[med-svn] [abyss] 08/14: Merge tag 'upstream/1.3.6'

[Charles Plessy]

This is an automated email from the git hooks/post-receive script.

plessy pushed a commit to branch master
in repository abyss.

commit c82f44153c59125f93ac5ac5a96e56b97aba739b
Merge: 55af673 b391f1f
Author: Charles Plessy <plessy at debian.org>
Date:   Sun Sep 8 11:22:27 2013 +0900

    Merge tag 'upstream/1.3.6'
    
    Upstream version 1.3.6
    
    # gpg: Signature faite le dim. 08 sept. 2013 11:22:27 JST avec la clef RSA d'identifiant 2295D502
    # gpg: Bonne signature de « Charles Plessy <plessy at debian.org> »

 ._depcomp                    |  Bin 368 -> 0 bytes
 ABYSS/Makefile.in            |  223 ++++++++++++-------
 AdjList/Makefile.in          |  223 ++++++++++++-------
 Align/Makefile.in            |  341 +++++++++++++++++------------
 Align/mergepairs.cc          |    2 +-
 Assembly/Makefile.in         |  290 +++++++++++++++----------
 ChangeLog                    |   37 ++++
 Common/BitUtil.h             |   42 ++--
 Common/Histogram.h           |   45 ++--
 Common/Makefile.in           |  402 +++++++++++++++++++---------------
 Common/Sequence.cpp          |   47 +++-
 Consensus/Makefile.in        |  223 ++++++++++++-------
 DAssembler/Makefile.in       |  247 +++++++++++++--------
 DataLayer/FastaReader.cpp    |    8 +-
 DataLayer/Makefile.in        |  309 +++++++++++++++++----------
 DataLayer/fac.cc             |   40 +++-
 DistanceEst/Makefile.in      |  247 +++++++++++++--------
 FMIndex/Makefile.in          |  254 ++++++++++++++--------
 FMIndex/abyss-dawg.cc        |    2 -
 FMIndex/count.cc             |    2 -
 FilterGraph/FilterGraph.cpp  |   39 +++-
 FilterGraph/Makefile.in      |  223 ++++++++++++-------
 Graph/AdjIO.h                |    7 +-
 Graph/Makefile.in            |  293 +++++++++++++++----------
 KAligner/Makefile.in         |  247 +++++++++++++--------
 Layout/Makefile.in           |  223 ++++++++++++-------
 Makefile.am                  |    2 +-
 Makefile.in                  |  288 +++++++++++++------------
 Map/Makefile.in              |  261 ++++++++++++++---------
 Map/index.cc                 |    2 -
 Map/map.cc                   |   39 +++-
 Map/overlap.cc               |    2 -
 MergePaths/Makefile.in       |  261 ++++++++++++++---------
 Misc/Makefile.in             |  182 +++++++++++++---
 Overlap/Makefile.in          |  223 ++++++++++++-------
 Parallel/Makefile.in         |  295 +++++++++++++++----------
 ParseAligns/Makefile.in      |  258 +++++++++++++---------
 ParseAligns/abyss-fixmate.cc |   95 ++++++++-
 PathOverlap/Makefile.in      |  223 ++++++++++++-------
 PopBubbles/Makefile.in       |  223 ++++++++++++-------
 PopBubbles/PopBubbles.cpp    |   15 +-
 README.html                  |   26 ++-
 README.md                    |   18 +-
 Scaffold/Makefile.in         |  261 ++++++++++++++---------
 SimpleGraph/Makefile.in      |  223 ++++++++++++-------
 aclocal.m4                   |  485 ++++++++++++++++++++++++++++--------------
 bin/Makefile.in              |  109 +++++++---
 bin/abyss-pe                 |    2 +-
 compile                      |  347 ++++++++++++++++++++++++++++++
 config.h.in                  |    9 +-
 configure                    |  275 +++++++++++++++++++++---
 configure.ac                 |   17 +-
 depcomp                      |  454 +++++++++++++++++++++++----------------
 dialign/Makefile.in          |  191 +++++++++++------
 doc/ABYSS.1                  |    2 +-
 doc/Makefile.in              |  123 ++++++-----
 doc/abyss-pe.1               |    2 +-
 doc/abyss-tofastq.1          |    2 +-
 doxygen.conf                 |   16 +-
 kmerprint/Makefile.in        |  194 +++++++++++------
 missing                      |  405 +++++++++++++----------------------
 61 files changed, 6136 insertions(+), 3410 deletions(-)

-- 
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