[med-svn] [gmap] branch master updated (988d7b7 -> 1428cfc)

[Alex Mestiashvili]

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

      from  988d7b7   Update changelog, upload to unstable
       new  f9bd6b9   Imported Upstream version 2016-07-11.v2
       new  c07d7ab   Merge tag 'upstream/2016-07-11.v2'
       new  d0e45f4   Update copyright format string
       new  1428cfc   Update changelog, upload to unstable

The 4 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
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Summary of changes:
 ChangeLog         |  109 +++
 Makefile.in       |    2 +-
 TODO              |    3 -
 VERSION           |    2 +-
 configure         |   56 +-
 configure.ac      |   21 +-
 debian/changelog  |    7 +
 debian/copyright  |    2 +-
 src/ChangeLog     |    0
 src/Makefile.am   |    4 +-
 src/Makefile.in   |  129 ++-
 src/compile       |  165 ----
 src/doublelist.c  |   18 +-
 src/doublelist.h  |    4 +-
 src/filestring.c  |  209 ++++-
 src/gmap.c        |   24 +-
 src/gsnap.c       |   12 +-
 src/indel.c       |    8 +-
 src/intlist.c     |   19 +-
 src/intlist.h     |    4 +-
 src/pair.c        |   99 +-
 src/pair.h        |    4 +-
 src/resulthr.c    |   10 +-
 src/resulthr.h    |    5 +-
 src/samprint.c    |   19 +-
 src/sarray-read.c |  387 +++++++-
 src/sedgesort.c   |  203 +++++
 src/sedgesort.h   |    9 +
 src/shortread.c   |  170 +++-
 src/splice.c      |   21 +-
 src/stage1hr.c    | 2636 ++++++++++++++++++++++++++++++++++++++++++-----------
 src/stage3.c      |   11 +-
 src/stage3.h      |    4 +-
 src/stage3hr.c    |  437 ++++++---
 src/stage3hr.h    |    4 +-
 src/substring.c   |   71 +-
 src/substring.h   |    4 +-
 src/uintlist.c    |   17 +-
 src/uintlist.h    |    4 +-
 src/uniqscan.c    |    6 +-
 src/univdiag.c    |   22 +
 src/univdiag.h    |    4 +-
 42 files changed, 3831 insertions(+), 1114 deletions(-)
 delete mode 100644 TODO
 delete mode 100644 src/ChangeLog
 delete mode 100644 src/compile
 create mode 100644 src/sedgesort.c
 create mode 100644 src/sedgesort.h

-- 
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