[med-svn] [gmap] branch master updated (02c26bc -> 7cd9e2f)

[Alex Mestiashvili]

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

      from  02c26bc   d/changelog: upload to unstable d/control,copyright,docs: applied wrap-and-sort
       new  fda1ac5   Imported Upstream version 2015-09-29
       new  6aa4797   Merge tag 'upstream/2015-09-29'
       new  7cd9e2f   d/changelog: imported new upstream version 2015-09-29  upload to unstable

The 3 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 +-
 debian/changelog      |    6 +
 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 +-
 33 files changed, 3310 insertions(+), 2537 deletions(-)
 delete mode 100644 TODO
 delete mode 100644 src/ChangeLog

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