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commit 4dcaffe5f428325eb8f80a87e24461766310465f Merge: 011a4f9 4bf6973 Author: Afif Elghraoui <a...@ghraoui.name> Date: Thu Oct 15 23:28:04 2015 -0700 Merge tag 'upstream/0_20151014+gitbe5d1bf' Upstream version 0~20151014+gitbe5d1bf .gitignore | 9 +- .travis.yml | 6 +- Makefile | 36 --- README.md | 24 +- alignment/Makefile | 113 ------- .../algorithms/anchoring/MapBySuffixArrayImpl.hpp | 20 +- alignment/algorithms/sorting/DifferenceCovers.cpp | 3 +- .../algorithms/sorting/LightweightSuffixArray.cpp | 11 +- alignment/algorithms/sorting/MultikeyQuicksort.cpp | 2 +- alignment/algorithms/sorting/qsufsort.hpp | 5 +- alignment/build.mk | 1 + alignment/bwt/Occ.hpp | 2 +- alignment/bwt/PackedHash.hpp | 14 +- .../datastructures/alignment/FilterCriteria.cpp | 2 + alignment/files/FragmentCCSIterator.cpp | 3 +- alignment/files/ReaderAgglomerate.cpp | 52 +++- alignment/files/ReaderAgglomerate.hpp | 4 + alignment/format/BAMPrinter.hpp | 18 +- alignment/format/BAMPrinterImpl.hpp | 67 +++- alignment/format/SAMHeaderPrinter.cpp | 25 +- alignment/format/SAMPrinter.cpp | 7 +- alignment/format/SAMPrinter.hpp | 1 + alignment/format/SAMPrinterImpl.hpp | 14 +- alignment/makefile | 47 +++ alignment/simple.mk | 82 ----- alignment/simulator/ContextOutputList.hpp | 2 +- alignment/simulator/ContextSet.cpp | 4 +- alignment/simulator/OutputSampleListSet.hpp | 3 +- alignment/suffixarray/LCPTable.hpp | 21 +- alignment/suffixarray/SuffixArray.hpp | 1 - alignment/suffixarray/ssort.hpp | 6 +- alignment/tuples/TupleCountTableImpl.hpp | 5 +- alignment/tuples/TupleListImpl.hpp | 1 - alignment/utils/RegionUtils.cpp | 111 +------ alignment/utils/RegionUtils.hpp | 48 --- alignment/utils/RegionUtilsImpl.hpp | 231 +++----------- common.mk | 84 ----- configure.py | 339 +++++++++++++++++++++ hdf/BufferedHDF2DArrayImpl.hpp | 15 +- hdf/BufferedHDFArrayImpl.hpp | 3 +- hdf/HDFAtom.cpp | 9 +- hdf/HDFAtom.hpp | 37 ++- hdf/HDFAttributable.cpp | 6 +- hdf/HDFAttributable.hpp | 4 +- hdf/HDFBasReader.hpp | 240 ++++++++------- hdf/HDFBaseCallsWriter.cpp | 326 ++++++++++++++++++++ hdf/HDFBaseCallsWriter.hpp | 233 ++++++++++++++ hdf/HDFBaxWriter.cpp | 141 +++++++++ hdf/HDFBaxWriter.hpp | 172 +++++++++++ hdf/HDFCmpFile.hpp | 14 +- hdf/HDFCmpReader.hpp | 1 + hdf/HDFCmpRefAlignmentGroup.hpp | 3 +- hdf/HDFData.cpp | 10 +- hdf/HDFData.hpp | 10 +- hdf/HDFPlsReader.hpp | 16 +- hdf/HDFRegionTableReader.cpp | 115 ++++--- hdf/HDFRegionTableReader.hpp | 30 +- hdf/HDFRegionsWriter.cpp | 99 ++++++ hdf/HDFRegionsWriter.hpp | 101 ++++++ hdf/HDFScanDataReader.cpp | 29 +- hdf/HDFScanDataReader.hpp | 7 +- hdf/HDFScanDataWriter.cpp | 127 +++++--- hdf/HDFScanDataWriter.hpp | 55 +++- hdf/HDFWriteBuffer.hpp | 3 +- hdf/HDFWriterBase.cpp | 98 ++++++ hdf/HDFWriterBase.hpp | 88 ++++++ hdf/HDFZMWMetricsWriter.cpp | 142 +++++++++ hdf/HDFZMWMetricsWriter.hpp | 117 +++++++ hdf/HDFZMWWriter.cpp | 144 +++++++++ hdf/HDFZMWWriter.hpp | 120 ++++++++ hdf/Makefile | 94 ------ hdf/build.mk | 1 + hdf/makefile | 33 ++ makefile | 31 ++ pbdata/.gitignore | 2 + pbdata/CCSSequence.cpp | 21 +- pbdata/CCSSequence.hpp | 22 +- pbdata/CompressedDNASequence.hpp | 6 +- pbdata/CompressedSequenceImpl.hpp | 13 +- pbdata/DNASequence.cpp | 30 +- pbdata/DNASequence.hpp | 15 +- pbdata/Enumerations.h | 47 ++- pbdata/FASTAReader.cpp | 11 +- pbdata/FASTASequence.cpp | 38 +-- pbdata/FASTASequence.hpp | 16 +- pbdata/FASTQReader.cpp | 2 +- pbdata/FASTQSequence.cpp | 50 ++- pbdata/FASTQSequence.hpp | 41 ++- pbdata/MD5Utils.cpp | 5 +- pbdata/Makefile | 85 ------ pbdata/PacBioDefs.h | 180 +++++++++++ pbdata/PackedDNASequence.cpp | 6 +- pbdata/ReverseCompressIndex.cpp | 3 +- pbdata/SMRTSequence.cpp | 289 +++++++++++++----- pbdata/SMRTSequence.hpp | 161 +++++++--- pbdata/StringUtils.cpp | 52 +--- pbdata/StringUtils.hpp | 2 +- pbdata/build.mk | 1 + pbdata/makefile | 39 +++ pbdata/matrix/FlatMatrixImpl.hpp | 9 +- pbdata/matrix/MatrixImpl.hpp | 7 +- pbdata/metagenome/SequenceIndexDatabaseImpl.hpp | 16 +- pbdata/metagenome/TitleTable.cpp | 10 +- pbdata/reads/BaseFile.cpp | 6 +- pbdata/reads/PulseBaseCommon.cpp | 39 ++- pbdata/reads/PulseBaseCommon.hpp | 39 ++- pbdata/reads/PulseFile.cpp | 40 ++- pbdata/reads/PulseFileImpl.hpp | 4 +- pbdata/reads/ReadInterval.hpp | 19 +- pbdata/reads/RegionAnnotation.cpp | 49 +++ pbdata/reads/RegionAnnotation.hpp | 241 +++++++++++++++ pbdata/reads/RegionAnnotations.cpp | 179 +++++++++++ pbdata/reads/RegionAnnotations.hpp | 122 ++++++++ pbdata/reads/RegionTable.cpp | 239 +++++++-------- pbdata/reads/RegionTable.hpp | 166 ++++++---- pbdata/reads/RegionTypeMap.cpp | 89 ++++++ pbdata/reads/RegionTypeMap.hpp | 85 ++++++ pbdata/reads/ScanData.cpp | 155 +++++++++- pbdata/reads/ScanData.hpp | 86 +++++- pbdata/sam/SAMReaderImpl.hpp | 2 +- pbdata/utils.hpp | 5 +- pbdata/utils/SMRTReadUtils.cpp | 4 +- pbdata/utils/SMRTTitle.hpp | 14 + pbdata/utilsImpl.hpp | 32 +- rules.mk | 28 ++ simple.mk | 16 - travis.sh | 14 + unittest/.gitignore | 1 + unittest/Makefile | 41 --- unittest/alignment/Makefile | 9 +- unittest/alignment/files/CCSIterator_gtest.cpp | 2 - .../alignment/files/FragmentCCSIterator_gtest.cpp | 5 +- .../files/FragmentCCSIterator_other_gtest.cpp | 100 ++++++ .../alignment/files/ReaderAgglomerate_gtest.cpp | 16 + unittest/alignment/utils/RegionUtils_gtest.cpp | 1 - unittest/build.mk | 27 ++ unittest/common.mk | 64 ---- unittest/hdf/HDFPlsReader_gtest.cpp | 3 +- unittest/hdf/HDFScanDataWriter_gtest.cpp | 2 + unittest/hdf/Makefile | 9 +- unittest/makefile | 120 ++++++++ unittest/pbdata/CCSSequence_gtest.cpp | 8 +- unittest/pbdata/DNASequence_gtest.cpp | 2 +- unittest/pbdata/Makefile | 9 +- unittest/pbdata/SMRTSequence_gtest.cpp | 6 +- unittest/pbdata/StringUtils_gtest.cpp | 44 ++- unittest/pbdata/reads/RegionAnnotations_gtest.cpp | 203 ++++++++++++ unittest/pbdata/reads/RegionTypeMap_gtest.cpp | 61 ++++ 148 files changed, 5744 insertions(+), 1939 deletions(-) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/pbseqlib.git _______________________________________________ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit