[med-svn] [libbpp-seq-omics] 04/10: Merge tag 'upstream/2.2.0'

[Andreas Tille]

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

commit 607af2a94b0801a371b76441e0151657e56e37b4
Merge: d45f80e e1f3f06
Author: Andreas Tille <tille at debian.org>
Date:   Wed Apr 13 16:41:56 2016 +0200

    Merge tag 'upstream/2.2.0'
    
    Upstream version 2.2.0
    
    Conflicts:
    	debian/changelog

 BppSeqOmics.tag                                    | 4984 ++++++++++++++++++++
 CMakeLists.txt                                     |    5 +-
 ChangeLog                                          |    8 +
 Doxyfile                                           |    2 +-
 bpp-seq-omics.spec                                 |    5 +-
 debian/control                                     |    6 +-
 debian/copyright                                   |    6 +-
 genIncludes.sh                                     |   35 +
 src/Bpp/Seq/Feature/SequenceFeatureTools.cpp       |   11 +-
 src/Bpp/Seq/Feature/SequenceFeatureTools.h         |    6 +-
 src/Bpp/Seq/Io/Maf/BlockMergerMafIterator.cpp      |    4 +-
 ...stener.cpp => CoordinatesOutputMafIterator.cpp} |   55 +-
 ...afIterator.h => CoordinatesOutputMafIterator.h} |   58 +-
 src/Bpp/Seq/Io/Maf/EntropyFilterMafIterator.cpp    |    4 +-
 src/Bpp/Seq/Io/Maf/FeatureExtractorMafIterator.cpp |   24 +-
 src/Bpp/Seq/Io/Maf/FeatureFilterMafIterator.cpp    |   24 +-
 src/Bpp/Seq/Io/Maf/IterationListener.cpp           |    6 +-
 src/Bpp/Seq/Io/Maf/MafParser.cpp                   |    3 +-
 src/Bpp/Seq/Io/Maf/MafSequence.h                   |   17 +-
 src/Bpp/Seq/Io/Maf/MafStatistics.cpp               |  309 +-
 src/Bpp/Seq/Io/Maf/MafStatistics.h                 |  269 +-
 .../Seq/Io/Maf/OrphanSequenceFilterMafIterator.h   |    9 +-
 src/Bpp/Seq/Io/Maf/OutputAlignmentMafIterator.cpp  |    7 +-
 src/Bpp/Seq/Io/Maf/OutputAlignmentMafIterator.h    |    4 +-
 .../Seq/Io/Maf/SequenceStatisticsMafIterator.cpp   |    4 +-
 src/Bpp/Seq/Io/Maf/SequenceStatisticsMafIterator.h |    6 +-
 src/Bpp/Seq/Io/Maf/VcfOutputMafIterator.cpp        |   51 +-
 src/Bpp/Seq/Io/Maf/VcfOutputMafIterator.h          |   25 +-
 src/Bpp/Seq/Io/Maf/WindowSplitMafIterator.h        |    2 +-
 src/CMakeLists.txt                                 |    2 +
 30 files changed, 5787 insertions(+), 164 deletions(-)

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