[med-svn] [libbpp-seq-omics] branch master updated (9cb0f5e -> 339906c)

[Andreas Tille]

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

      from  9cb0f5e   Better short description.
       new  cffc5d3   New upstream version, d/watch: point to github
       new  7b9eb57   New upstream version 2.3.1
       new  63b2bad   Updated version 2.3.1 from 'upstream/2.3.1'
       new  c3add48   debhelper 10
       new  9b93b4c   Adapt package names to soversion change, Hardening
       new  339906c   Upload to unstable

The 6 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                                   |   10 +
 debian/compat                                      |    2 +-
 debian/control                                     |   12 +-
 debian/rules                                       |   25 +-
 debian/watch                                       |    5 +-
 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 +-
 62 files changed, 3631 insertions(+), 6844 deletions(-)
 delete mode 100644 BppSeqOmics.tag
 create mode 100644 CTestConfig.cmake
 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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