[med-svn] [bwa] branch upstream updated (e513f4d -> 30f8d35)

[Andreas Tille]

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tille pushed a change to branch upstream
in repository bwa.

      from  e513f4d   Imported Upstream version 0.7.8
       new  30f8d35   Imported Upstream version 0.7.9a

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:
 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 +-
 fastmap.c       | 114 ++++++---
 kbtree.h        |   2 +-
 ksw.c           | 116 ++++++----
 main.c          |   2 +-
 21 files changed, 1744 insertions(+), 508 deletions(-)
 rename NEWS => NEWS.md (85%)
 create mode 100644 bwa-helper.js
 create mode 100644 bwamem_extra.c

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