[med-svn] [libbpp-seq-omics] branch upstream updated (e1f3f06 -> 7b9eb57)

[Andreas Tille]

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tille pushed a change to branch upstream
in repository libbpp-seq-omics.

      from  e1f3f06   Imported Upstream version 2.2.0
       new  7b9eb57   New upstream version 2.3.1

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:
 BppSeqOmics.tag                                    | 4984 --------------------
 CMakeLists.txt                                     |  172 +-
 CTestConfig.cmake                                  |   13 +
 ChangeLog                                          |   41 +
 Doxyfile                                           | 2662 ++++++-----
 INSTALL.txt                                        |   19 +-
 bpp-seq-omics.spec                                 |  137 +-
 debian/changelog                                   |   19 -
 debian/compat                                      |    1 -
 debian/control                                     |   25 -
 debian/copyright                                   |   66 -
 debian/libbpp-seq-omics-dev.install                |    3 -
 debian/libbpp-seq-omics1.install                   |    1 -
 debian/postinst                                    |   57 -
 debian/postrm                                      |   59 -
 debian/prerm                                       |   41 -
 debian/rules                                       |  122 -
 debian/source/format                               |    1 -
 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} |   43 +-
 .../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 +-
 68 files changed, 3608 insertions(+), 7208 deletions(-)
 delete mode 100644 BppSeqOmics.tag
 create mode 100644 CTestConfig.cmake
 delete mode 100644 debian/changelog
 delete mode 100644 debian/compat
 delete mode 100644 debian/control
 delete mode 100644 debian/copyright
 delete mode 100644 debian/libbpp-seq-omics-dev.install
 delete mode 100644 debian/libbpp-seq-omics1.install
 delete mode 100755 debian/postinst
 delete mode 100755 debian/postrm
 delete mode 100755 debian/prerm
 delete mode 100755 debian/rules
 delete mode 100644 debian/source/format
 delete mode 100755 genIncludes.sh
 create mode 100644 package.cmake.in
 create mode 100644 src/Bpp/Seq/Feature/Bed/BedGraphFeatureReader.cpp
 copy src/Bpp/Seq/Feature/{Gff/GffFeatureReader.h => Bed/BedGraphFeatureReader.h} (71%)
 create mode 100644 src/Bpp/Seq/Io/Maf/CoordinateTranslatorMafIterator.cpp
 copy src/Bpp/Seq/Io/Maf/{FeatureExtractorMafIterator.h => CoordinateTranslatorMafIterator.h} (52%)
 create mode 100644 src/Bpp/Seq/Io/Maf/MsmcOutputMafIterator.cpp
 copy src/Bpp/Seq/Io/Maf/{VcfOutputMafIterator.h => MsmcOutputMafIterator.h} (56%)
 create mode 100644 src/Bpp/Seq/Io/Maf/PlinkOutputMafIterator.cpp
 create mode 100644 src/Bpp/Seq/Io/Maf/PlinkOutputMafIterator.h
 copy src/Bpp/Seq/Io/Maf/{CoordinatesOutputMafIterator.cpp => RemoveEmptySequencesMafIterator.cpp} (62%)
 copy src/Bpp/Seq/Io/Maf/{ChromosomeMafIterator.h => RemoveEmptySequencesMafIterator.h} (64%)
 create mode 100644 src/Bpp/Seq/Io/Maf/SequenceLDhotOutputMafIterator.cpp
 copy src/Bpp/Seq/Io/Maf/{VcfOutputMafIterator.h => SequenceLDhotOutputMafIterator.h} (50%)

-- 
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