[med-svn] [gmap] branch upstream updated (1f0c49c -> fda1ac5)

[Alex Mestiashvili]

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

      from  1f0c49c   Imported Upstream version 2015-07-23
       new  fda1ac5   Imported Upstream version 2015-09-29

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             |   93 ++
 Makefile.in           |    2 +-
 TODO                  |    3 -
 VERSION               |    2 +-
 configure             |   24 +-
 src/ChangeLog         |    0
 src/Makefile.in       |    2 +-
 src/chimera.c         |   75 +-
 src/chimera.h         |    5 +-
 src/dynprog_genome.c  | 4254 +++++++++++++++++++++++++------------------------
 src/genome.c          |    4 +-
 src/gmap.c            |   85 +-
 src/gsnap.c           |   87 +-
 src/inbuffer.c        |    8 +-
 src/oligoindex_hr.c   |   55 +-
 src/outbuffer.c       |    4 +-
 src/pair.c            |   76 +-
 src/pair.h            |    5 +-
 src/samprint.c        |  164 +-
 src/samprint.h        |    5 +-
 src/sarray-read.c     |   59 +-
 src/splice.c          |   10 +-
 src/stage1.c          |   28 +-
 src/stage1hr.c        |  408 +++--
 src/stage1hr.h        |    9 +-
 src/stage3.c          |   78 +-
 src/stage3hr.c        |  221 ++-
 src/stage3hr.h        |   10 +-
 src/substring.c       |   11 +-
 src/substring.h       |    5 +-
 src/uniqscan.c        |   14 +-
 util/gmap_build.pl.in |   35 +-
 32 files changed, 3304 insertions(+), 2537 deletions(-)
 delete mode 100644 TODO
 delete mode 100644 src/ChangeLog

-- 
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/gmap.git