[med-svn] [gmap] branch upstream updated (eff24d5 -> 536c54f)

[Alex Mestiashvili]

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

      from  eff24d5   Imported Upstream version 2014-06-10
       new  536c54f   Imported Upstream version 2014-07-04

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:
 ChangeLog            |  102 +++
 VERSION              |    2 +-
 configure            |   24 +-
 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 +-
 32 files changed, 4635 insertions(+), 3158 deletions(-)

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