This is an automated email from the git hooks/post-receive script. tille pushed a commit to branch master in repository libbpp-seq-omics.
commit 63b2badde2b018d2578d0b1a484983f87e5af2ba Merge: cffc5d3 7b9eb57 Author: Andreas Tille <[email protected]> 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(-) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/libbpp-seq-omics.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
