[med-svn] [bwa] branch upstream updated (ad3b39d -> 41430b9)

[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  ad3b39d   Imported Upstream version 0.7.10
       new  41430b9   Imported Upstream version 0.7.12

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.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(-)
 create mode 100644 README-alt.md
 delete mode 100644 bwa-helper.js
 create mode 100644 bwakit/README.md
 create mode 100644 bwakit/bwa-postalt.js
 create mode 100755 bwakit/run-HLA
 create mode 100755 bwakit/run-bwamem
 create mode 100755 bwakit/run-gen-ref
 create mode 100644 bwakit/typeHLA-selctg.js
 create mode 100644 bwakit/typeHLA.js
 create mode 100755 bwakit/typeHLA.sh
 create mode 100644 bwashm.c

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