This is an automated email from the git hooks/post-receive script. afif-guest pushed a commit to branch master in repository blasr.
commit 71819370d7ad50aedd34d7f9e280a2046e43d0d5 Merge: df881fc 255f617 Author: Afif Elghraoui <[email protected]> Date: Sat Dec 12 21:30:21 2015 -0800 Merge tag 'upstream/0_20150925+git77862af' Upstream version 0~20150925+git77862af .gitignore | 4 + Blasr.cpp | 34 + MANUAL.md | 84 - Makefile | 59 - README.INSTALL.md | 72 + README.MANUAL.md | 38 + README.md | 52 +- blasr_git_common.mk | 15 - blasr_gitp4.mk | 24 - common.mk | 139 - configure.py | 104 +- ctest/hitpolicy.t | 14 +- ctest/useccsallLargeGenome.t | 3 +- extrautils/GNUmakefile | 45 - extrautils/Makefile | 78 - extrautils/makefile | 49 + extrautils/p4.mk | 79 - libcpp.makefile | 9 - libcpp/.gitignore | 7 - libcpp/.travis.yml | 22 - libcpp/README.md | 47 - libcpp/alignment/MappingMetrics.cpp | 299 - libcpp/alignment/MappingMetrics.hpp | 133 - .../algorithms/alignment/AffineGuidedAlign.hpp | 589 - .../algorithms/alignment/AffineKBandAlign.hpp | 406 - .../algorithms/alignment/AlignmentFormats.hpp | 6 - .../algorithms/alignment/AlignmentUtils.cpp | 43 - .../algorithms/alignment/AlignmentUtils.hpp | 139 - .../algorithms/alignment/AlignmentUtilsImpl.hpp | 548 - .../algorithms/alignment/BaseScoreFunction.cpp | 11 - .../algorithms/alignment/BaseScoreFunction.hpp | 17 - .../alignment/DistanceMatrixScoreFunction.hpp | 40 - .../alignment/DistanceMatrixScoreFunctionImpl.hpp | 96 - .../alignment/algorithms/alignment/ExtendAlign.cpp | 79 - .../alignment/algorithms/alignment/ExtendAlign.hpp | 416 - .../alignment/algorithms/alignment/FullQVAlign.hpp | 132 - .../alignment/algorithms/alignment/GraphPaper.hpp | 31 - .../algorithms/alignment/GraphPaperImpl.hpp | 175 - .../alignment/algorithms/alignment/GuidedAlign.cpp | 226 - .../alignment/algorithms/alignment/GuidedAlign.hpp | 600 - .../algorithms/alignment/IDSScoreFunction.cpp | 158 - .../algorithms/alignment/IDSScoreFunction.hpp | 109 - .../alignment/algorithms/alignment/KBandAlign.cpp | 30 - .../alignment/algorithms/alignment/KBandAlign.hpp | 381 - .../algorithms/alignment/OneGapAlignment.hpp | 374 - .../alignment/QualityValueScoreFunction.cpp | 90 - .../alignment/QualityValueScoreFunction.hpp | 56 - libcpp/alignment/algorithms/alignment/SDPAlign.hpp | 64 - .../algorithms/alignment/SDPAlignImpl.hpp | 614 - libcpp/alignment/algorithms/alignment/SWAlign.hpp | 17 - .../alignment/algorithms/alignment/SWAlignImpl.hpp | 389 - .../algorithms/alignment/ScoreMatrices.cpp | 58 - .../algorithms/alignment/ScoreMatrices.hpp | 18 - .../algorithms/alignment/StringToScoreMatrix.cpp | 26 - .../algorithms/alignment/StringToScoreMatrix.hpp | 9 - .../algorithms/alignment/sdp/FragmentSort.hpp | 19 - .../algorithms/alignment/sdp/FragmentSortImpl.hpp | 16 - .../sdp/NonoverlappingSparseDynamicProgramming.h | 193 - .../algorithms/alignment/sdp/SDPColumn.hpp | 23 - .../algorithms/alignment/sdp/SDPFragment.cpp | 27 - .../algorithms/alignment/sdp/SDPFragment.hpp | 132 - .../alignment/algorithms/alignment/sdp/SDPSet.hpp | 52 - .../algorithms/alignment/sdp/SDPSetImpl.hpp | 113 - .../alignment/sdp/SparseDynamicProgramming.cpp | 18 - .../alignment/sdp/SparseDynamicProgramming.hpp | 37 - .../alignment/sdp/SparseDynamicProgrammingImpl.hpp | 266 - .../alignment/sdp/VariableLengthSDPFragment.h | 51 - .../alignment/algorithms/anchoring/BWTSearch.cpp | 85 - .../alignment/algorithms/anchoring/BWTSearch.hpp | 35 - .../algorithms/anchoring/BWTSearchImpl.hpp | 14 - .../algorithms/anchoring/BasicEndpoint.hpp | 50 - .../algorithms/anchoring/BasicEndpointImpl.hpp | 78 - .../algorithms/anchoring/ClusterProbability.cpp | 45 - .../algorithms/anchoring/ClusterProbability.hpp | 13 - .../alignment/algorithms/anchoring/Coordinate.cpp | 12 - .../alignment/algorithms/anchoring/Coordinate.hpp | 45 - .../algorithms/anchoring/FindMaxInterval.cpp | 23 - .../algorithms/anchoring/FindMaxInterval.hpp | 175 - .../algorithms/anchoring/FindMaxIntervalImpl.hpp | 945 - .../alignment/algorithms/anchoring/GlobalChain.hpp | 37 - .../algorithms/anchoring/GlobalChainImpl.hpp | 225 - .../alignment/algorithms/anchoring/LISPValue.hpp | 24 - .../algorithms/anchoring/LISPValueImpl.hpp | 165 - .../algorithms/anchoring/LISPValueWeightor.hpp | 52 - .../algorithms/anchoring/LISPValueWeightorImpl.hpp | 112 - .../algorithms/anchoring/LISQValueWeightor.hpp | 35 - .../algorithms/anchoring/LISSizeWeightor.hpp | 14 - .../algorithms/anchoring/LISSizeWeightorImpl.hpp | 13 - .../anchoring/LongestIncreasingSubsequence.hpp | 31 - .../anchoring/LongestIncreasingSubsequenceImpl.hpp | 135 - .../algorithms/anchoring/MapBySuffixArray.hpp | 44 - .../algorithms/anchoring/MapBySuffixArrayImpl.hpp | 315 - .../algorithms/anchoring/PrioritySearchTree.hpp | 69 - .../anchoring/PrioritySearchTreeImpl.hpp | 296 - .../algorithms/anchoring/ScoreAnchors.hpp | 46 - .../algorithms/anchoring/ScoreAnchorsImpl.hpp | 179 - .../algorithms/compare/CompareStrings.hpp | 81 - .../algorithms/sorting/DifferenceCovers.cpp | 15 - .../algorithms/sorting/DifferenceCovers.hpp | 16 - libcpp/alignment/algorithms/sorting/Karkkainen.hpp | 134 - .../algorithms/sorting/LightweightSuffixArray.cpp | 405 - .../algorithms/sorting/LightweightSuffixArray.hpp | 103 - .../algorithms/sorting/MultikeyQuicksort.cpp | 197 - .../algorithms/sorting/MultikeyQuicksort.hpp | 48 - libcpp/alignment/algorithms/sorting/qsufsort.cpp | 302 - libcpp/alignment/algorithms/sorting/qsufsort.hpp | 376 - libcpp/alignment/anchoring/AnchorParameters.hpp | 35 - libcpp/alignment/build.mk | 1 - libcpp/alignment/bwt/BWT.hpp | 316 - libcpp/alignment/bwt/Occ.hpp | 217 - libcpp/alignment/bwt/PackedHash.hpp | 350 - libcpp/alignment/bwt/Pos.hpp | 47 - .../datastructures/alignment/AlignedPair.h | 19 - .../datastructures/alignment/Alignment.cpp | 512 - .../datastructures/alignment/Alignment.hpp | 184 - .../alignment/AlignmentCandidate.cpp | 26 - .../alignment/AlignmentCandidate.hpp | 370 - .../datastructures/alignment/AlignmentContext.cpp | 35 - .../datastructures/alignment/AlignmentContext.hpp | 32 - .../datastructures/alignment/AlignmentGapList.h | 26 - .../datastructures/alignment/AlignmentMap.cpp | 22 - .../datastructures/alignment/AlignmentMap.hpp | 20 - .../datastructures/alignment/AlignmentStats.cpp | 29 - .../datastructures/alignment/AlignmentStats.hpp | 25 - .../datastructures/alignment/ByteAlignment.h | 347 - .../alignment/datastructures/alignment/CmpFile.cpp | 6 - .../alignment/datastructures/alignment/CmpFile.hpp | 33 - .../alignment/CmpIndexedStringTable.h | 67 - .../datastructures/alignment/CmpReadGroupTable.h | 22 - .../datastructures/alignment/CmpRefSeqTable.h | 22 - .../datastructures/alignment/FilterCriteria.cpp | 371 - .../datastructures/alignment/FilterCriteria.hpp | 165 - libcpp/alignment/datastructures/alignment/Path.h | 23 - .../alignment/SAMToAlignmentCandidateAdapter.cpp | 461 - .../alignment/SAMToAlignmentCandidateAdapter.hpp | 79 - .../alignmentset/AlignmentSetToCmpH5Adapter.hpp | 84 - .../AlignmentSetToCmpH5AdapterImpl.hpp | 256 - .../alignmentset/SAMQVConversion.cpp | 27 - .../alignmentset/SAMQVConversion.hpp | 15 - .../alignmentset/SAMSupplementalQVList.cpp | 71 - .../alignmentset/SAMSupplementalQVList.hpp | 27 - .../datastructures/anchoring/AnchorParameters.cpp | 44 - .../datastructures/anchoring/AnchorParameters.hpp | 35 - .../datastructures/anchoring/ClusterList.cpp | 75 - .../datastructures/anchoring/ClusterList.hpp | 25 - .../datastructures/anchoring/MatchPos.cpp | 59 - .../datastructures/anchoring/MatchPos.hpp | 192 - .../datastructures/anchoring/WeightedInterval.cpp | 181 - .../datastructures/anchoring/WeightedInterval.hpp | 85 - libcpp/alignment/files/BaseSequenceIO.cpp | 77 - libcpp/alignment/files/BaseSequenceIO.hpp | 26 - libcpp/alignment/files/CCSIterator.cpp | 28 - libcpp/alignment/files/CCSIterator.hpp | 21 - libcpp/alignment/files/FragmentCCSIterator.cpp | 109 - libcpp/alignment/files/FragmentCCSIterator.hpp | 23 - libcpp/alignment/files/ReaderAgglomerate.cpp | 505 - libcpp/alignment/files/ReaderAgglomerate.hpp | 136 - libcpp/alignment/files/ReaderAgglomerateImpl.hpp | 44 - libcpp/alignment/format/BAMPrinter.hpp | 29 - libcpp/alignment/format/BAMPrinterImpl.hpp | 168 - .../alignment/format/CompareSequencesPrinter.cpp | 10 - .../alignment/format/CompareSequencesPrinter.hpp | 21 - .../format/CompareSequencesPrinterImpl.hpp | 77 - libcpp/alignment/format/IntervalPrinter.cpp | 70 - libcpp/alignment/format/IntervalPrinter.hpp | 21 - libcpp/alignment/format/SAMHeaderPrinter.cpp | 432 - libcpp/alignment/format/SAMHeaderPrinter.hpp | 311 - libcpp/alignment/format/SAMPrinter.cpp | 188 - libcpp/alignment/format/SAMPrinter.hpp | 93 - libcpp/alignment/format/SAMPrinterImpl.hpp | 304 - libcpp/alignment/format/StickAlignmentPrinter.hpp | 123 - libcpp/alignment/format/SummaryPrinter.cpp | 26 - libcpp/alignment/format/SummaryPrinter.hpp | 14 - libcpp/alignment/format/VulgarPrinter.hpp | 53 - libcpp/alignment/format/XMLPrinter.hpp | 84 - libcpp/alignment/ipc/SharedMemoryAllocator.hpp | 33 - libcpp/alignment/makefile | 52 - libcpp/alignment/old.Makefile | 113 - libcpp/alignment/qvs/QualityValueProfile.cpp | 41 - libcpp/alignment/qvs/QualityValueProfile.hpp | 23 - libcpp/alignment/simulator/CDFMap.hpp | 44 - libcpp/alignment/simulator/ContextOutputList.hpp | 100 - libcpp/alignment/simulator/ContextSample.cpp | 53 - libcpp/alignment/simulator/ContextSample.hpp | 30 - libcpp/alignment/simulator/ContextSet.cpp | 35 - libcpp/alignment/simulator/ContextSet.hpp | 19 - libcpp/alignment/simulator/LengthHistogram.cpp | 58 - libcpp/alignment/simulator/LengthHistogram.hpp | 24 - libcpp/alignment/simulator/OutputList.hpp | 57 - libcpp/alignment/simulator/OutputSample.hpp | 59 - libcpp/alignment/simulator/OutputSampleList.hpp | 33 - libcpp/alignment/simulator/OutputSampleListSet.hpp | 123 - libcpp/alignment/simulator/QualitySample.cpp | 77 - libcpp/alignment/simulator/QualitySample.hpp | 28 - .../statistics/AnchorDistributionTable.hpp | 43518 ------------------- .../statistics/LookupAnchorDistribution.cpp | 58 - .../statistics/LookupAnchorDistribution.hpp | 10 - libcpp/alignment/statistics/StatUtils.cpp | 45 - libcpp/alignment/statistics/StatUtils.hpp | 165 - libcpp/alignment/statistics/StatUtilsImpl.hpp | 57 - .../alignment/statistics/VarianceAccumulator.hpp | 28 - .../statistics/VarianceAccumulatorImpl.hpp | 60 - libcpp/alignment/statistics/cdfs.cpp | 53 - libcpp/alignment/statistics/cdfs.hpp | 418 - libcpp/alignment/statistics/pdfs.cpp | 36 - libcpp/alignment/statistics/pdfs.hpp | 18 - libcpp/alignment/suffixarray/LCPTable.hpp | 182 - libcpp/alignment/suffixarray/SharedSuffixArray.hpp | 83 - libcpp/alignment/suffixarray/SuffixArray.hpp | 1197 - libcpp/alignment/suffixarray/SuffixArrayTypes.hpp | 17 - libcpp/alignment/suffixarray/ssort.hpp | 449 - libcpp/alignment/tuples/BaseTuple.cpp | 53 - libcpp/alignment/tuples/BaseTuple.hpp | 27 - libcpp/alignment/tuples/CompressedDNATuple.hpp | 63 - libcpp/alignment/tuples/CountedTuple.h | 16 - libcpp/alignment/tuples/DNATuple.cpp | 94 - libcpp/alignment/tuples/DNATuple.hpp | 103 - libcpp/alignment/tuples/DNATupleImpl.hpp | 200 - libcpp/alignment/tuples/DNATupleList.h | 53 - libcpp/alignment/tuples/HashedTupleList.hpp | 61 - libcpp/alignment/tuples/HashedTupleListImpl.hpp | 144 - libcpp/alignment/tuples/TupleCountTable.hpp | 33 - libcpp/alignment/tuples/TupleCountTableImpl.hpp | 101 - libcpp/alignment/tuples/TupleList.hpp | 64 - libcpp/alignment/tuples/TupleListImpl.hpp | 134 - libcpp/alignment/tuples/TupleMask.h | 13 - libcpp/alignment/tuples/TupleMatching.hpp | 25 - libcpp/alignment/tuples/TupleMatchingImpl.hpp | 106 - libcpp/alignment/tuples/TupleMetrics.cpp | 16 - libcpp/alignment/tuples/TupleMetrics.hpp | 19 - libcpp/alignment/tuples/TupleOperations.h | 7 - libcpp/alignment/tuples/TupleTranslations.h | 4 - libcpp/alignment/tuples/tuple.h | 82 - libcpp/alignment/utils/FileOfFileNames.cpp | 102 - libcpp/alignment/utils/FileOfFileNames.hpp | 27 - libcpp/alignment/utils/FileUtils.cpp | 61 - libcpp/alignment/utils/FileUtils.hpp | 27 - libcpp/alignment/utils/LogUtils.cpp | 55 - libcpp/alignment/utils/LogUtils.hpp | 15 - libcpp/alignment/utils/PhredUtils.cpp | 13 - libcpp/alignment/utils/PhredUtils.hpp | 8 - libcpp/alignment/utils/RangeUtils.cpp | 107 - libcpp/alignment/utils/RangeUtils.hpp | 56 - libcpp/alignment/utils/RegionUtils.cpp | 302 - libcpp/alignment/utils/RegionUtils.hpp | 132 - libcpp/alignment/utils/RegionUtilsImpl.hpp | 215 - libcpp/alignment/utils/SimpleXMLUtils.hpp | 99 - libcpp/alignment/utils/TimeUtils.cpp | 20 - libcpp/alignment/utils/TimeUtils.hpp | 7 - libcpp/configure.py | 268 - libcpp/hdf/BufferedHDF2DArray.cpp | 79 - libcpp/hdf/BufferedHDF2DArray.hpp | 158 - libcpp/hdf/BufferedHDF2DArrayImpl.hpp | 379 - libcpp/hdf/BufferedHDFArray.cpp | 92 - libcpp/hdf/BufferedHDFArray.hpp | 207 - libcpp/hdf/BufferedHDFArrayImpl.hpp | 435 - libcpp/hdf/DatasetCollection.cpp | 61 - libcpp/hdf/DatasetCollection.hpp | 41 - libcpp/hdf/DatasetCollectionImpl.hpp | 29 - libcpp/hdf/HDF2DArray.hpp | 25 - libcpp/hdf/HDFAlnGroup.hpp | 50 - libcpp/hdf/HDFAlnGroupGroup.cpp | 52 - libcpp/hdf/HDFAlnGroupGroup.hpp | 27 - libcpp/hdf/HDFAlnInfoGroup.cpp | 102 - libcpp/hdf/HDFAlnInfoGroup.hpp | 46 - libcpp/hdf/HDFArray.hpp | 85 - libcpp/hdf/HDFAtom.cpp | 159 - libcpp/hdf/HDFAtom.hpp | 176 - libcpp/hdf/HDFAttributable.cpp | 41 - libcpp/hdf/HDFAttributable.hpp | 23 - libcpp/hdf/HDFBasReader.cpp | 46 - libcpp/hdf/HDFBasReader.hpp | 1178 - libcpp/hdf/HDFBasWriter.hpp | 390 - libcpp/hdf/HDFCCSReader.hpp | 257 - libcpp/hdf/HDFCmpData.hpp | 36 - libcpp/hdf/HDFCmpExperimentGroup.cpp | 193 - libcpp/hdf/HDFCmpExperimentGroup.hpp | 70 - libcpp/hdf/HDFCmpFile.hpp | 844 - libcpp/hdf/HDFCmpReader.hpp | 663 - libcpp/hdf/HDFCmpRefAlignmentGroup.hpp | 102 - libcpp/hdf/HDFCmpRootGroup.hpp | 66 - libcpp/hdf/HDFCmpSupportedFields.cpp | 25 - libcpp/hdf/HDFCmpSupportedFields.hpp | 13 - libcpp/hdf/HDFCommonFG.hpp | 13 - libcpp/hdf/HDFConfig.hpp | 7 - libcpp/hdf/HDFData.cpp | 74 - libcpp/hdf/HDFData.hpp | 52 - libcpp/hdf/HDFFile.cpp | 53 - libcpp/hdf/HDFFile.hpp | 32 - libcpp/hdf/HDFFileLogGroup.hpp | 55 - libcpp/hdf/HDFGroup.cpp | 58 - libcpp/hdf/HDFGroup.hpp | 36 - libcpp/hdf/HDFMovieInfoGroup.hpp | 79 - libcpp/hdf/HDFNewBasReader.cpp | 72 - libcpp/hdf/HDFNewBasReader.hpp | 39 - libcpp/hdf/HDFPlsReader.hpp | 542 - libcpp/hdf/HDFPlsWriter.hpp | 195 - libcpp/hdf/HDFPulseDataFile.cpp | 151 - libcpp/hdf/HDFPulseDataFile.hpp | 67 - libcpp/hdf/HDFRefGroupGroup.hpp | 65 - libcpp/hdf/HDFRefInfoGroup.hpp | 84 - libcpp/hdf/HDFRegionTableReader.cpp | 149 - libcpp/hdf/HDFRegionTableReader.hpp | 47 - libcpp/hdf/HDFRegionTableWriter.hpp | 140 - libcpp/hdf/HDFSMRTSequenceReader.hpp | 71 - libcpp/hdf/HDFScanDataReader.cpp | 262 - libcpp/hdf/HDFScanDataReader.hpp | 101 - libcpp/hdf/HDFScanDataWriter.cpp | 164 - libcpp/hdf/HDFScanDataWriter.hpp | 71 - libcpp/hdf/HDFSentinalFile.hpp | 21 - libcpp/hdf/HDFUtils.cpp | 82 - libcpp/hdf/HDFUtils.hpp | 44 - libcpp/hdf/HDFWriteBuffer.hpp | 52 - libcpp/hdf/HDFZMWReader.cpp | 136 - libcpp/hdf/HDFZMWReader.hpp | 45 - libcpp/hdf/build.mk | 1 - libcpp/hdf/makefile | 28 - libcpp/hdf/old.Makefile | 94 - libcpp/makefile | 32 - libcpp/old.Makefile | 28 - libcpp/pbdata/.gitignore | 2 - libcpp/pbdata/CCSSequence.cpp | 35 - libcpp/pbdata/CCSSequence.hpp | 43 - libcpp/pbdata/ChangeListID.cpp | 64 - libcpp/pbdata/ChangeListID.hpp | 38 - libcpp/pbdata/CommandLineParser.cpp | 846 - libcpp/pbdata/CommandLineParser.hpp | 175 - libcpp/pbdata/Compare4BitCompressed.hpp | 98 - libcpp/pbdata/CompressedDNASequence.hpp | 89 - libcpp/pbdata/CompressedSequence.hpp | 100 - libcpp/pbdata/CompressedSequenceImpl.hpp | 343 - libcpp/pbdata/DNASequence.cpp | 402 - libcpp/pbdata/DNASequence.hpp | 183 - libcpp/pbdata/Enumerations.h | 39 - libcpp/pbdata/FASTAReader.cpp | 420 - libcpp/pbdata/FASTAReader.hpp | 80 - libcpp/pbdata/FASTASequence.cpp | 246 - libcpp/pbdata/FASTASequence.hpp | 91 - libcpp/pbdata/FASTQReader.cpp | 89 - libcpp/pbdata/FASTQReader.hpp | 24 - libcpp/pbdata/FASTQSequence.cpp | 651 - libcpp/pbdata/FASTQSequence.hpp | 146 - libcpp/pbdata/GFFFile.cpp | 39 - libcpp/pbdata/GFFFile.hpp | 33 - libcpp/pbdata/MD5Utils.cpp | 464 - libcpp/pbdata/MD5Utils.hpp | 113 - libcpp/pbdata/MD5UtilsImpl.hpp | 57 - libcpp/pbdata/NucConversion.cpp | 409 - libcpp/pbdata/NucConversion.hpp | 50 - libcpp/pbdata/PackedDNASequence.cpp | 233 - libcpp/pbdata/PackedDNASequence.hpp | 60 - libcpp/pbdata/ReverseCompressIndex.cpp | 40 - libcpp/pbdata/ReverseCompressIndex.hpp | 25 - libcpp/pbdata/SMRTSequence.cpp | 283 - libcpp/pbdata/SMRTSequence.hpp | 115 - libcpp/pbdata/SeqUtils.hpp | 17 - libcpp/pbdata/SeqUtilsImpl.hpp | 47 - libcpp/pbdata/StringUtils.cpp | 133 - libcpp/pbdata/StringUtils.hpp | 71 - libcpp/pbdata/Types.h | 21 - libcpp/pbdata/VectorUtils.hpp | 17 - libcpp/pbdata/alignment/CmpAlignment.cpp | 219 - libcpp/pbdata/alignment/CmpAlignment.hpp | 126 - libcpp/pbdata/alignment/CmpAlignmentImpl.hpp | 6 - libcpp/pbdata/amos/AfgBasWriter.cpp | 102 - libcpp/pbdata/amos/AfgBasWriter.hpp | 59 - libcpp/pbdata/build.mk | 1 - libcpp/pbdata/defs.h | 19 - libcpp/pbdata/loadpulses/MetricField.cpp | 87 - libcpp/pbdata/loadpulses/MetricField.hpp | 115 - .../pbdata/loadpulses/MovieAlnIndexLookupTable.cpp | 54 - .../pbdata/loadpulses/MovieAlnIndexLookupTable.hpp | 117 - libcpp/pbdata/makefile | 40 - libcpp/pbdata/matrix/FlatMatrix.hpp | 98 - libcpp/pbdata/matrix/FlatMatrixImpl.hpp | 192 - libcpp/pbdata/matrix/Matrix.hpp | 50 - libcpp/pbdata/matrix/MatrixImpl.hpp | 117 - libcpp/pbdata/metagenome/FindRandomSequence.hpp | 70 - libcpp/pbdata/metagenome/SequenceIndexDatabase.hpp | 96 - .../metagenome/SequenceIndexDatabaseImpl.hpp | 347 - libcpp/pbdata/metagenome/TitleTable.cpp | 109 - libcpp/pbdata/metagenome/TitleTable.hpp | 39 - libcpp/pbdata/mklibconfig.sh | 32 - libcpp/pbdata/old.Makefile | 87 - libcpp/pbdata/qvs/QualityTransform.cpp | 23 - libcpp/pbdata/qvs/QualityTransform.hpp | 26 - libcpp/pbdata/qvs/QualityValue.cpp | 65 - libcpp/pbdata/qvs/QualityValue.hpp | 31 - libcpp/pbdata/qvs/QualityValueVector.hpp | 47 - libcpp/pbdata/qvs/QualityValueVectorImpl.hpp | 99 - libcpp/pbdata/reads/BaseFile.cpp | 82 - libcpp/pbdata/reads/BaseFile.hpp | 49 - libcpp/pbdata/reads/BaseFileImpl.hpp | 11 - libcpp/pbdata/reads/HoleXY.cpp | 14 - libcpp/pbdata/reads/HoleXY.hpp | 14 - libcpp/pbdata/reads/PulseBaseCommon.cpp | 37 - libcpp/pbdata/reads/PulseBaseCommon.hpp | 26 - libcpp/pbdata/reads/PulseFile.cpp | 76 - libcpp/pbdata/reads/PulseFile.hpp | 53 - libcpp/pbdata/reads/PulseFileImpl.hpp | 21 - libcpp/pbdata/reads/ReadInterval.hpp | 18 - libcpp/pbdata/reads/ReadType.cpp | 43 - libcpp/pbdata/reads/ReadType.hpp | 18 - libcpp/pbdata/reads/RegionTable.cpp | 159 - libcpp/pbdata/reads/RegionTable.hpp | 95 - libcpp/pbdata/reads/ScanData.cpp | 12 - libcpp/pbdata/reads/ScanData.hpp | 20 - libcpp/pbdata/reads/ZMWGroupEntry.cpp | 8 - libcpp/pbdata/reads/ZMWGroupEntry.hpp | 17 - libcpp/pbdata/saf/AlnGroup.cpp | 12 - libcpp/pbdata/saf/AlnGroup.hpp | 14 - libcpp/pbdata/saf/AlnInfo.hpp | 17 - libcpp/pbdata/saf/MovieInfo.cpp | 13 - libcpp/pbdata/saf/MovieInfo.hpp | 19 - libcpp/pbdata/saf/RefGroup.cpp | 25 - libcpp/pbdata/saf/RefGroup.hpp | 21 - libcpp/pbdata/saf/RefInfo.cpp | 20 - libcpp/pbdata/saf/RefInfo.hpp | 26 - libcpp/pbdata/sam/AlignmentSet.hpp | 31 - libcpp/pbdata/sam/AlignmentSetImpl.hpp | 31 - libcpp/pbdata/sam/CigarString.h | 23 - libcpp/pbdata/sam/ReadGroup.cpp | 51 - libcpp/pbdata/sam/ReadGroup.hpp | 40 - libcpp/pbdata/sam/ReferenceSequence.cpp | 47 - libcpp/pbdata/sam/ReferenceSequence.hpp | 72 - libcpp/pbdata/sam/SAMAlignment.cpp | 199 - libcpp/pbdata/sam/SAMAlignment.hpp | 97 - libcpp/pbdata/sam/SAMFlag.h | 48 - libcpp/pbdata/sam/SAMHeader.cpp | 31 - libcpp/pbdata/sam/SAMHeader.hpp | 18 - libcpp/pbdata/sam/SAMKeywordValuePair.cpp | 51 - libcpp/pbdata/sam/SAMKeywordValuePair.hpp | 50 - libcpp/pbdata/sam/SAMKeywordValuePairImpl.hpp | 32 - libcpp/pbdata/sam/SAMReader.hpp | 61 - libcpp/pbdata/sam/SAMReaderImpl.hpp | 197 - libcpp/pbdata/utils.hpp | 20 - libcpp/pbdata/utils/BitUtils.cpp | 99 - libcpp/pbdata/utils/BitUtils.hpp | 14 - libcpp/pbdata/utils/SMRTReadUtils.cpp | 45 - libcpp/pbdata/utils/SMRTReadUtils.hpp | 18 - libcpp/pbdata/utils/SMRTTitle.cpp | 52 - libcpp/pbdata/utils/SMRTTitle.hpp | 24 - libcpp/pbdata/utilsImpl.hpp | 32 - libcpp/rules.mk | 17 - libcpp/simple.mk | 16 - libcpp/unittest/.gitignore | 1 - libcpp/unittest/Makefile | 151 - libcpp/unittest/alignment/Makefile | 35 - .../alignment/AlignmentMap_gtest.cpp | 63 - .../alignment/CmpIndexedStringTable_gtest.cpp | 143 - .../unittest/alignment/files/CCSIterator_gtest.cpp | 66 - .../alignment/files/FragmentCCSIterator_gtest.cpp | 104 - .../alignment/files/ReaderAgglomerate_gtest.cpp | 129 - .../alignment/format/SAMHeaderPrinter_gtest.cpp | 138 - .../unittest/alignment/format/SAMPrinter_gtest.cpp | 45 - .../unittest/alignment/utils/FileUtils_gtest.cpp | 54 - .../unittest/alignment/utils/RangeUtils_gtest.cpp | 63 - .../unittest/alignment/utils/RegionUtils_gtest.cpp | 236 - libcpp/unittest/build.mk | 27 - libcpp/unittest/common.mk | 64 - libcpp/unittest/hdf/HDF2DArray_gtest.cpp | 96 - libcpp/unittest/hdf/HDFBasReader_gtest.cpp | 56 - libcpp/unittest/hdf/HDFCCSReader_gtest.cpp | 68 - libcpp/unittest/hdf/HDFPlsReader_gtest.cpp | 49 - libcpp/unittest/hdf/HDFScanDataReader_gtest.cpp | 52 - libcpp/unittest/hdf/HDFScanDataWriter_gtest.cpp | 36 - libcpp/unittest/hdf/HDFUtils_gtest.cpp | 38 - libcpp/unittest/hdf/HDFZMWReader_gtest.cpp | 125 - libcpp/unittest/hdf/Makefile | 26 - libcpp/unittest/normal.Makefile | 9 - libcpp/unittest/normal.defines.mk | 54 - libcpp/unittest/pbdata/CCSSequence_gtest.cpp | 117 - libcpp/unittest/pbdata/ChangeListID_gtest.cpp | 34 - libcpp/unittest/pbdata/DNASequence_gtest.cpp | 279 - libcpp/unittest/pbdata/FASTAReader_gtest.cpp | 65 - libcpp/unittest/pbdata/FASTASequence_gtest.cpp | 143 - libcpp/unittest/pbdata/FASTQReader_gtest.cpp | 90 - libcpp/unittest/pbdata/Makefile | 31 - libcpp/unittest/pbdata/NucConversion_gtest.cpp | 105 - libcpp/unittest/pbdata/SMRTSequence_gtest.cpp | 62 - libcpp/unittest/pbdata/ScanData_gtest.cpp | 31 - libcpp/unittest/pbdata/SeqUtils_gtest.cpp | 50 - libcpp/unittest/pbdata/StringUtils_gtest.cpp | 80 - libcpp/unittest/pbdata/VectorUtils_gtest.cpp | 38 - libcpp/unittest/pbdata/defs_gtest.cpp | 44 - .../pbdata/metagenome/TitleTable_gtest.cpp | 32 - .../pbdata/qvs/QualityValueVector_gtest.cpp | 50 - libcpp/unittest/pbdata/reads/ReadType_gtest.cpp | 57 - libcpp/unittest/pbdata/saf/AlnGroup_gtest.cpp | 44 - libcpp/unittest/pbdata/saf/MovieInfo_gtest.cpp | 43 - libcpp/unittest/pbdata/saf/RefInfo_gtest.cpp | 45 - libcpp/unittest/pbdata/testdata.h | 71 - libcpp/unittest/pbdata/utils/SMRTTitle_gtest.cpp | 28 - libcpp/unittest/pbdata/utils_gtest.cpp | 37 - GNUmakefile => makefile | 35 +- p4.common.mk | 147 - p4.fetch.tmpmk | 10 - p4.mk | 76 - rules.mk | 16 +- travis.sh | 2 +- utils/.gitignore | 8 + utils/Makefile | 64 - utils/{GNUmakefile => makefile} | 28 +- utils/p4.mk | 65 - yli.common.mk | 94 - yli.makefile | 80 - 506 files changed, 337 insertions(+), 96096 deletions(-) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/blasr.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
