[med-svn] [abyss] 06/14: Merge tag 'upstream/1.3.5'

[Charles Plessy]

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plessy pushed a commit to branch master
in repository abyss.

commit 55af673f34253e8ebf3ea61120664266e558762d
Merge: 9ec0c9c e05ee57
Author: Charles Plessy <plessy at debian.org>
Date:   Sun Sep 8 11:22:19 2013 +0900

    Merge tag 'upstream/1.3.5'
    
    Upstream version 1.3.5
    
    # gpg: Signature faite le dim. 08 sept. 2013 11:22:19 JST avec la clef RSA d'identifiant 2295D502
    # gpg: Bonne signature de « Charles Plessy <plessy at debian.org> »

 ._depcomp                              |  Bin 0 -> 368 bytes
 ABYSS/Makefile.in                      |    1 +
 AdjList/AdjList.cpp                    |    8 +-
 AdjList/Makefile.in                    |    1 +
 Align/Makefile.am                      |   17 +-
 Align/Makefile.in                      |   48 ++++-
 Align/Options.h                        |   11 ++
 Align/align.cc                         |    7 +-
 Align/mergepairs.cc                    |  333 ++++++++++++++++++++++++++++++++
 Align/smith_waterman.cpp               |   24 +--
 Assembly/Makefile.in                   |    1 +
 Assembly/Options.cpp                   |    4 +-
 COPYRIGHT                              |   12 +-
 ChangeLog                              |   60 ++++++
 Common/ContigProperties.h              |    4 +
 Common/Makefile.in                     |    1 +
 Common/SAM.h                           |   21 ++
 Common/SeqExt.h                        |   10 +-
 Common/Uncompress.cpp                  |   57 +++++-
 Consensus/Consensus.cpp                |    7 +-
 Consensus/Makefile.in                  |    1 +
 DAssembler/DAssembler.cpp              |    7 +-
 DAssembler/Makefile.in                 |    1 +
 DataLayer/FastaReader.cpp              |   25 ++-
 DataLayer/FastaReader.h                |    5 +-
 DataLayer/Makefile.in                  |    1 +
 DataLayer/abyss-tofastq.cc             |    4 +-
 DataLayer/fac.cc                       |    9 +-
 DistanceEst/DistanceEst.cpp            |   48 +++--
 DistanceEst/MLE.cpp                    |    2 +-
 DistanceEst/Makefile.in                |    1 +
 FMIndex/Makefile.in                    |    1 +
 FMIndex/abyss-dawg.cc                  |    4 +-
 FMIndex/count.cc                       |    4 +-
 FilterGraph/FilterGraph.cpp            |    7 +-
 FilterGraph/Makefile.in                |    1 +
 Graph/AdjIO.h                          |    5 +
 Graph/ContigGraphAlgorithms.h          |    2 +-
 Graph/GraphAlgorithms.h                |    6 +-
 Graph/Makefile.in                      |    1 +
 Graph/gc.cc                            |    4 +-
 Graph/todot.cc                         |    4 +-
 KAligner/KAligner.cpp                  |    6 +-
 KAligner/Makefile.in                   |    1 +
 LICENSE                                |    2 +-
 Layout/Makefile.am                     |    5 +
 {ABYSS => Layout}/Makefile.in          |   69 +++----
 Layout/layout.cc                       |  319 ++++++++++++++++++++++++++++++
 Makefile.am                            |    2 +
 Makefile.in                            |    8 +-
 Map/Makefile.in                        |    1 +
 Map/index.cc                           |    4 +-
 Map/map.cc                             |   20 +-
 Map/overlap.cc                         |   53 ++++-
 MergePaths/Makefile.in                 |    1 +
 MergePaths/MergeContigs.cpp            |   10 +-
 MergePaths/MergePaths.cpp              |    7 +-
 MergePaths/PathConsensus.cpp           |    6 +-
 Misc/Makefile.am                       |   12 ++
 {bin => Misc}/Makefile.in              |  166 +++++++---------
 Misc/samtobreak.hs                     |  327 +++++++++++++++++++++++++++++++
 Overlap/Makefile.in                    |    1 +
 Overlap/Overlap.cpp                    |    4 +-
 Parallel/Makefile.in                   |    1 +
 Parallel/NetworkSequenceCollection.cpp |   13 +-
 Parallel/parallelAbyss.cpp             |    4 +
 ParseAligns/Makefile.in                |    1 +
 ParseAligns/ParseAligns.cpp            |    4 +-
 ParseAligns/abyss-fixmate.cc           |   41 +++-
 PathOverlap/Makefile.in                |    1 +
 PathOverlap/PathOverlap.cpp            |    7 +-
 PopBubbles/Makefile.in                 |    1 +
 PopBubbles/PopBubbles.cpp              |    7 +-
 README.html                            |   19 +-
 README.md                              |   15 +-
 Scaffold/Makefile.in                   |    1 +
 Scaffold/drawgraph.cc                  |    7 +-
 Scaffold/junction.cc                   |    7 +-
 Scaffold/scaffold.cc                   |   31 ++-
 SimpleGraph/Makefile.in                |    1 +
 SimpleGraph/SimpleGraph.cpp            |    7 +-
 bin/Makefile.in                        |    1 +
 bin/abyss-pe                           |   31 +--
 configure                              |  137 +++++++++++--
 configure.ac                           |   12 +-
 depcomp                                |  189 ++++++++++++------
 dialign/Makefile.in                    |    1 +
 doc/ABYSS.1                            |   12 +-
 doc/Makefile.in                        |    1 +
 doc/abyss-pe.1                         |   16 +-
 doc/abyss-tofastq.1                    |    4 +-
 doc/flowchart.pdf                      |  Bin 77904 -> 165274 bytes
 install-sh                             |   35 ++--
 kmerprint/Makefile.in                  |    1 +
 kmerprint/kmerprint.cc                 |  103 +++++++---
 missing                                |  148 +++++---------
 96 files changed, 2176 insertions(+), 477 deletions(-)

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