[med-svn] [libbpp-seq-omics] 03/06: Updated version 2.3.1 from 'upstream/2.3.1'

[Andreas Tille]

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tille pushed a commit to branch master
in repository libbpp-seq-omics.

commit 63b2badde2b018d2578d0b1a484983f87e5af2ba
Merge: cffc5d3 7b9eb57
Author: Andreas Tille <tille at debian.org>
Date:   Tue Jun 13 23:19:43 2017 +0200

    Updated version 2.3.1 from 'upstream/2.3.1'
    
    with Debian dir 608c9ab6aed03aa88727f9d17c8a8f8f4c059e54

 BppSeqOmics.tag                                    | 4984 --------------------
 CMakeLists.txt                                     |  172 +-
 CTestConfig.cmake                                  |   13 +
 ChangeLog                                          |   41 +
 Doxyfile                                           | 2662 ++++++-----
 INSTALL.txt                                        |   19 +-
 bpp-seq-omics.spec                                 |  137 +-
 genIncludes.sh                                     |   35 -
 package.cmake.in                                   |   26 +
 src/Bpp/Seq/Feature/Bed/BedGraphFeatureReader.cpp  |  105 +
 .../BedGraphFeatureReader.h}                       |   57 +-
 src/Bpp/Seq/Feature/Gff/GffFeatureReader.cpp       |    4 +-
 src/Bpp/Seq/Feature/Gff/GffFeatureReader.h         |    8 +-
 src/Bpp/Seq/Feature/Gtf/GtfFeatureReader.cpp       |    4 +-
 src/Bpp/Seq/Feature/Gtf/GtfFeatureReader.h         |    8 +-
 src/Bpp/Seq/Feature/SequenceFeature.h              |  150 +-
 src/Bpp/Seq/Feature/SequenceFeatureTools.cpp       |   11 +
 src/Bpp/Seq/Feature/SequenceFeatureTools.h         |   14 +
 src/Bpp/Seq/Io/Maf/AlignmentFilterMafIterator.cpp  |   72 +-
 src/Bpp/Seq/Io/Maf/AlignmentFilterMafIterator.h    |  105 +-
 src/Bpp/Seq/Io/Maf/BlockMergerMafIterator.cpp      |    4 +-
 src/Bpp/Seq/Io/Maf/ConcatenateMafIterator.cpp      |   25 +-
 src/Bpp/Seq/Io/Maf/ConcatenateMafIterator.h        |   11 +-
 .../Seq/Io/Maf/CoordinateTranslatorMafIterator.cpp |  136 +
 ...terator.h => CoordinateTranslatorMafIterator.h} |   72 +-
 .../Seq/Io/Maf/CoordinatesOutputMafIterator.cpp    |    6 +
 src/Bpp/Seq/Io/Maf/CoordinatesOutputMafIterator.h  |   10 +-
 src/Bpp/Seq/Io/Maf/FeatureExtractorMafIterator.cpp |   23 +-
 src/Bpp/Seq/Io/Maf/FeatureExtractorMafIterator.h   |    4 +-
 src/Bpp/Seq/Io/Maf/FeatureFilterMafIterator.cpp    |    6 +-
 src/Bpp/Seq/Io/Maf/FullGapFilterMafIterator.cpp    |    6 +-
 src/Bpp/Seq/Io/Maf/IterationListener.h             |    2 +-
 src/Bpp/Seq/Io/Maf/MafParser.cpp                   |   51 +-
 src/Bpp/Seq/Io/Maf/MafParser.h                     |   43 +-
 src/Bpp/Seq/Io/Maf/MafSequence.h                   |   36 +-
 src/Bpp/Seq/Io/Maf/MafStatistics.cpp               |  159 +-
 src/Bpp/Seq/Io/Maf/MafStatistics.h                 |  107 +-
 src/Bpp/Seq/Io/Maf/MaskFilterMafIterator.cpp       |    8 +-
 src/Bpp/Seq/Io/Maf/MsmcOutputMafIterator.cpp       |  113 +
 ...OutputMafIterator.h => MsmcOutputMafIterator.h} |   65 +-
 src/Bpp/Seq/Io/Maf/OutputAlignmentMafIterator.cpp  |   20 +-
 src/Bpp/Seq/Io/Maf/OutputAlignmentMafIterator.h    |   59 +-
 src/Bpp/Seq/Io/Maf/OutputMafIterator.cpp           |    2 +-
 src/Bpp/Seq/Io/Maf/PlinkOutputMafIterator.cpp      |  124 +
 src/Bpp/Seq/Io/Maf/PlinkOutputMafIterator.h        |  144 +
 ...tor.cpp => RemoveEmptySequencesMafIterator.cpp} |   40 +-
 ...terator.h => RemoveEmptySequencesMafIterator.h} |   50 +-
 .../Seq/Io/Maf/SequenceLDhotOutputMafIterator.cpp  |  139 +
 ...Iterator.h => SequenceLDhotOutputMafIterator.h} |   80 +-
 src/Bpp/Seq/Io/Maf/SequenceStreamToMafIterator.cpp |    2 +-
 src/Bpp/Seq/Io/Maf/SequenceStreamToMafIterator.h   |    4 +-
 src/Bpp/Seq/Io/Maf/VcfOutputMafIterator.cpp        |    3 +
 src/Bpp/Seq/Io/Maf/VcfOutputMafIterator.h          |   10 +-
 src/Bpp/Seq/Io/Maf/WindowSplitMafIterator.cpp      |   16 +-
 src/Bpp/Seq/Io/Maf/WindowSplitMafIterator.h        |    7 +-
 src/CMakeLists.txt                                 |  148 +-
 test/CMakeLists.txt                                |   66 +-
 57 files changed, 3616 insertions(+), 6812 deletions(-)

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