[med-svn] [gmap] branch master updated (493c311 -> 29dae58)

[Alex Mestiashvili]

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

malex-guest pushed a change to branch master
in repository gmap.

      from  493c311    d/manpages: install gmap_build  d/copyright: included full text of BSD license  d/gmap_setup.1: binary is deprecated and removed from the distribution
       new  6f22792    d/copyright: fix copyright-refers-to-symlink-license
       new  536c54f   Imported Upstream version 2014-07-04
       new  a78521e   Merge tag 'upstream/2014-07-04'
       new  d5bfa54    d/changelog: new upstream release  d/*.1: updated man pages
       new  6bef46f   d/docs: add AUTHORS d/control: removed help2man from Build-Depends:
       new  29dae58   upload to unstable

The 6 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:
 ChangeLog            |  102 +++
 VERSION              |    2 +-
 configure            |   24 +-
 debian/changelog     |    8 +-
 debian/control       |    1 -
 debian/copyright     |    2 +-
 debian/docs          |    1 +
 debian/gmap.1        |    2 +-
 debian/gmap_build.1  |    6 +-
 debian/gsnap.1       |    2 +-
 src/access.c         |  134 ++--
 src/dynprog.c        |    9 +-
 src/dynprog_end.c    |  532 ++++++--------
 src/dynprog_simd.c   |   40 +-
 src/dynprog_simd.h   |    2 +-
 src/dynprog_single.c |   63 +-
 src/genome.c         |   14 +-
 src/genome.h         |    8 +-
 src/genome128_hr.c   |  367 +++++-----
 src/gmap.c           |   27 +-
 src/gmapindex.c      |   23 +-
 src/intlist.c        |   16 +-
 src/intlist.h        |    4 +-
 src/samprint.c       |   10 +-
 src/sarray-read.c    |  617 ++++++++++------
 src/sarray-write.c   |  742 ++++++++++++++++++--
 src/sarray-write.h   |    6 +-
 src/splice.c         | 1046 ++++++++++++++++++----------
 src/splice.h         |   57 +-
 src/splicetrie.c     |  419 +++++------
 src/stage1hr.c       | 1132 ++++++++++++++++--------------
 src/stage3.c         |  129 ++--
 src/stage3hr.c       | 1893 +++++++++++++++++++++++++++++---------------------
 src/stage3hr.h       |   19 +-
 src/substring.c      |  316 +++------
 src/uint8list.c      |   16 +-
 src/uint8list.h      |    4 +-
 src/uintlist.c       |   16 +-
 src/uintlist.h       |    4 +-
 39 files changed, 4649 insertions(+), 3166 deletions(-)

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