright |   5 +-
 fastmap.c        | 114 ++++++---
 kbtree.h         |   2 +-
 ksw.c            | 116 +++++----
 main.c           |   2 +-
 23 files changed, 1755 insertions(+), 509 deletions(-)
 rename NEWS => NEWS.md (85%)
 create mode 100644 bwa-helper.js
 create mode 100644 bwamem_extra.c

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