[med-svn] [gmap] branch upstream updated (8ab5509 -> f9bd6b9)

[Alex Mestiashvili]

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

      from  8ab5509   Imported Upstream version 2016-06-09
       new  f9bd6b9   Imported Upstream version 2016-07-11.v2

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         |  109 +++
 Makefile.in       |    2 +-
 TODO              |    3 -
 VERSION           |    2 +-
 configure         |   56 +-
 configure.ac      |   21 +-
 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 +-
 40 files changed, 3823 insertions(+), 1113 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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