[med-svn] [blasr] 03/12: Imported Upstream version 0~20150925+git77862af
Afif Elghraoui
afif-guest at moszumanska.debian.org
Mon Dec 14 21:14:42 UTC 2015
This is an automated email from the git hooks/post-receive script.
afif-guest pushed a commit to branch master
in repository blasr.
commit 255f61754358d6f26dce7244a7a305614c12c9df
Author: Afif Elghraoui <afif at ghraoui.name>
Date: Sat Dec 12 21:30:17 2015 -0800
Imported 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(-)
diff --git a/.gitignore b/.gitignore
new file mode 100644
index 0000000..bfdb47f
--- /dev/null
+++ b/.gitignore
@@ -0,0 +1,4 @@
+defines.mk
+*.d
+*.o
+blasr
diff --git a/Blasr.cpp b/Blasr.cpp
index 95aee11..f7a4276 100644
--- a/Blasr.cpp
+++ b/Blasr.cpp
@@ -3533,6 +3533,23 @@ void MapReads(MappingData<T_SuffixArray, T_GenomeSequence, T_Tuple> *mapData) {
}
}
}
+ // Fix for memory leakage bug due to undeleted Alignment Candidate objectts which wasn't selected
+ // for printing
+ // delete all AC which are in complement of SelectedAlignmemntPtrs vector
+ // namely (SelectedAlignmentPtrs/alignmentPtrs)
+ for (int ii = 0; ii < alignmentPtrs.size(); ii++)
+ {
+ int found =0;
+ for (int jj = 0; jj < selectedAlignmentPtrs.size(); jj++)
+ {
+ if (alignmentPtrs[ii] == selectedAlignmentPtrs[jj] )
+ {
+ found = 1;
+ break;
+ }
+ }
+ if (found == 0) delete alignmentPtrs[ii];
+ }
subreadSequence.Free();
subreadSequenceRC.Free();
} // End of looping over subread intervals within [startIndex, endIndex).
@@ -3743,6 +3760,23 @@ void MapReads(MappingData<T_SuffixArray, T_GenomeSequence, T_Tuple> *mapData) {
} // End of alignining all subreads to where the de novo ccs has aligned to.
} // End of if readIsCCS and !params.useCcsOnly
+ // Fix for memory leakage due to undeleted Alignment Candidate objectts not selected
+ // for printing
+ // delete all AC which are in complement of SelectedAlignmemntPtrs vector
+ // namely (SelectedAlignmentPtrs/alignmentPtrs)
+ for (int ii = 0; ii < alignmentPtrs.size(); ii++)
+ {
+ int found =0;
+ for (int jj = 0; jj < selectedAlignmentPtrs.size(); jj++)
+ {
+ if (alignmentPtrs[ii] == selectedAlignmentPtrs[jj] )
+ {
+ found = 1;
+ break;
+ }
+ }
+ if (found == 0) delete alignmentPtrs[ii];
+ }
} // End of if not (readIsCCS == false and params.mapSubreadsSeparately)
PrintAllReadAlignments(allReadAlignments, alignmentContext,
diff --git a/MANUAL.md b/MANUAL.md
deleted file mode 100644
index 92b96b0..0000000
--- a/MANUAL.md
+++ /dev/null
@@ -1,84 +0,0 @@
-##NEWS:Refactored blasr has been online! Try it out!##
-
-
-##Installation##
-
-###1. Download source code###
- In order to download blasr source code from github,
-
- + > git clone git at github.com:PacificBiosciences/blasr.git --recursive
-
- To sync your local repo with latest from github blasr master branch
-
- + > git pull -u origin master && git submodule update --init --recursive
-
-###2. Requirements###
-
- To build BLASR, you must have hdf 1.8.12 or above installed and
- configured with c++ support (you should have the library
- libhdf5_cpp.a). If you are intalling the entire PacBio secondary
- analysis software suite, appropriate hdf libraries are already
- distributed and no configuration is necessary. Otherwise, it is
- necessary to point two environment variables:
-
- + **HDF5_INC**, which points to locations of the HDF5 headers
- (e.g., hdf5.h)
-
- + **HDF5_LIB**, which points to the HDF5 library (e.g., hdf5*.a,
- and hdf5*.so)
-
- You may edit file blasr_git_common.mk in order sepcify HDF5_INC and HDF5_LIB.
- Alternatively, you may export them from command line.
-
- + > export HDF5_INC=path_to_your_hdf5_include && export HDF5_LIB=path_to_your_hdf5_lib
-
-###3. Build blasr only###
-
- + > make blasr
- + > ./blasr
-
-###4. Build the source tree, including other executables###
-
- + > make
- + > ls utils # Frequently used executables will be under utils.
-
-
-##Running BLASR##
-
- Typing 'blasr -h' or 'blasr -help' on the command line will give you a
- list of options. At the least, provide a fasta, fastq, or bas.h5 file,
- and a genome.
-
- *Some typical use cases:*
-
- Align reads from reads.bas.h5 to ecoli_K12 genome, and output in SAM format.
-
- + > blasr reads.bas.h5 ecoli_K12.fasta -sam
-
- Same as above, but with soft clipping
-
- + > blasr reads.bas.h5 ecoli_K12.fasta -sam -clipping soft
-
- Use multiple threads
-
- + > blasr reads.bas.h5 ecoli_K12.fasta -sam -clipping soft -out alignments.sam -nproc 16
-
- Include a larger minimal match, for faster but less sensitive alignments
-
- + > blasr reads.bas.h5 ecoli_K12.fasta -sam -clipping soft -minMatch 15
-
- Produce alignments in a pairwise human readable format
-
- + > blasr reads.bas.h5 ecoli_K12.fasta -m 0
-
- Use a precomputed suffix array for faster startup
-
- + > sawriter hg19.fasta.sa hg19.fasta #First precompute the suffix array
- + > blasr reads.bas.h5 hg19.fasta -sa hg19.fasta.sa
-
- Use a precomputed BWT-FM index for smaller runtime memory footprint, but slower alignments.
-
- + > sa2bwt hg19.fasta hg19.fasta.sa hg19.fasta.bwt
- + > blasr reads.bas.h5 hg19.fasta -bwt hg19.fasta.bwt
-
-
diff --git a/Makefile b/Makefile
deleted file mode 100644
index 938351b..0000000
--- a/Makefile
+++ /dev/null
@@ -1,59 +0,0 @@
-SHELL=bash -e -E
-
-.PHONY: all pblib makeutils gtest cramtests cramfast check clean cleanall cleanlib
-
-include common.mk
-
-SRCS := $(wildcard *.cpp)
-OBJS := $(SRCS:.cpp=.o)
-DEPS := $(SRCS:.cpp=.d)
-EXE = blasr
-UTILS = utils
-
-all : CXXFLAGS ?= $(DEFAULTCXXFLAG)
-debug : CXXFLAGS ?= $(DEBUGCXXFLAG)
-profile : CXXFLAGS ?= $(PROFILECXXFLAG)
-g: CXXFLAGS += $(GCXXFLAG)
-g: LIBS = $(GLIBS)
-
-
-all debug profile g: $(EXE) makeutils
-
-$(EXE): $(SRCS) $(PBLIB)
- $(CXX) $(CXXOPTS) $(CXXFLAGS) $(INCDIRS) -MF"$(@:%=%.d)" $(STATIC) -o $@ $(SRCS) $(LIBDIRS) $(LIBS)
-
-# DON'T use pbbam which is not on github.
-PBINCROOT:=$(abspath libcpp)
-pblib: $(PBINCROOT)/configure.py $(PBINCROOT)/makefile
- cd $(PBINCROOT) && NOPBBAM=true HDF5_LIB=${HDF5_LIB}/libhdf5.so ./configure.py
- cd $(PBINCROOT) && ${MAKE}
-
-makeutils:
- make -C $(UTILS) $(MODE)
-
-CTESTS := $(wildcard ctest/*.t)
-SLOW_CTESTS := ctest/bug25328.t ctest/useccsallLargeGenome.t
-
-cramtests: $(EXE) $(UTILS)
- cram -v --shell=/bin/bash $(CTESTS)
- make -C $(UTILS) cramtests
-
-cramfast: $(EXE) $(UTILS)
- cram -v --shell=/bin/bash $(filter-out $(SLOW_CTESTS),$(CTESTS))
- make -C $(UTILS) cramfast
-
-gtest: $(EXE)
- make -C $(PBINCROOT) gtest
-
-check: gtest cramtests
-
-cleanall: cleanlib clean
-
-cleanlib: $(PBINCROOT)/Makefile
- @make -C $(PBINCROOT) cleanall
-
-clean:
- @rm -f $(EXE) $(OBJS) $(DEPS) blasr.d
- @make -C $(UTILS) clean
-
--include $(DEPS)
diff --git a/README.INSTALL.md b/README.INSTALL.md
new file mode 100644
index 0000000..b892078
--- /dev/null
+++ b/README.INSTALL.md
@@ -0,0 +1,72 @@
+## Installation
+
+### Download source code
+
+* To pull this project from git hub to your local system:
+
+ git clone git://github.com/PacificBiosciences/blasr.git blasr
+
+* To sync your code with the latest git code base:
+
+ git pull -u origin master && git submodule update --init
+
+### Requirements
+
+* To configure:
+
+ ./configure.py --no-pbbam
+
+* or with HDF5 directories (and note that `HDF5_LIB` is a *directory* here):
+
+ ./configure.py --no-pbbam HDF5_INCLUDE=... HDF5_LIB=...
+
+To build BLASR, you must have hdf 1.8.12 or above installed and
+ configured with c++ support (you should have the library
+ libhdf5_cpp.a). If you are intalling the entire PacBio secondary
+ analysis software suite, appropriate hdf libraries are already
+ distributed and no configuration is necessary. Otherwise, it is
+ necessary to point two environment variables:
+
+ + **HDF5_INCLUDE**, which points to directory of the HDF5 headers
+ (e.g., hdf5.h)
+
+ + **HDF5_LIB**, which points to the HDF5 library directory (e.g., hdf5*.a,
+ and hdf5*.so)
+
+ You may pass arguments to `configure.py` as above, or you may export them from command line:
+
+ export HDF5_INC=path_to_your_hdf5_include && export HDF5_LIB=path_to_your_hdf5_lib
+
+### Build
+
+* To make the 'libcpp' libraries:
+
+ make build-submodule
+
+* To make 'blasr' only:
+
+ make blasr
+
+* To compile all tools, including blasr, pls2fasta, loadPulses, sawriter:
+
+ make
+
+ * Frequently used executables will be under utils.
+
+* To test (with **cram** installed):
+
+ #make cramtests
+ make cramfast
+ ## Currently:
+ ## Ran 22 tests, 0 skipped, 4 failed.
+
+* To clean all compiled tools and lib:
+
+ make cleanall
+
+* To clean compiled tools without cleaning lib:
+
+ make clean
+
+ make blasr
+ ./blasr
diff --git a/README.MANUAL.md b/README.MANUAL.md
new file mode 100644
index 0000000..c1d12f6
--- /dev/null
+++ b/README.MANUAL.md
@@ -0,0 +1,38 @@
+## Running BLASR
+
+ Typing 'blasr -h' or 'blasr -help' on the command line will give you a
+ list of options. At the least, provide a fasta, fastq, or bas.h5 file,
+ and a genome.
+
+### Some typical use cases
+
+Align reads from reads.bas.h5 to ecoli_K12 genome, and output in SAM format.
+
+ blasr reads.bas.h5 ecoli_K12.fasta -sam
+
+Same as above, but with soft clipping
+
+ blasr reads.bas.h5 ecoli_K12.fasta -sam -clipping soft
+
+Use multiple threads
+
+ blasr reads.bas.h5 ecoli_K12.fasta -sam -clipping soft -out alignments.sam -nproc 16
+
+Include a larger minimal match, for faster but less sensitive alignments
+
+ blasr reads.bas.h5 ecoli_K12.fasta -sam -clipping soft -minMatch 15
+
+Produce alignments in a pairwise human readable format
+
+ blasr reads.bas.h5 ecoli_K12.fasta -m 0
+
+Use a precomputed suffix array for faster startup
+
+ sawriter hg19.fasta.sa hg19.fasta #First precompute the suffix array
+ blasr reads.bas.h5 hg19.fasta -sa hg19.fasta.sa
+
+Use a precomputed BWT-FM index for smaller runtime memory footprint, but slower alignments.
+
+ sa2bwt hg19.fasta hg19.fasta.sa hg19.fasta.bwt
+ blasr reads.bas.h5 hg19.fasta -bwt hg19.fasta.bwt
+
diff --git a/README.md b/README.md
index 8bc8e40..c7724ce 100644
--- a/README.md
+++ b/README.md
@@ -1,52 +1,2 @@
-# NEWS: refactored blasr has been put online. Please try it out!
+See Blasr [README.INSTALL.md](README.INSTALL.md) and [README.MANUAL.md](README.MANUAL.md).
-Blasr installation and maual:
-
- more Manual.md
-
-To pull this project from git hub to your local system:
-
- git clone git at github.com:PacificBiosciences/blasr.git blasr --recursive
-
-To sync your code with the latest git code base:
-
- git pull -u origin master && git submodule update --init --recursive
-
-To specify HDF5 headers and lib on your system:
-
- export HDF5_INCLUDE=path_to_your_hdf5_include && export HDF5_LIB=path_to_your_hdf5_lib
-
-To configure:
-
- ./configure.py --no-pbbam
-
-or with HDF5 directories (and note that `HDF5_LIB` is a *directory* here):
-
- ./configure.py --no-pbbam HDF5_INCLUDE=... HDF5_LIB=...
-
-To make the 'libcpp' libraries:
-
- make build-submodule
-
-To make 'blasr' only:
-
- make blasr
-
-To compile all tools, including blasr, pls2fasta, loadPulses, sawriter:
-
- make
-
-To test (with **cram** installed):
-
- #make cramtests
- make cramfast
- ## Currently:
- ## Ran 22 tests, 0 skipped, 4 failed.
-
-To clean all compiled tools and lib:
-
- make cleanall
-
-To clean compiled tools without cleaning lib:
-
- make clean
diff --git a/blasr_git_common.mk b/blasr_git_common.mk
deleted file mode 100644
index 5834a55..0000000
--- a/blasr_git_common.mk
+++ /dev/null
@@ -1,15 +0,0 @@
-# Set HDF5_INC and HDF5_LIB, the path to hdf5 headers and library.
-#
-# Directory HDF5_INC should contain hdf headers (e.g.,
-# hdf5.h).
-#
-# Directory HDF5_LIB should contain hdf5 libraries (e.g.,
-# libhdf5*.a libhdf5*.so).
-#
-# !! Note HDF5_INC and HDF5_LIB must be absolute paths!
-#############################################################
-
-HDF5_INC?=/home/UNIXHOME/yli/yliWorkspace/software/smrtanalysis/prebuilt.out/hdf5/hdf5-1.8.12/centos-5/include
-HDF5_LIB?=/home/UNIXHOME/yli/yliWorkspace/software/smrtanalysis/prebuilt.out/hdf5/hdf5-1.8.12/centos-5/lib
-
-#############################################################
diff --git a/blasr_gitp4.mk b/blasr_gitp4.mk
deleted file mode 100644
index 0b05708..0000000
--- a/blasr_gitp4.mk
+++ /dev/null
@@ -1,24 +0,0 @@
-SHELL=/bin/bash -e -E
-
-.PHONY: curdir submodules p4togit pullfromgit
-
-# git p4 operations
-curdir = $(shell pwd)
-
-submodules = libcpp
-
-p4togit: $(submodules)
- @for submodule in $(submodules); do \
- cd $$submodule; echo Rebasing submodule $$submodule; git p4 sync; git p4 rebase; git push -u origin master; cd $(curdir);\
- done
- @for submodule in $(submodules); do \
- echo Adding submodule $$submodle to blasr; git add $$submodule; \
- done
- @git commit -m "Push latest $(submodules) from p4 to github"
- @git push -u origin master || echo push failed
-
-# To help users sync all submodules from github to local.
-pullfromgit:
- @git pull -u origin master
- @git submodule update --init --recursive
-
diff --git a/common.mk b/common.mk
deleted file mode 100644
index 9f2723c..0000000
--- a/common.mk
+++ /dev/null
@@ -1,139 +0,0 @@
-OS := $(shell uname)
-
-# Determine where is PBINCROOT, either from github or PacBio SMRTAnalysis package.
-PBINCROOT ?= $(realpath ../../lib/cpp/)
-PREBUILT ?= $(realpath ../../../prebuilt.out)
-THIRD_PARTY_PREFIX ?= $(realpath ..)
-
-#####include $(PBINCROOT)/common.mk
-#####include $(PBINCROOT)/rules.mk
-
-LIBBLASR_INCLUDE := $(PBINCROOT)/alignment
-LIBPBIHDF_INCLUDE := $(PBINCROOT)/hdf
-LIBPBDATA_INCLUDE := $(PBINCROOT)/pbdata
-PBBAM_INCLUDE := $(PBBAM)/include
-HTSLIB_INCLUDE := $(PBBAM)/../htslib/htslib
-HDF5_INCLUDE := $(HDF5_INC)
-ZLIB_INCLUDE := $(ZLIB_ROOT)/include
-
-LIBBLASR_LIB := $(PBINCROOT)/alignment
-LIBPBIHDF_LIB := $(PBINCROOT)/hdf
-LIBPBDATA_LIB := $(PBINCROOT)/pbdata
-PBBAM_LIB := $(PBBAM)/lib
-HTSLIB_LIB := $(PBBAM)/../htslib
-HDF5_LIB := $(HDF5_LIB)
-ZLIB_LIB := $(ZLIB_ROOT)/lib
-
-
-LIBPBIHDF_CPP_LIBFLAG := -lhdf5_cpp
-LIBPBIHDF_LIBFLAG := -lhdf5
-
-LIBBLASR_LIBFLAGS := -lblasr
-LIBPBIHDF_LIBFLAGS := -lpbihdf
-LIBPBDATA_LIBFLAGS := -lpbdata
-PBBAM_LIBFLAGS := -lpbbam
-HTSLIB_LIBFLAGS := -lhts
-HDF5_LIBFLAGS := $(LIBHDF5_CPP_LIBFLAG) $(LIBHDF5_LIBFLAG)
-ZLIB_LIBFLAGS := -lz
-
-
-INCDIRS = -I$(LIBBLASR_INCLUDE) \
- -I$(LIBPBIHDF_INCLUDE) \
- -I$(LIBPBDATA_INCLUDE) \
- -I$(HDF5_INCLUDE)
-
-LIBDIRS = -L$(LIBBLASR_LIB) \
- -L$(LIBPBIHDF_LIB) \
- -L$(LIBPBDATA_LIB) \
- -L$(HDF5_LIB)
-
-ifneq ($(ZLIB_ROOT), notfound)
- # NOTE: The zlib include directory is not needed since we do not
- # refer to any zlib include files directly in the blasr source
- # code. But we do need to link to the zlib library (static
- # or shared), since htslib depends on it.
- # INCDIRS += -I$(ZLIB_INCLUDE)
- LIBDIRS += -L$(ZLIB_LIB)
-endif
-
-CXXOPTS := -std=c++0x -pedantic \
- -Wall -Wuninitialized -Wno-div-by-zero \
- -MMD -MP -w -fpermissive
-
-DEFAULTCXXFLAG := -O3
-DEBUGCXXFLAG := -g -ggdb -fno-inline
-PROFILECXXFLAG := -Os -pg
-GCXXFLAG := -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer
-
-LIBS := $(LIBBLASR_LIBFLAGS) $(LIBPBIHDF_LIBFLAGS) $(LIBPBDATA_LIBFLAGS)
-PBBAMLIBS := $(PBBAM_LIBFLAGS)
-ifneq ($(SHARED_LIB),)
- PBBAMLIBS += $(HTSLIB_LIBFLAGS)
-else
- ifneq ($(wildcard "$(HTSLIB_LIB)/libhts.a"),"")
- PBBAMLIBS += $(HTSLIB_LIB)/libhts.a
- else
- PBBAMLIBS += $(HTSLIB_LIBFLAGS)
- endif
-endif
-
-ifneq ($(SHARED_LIB),)
- LIBS += $(HDF5_LIBFLAGS)
-else
- ifneq ($(wildcard "$(HDF5_LIB)/libhdf5_cpp.a"),"")
- LIBS += $(HDF5_LIB)/libhdf5_cpp.a $(HDF5_LIB)/libhdf5.a
- else
- LIBS += $(HDF5_LIBFLAGS)
- endif
-endif
-
-ifeq ($(origin nopbbam), undefined)
- INCDIRS += -I$(PBBAM_INCLUDE) \
- -I$(HTSLIB_INCLUDE) \
- -I$(BOOST_INCLUDE)
-
-
- LIBDIRS += -L$(PBBAM_LIB) \
- -L$(HTSLIB_LIB)
-
- LIBS += $(PBBAMLIBS)
-endif
-
-LIBS += $(ZLIB_LIBFLAGS)
-LIBS += -lpthread
-
-# NOTE: libdl is not needed when we are linking with shared libraries, but
-# is is needed for static linking, since the hdf5 library depends on it
-ifeq ($(SHARED_LIB),)
- LIBS += -ldl
-endif
-
-ifneq ($(SHARED_LIB),)
- STATIC :=
-else
- ifneq ($(OS), Darwin)
- STATIC := -static
- else
- STATIC :=
- endif
-endif
-
-ifneq ($(OS), Darwin)
- LIBS += -lrt
-else
- LIBS += -lsz
-endif
-
-# -lhdf5, -lhdf5_cpp, -lz required for HDF5
-# -lpbbam -lhts for BAM
-# -lpthread for multi-threading
-# -lrt for clock_gettime
-# -ldl for dlopen dlclose
-
-GLIBS = -Wl --eh-frame-hdr -fno-builtin-malloc -L$(HOME)/lib -ltcmalloc -lunwind -lprofiler $(LIBS)
-
-PBLIB :=
-ifeq ($(NO_SUBMAKES),)
- PBLIB := pblib
-endif
-
diff --git a/configure.py b/configure.py
index 126c362..9b7927c 100755
--- a/configure.py
+++ b/configure.py
@@ -8,23 +8,25 @@ import contextlib
import optparse
import os
import sys
+import warnings
#DEFAULTCXXFLAG := -O3
#DEBUGCXXFLAG := -g -ggdb -fno-inline
#PROFILECXXFLAG := -Os -pg
#GCXXFLAG := -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer
-ROOT = '${ROOT}'
+ROOT = os.path.abspath(os.path.dirname(__file__))
def log(msg):
sys.stderr.write(msg)
sys.stderr.write('\n')
def shell(cmd):
- log(cmd)
+ log('`%s`'%cmd)
status, output = commands.getstatusoutput(cmd)
if status:
raise Exception('%d <- %r' %(status, cmd))
+ log(output)
return output
def system(cmd):
@@ -34,6 +36,10 @@ def system(cmd):
raise Exception('%d <- %r' %(status, cmd))
return
+def mkdirs(path):
+ if not os.path.isdir(path):
+ os.makedirs(path)
+
@contextlib.contextmanager
def cd(nwd):
cwd = os.getcwd()
@@ -46,8 +52,8 @@ def cd(nwd):
def update_content(fn, content):
current_content = open(fn).read() if os.path.exists(fn) else None
if content != current_content:
- log('writing to %r' %fn)
- log('"""\n' + content + '"""')
+ log('writing to %r:' %fn)
+ log('"""\n' + content + '"""\n----')
open(fn, 'w').write(content)
def get_OS_STRING():
@@ -87,43 +93,35 @@ def compose_defines_pacbio(envin):
#setifenvf(env, envin, 'PREBUILT', get_PREBUILT)
nondefaults = set([
'CXX',
- 'LIBPBDATA_INCLUDE', 'LIBPBDATA_LIB', 'LIBPBDATA_LIBFLAGS',
- 'LIBPBIHDF_INCLUDE', 'LIBPBIHDF_LIB', 'LIBPBIHDF_LIBFLAGS',
- 'LIBBLASR_INCLUDE', 'LIBBLASR_LIB', 'LIBBLASR_LIBFLAGS',
- 'HDF5_INCLUDE', 'HDF5_LIB', 'HDF5_LIBFLAGS',
- 'PBBAM_INCLUDE', 'PBBAM_LIB', 'PBBAM_LIBFLAGS',
- 'HTSLIB_INCLUDE', 'HTSLIB_LIB', 'HTSLIB_LIBFLAGS',
- 'BOOST_INCLUDE',
+ 'LIBPBDATA_INC', 'LIBPBDATA_LIB', 'LIBPBDATA_LIBFLAGS',
+ 'LIBPBIHDF_INC', 'LIBPBIHDF_LIB', 'LIBPBIHDF_LIBFLAGS',
+ 'LIBBLASR_INC', 'LIBBLASR_LIB', 'LIBBLASR_LIBFLAGS',
+ 'HDF5_INC', 'HDF5_LIB', 'HDF5_LIBFLAGS',
+ 'PBBAM_INC', 'PBBAM_LIB', 'PBBAM_LIBFLAGS',
+ 'HTSLIB_INC', 'HTSLIB_LIB', 'HTSLIB_LIBFLAGS',
+ 'BOOST_INC',
+ 'GCC_LIB',
'ZLIB_LIB', 'ZLIB_LIBFLAGS',
'PTHREAD_LIBFLAGS',
'DL_LIBFLAGS',
+ 'RT_LIBFLAGS',
])
update_env_if(env, envin, nondefaults)
return compose_defs_env(env)
-def update(content_defines_mk):
- """ Write these relative to the same directory as *this* file.
- """
- thisdir = os.path.dirname(os.path.abspath(__file__))
- fn_defines_mk = os.path.join(thisdir, 'defines.mk')
- update_content(fn_defines_mk, content_defines_mk)
-
-def configure_pacbio(envin, shared):
+def configure_pacbio(envin, shared, build_dir):
content1 = compose_defines_pacbio(envin)
- if shared:
- content1 += 'LDLIBS+=-lrt\n'
- else:
+ if not shared:
content1 += 'LDFLAGS+=-static\n'
- content1 += 'SUB_CONF_FLAGS+=--shared\n'
- update(content1)
+ update_content(os.path.join(build_dir, 'defines.mk'), content1)
def set_defs_submodule_defaults(env, nopbbam):
subdir = os.path.join(ROOT, 'libcpp')
defaults = {
- 'LIBPBDATA_INCLUDE': os.path.join(subdir, 'pbdata'),
- 'LIBBLASR_INCLUDE': os.path.join(subdir, 'alignment'),
- #'LIBPBIHDF_INCLUDE': '' if nopbbam else os.path.join(subdir, 'hdf'),
+ 'LIBPBDATA_INC': os.path.join(subdir, 'pbdata'),
+ 'LIBBLASR_INC': os.path.join(subdir, 'alignment'),
+ #'LIBPBIHDF_INC': '' if nopbbam else os.path.join(subdir, 'hdf'),
'LIBPBDATA_LIB': os.path.join(subdir, 'pbdata'),
'LIBBLASR_LIB': os.path.join(subdir, 'alignment'),
#'LIBPBIHDF_LIB': '' if nopbbam else os.path.join(subdir, 'hdf'),
@@ -132,13 +130,17 @@ def set_defs_submodule_defaults(env, nopbbam):
if k not in env:
env[k] = defaults[k]
+def update_defaults_for_os(env):
+ OS = shell('uname')
+ if 'Darwin' in OS:
+ #-lsz (for static builds?)
+ env['RT_LIBFLAGS'] = ''
+
def set_defs_defaults(env, nopbbam):
- # OS := $(shell uname)
- # if Darwin, -lsz (for static builds?)
defaults = {
- 'LIBBLASR_INCLUDE': os.path.join(ROOT, 'libcpp', 'alignment'),
- 'LIBPBDATA_INCLUDE': os.path.join(ROOT, 'libcpp', 'pbdata'),
- 'LIBPBIHDF_INCLUDE': os.path.join(ROOT, 'libcpp', 'hdf'),
+ 'LIBBLASR_INC': os.path.join(ROOT, 'libcpp', 'alignment'),
+ 'LIBPBDATA_INC': os.path.join(ROOT, 'libcpp', 'pbdata'),
+ 'LIBPBIHDF_INC': os.path.join(ROOT, 'libcpp', 'hdf'),
'LIBBLASR_LIB': os.path.join(ROOT, 'libcpp', 'alignment'),
'LIBPBDATA_LIB': os.path.join(ROOT, 'libcpp', 'pbdata'),
'LIBPBIHDF_LIB': os.path.join(ROOT, 'libcpp', 'hdf'),
@@ -146,19 +148,24 @@ def set_defs_defaults(env, nopbbam):
'LIBPBDATA_LIBFLAGS': '-lpbdata',
'LIBPBIHDF_LIBFLAGS': '-lpbihdf',
'HDF5_LIBFLAGS': '-lhdf5_cpp -lhdf5',
+ 'RT_LIBFLAGS': '-lrt',
'ZLIB_LIBFLAGS': '-lz',
'PTHREAD_LIBFLAGS': '-lpthread',
'DL_LIBFLAGS': '-ldl', # neeeded by HDF5 always
'SHELL': 'bash -xe',
}
+ try:
+ update_defaults_for_os(defaults)
+ except Exception as e:
+ warnings.warn(e)
#setifenvf(defaults, env, 'OS_STRING', get_OS_STRING)
#setifenvf(defaults, env, 'PREBUILT', get_PREBUILT)
pbbam_defaults = {
'PBBAM_LIBFLAGS': '-lpbbam',
'HTSLIB_LIBFLAGS': '-lhts',
'ZLIB_LIBFLAGS': '-lz',
- 'PTHREAD_LIBFLAGS': '-lpthread',
- 'DL_LIBFLAGS': '-ldl', # neeeded by HDF5 always
+ #'PTHREAD_LIBFLAGS': '-lpthread',
+ #'DL_LIBFLAGS': '-ldl', # neeeded by HDF5 always
}
if not nopbbam:
defaults.update(pbbam_defaults)
@@ -183,21 +190,44 @@ def parse_args(args):
help='Set variables to use our git-submodules, which must be pulled and built first. (Implies --no-pbbam.)')
parser.add_option('--shared', action='store_true',
help='Build for dynamic linking.')
+ parser.add_option('--build-dir',
+ help='Can be different from source directory, but only when *not* also building submodule.')
return parser.parse_args(list(args))
+def symlink_makefile(build_dir_root, src_dir_root, makefilename, relpath):
+ src_dir = os.path.join(src_dir_root, relpath)
+ build_dir = os.path.join(build_dir_root, relpath)
+ src_name = os.path.join(src_dir, 'makefile')
+ dst_name = os.path.join(build_dir, 'makefile')
+ if os.path.lexists(dst_name):
+ os.unlink(dst_name)
+ print('%r <- %r' %(src_name, dst_name))
+ mkdirs(build_dir)
+ os.symlink(src_name, dst_name)
+
+def symlink_makefiles(build_dir):
+ symlink_makefile(build_dir, ROOT, 'makefile', '.')
+ symlink_makefile(build_dir, ROOT, 'makefile', 'utils')
+ symlink_makefile(build_dir, ROOT, 'makefile', 'extrautils')
+
def main(prog, *args):
"""We are still deciding what env-vars to use, if any.
"""
# Set up an alias, until everything uses one consistently.
- if 'HDF5_INC' in os.environ and 'HDF5_INCLUDE' not in os.environ:
- os.environ['HDF5_INCLUDE'] = os.environ['HDF5_INC']
conf, makevars = parse_args(args)
+ if conf.build_dir is not None:
+ symlink_makefiles(conf.build_dir)
+ else:
+ conf.build_dir = '.'
+ conf.build_dir = os.path.abspath(conf.build_dir)
envin = get_make_style_env(os.environ, makevars)
+ if 'HDF5_INCLUDE' in envin and 'HDF5_INC' not in envin:
+ envin['HDF5_INC'] = envin['HDF5_INCLUDE']
if conf.submodules:
set_defs_submodule_defaults(envin, conf.no_pbbam)
conf.no_pbbam = True
set_defs_defaults(envin, conf.no_pbbam)
- configure_pacbio(envin, conf.shared)
+ configure_pacbio(envin, conf.shared, conf.build_dir)
if __name__=="__main__":
diff --git a/ctest/hitpolicy.t b/ctest/hitpolicy.t
index 062a4ae..2a90e19 100644
--- a/ctest/hitpolicy.t
+++ b/ctest/hitpolicy.t
@@ -35,22 +35,32 @@ Test hitpolicy allbest
Test hitpolicy random
$ O=$OUTDIR/hitpolicy_random.m4
+ $ O2=$OUTDIR/hitpolicy_random_2.m4
$ X=$STDDIR/hitpolicy_random.m4
$ $EXEC $I $R -out $O -m 4 -hitPolicy random -randomSeed 1
[INFO]* (glob)
[INFO]* (glob)
+ $ $EXEC $I $R -out $O2 -m 4 -hitPolicy random -randomSeed 1
+ [INFO]* (glob)
+ [INFO]* (glob)
$ sort $O > $TMP1 && mv $TMP1 $O
- $ diff $O $X && echo $?
+ $ sort $O2 > $TMP2 && mv $TMP2 $O2
+ $ diff $O $O2 && echo $?
0
Test hitpolicy randombest bam inputs, nproc > 1, fixed seed
$ O=$OUTDIR/hitpolicy_randombest_bam_in.m4
+ $ O2=$OUTDIR/hitpolicy_randombest_bam_in_2.m4
$ X=$STDDIR/hitpolicy_randombest_bam_in.m4
$ $EXEC $I $R -out $O -m 4 -hitPolicy randombest -randomSeed 1 -nproc 10
[INFO]* (glob)
[INFO]* (glob)
+ $ $EXEC $I $R -out $O2 -m 4 -hitPolicy randombest -randomSeed 1 -nproc 10
+ [INFO]* (glob)
+ [INFO]* (glob)
$ sort $O > $TMP1 && mv $TMP1 $O
- $ diff $O $X && echo $?
+ $ sort $O2 > $TMP1 && mv $TMP1 $O2
+ $ diff $O $O2 && echo $?
0
Test hitpolicy randombest bax inputs, nproc > 1, fixed seed
diff --git a/ctest/useccsallLargeGenome.t b/ctest/useccsallLargeGenome.t
index 5ab7ac1..ac93834 100644
--- a/ctest/useccsallLargeGenome.t
+++ b/ctest/useccsallLargeGenome.t
@@ -10,4 +10,5 @@ Test -useccsall with Large genome.
$ $EXEC $BASFILE $REFFA -out $OUTFILE -m 4 -sa $REFSA -holeNumbers 109020
[INFO]* (glob)
[INFO]* (glob)
- $ diff $STDDIR/intflow_2014_06_10.m4 $OUTFILE
+ $ sort $OUTFILE > $TMP1 && sort $STDDIR/intflow_2014_06_10.m4 > $TMP2 && diff $TMP1 $TMP2 && echo $?
+ 0
diff --git a/extrautils/GNUmakefile b/extrautils/GNUmakefile
deleted file mode 100644
index 5d7da34..0000000
--- a/extrautils/GNUmakefile
+++ /dev/null
@@ -1,45 +0,0 @@
-.PHONY=all cramtests
-
-ROOT:=..
-include ${ROOT}/defines.mk
-include ${ROOT}/rules.mk
-
-CXXOPTS := -std=c++0x -pedantic \
- -Wall -Wuninitialized -Wno-div-by-zero \
- -MMD -MP -w -fpermissive
-CXXFLAGS += ${CXXOPTS} ${GCXXFLAGS}
-
-EXE = sa2bwt bwt2sa alchemy excrep evolve bsdb simpleShredder swMatcher \
- samodify sals printTupleCountTable cmpH5StoreQualityByContext ccsh5tobam
-
-LD_LIBRARY_PATH=${HDF5_LIB}:${LIBBLASR_LIB}:${LIBPBIHDF_LIB}:${LIBPBDATA_LIB}
-export LD_LIBRARY_PATH
-
-
-all: ${EXE}
-
-${EXE}:
- ${CXX} -o $@ $< ${CXXFLAGS} ${CPPFLAGS} -MF"${@:%=%.d}" ${STATIC} ${LDFLAGS} ${LDLIBS}
-
-sa2bwt: SuffixArrayToBWT.cpp
-bwt2sa: BwtToSuffixArray.cpp
-alchemy: BasH5Simulator.cpp
-excrep: ExciseRepeats.cpp
-evolve: Evolve.cpp
-bsdb: BuildSequenceDB.cpp
-simpleShredder: SimpleShredder.cpp
-swMatcher: SWMatcher.cpp
-samodify: SAModify.cpp
-sals: SALS.cpp
-printTupleCountTable: PrintTupleCountTable.cpp
-cmpH5StoreQualityByContext: StoreQualityByContextFromCmpH5.cpp
-ccsh5tobam: CCSH5ToBam.cpp
-
-CTESTS := $(wildcard ctest/*.t)
-
-cramtests: ${EXE}
- cram -v --shell=/bin/bash ${CTESTS}
-
-clean:
- @rm -f ${EXE}
- @rm -f *.d *.o
diff --git a/extrautils/Makefile b/extrautils/Makefile
deleted file mode 100644
index 0e05bd5..0000000
--- a/extrautils/Makefile
+++ /dev/null
@@ -1,78 +0,0 @@
-SHELL=/bin/bash -e -E
-
-.PHONY=all cramtests
-
-PBINCROOT ?= $(realpath ../../../lib/cpp/)
-PREBUILT ?= $(realpath ../../../../prebuilt.out)
-THIRD_PARTY_PREFIX := $(realpath ../..)
-
-include ../common.mk
-
-all : CXXFLAGS ?= $(DEFAULTCXXFLAG)
-
-debug : CXXFLAGS ?= $(DEBUGCXXFLAG)
-
-profile : CXXFLAGS ?= $(PROFILECXXFLAG)
-
-g: CXXFLAGS += $(GCXXFLAG)
-g: LIBS = $(GLIBS)
-
-exe = sa2bwt bwt2sa alchemy excrep evolve bsdb simpleShredder swMatcher \
- samodify sals printTupleCountTable cmpH5StoreQualityByContext ccsh5tobam
-
-all debug profile g: $(exe)
-
-sa2bwt: SuffixArrayToBWT.cpp $(PBLIB)
- $(CXX) $(CXXOPTS) $(CXXFLAGS) $(INCDIRS) -MF"$(@:%=%.d)" $(STATIC) -o $@ $< $(LIBDIRS) $(LIBS)
-
-bwt2sa: BwtToSuffixArray.cpp $(PBLIB)
- $(CXX) $(CXXOPTS) $(CXXFLAGS) $(INCDIRS) -MF"$(@:%=%.d)" $(STATIC) -o $@ $< $(LIBDIRS) $(LIBS)
-
-alchemy: BasH5Simulator.cpp $(PBLIB)
- $(CXX) $(CXXOPTS) $(CXXFLAGS) $(INCDIRS) -MF"$(@:%=%.d)" $(STATIC) -o $@ $< $(LIBDIRS) $(LIBS)
-
-excrep: ExciseRepeats.cpp $(PBLIB)
- $(CXX) $(CXXOPTS) $(CXXFLAGS) $(INCDIRS) -MF"$(@:%=%.d)" $(STATIC) -o $@ $< $(LIBDIRS) $(LIBS)
-
-evolve: Evolve.cpp $(PBLIB)
- $(CXX) $(CXXOPTS) $(CXXFLAGS) $(INCDIRS) -MF"$(@:%=%.d)" $(STATIC) -o $@ $< $(LIBDIRS) $(LIBS)
-
-bsdb: BuildSequenceDB.cpp $(PBLIB)
- $(CXX) $(CXXOPTS) $(CXXFLAGS) $(INCDIRS) -MF"$(@:%=%.d)" $(STATIC) -o $@ $< $(LIBDIRS) $(LIBS)
-
-simpleShredder: SimpleShredder.cpp $(PBLIB)
- $(CXX) $(CXXOPTS) $(CXXFLAGS) $(INCDIRS) -MF"$(@:%=%.d)" $(STATIC) -o $@ $< $(LIBDIRS) $(LIBS)
-
-swMatcher: SWMatcher.cpp $(PBLIB)
- $(CXX) $(CXXOPTS) $(CXXFLAGS) $(INCDIRS) -MF"$(@:%=%.d)" $(STATIC) -o $@ $< $(LIBDIRS) $(LIBS)
-
-samodify: SAModify.cpp $(PBLIB)
- $(CXX) $(CXXOPTS) $(CXXFLAGS) $(INCDIRS) -MF"$(@:%=%.d)" $(STATIC) -o $@ $< $(LIBDIRS) $(LIBS)
-
-sals: SALS.cpp $(PBLIB)
- $(CXX) $(CXXOPTS) $(CXXFLAGS) $(INCDIRS) -MF"$(@:%=%.d)" $(STATIC) -o $@ $< $(LIBDIRS) $(LIBS)
-
-printTupleCountTable: PrintTupleCountTable.cpp $(PBLIB)
- $(CXX) $(CXXOPTS) $(CXXFLAGS) $(INCDIRS) -MF"$(@:%=%.d)" $(STATIC) -o $@ $< $(LIBDIRS) $(LIBS)
-
-cmpH5StoreQualityByContext: StoreQualityByContextFromCmpH5.cpp $(PBLIB)
- $(CXX) $(CXXOPTS) $(CXXFLAGS) $(INCDIRS) -MF"$(@:%=%.d)" $(STATIC) -o $@ $< $(LIBDIRS) $(LIBS)
-
-ccsh5tobam: CCSH5ToBam.cpp $(PBLIB)
- $(CXX) $(CXXOPTS) $(CXXFLAGS) $(INCDIRS) -MF"$(@:%=%.d)" $(STATIC) -o $@ $< $(LIBDIRS) $(LIBS)
-
-pblib: $(PBINCROOT)/Makefile
- make -C $(PBINCROOT)
-
-.INTERMEDIATE: $(OBJS)
-
-CTESTS = $(wildcard ctest/*.t)
-cramtests: $(EXE)
- cram --shell=/bin/bash $(CTESTS)
-
-clean:
- @rm -f $(exe)
- @rm -f $(OBJS) $(DEPS)
- @rm *.o *.d
-
--include $(DEPS)
diff --git a/extrautils/makefile b/extrautils/makefile
new file mode 100644
index 0000000..c897e37
--- /dev/null
+++ b/extrautils/makefile
@@ -0,0 +1,49 @@
+.PHONY=all cramtests
+
+SRCDIR:=$(dir $(realpath $(lastword $(MAKEFILE_LIST))))
+-include ${CURDIR}/../defines.mk
+include ${SRCDIR}/../rules.mk
+
+CXXOPTS := -std=c++0x -pedantic \
+ -Wall -Wuninitialized -Wno-div-by-zero \
+ -MMD -MP -w -fpermissive
+CXXFLAGS += ${CXXOPTS} ${GCXXFLAGS}
+
+EXE = sa2bwt bwt2sa alchemy excrep evolve bsdb simpleShredder swMatcher \
+ samodify sals printTupleCountTable cmpH5StoreQualityByContext ccsh5tobam
+
+LD_LIBRARY_PATH=${HDF5_LIB}:${LIBBLASR_LIB}:${LIBPBIHDF_LIB}:${LIBPBDATA_LIB}
+export LD_LIBRARY_PATH
+
+vpath %.cpp ${SRCDIR}
+
+all: ${EXE}
+
+${EXE}:
+ ${CXX} -o $@ $< ${CXXFLAGS} ${CPPFLAGS} -MF"${@:%=%.d}" ${STATIC} ${LDFLAGS} ${LDLIBS}
+
+sa2bwt: SuffixArrayToBWT.o
+bwt2sa: BwtToSuffixArray.o
+alchemy: BasH5Simulator.o
+excrep: ExciseRepeats.o
+evolve: Evolve.o
+bsdb: BuildSequenceDB.o
+simpleShredder: SimpleShredder.o
+swMatcher: SWMatcher.o
+samodify: SAModify.o
+sals: SALS.o
+printTupleCountTable: PrintTupleCountTable.o
+cmpH5StoreQualityByContext: StoreQualityByContextFromCmpH5.o
+ccsh5tobam: CCSH5ToBam.o
+
+CTESTS := \
+ctest/alchemy.t ctest/ccsh5tobam.t ctest/printTupleCountTable.t ctest/sals.t ctest/swmatcher.t \
+ctest/bwt2sa.t ctest/cmpH5StoreQualityByContext.t ctest/sa2bwt.t ctest/samodify.t
+
+
+cramtests: ${EXE}
+ cram -v --shell=/bin/bash ${CTESTS}
+
+clean:
+ @rm -f ${EXE}
+ @rm -f *.d *.o
diff --git a/extrautils/p4.mk b/extrautils/p4.mk
deleted file mode 100644
index 7e41029..0000000
--- a/extrautils/p4.mk
+++ /dev/null
@@ -1,79 +0,0 @@
-# This p4.mk is only used to make
-# //depot/software/smrtanalysis/bioinformatics/tools/blasr
-# on PacBio internal p4 build.
-
-SHELL=/bin/bash -e -E
-
-.PHONY=all cramtests
-
-PBINCROOT ?= $(realpath ../../../lib/cpp/)
-PREBUILT ?= $(realpath ../../../../prebuilt.out)
-THIRD_PARTY_PREFIX := $(realpath ../..)
-
-include ../p4.common.mk
-
-all : CXXFLAGS ?= $(DEFAULTCXXFLAG)
-debug : CXXFLAGS ?= $(DEBUGCXXFLAG)
-profile : CXXFLAGS ?= $(PROFILECXXFLAG)
-g: CXXFLAGS += $(GCXXFLAG)
-g: LIBS = $(GLIBS)
-
-exe = sa2bwt bwt2sa alchemy excrep evolve bsdb simpleShredder swMatcher \
- samodify sals printTupleCountTable cmpH5StoreQualityByContext ccsh5tobam
-
-all debug profile g: $(exe)
-
-sa2bwt: SuffixArrayToBWT.cpp $(PBLIB)
- $(CXX) $(CXXOPTS) $(CXXFLAGS) $(INCDIRS) -MF"$(@:%=%.d)" $(STATIC) -o $@ $< $(LIBDIRS) $(LIBS)
-
-bwt2sa: BwtToSuffixArray.cpp $(PBLIB)
- $(CXX) $(CXXOPTS) $(CXXFLAGS) $(INCDIRS) -MF"$(@:%=%.d)" $(STATIC) -o $@ $< $(LIBDIRS) $(LIBS)
-
-alchemy: BasH5Simulator.cpp $(PBLIB)
- $(CXX) $(CXXOPTS) $(CXXFLAGS) $(INCDIRS) -MF"$(@:%=%.d)" $(STATIC) -o $@ $< $(LIBDIRS) $(LIBS)
-
-excrep: ExciseRepeats.cpp $(PBLIB)
- $(CXX) $(CXXOPTS) $(CXXFLAGS) $(INCDIRS) -MF"$(@:%=%.d)" $(STATIC) -o $@ $< $(LIBDIRS) $(LIBS)
-
-evolve: Evolve.cpp $(PBLIB)
- $(CXX) $(CXXOPTS) $(CXXFLAGS) $(INCDIRS) -MF"$(@:%=%.d)" $(STATIC) -o $@ $< $(LIBDIRS) $(LIBS)
-
-bsdb: BuildSequenceDB.cpp $(PBLIB)
- $(CXX) $(CXXOPTS) $(CXXFLAGS) $(INCDIRS) -MF"$(@:%=%.d)" $(STATIC) -o $@ $< $(LIBDIRS) $(LIBS)
-
-simpleShredder: SimpleShredder.cpp $(PBLIB)
- $(CXX) $(CXXOPTS) $(CXXFLAGS) $(INCDIRS) -MF"$(@:%=%.d)" $(STATIC) -o $@ $< $(LIBDIRS) $(LIBS)
-
-swMatcher: SWMatcher.cpp $(PBLIB)
- $(CXX) $(CXXOPTS) $(CXXFLAGS) $(INCDIRS) -MF"$(@:%=%.d)" $(STATIC) -o $@ $< $(LIBDIRS) $(LIBS)
-
-samodify: SAModify.cpp $(PBLIB)
- $(CXX) $(CXXOPTS) $(CXXFLAGS) $(INCDIRS) -MF"$(@:%=%.d)" $(STATIC) -o $@ $< $(LIBDIRS) $(LIBS)
-
-sals: SALS.cpp $(PBLIB)
- $(CXX) $(CXXOPTS) $(CXXFLAGS) $(INCDIRS) -MF"$(@:%=%.d)" $(STATIC) -o $@ $< $(LIBDIRS) $(LIBS)
-
-printTupleCountTable: PrintTupleCountTable.cpp $(PBLIB)
- $(CXX) $(CXXOPTS) $(CXXFLAGS) $(INCDIRS) -MF"$(@:%=%.d)" $(STATIC) -o $@ $< $(LIBDIRS) $(LIBS)
-
-cmpH5StoreQualityByContext: StoreQualityByContextFromCmpH5.cpp $(PBLIB)
- $(CXX) $(CXXOPTS) $(CXXFLAGS) $(INCDIRS) -MF"$(@:%=%.d)" $(STATIC) -o $@ $< $(LIBDIRS) $(LIBS)
-
-ccsh5tobam: CCSH5ToBam.cpp $(PBLIB)
- $(CXX) $(CXXOPTS) $(CXXFLAGS) $(INCDIRS) -MF"$(@:%=%.d)" $(STATIC) -o $@ $< $(LIBDIRS) $(LIBS)
-
-pblib:
- make -C .. -f p4.mk mkliba
-
-.INTERMEDIATE: $(OBJS)
-
-CTESTS = $(wildcard ctest/*.t)
-cramtests: $(EXE)
- cram --shell=/bin/bash $(CTESTS)
-
-clean:
- @rm -f $(exe)
- @rm -f $(OBJS) $(DEPS)
- @rm *.o *.d
-
--include $(DEPS)
diff --git a/libcpp.makefile b/libcpp.makefile
deleted file mode 100644
index d4f9c40..0000000
--- a/libcpp.makefile
+++ /dev/null
@@ -1,9 +0,0 @@
-include defines.mk
-
-# Note that, for now, HDF5_LIB is a directory here, and a file in libcpp.
-# I do not know why buildctl has set that up, but we follow the mobs
-# adaptors for now.
-
-pblib: libcpp/configure.py libcpp/makefile
- cd libcpp && NOPBBAM=true HDF5_LIB=${HDF5_LIB}/libhdf5.so ./configure.py
- ${MAKE} -C libcpp
diff --git a/libcpp/.gitignore b/libcpp/.gitignore
deleted file mode 100644
index d67c0ce..0000000
--- a/libcpp/.gitignore
+++ /dev/null
@@ -1,7 +0,0 @@
-*.o
-*.d
-*.a
-*.so
-defines.mk
-/pbdata/libconfig.h
-/hdf/hdf5-1.8.12-headers/
diff --git a/libcpp/.travis.yml b/libcpp/.travis.yml
deleted file mode 100644
index 5efbc08..0000000
--- a/libcpp/.travis.yml
+++ /dev/null
@@ -1,22 +0,0 @@
-language: cpp
-script:
- - NOPBBAM=1 ./configure.py
- - make -j all
-# - make -j gtest
-compiler:
- - gcc
-# - clang
-install:
-- if [ "$CXX" = "g++" ]; then export CXX="g++-4.8" CC="gcc-4.8"; fi
-addons:
- apt:
- sources:
- - ubuntu-toolchain-r-test
- packages:
- - gcc-4.8
- - g++-4.8
-# - clang
-# - libhdf5-serial-1.8.4
-notifications:
- email: false
-sudo: false
diff --git a/libcpp/README.md b/libcpp/README.md
deleted file mode 100644
index 91745bc..0000000
--- a/libcpp/README.md
+++ /dev/null
@@ -1,47 +0,0 @@
-[](https://travis-ci.org/PacificBiosciences/blasr_libcpp)
-#What is blasr_libcpp#
-
-**Blasr_libcpp** is a *library* used by **blasr** and other executables such as samtoh5, loadPulses for analyzing PacBio sequences. This library contains three sub-directories, including pbdata, hdf and alignment.
-+ pbdata
- - contains source code for handling Pacbio sequences and can build lib ```libpbdata```.
-+ hdf
- - contains source code for handling Pacbio hdf5 files (e.g., *.pls.h5, *.rgn.h5, *.bas.h5) and builds ```libpbhdf```.
-+ alignment
- - contains source code for aligning Pacbio reads to target sequences used in blasr and builds ```libblasr```.
-
-## Building
-```
-./configure.py
-make -j all
-```
-By default, that will skip pbbam, and it will download HDF5 headers.
-
-## configure.py
-This is a WIP. It generates `defines.mk` based on the environment and command-line flags.
-In theory, it will allow simpler configuration. We might soon have different executables for
-different environments.
-
-It also generates `pbdata/libconfig.h`.
-
-By configuring up-front, we avoid race conditions, and we simplify the makefiles. For extra
-simplicity, we use the same `defines.mk` for all 3 sub-dirs.
-
-## unittest
-There is at least one failing for now, and we cannot run them in Travis without installing HDF5. TODO.
-
-(unittests mostly pass in Jenkins. We will get them into Travis later.)
-
-##Appendix: Dependencies##
-- libpbdata
- - does **not** depend on ```libhdf5```
- - should build without the ```pbbam``` library *for now*
-
-- libpbihdf
- - depends on the ```libpbdata``` and ```libhdf5``` libraries to build
-
-- alignment
- - depends on the ```libpbdata``` library to build
- - can build either with or without the ```libpbihdf``` library
- - can build either with or without the ```pbbam``` library
-- hts
- - if you use pbbam, you will need [HTSLib](https://github.com/samtools/htslib)
diff --git a/libcpp/alignment/MappingMetrics.cpp b/libcpp/alignment/MappingMetrics.cpp
deleted file mode 100644
index 1a5650e..0000000
--- a/libcpp/alignment/MappingMetrics.cpp
+++ /dev/null
@@ -1,299 +0,0 @@
-#include <iomanip>
-#include <unistd.h>
-#include "MappingMetrics.hpp"
-//In order to use clock_gettime in LINUX, add -lrt
-
-#ifdef __APPLE__
-#pragma weak clock_gettime
-int clock_gettime(clockid_t clk_id, struct timespec *tp) {
- kern_return_t ret;
- clock_serv_t clk;
- clock_id_t clk_serv_id;
- mach_timespec_t tm;
-
- uint64_t start, end, delta, nano;
-
- task_basic_info_data_t tinfo;
- task_thread_times_info_data_t ttinfo;
- mach_msg_type_number_t tflag;
-
- int retval = -1;
- switch (clk_id) {
- case CLOCK_REALTIME:
- case CLOCK_MONOTONIC:
- clk_serv_id = clk_id == CLOCK_REALTIME ? CALENDAR_CLOCK : SYSTEM_CLOCK;
- if (KERN_SUCCESS == (ret = host_get_clock_service(mach_host_self(), clk_serv_id, &clk))) {
- if (KERN_SUCCESS == (ret = clock_get_time(clk, &tm))) {
- tp->tv_sec = tm.tv_sec;
- tp->tv_nsec = tm.tv_nsec;
- retval = 0;
- }
- }
- if (KERN_SUCCESS != ret) {
- errno = EINVAL;
- retval = -1;
- }
- break;
- case CLOCK_PROCESS_CPUTIME_ID:
- case CLOCK_THREAD_CPUTIME_ID:
- start = mach_absolute_time();
- if (clk_id == CLOCK_PROCESS_CPUTIME_ID) {
- getpid();
- } else {
- sched_yield();
- }
- end = mach_absolute_time();
- delta = end - start;
- if (0 == __clock_gettime_inf.denom) {
- mach_timebase_info(&__clock_gettime_inf);
- }
- nano = delta * __clock_gettime_inf.numer / __clock_gettime_inf.denom;
- tp->tv_sec = nano * 1e-9;
- tp->tv_nsec = nano - (tp->tv_sec * 1e9);
- retval = 0;
- break;
- default:
- errno = EINVAL;
- retval = -1;
- }
- return retval;
-}
-#endif // __APPLE__
-
-Timer::Timer(std::string _header) {
- keepHistogram = false;
- keepList = false;
- totalElapsedClock = 0;
- header = _header;
- elapsedClockMsec = 0;
- elapsedTime = 0.0;
-}
-
-int Timer::ListSize() {
- return msecList.size();
-}
-
-void Timer::PrintHeader(std::ostream &out) {
- if (msecList.size() > 0) {
- out << header << " ";
- }
-}
-
-void Timer::PrintListValue(std::ostream &out, int index) {
- if (msecList.size() > 0) {
- out << msecList[index] << " ";
- }
-}
-void Timer::Tick() {
- clock_gettime(CLOCK_THREAD_CPUTIME_ID, &cpuclock[0]);
-}
-
-void Timer::SetStoreElapsedTime(bool value) {
- keepList = value;
-}
-
-void Timer::SetStoreHistgram(bool value) {
- keepHistogram = value;
-}
-
-void Timer::Tock() {
- clock_gettime(CLOCK_THREAD_CPUTIME_ID, &cpuclock[1]);
- elapsedClockMsec = (cpuclock[1].tv_nsec - cpuclock[0].tv_nsec)/1000;
- totalElapsedClock += elapsedClockMsec;
- elapsedTime = ((1.0)*elapsedClockMsec);
- if (keepHistogram) {
- // keep a histogram in number of milliseconds per operation
- if (histogram.find(elapsedClockMsec) == histogram.end()) {
- histogram[elapsedClockMsec] = 1;
- }
- else {
- histogram[elapsedClockMsec]++;
- }
- }
- if (keepList) {
- msecList.push_back(elapsedClockMsec);
- }
-}
-
-void Timer::Add(const Timer &rhs) {
- elapsedClockMsec += rhs.elapsedClockMsec;
- elapsedTime += rhs.elapsedTime;
- totalElapsedClock += rhs.totalElapsedClock;
- msecList.insert(msecList.end(), rhs.msecList.begin(), rhs.msecList.end());
-}
-
-void Timer::SetHeader(std::string _header) {
- header = _header;
-}
-
-void MappingClocks::AddCells(int nCells) {
- nCellsPerSample.push_back(nCells);
-}
-
-void MappingClocks::AddBases(int nBases) {
- nBasesPerSample.push_back(nBases);
-}
-
-int MappingClocks::GetSize() {
- return total.ListSize();
-}
-
-MappingClocks::MappingClocks() {
- total.SetHeader("Total");
- findAnchors.SetHeader("FindAnchors");
- mapToGenome.SetHeader("MapToGenome");
- sortMatchPosList.SetHeader("SortMatchPosList");
- findMaxIncreasingInterval.SetHeader("FindMaxIncreasingInterval");
- alignIntervals.SetHeader("AlignIntervals");
-}
-
-void MappingClocks::PrintHeader(std::ostream &out) {
- total.PrintHeader(out);
- findAnchors.PrintHeader(out);
- mapToGenome.PrintHeader(out);
- sortMatchPosList.PrintHeader(out);
- findMaxIncreasingInterval.PrintHeader(out);
- alignIntervals.PrintHeader(out);
-}
-
-void MappingClocks::PrintList(std::ostream &out, int index) {
-
- total.PrintListValue(out,index);
- findAnchors.PrintListValue(out,index);
- mapToGenome.PrintListValue(out,index);
- sortMatchPosList.PrintListValue(out,index);
- findMaxIncreasingInterval.PrintListValue(out,index);
- alignIntervals.PrintListValue(out,index);
- if (nCellsPerSample.size() > 0) {
- out << nCellsPerSample[index] << " ";
- }
- if (nBasesPerSample.size() > 0) {
- out << nBasesPerSample[index] << " ";
- }
- out << std::endl;
-}
-
-void MappingClocks::SetStoreList(bool value) {
- total.SetStoreElapsedTime(value);
- findAnchors.SetStoreElapsedTime(value);
- mapToGenome.SetStoreElapsedTime(value);
- sortMatchPosList.SetStoreElapsedTime(value);
- findMaxIncreasingInterval.SetStoreElapsedTime(value);
- alignIntervals.SetStoreElapsedTime(value);
-}
-
-void MappingClocks::AddClockTime(const MappingClocks &rhs) {
- total.Add(rhs.total);
- findAnchors.Add(rhs.findAnchors);
- mapToGenome.Add(rhs.mapToGenome);
- sortMatchPosList.Add(rhs.sortMatchPosList);
- findMaxIncreasingInterval.Add(rhs.findMaxIncreasingInterval);
- alignIntervals.Add(rhs.alignIntervals);
-}
-
-MappingMetrics::MappingMetrics() {
- numReads = 0;
- numMappedReads = 0;
- numMappedBases = 0;
- anchorsPerRead = 0;
- totalAnchorsForMappedReads = 0;
- totalAnchors = 0;
-}
-void MappingMetrics::StoreSDPPoint(int nBases, int nSDPAnchors, int nClock) {
- sdpBases.push_back(nBases);
- sdpAnchors.push_back(nSDPAnchors);
- sdpClock.push_back(nClock);
-}
-
-void MappingMetrics::SetStoreList(bool value) {
- clocks.SetStoreList(value);
-}
-
-void MappingMetrics::PrintSeconds(std::ostream& out, long sec ){
- out << sec << " Msec";
-}
-
-void MappingMetrics::PrintFraction(std::ostream &out, float frac) {
- out << std::setprecision(2) << frac;
-}
-
-void MappingMetrics::RecordNumAlignedBases(int nBases) {
- mappedBases.push_back(nBases);
-}
-
-void MappingMetrics::RecordNumCells(int nCells) {
- cellsPerAlignment.push_back(nCells);
-}
-
-void MappingMetrics::Collect(MappingMetrics &rhs) {
- clocks.AddClockTime(rhs.clocks);
- totalAnchors += rhs.totalAnchors;
- numReads += rhs.numReads;
- numMappedReads += rhs.numMappedReads;
- totalAnchorsForMappedReads += rhs.totalAnchorsForMappedReads;
- mappedBases.insert(mappedBases.end(), rhs.mappedBases.begin(), rhs.mappedBases.end());
- cellsPerAlignment.insert(cellsPerAlignment.end(), rhs.cellsPerAlignment.begin(), rhs.cellsPerAlignment.end());
-}
-
-void MappingMetrics::CollectSDPMetrics(MappingMetrics &rhs) {
- sdpAnchors.insert(sdpAnchors.end(), rhs.sdpAnchors.begin(), rhs.sdpAnchors.end());
- sdpBases.insert(sdpBases.end(), rhs.sdpBases.begin(), rhs.sdpBases.end());
- sdpClock.insert(sdpClock.end(), rhs.sdpClock.begin(), rhs.sdpClock.end());
-}
-
-void MappingMetrics::PrintSDPMetrics(std::ostream &out) {
- out << "nbases ncells time" << std::endl;
- int i;
- for (i = 0; i < sdpAnchors.size(); i++) {
- out << sdpBases[i] << " " << sdpAnchors[i] << " " << sdpClock[i] << std::endl;
- }
-}
-
-void MappingMetrics::PrintFullList(std::ostream &out) {
- //
- // Print the full header
- //
- clocks.PrintHeader(out);
- out << " MappedBases Cells " << std::endl;
- //
- // Print all values: clocks + bases and cells.
- //
- int i;
- for (i = 0; i < clocks.GetSize(); i++) {
- clocks.PrintList(out,i);
- // out << mappedBases[i] << " " << cellsPerAlignment[i] << endl;
- }
-}
-
-void MappingMetrics::PrintSummary(std::ostream &out) {
- out << "Examined " << numReads << std::endl;
- out << "Mapped " << numMappedReads << std::endl;
- out << "Total mapping time\t";
- PrintSeconds(out, clocks.total.elapsedClockMsec);
- out << " \t";
- PrintSeconds(out, (1.0*clocks.total.elapsedClockMsec)/numReads);
- out << " /read" << std::endl;
- out << " find anchors\t";
- PrintSeconds(out, clocks.mapToGenome.elapsedClockMsec);
- out << " \t";
- PrintSeconds(out, (1.0*clocks.mapToGenome.elapsedClockMsec)/numReads);
- out << std::endl;
- out << " sort anchors\t";
- PrintSeconds(out, clocks.sortMatchPosList.elapsedClockMsec);
- out << " \t";
- PrintSeconds(out, (1.0*clocks.sortMatchPosList.elapsedClockMsec)/numReads);
- out << std::endl;
- out << " find max interval\t";
- PrintSeconds(out, clocks.findMaxIncreasingInterval.elapsedClockMsec);
- out << " \t";
- PrintSeconds(out, (1.0*clocks.findMaxIncreasingInterval.elapsedClockMsec)/numReads);
- out << std::endl;
- out << "Total anchors: " << totalAnchors << std::endl;
- out << " Anchors per read: " << (1.0*totalAnchors) / numReads << std::endl;
- out << "Total mapped: " << totalAnchorsForMappedReads << std::endl;
- out << " Anchors per mapped read: " << (1.0*totalAnchorsForMappedReads) / numMappedReads << std::endl;
-}
-
-void MappingMetrics::AddClock(MappingClocks &clocks) {
- clocks.AddClockTime(clocks);
-}
diff --git a/libcpp/alignment/MappingMetrics.hpp b/libcpp/alignment/MappingMetrics.hpp
deleted file mode 100644
index 83bc07c..0000000
--- a/libcpp/alignment/MappingMetrics.hpp
+++ /dev/null
@@ -1,133 +0,0 @@
-#ifndef _BLASR_MAPPING_METRICS_HPP_
-#define _BLASR_MAPPING_METRICS_HPP_
-
-#include <iostream>
-#include <time.h>
-#include <map>
-#include <vector>
-//In order to use clock_gettime in LINUX, add -lrt
-#ifdef __APPLE__
-#include <mach/mach.h>
-#include <mach/clock.h>
-#include <mach/mach_time.h>
-#include <errno.h>
-
-typedef enum {
- CLOCK_REALTIME,
- CLOCK_MONOTONIC,
- CLOCK_PROCESS_CPUTIME_ID,
- CLOCK_THREAD_CPUTIME_ID
-} clockid_t;
-static mach_timebase_info_data_t __clock_gettime_inf;
-
-int clock_gettime(clockid_t clk_id, struct timespec *tp);
-#endif // __APPLE__
-
-class Timer {
-public:
- bool keepHistogram, keepList;
- timespec cpuclock[2];
- int elapsedClockMsec;
- float elapsedTime;
- std::map<int,int> histogram;
- std::vector<int> msecList;
- long long totalElapsedClock;
- std::string header;
-
-
- Timer(std::string _header="");
-
- int ListSize();
-
- void PrintHeader(std::ostream &out);
-
- void PrintListValue(std::ostream &out, int index);
-
- void Tick();
-
- void SetStoreElapsedTime(bool value);
-
- void SetStoreHistgram(bool value);
-
- void Tock();
-
- void Add(const Timer &rhs);
-
- void SetHeader(std::string _header);
-
-};
-
-
-class MappingClocks {
-public:
- Timer total;
- Timer findAnchors;
- Timer mapToGenome;
- Timer sortMatchPosList;
- Timer findMaxIncreasingInterval;
- Timer alignIntervals;
- std::vector<int> nCellsPerSample;
- std::vector<int> nBasesPerSample;
-
- void AddCells(int nCells);
-
- void AddBases(int nBases);
-
- int GetSize();
-
- MappingClocks();
-
- void PrintHeader(std::ostream &out);
-
- void PrintList(std::ostream &out, int index);
-
- void SetStoreList(bool value=true);
-
- void AddClockTime(const MappingClocks &rhs);
-};
-
-
-class MappingMetrics {
-public:
- MappingClocks clocks;
- int numReads;
- int numMappedReads;
- int numMappedBases;
- std::vector<int> mappedBases;
- std::vector<int> cellsPerAlignment;
- std::vector<int> anchorsPerAlignment;
- std::vector<int> sdpAnchors, sdpBases, sdpClock;
- long totalAnchors;
- int anchorsPerRead;
- long totalAnchorsForMappedReads;
-
- MappingMetrics();
-
- void StoreSDPPoint(int nBases, int nSDPAnchors, int nClock);
-
- void SetStoreList(bool value=true);
-
- void PrintSeconds(std::ostream &out, long sec);
-
- void PrintFraction(std::ostream &out, float frac);
-
- void RecordNumAlignedBases(int nBases);
-
- void RecordNumCells(int nCells);
-
- void Collect(MappingMetrics &rhs);
-
- void CollectSDPMetrics(MappingMetrics &rhs);
-
- void PrintSDPMetrics(std::ostream &out);
-
- void PrintFullList(std::ostream &out);
-
- void PrintSummary(std::ostream &out);
-
- void AddClock(MappingClocks &clocks);
-};
-
-
-
-#endif // _BLASR_MAPPING_METRICS_HPP_
diff --git a/libcpp/alignment/algorithms/alignment/AffineGuidedAlign.hpp b/libcpp/alignment/algorithms/alignment/AffineGuidedAlign.hpp
deleted file mode 100644
index 4080489..0000000
--- a/libcpp/alignment/algorithms/alignment/AffineGuidedAlign.hpp
+++ /dev/null
@@ -1,589 +0,0 @@
-#ifndef _BLASR_AFFINE_GUIDE_ALIGNMENT_HPP_
-#define _BLASR_AFFINE_GUIDE_ALIGNMENT_HPP_
-
-#include "GuidedAlign.hpp"
-template<typename QSequence, typename TSequence, typename T_ScoreFn>
-int AffineGuidedAlign(QSequence &origQSeq, TSequence &origTSeq, Alignment &guideAlignment,
- T_ScoreFn &scoreFn,
- int bandSize,
- Alignment &alignment,
- std::vector<int> &scoreMat,
- std::vector<Arrow> &pathMat,
- std::vector<double> &probMat,
- std::vector<double> &optPathProbMat,
- std::vector<float> &lnSubPValueVect,
- std::vector<float> &lnInsPValueVect,
- std::vector<float> &lnDelPValueVect,
- std::vector<float> &lnMatchPValueVect,
- AlignmentType alignType=Global,
- bool computeProb=false) {
-
- Guide guide;
- AlignmentToGuide(guideAlignment, guide, bandSize);
- StoreMatrixOffsets(guide);
- int guideSize = ComputeMatrixNElem(guide);
-
- //
- // Make a copy of the sequences that is guaranteed to be in 3-bit format for faster alignment.
- // (mabybe eventually reuse the qseq and tseq memory)
- //
- QSequence qSeq;
- TSequence tSeq;
- qSeq.Assign(origQSeq);
- tSeq.Assign(origTSeq);
-
- int matrixNElem = ComputeMatrixNElem(guide);
- StoreMatrixOffsets(guide);
-
- /*
- * The following code is useful to produce images of the dp-matrix.
- * Make sure the sequenences are less than 5kb each though.
-
- Matrix<float> probMatrix;
- probMatrix.Resize(qSeq.length, tSeq.length);
- probMatrix.Initialize(0);
- ofstream matrixOut;
- stringstream matrixOutNameStrm;
- matrixOutNameStrm << "probMatrix_"<< runIndex << ".dat";
- matrixOut.open(matrixOutNameStrm.str().c_str());
- */
-
- if (computeProb) {
- //
- // Convert phred scale to proper ln for faster manipulation later on.
- //
- QVToLogPScale(qSeq.substitutionQV, qSeq.length, lnSubPValueVect);
- QVToLogPScale(qSeq.insertionQV, qSeq.length, lnInsPValueVect);
- QVToLogPScale(qSeq.deletionQV, qSeq.length, lnDelPValueVect);
- if (lnMatchPValueVect.size() < qSeq.length) {
- lnMatchPValueVect.resize(qSeq.length);
- }
- //
- // Normalize probability std::vectors so that the probability of transition from each cell is 1.
- //
- int i;
- for (i = 0; i < qSeq.length; i++) {
- float subSum = LogSumOfTwo(lnSubPValueVect[i], QVToLogPScale(scoreFn.substitutionPrior)); // prior on substitution rate
- float denominator = LogSumOfThree(lnDelPValueVect[i], lnInsPValueVect[i], subSum);
- lnDelPValueVect[i] = lnDelPValueVect[i] - denominator;
- lnSubPValueVect[i] = lnSubPValueVect[i] - denominator;
- lnInsPValueVect[i] = lnInsPValueVect[i] - denominator;
- lnMatchPValueVect[i] = subSum - denominator;
- }
-
- }
-
-
-
- //
- // Make sure the alignments can fit in the reused buffers.
- //
- std::vector<int> affineInsScoreMat, affineDelScoreMat;
- std::vector<Arrow> affineInsPathMat, affineDelPathMat;
- affineInsScoreMat.resize(matrixNElem);
- fill(affineInsScoreMat.begin(), affineInsScoreMat.end(), 0);
- affineDelScoreMat.resize(matrixNElem);
- fill(affineDelScoreMat.begin(), affineDelScoreMat.end(), 0);
- affineInsPathMat.resize(matrixNElem);
- fill(affineInsPathMat.begin(), affineInsPathMat.end(), NoArrow);
- affineDelPathMat.resize(matrixNElem);
- fill(affineDelPathMat.begin(), affineDelPathMat.end(), NoArrow);
-
-
- if (scoreMat.size() < matrixNElem) {
- scoreMat.resize(matrixNElem);
- pathMat.resize(matrixNElem);
- fill(scoreMat.begin(), scoreMat.end(), 0);
- fill(pathMat.begin(), pathMat.end(), NoArrow);
- }
- if (computeProb) {
- if (probMat.size() < matrixNElem) {
- probMat.resize(matrixNElem);
- optPathProbMat.resize(matrixNElem);
- }
- }
-
- //
- // Initialze matrices. Only initialize up to matrixNElem rather
- // than matrix.size() because the matrix.size() unnecessary space
- // may be allocated.
- //
-
- std::fill(scoreMat.begin(), scoreMat.begin() + matrixNElem, 0);
- std::fill(pathMat.begin(), pathMat.begin() + matrixNElem, NoArrow);
- if (computeProb) {
- std::fill(probMat.begin(), probMat.begin() + matrixNElem, 0);
- std::fill(optPathProbMat.begin(), optPathProbMat.begin() + matrixNElem, 0);
- }
- //
- // Initialize boundary conditions.
- //
- int q, t;
- int bufferIndex;
- // start alignemnt at the beginning of the guide, and align to the
- // end of the guide.
- if (guide.size() == 0) {
- qSeq.Free();
- tSeq.Free();
- return 0;
- }
- int qStart = guide[1].q;
- int tStart = guide[1].t;
- int qEnd = guide[guide.size()-1].q+1;
- int tEnd = guide[guide.size()-1].t+1;
-
- GetBufferIndexFunctor GetBufferIndex;
- GetBufferIndex.seqRowOffset = qStart;
- GetBufferIndex.guideSize = guide.size();
- int indicesAreValid, delIndexIsValid, insIndexIsValid, matchIndexIsValid;
- bufferIndex = -1;
- indicesAreValid = GetBufferIndex(guide, qStart-1, tStart-1, bufferIndex);
- assert(indicesAreValid);
- scoreMat[bufferIndex] = 0;
- pathMat[bufferIndex] = NoArrow;
- int matchIndex, insIndex, delIndex, curIndex;
-
- //
- // Initialize deletion row.
- //
- if (computeProb) {
- probMat[0] = optPathProbMat[0] = 0;
- }
- for (t = tStart; t < tStart + guide[0].tPost; t++) {
- curIndex=-1;
- indicesAreValid = GetBufferIndex(guide, qStart-1, t, curIndex);
- if (indicesAreValid == 0 ) {
- cout << "QSeq" << endl;
- (static_cast<DNASequence*>(&origQSeq))->PrintSeq(cout);
- cout << "TSeq" << endl;
- (static_cast<DNASequence*>(&origTSeq))->PrintSeq(cout);
- assert(0);
- }
- delIndex = -1;
- delIndexIsValid = GetBufferIndex(guide, qStart-1, t-1, delIndex);
- if (delIndexIsValid) {
- if (alignType == Global) {
- scoreMat[curIndex] = scoreMat[delIndex] + scoreFn.del;
- }
- else if (alignType == Local) {
- scoreMat[curIndex] = 0;
- }
- affineDelScoreMat[curIndex] = scoreFn.del;
- affineDelPathMat[curIndex] = AffineDelOpen;
- affineInsPathMat[curIndex] = AffineInsOpen;
- affineInsScoreMat[curIndex] = scoreFn.ins;
- pathMat[curIndex] = Left;
- if (computeProb) {
- if (qSeq.qual.Empty() == false) {
- optPathProbMat[curIndex] = probMat[curIndex] = probMat[delIndex] + QVToLogPScale(scoreFn.globalDeletionPrior);
- }
- }
- }
- }
-
- //
- // Initialize stripe along the top of the grid.
- //
- for (q = qStart ; q < qStart + bandSize and q < qEnd; q++) {
- insIndex = -1;
- insIndexIsValid = GetBufferIndex(guide, q-1, tStart-1, // diagonal from t-start
- insIndex);
- curIndex = -1;
- indicesAreValid = GetBufferIndex(guide, q, tStart-1, curIndex);
-
- if (insIndexIsValid and indicesAreValid) {
- assert(insIndex >= 0);
- assert(curIndex >= 0);
- if (alignType == Global) {
- scoreMat[curIndex] = scoreMat[insIndex] + scoreFn.ins;
- }
- else {
- scoreMat[curIndex] = 0;
- }
- affineInsScoreMat[curIndex] = scoreFn.ins;
- affineInsPathMat[curIndex] = AffineInsOpen;
- affineDelScoreMat[curIndex] = scoreFn.del;
- affineDelPathMat[curIndex] = AffineDelOpen;
- pathMat[curIndex] = Up;
- }
- }
-
- int matchScore, insScore, delScore,
- affineInsOpenScore, affineInsExtScore,
- affineDelOpenScore, affineDelExtScore;
-
- for (q = qStart; q < qEnd; q++) {
- int qi = q - qStart + 1;
- int tp = guide[qi].t;
- curIndex = matchIndex = insIndex = delIndex = -1;
-
- //
- // Do some work that will help define when matchIndex and insIndex
- // may be used. Once delIndex is computed once, it is valid for
- // all t positions.
- //
- int prevRowTEnd = -1;
- if ( qi > 0) {
- //
- // Define the boundaries of the column which may access previously
- // computed cells with a match.
- //
- prevRowTEnd = guide[qi-1].t + guide[qi-1].tPost;
- }
-
- for (t = tp - guide[qi].tPre ; t < guide[qi].t + guide[qi].tPost +1; t++) {
-
- if (q < qStart + bandSize and t == tp - guide[qi].tPre - 1) {
- // On the boundary condition, don't access the 1st element;
- t++;
- continue;
- }
- // Make sure the index is not past the end of the sequence.
- if (t < -1) continue;
- if (t >= tEnd) continue;
-
- //
- // No cells are available to use for insertion cost
- // computation.
- //
- if (t > prevRowTEnd) {
- insIndex = -1;
- }
- if (t > prevRowTEnd + 1) {
- matchIndex = -1;
- }
-
- //
- // Find the indices in the buffer. Since the rows are of
- // different sizes, one can't just use offsets from the buffer
- // index.
- //
-
- if (GetBufferIndex(guide, q-1,t-1, matchIndex)) {
- assert(matchIndex >= 0);
- matchScore = scoreMat[matchIndex] + scoreFn.Match(tSeq, t, qSeq, q);
- }
- else {
- matchScore = INF_INT;
- }
-
- if (GetBufferIndex(guide, q-1, t, insIndex)) {
- assert(insIndex >= 0);
- insScore = scoreMat[insIndex] + scoreFn.Insertion(tSeq,(DNALength) t, qSeq, (DNALength)q);
- affineInsExtScore = affineInsScoreMat[insIndex] + scoreFn.affineExtend; // 0 extension
- }
- else {
- insScore = INF_INT;
- affineInsExtScore = INF_INT;
- }
- if (GetBufferIndex(guide, q, t-1, delIndex)) {
- assert(delIndex >= 0);
- delScore = scoreMat[delIndex] + scoreFn.Deletion(tSeq, (DNALength) t, qSeq, (DNALength)q);
- affineDelExtScore = affineDelScoreMat[delIndex] + scoreFn.affineExtend;
- }
- else {
- delScore = INF_INT;
- affineDelExtScore = INF_INT;
- }
-
- int minScore = MIN(matchScore, MIN(insScore, MIN(delScore, MIN(affineInsExtScore, affineDelExtScore))));
- int result = GetBufferIndex(guide, q, t, curIndex);
- // This should only loop over valid cells.
- assert(result);
- assert(curIndex >= 0);
- scoreMat[curIndex] = minScore;
- if (minScore == INF_INT) {
- pathMat[curIndex] = NoArrow;
- }
- else {
- assert(result == 1);
- if (minScore == matchScore) {
- pathMat[curIndex] = Diagonal;
- }
- else if (minScore == delScore) {
- pathMat[curIndex] = Left;
- }
- else if (minScore == insScore) {
- pathMat[curIndex] = Up;
- }
- else if (minScore == affineInsExtScore) {
- pathMat[curIndex] = AffineInsClose;
- }
- else {
- assert (minScore == affineDelExtScore) ;
- pathMat[curIndex] = AffineDelClose;
- }
- }
-
- // affineInsOpenScore = scoreMat[curIndex] + scoreFn.ins * 2;
- // affineDelOpenScore = scoreMat[curIndex] + scoreFn.del * 2;
-
- //
- // Set the penalty to initiate an affine gap here.
- //
- affineInsOpenScore = scoreMat[curIndex] + scoreFn.affineOpen;
- affineDelOpenScore = scoreMat[curIndex] + scoreFn.affineOpen;
-
- if (affineInsOpenScore == INF_INT and
- affineInsExtScore == INF_INT) {
- cout << q << " " << t << endl;
- cout << "All infinity, bad things will happen." << endl;
- cout << "the score mat here is : " << scoreMat[curIndex] << " and path " << pathMat[curIndex] << endl;
- assert(0);
- }
- if (affineInsOpenScore < affineInsExtScore) {
- affineInsPathMat[curIndex] = AffineInsOpen;
- affineInsScoreMat[curIndex] = affineInsOpenScore;
- }
- else {
- affineInsPathMat[curIndex] = AffineInsUp;
- affineInsScoreMat[curIndex] = affineInsExtScore;
- }
-
- if (affineDelOpenScore < affineDelExtScore) {
- affineDelPathMat[curIndex] = AffineDelOpen;
- affineDelScoreMat[curIndex] = affineDelOpenScore;
- }
- else {
- affineDelPathMat[curIndex] = AffineDelLeft;
- affineDelScoreMat[curIndex] = affineDelExtScore;
- }
- }
- }
- // Ok, for now just trace back from qend/tend
- q = qEnd-1;
- t = tEnd-1;
- std::vector<Arrow> optAlignment;
- int bufferIndexIsValid;
- int curMatrix = Match;
- while(q >= qStart or t >= tStart) {
- bufferIndex = -1;
- // cout << "backtrace: " << q << " "<< t << endl;
- bufferIndexIsValid = GetBufferIndex(guide, q, t, bufferIndex);
- assert(bufferIndexIsValid);
- assert(bufferIndex >= 0);
- Arrow arrow;
- // cout << q << " "<< t << " " << curMatrix << " " << arrow << endl;
- if (curMatrix == Match) {
- arrow = pathMat[bufferIndex];
- if (arrow == NoArrow) {
- tSeq.ToAscii();
- qSeq.ToAscii();
- int gi;
- for (gi = 0; gi < guide.size(); gi++) {
- cout << guide[gi].q << " " << guide[gi].t << " " << guide[gi].tPre << " " << guide[gi].tPost << endl;
- }
-
- cout << "qseq: "<< endl;
- (static_cast<DNASequence*>(&qSeq))->PrintSeq(cout);
- cout << "tseq: "<< endl;
- (static_cast<DNASequence*>(&tSeq))->PrintSeq(cout);
- cout << "ERROR, this path has gone awry at " << q << " " << t << " !" << endl;
- exit(1);
- }
-
- if (arrow == Diagonal) {
- optAlignment.push_back(arrow);
- q--;
- t--;
- }
- else if (arrow == Up) {
- optAlignment.push_back(arrow);
- q--;
- }
- else if (arrow == Left) {
- optAlignment.push_back(arrow);
- t--;
- }
- else if (arrow == AffineInsClose) {
- optAlignment.push_back(Up);
- curMatrix = AffineIns;
- q--;
- }
- else if (arrow == AffineDelClose) {
- t--;
- optAlignment.push_back(Left);
- curMatrix = AffineDel;
- }
- }
- else if (curMatrix == AffineIns) {
- arrow = affineInsPathMat[bufferIndex];
- if (arrow == AffineInsOpen) {
- curMatrix = Match;
- }
- else if (arrow == AffineInsUp) {
- q--;
- optAlignment.push_back(Up);
- }
- else {
- cout << "ERROR! Reached arrow " << arrow << " at " << q << " " << t << " in affine ins path mat. That is bad." << endl;
- assert(0);
- }
- }
- else {
- assert(curMatrix == AffineDel);
- arrow = affineDelPathMat[bufferIndex];
- if (arrow == AffineDelOpen) {
- curMatrix = Match;
- }
- else if (arrow == AffineDelLeft) {
- t--;
- optAlignment.push_back(Left);
- }
- else {
- cout << "ERROR! Reached arrow " << arrow << " at " << q << " " << t << " in affine del mat. This is also bad." << endl;
- assert(0);
- }
- }
- }
-
- alignment.nCells = ComputeMatrixNElem(guide);
- std::reverse(optAlignment.begin(), optAlignment.end());
- alignment.qPos = qStart;
- alignment.tPos = tStart;
- alignment.ArrowPathToAlignment(optAlignment);
- // StickPrintAlignment(alignment, qSeq, tSeq, cout);
- RemoveAlignmentPrefixGaps(alignment);
- int lastIndex = 0;
- tSeq.Free();
- qSeq.Free();
- lastIndex = -1;
- if (GetBufferIndex(guide, qEnd - 1, tEnd - 1, lastIndex)) {
- alignment.score = scoreMat[lastIndex];
- return scoreMat[lastIndex];
- }
- else {
- return 0;
- }
-}
-
-
-template<typename QSequence, typename TSequence, typename T_ScoreFn> //, typename T_BufferCache>
-int AffineGuidedAlign(QSequence &origQSeq, TSequence &origTSeq,
- T_ScoreFn &scoreFn,
- int bandSize,
- int sdpIns, int sdpDel, float sdpIndelRate,
- Alignment &alignment,
- AlignmentType alignType=Global,
- bool computeProb = false,
- int sdpTupleSize= 8) {
- Alignment sdpAlignment;
-
- int alignScore = SDPAlign(origQSeq, origTSeq,
- scoreFn, sdpTupleSize,
- sdpIns, sdpDel, sdpIndelRate,
- sdpAlignment); //, Local, false, false);
-
- int b;
- for (b = 0; b < sdpAlignment.blocks.size(); b++) {
- sdpAlignment.blocks[b].qPos += sdpAlignment.qPos;
- sdpAlignment.blocks[b].tPos += sdpAlignment.tPos;
- }
- sdpAlignment.tPos = 0;
- sdpAlignment.qPos = 0;
-
- return AffineGuidedAlign(origQSeq, origTSeq, sdpAlignment, scoreFn, bandSize, alignment,
- // fill in optional parameters
- alignType, computeProb);
-
-}
-
-
-//
-// Use Case: No guide yet exists for this alignment, but using
-// buffers. Run SDP alignment first, then refine on the guide.
-//
-
-template<typename QSequence, typename TSequence, typename T_ScoreFn, typename T_BufferCache>
-int AffineGuidedAlign(QSequence &origQSeq, TSequence &origTSeq,
- T_ScoreFn &scoreFn,
- int bandSize,
- int sdpIns, int sdpDel, float sdpIndelRate,
- T_BufferCache &buffers,
- Alignment &alignment,
- AlignmentType alignType=Global,
- bool computeProb = false,
- int sdpTupleSize= 8) {
-
- Alignment sdpAlignment;
-
- int alignScore = SDPAlign(origQSeq, origTSeq,
- scoreFn, sdpTupleSize,
- sdpIns, sdpDel, sdpIndelRate,
- sdpAlignment, buffers, Local, false, false);
-
- int b;
- for (b = 0; b < sdpAlignment.blocks.size(); b++) {
- sdpAlignment.blocks[b].qPos += sdpAlignment.qPos;
- sdpAlignment.blocks[b].tPos += sdpAlignment.tPos;
- }
- sdpAlignment.tPos = 0;
- sdpAlignment.qPos = 0;
-
- return AffineGuidedAlign(origQSeq, origTSeq, sdpAlignment, scoreFn, bandSize, buffers, alignment,
- // fill in optional parameters
- alignType, computeProb);
-}
-
-//
-// Use case, guide exists, using buffers
-//
-template<typename QSequence, typename TSequence, typename T_ScoreFn, typename T_BufferCache>
-int AffineGuidedAlign(QSequence &origQSeq, TSequence &origTSeq, Alignment &guideAlignment,
- T_ScoreFn &scoreFn,
- int bandSize,
- T_BufferCache &buffers,
- Alignment &alignment,
- AlignmentType alignType=Global,
- bool computeProb=false) {
- return AffineGuidedAlign(origQSeq, origTSeq, guideAlignment, scoreFn, bandSize, alignment,
- buffers.scoreMat,
- buffers.pathMat,
- buffers.probMat,
- buffers.optPathProbMat,
- buffers.lnSubPValueMat,
- buffers.lnInsPValueMat,
- buffers.lnDelPValueMat,
- buffers.lnMatchPValueMat, alignType, computeProb);
-}
-
-//
-// Missing the use case for guide does not exist, and not using
-// buffers. This is just a very long function declaration, so it's
-// not worth writing until it is needed.
-//
-
-
-//
-// Use case, guide exists, but not using buffers.
-//
-template<typename QSequence, typename TSequence, typename T_ScoreFn>
-int AffineGuidedAlign(QSequence &origQSeq, TSequence &origTSeq, Alignment &guideAlignment,
- T_ScoreFn &scoreFn,
- int bandSize,
- Alignment &alignment,
- AlignmentType alignType=Global,
- bool computeProb=false) {
-
- // Make synonyms for members of the buffers class for easier typing.
- std::vector<int> scoreMat;
- std::vector<Arrow> pathMat;
- std::vector<double> probMat;
- std::vector<double> optPathProbMat;
- std::vector<float> lnSubPValueVect;
- std::vector<float> lnInsPValueVect;
- std::vector<float> lnDelPValueVect;
- std::vector<float> lnMatchPValueVect;
-
- return AffineGuidedAlign(origQSeq, origTSeq, guideAlignment, scoreFn, bandSize, alignment,
- scoreMat,
- pathMat,
- probMat,
- optPathProbMat,
- lnSubPValueVect,
- lnInsPValueVect,
- lnDelPValueVect,
- lnMatchPValueVect, alignType, computeProb);
-}
-
-#endif // _BLASR_AFFINE_GUIDE_ALIGNMENT_HPP_
diff --git a/libcpp/alignment/algorithms/alignment/AffineKBandAlign.hpp b/libcpp/alignment/algorithms/alignment/AffineKBandAlign.hpp
deleted file mode 100644
index 82ba5f7..0000000
--- a/libcpp/alignment/algorithms/alignment/AffineKBandAlign.hpp
+++ /dev/null
@@ -1,406 +0,0 @@
-#ifndef _BLASR_AFFINE_KBAND_ALIGN_HPP_
-#define _BLASR_AFFINE_KBAND_ALIGN_HPP_
-
-#include <cassert>
-#include <vector>
-#include <iostream>
-#include "NucConversion.hpp"
-#include "defs.h"
-#include "matrix/FlatMatrix.hpp"
-#include "datastructures/alignment/Alignment.hpp"
-#include "KBandAlign.hpp"
-
-template<typename T_QuerySequence, typename T_TargetSequence, typename T_Alignment>
-int AffineKBandAlign(T_QuerySequence &pqSeq, T_TargetSequence &ptSeq,
- int matchMat[5][5],
- int hpInsOpen, int hpInsExtend, int insOpen, int insExtend,
- int del, int k,
- vector<int> &scoreMat,
- vector<Arrow> & pathMat,
- vector<int> &hpInsScoreMat,
- vector<Arrow> &hpInsPathMat,
- vector<int> &insScoreMat,
- vector<Arrow> &insPathMat,
- T_Alignment &alignment,
- AlignmentType alignType) {
-
- //
- // Make a copy of the sequences that is guaranteed to be in 3-bit format
- // for quick access to the score array.
- //
-
- int INF_SCORE = INF_INT - 1000;
- T_QuerySequence qSeq;
- T_TargetSequence tSeq;
- // CreateThreeBitSequence(pqSeq, qSeq);
- // CreateThreeBitSequence(ptSeq, tSeq);
- qSeq.seq = pqSeq.seq;
- qSeq.length= pqSeq.length;
- tSeq.seq = ptSeq.seq;
- tSeq.length = ptSeq.length;
-
-
- DNALength tLen, qLen;
- SetKBoundedLengths(tSeq.length, qSeq.length, k, tLen, qLen);
-
- //
- //
- // Allow for length up to diagonal + k + 1 for boundary.
- //
- // Allow for width:
- // diagonal (1)
- // up to k insertions (k)
- // up to k deletions (k)
- // boundary on left side of matrix (1)
- //
- // if (qLen + k > tLen and qLen < tLen) {
- // k = tLen - qLen +1;
- // }
- DNALength nCols = 2*k + 1;
- VectorIndex totalMatSize = (qLen + 1) * nCols;
-
-
- //
- // For now the scoreMat and path mat maintained outside this
- // function so that they may have different sizes from the affine
- // matrices.
- //
-
- if (scoreMat.size() < totalMatSize) {
- scoreMat.resize(totalMatSize);
- pathMat.resize(totalMatSize);
- }
-
- if (hpInsScoreMat.size() < totalMatSize) {
- hpInsScoreMat.resize(totalMatSize);
- hpInsPathMat.resize(totalMatSize);
- insScoreMat.resize(totalMatSize);
- insPathMat.resize(totalMatSize);
- }
-
- //
- // Initialze matrices
- //
- std::fill(scoreMat.begin(), scoreMat.begin() + totalMatSize, 0);
- std::fill(pathMat.begin(), pathMat.begin() + totalMatSize, NoArrow);
- std::fill(hpInsScoreMat.begin(), hpInsScoreMat.begin() + totalMatSize, 0);
- std::fill(hpInsPathMat.begin(), hpInsPathMat.begin() + totalMatSize, NoArrow);
- std::fill(insScoreMat.begin(), insScoreMat.begin() + totalMatSize, 0);
- std::fill(insPathMat.begin(), insPathMat.begin() + totalMatSize, NoArrow);
-
- //
- // Initialize the boundaries of the DP matrix.
- //
- int q, t;
-
- if (alignType != TargetFit) {
- insScoreMat[rc2index(0, k, nCols)] = 0;
- insPathMat[rc2index(0, k, nCols)] = AffineInsOpen;
-
- for (q = 1; q <=k && q < (int) qLen + 1; q++ ){
- insScoreMat[rc2index(q, k - q, nCols)] = q * insExtend + insOpen;
- insPathMat[rc2index(q, k-q, nCols)] = AffineInsUp;
- }
- }
- else if (alignType == TargetFit) {
- //
- // Allow free gap penalties at the beginning of the alignment.
- //
- insScoreMat[rc2index(0, k, nCols)] = 0;
- insPathMat[rc2index(0, k, nCols)] = AffineInsOpen;
- for (q = 1; q <= k && q < (int) qLen + 1; q++ ){
- insScoreMat[rc2index(q, k - q, nCols)] = 0;
- insPathMat[rc2index(q, k-q, nCols)] = AffineInsUp;
- }
- }
-
-
- //
- // Assign score for (0,0) position in matrix -- aligning a gap to a gap
- // which should just be a finished alignment. There is no cost for
- // gap-gap alignment.
- //
- hpInsScoreMat[rc2index(0,k,nCols)] = 0;
- hpInsPathMat[rc2index(0,k,nCols)] = AffineHPInsOpen;
-
- for (q = 1; q <= k && q < (int) qLen + 1; q++) {
- hpInsScoreMat[rc2index(q, k - q, nCols)] = q * hpInsExtend + hpInsOpen;
- hpInsPathMat[rc2index(q,k-q,nCols)] = AffineHPInsUp;
- }
-
- for (t = k+1; t < (int) nCols; t++ ) {
- hpInsScoreMat[rc2index(0, t, nCols)] = INF_SCORE;// hpInsOpen + (t - k) * hpInsExtend;//; //INF_SCORE;
- hpInsPathMat[t] = NoArrow; //AffineHPInsOpen ; //NoArrow;
- insScoreMat[t] = INF_SCORE; //insOpen + (t - k) * insExtend; //INF_SCORE;
- insPathMat[t] = NoArrow; //AffineInsOpen; //NoArrow;
- }
-
- for (q = 1; q <= k && q < (int) qLen + 1; q++) {
- scoreMat[rc2index(q, k - q, nCols)] = insScoreMat[rc2index(q,k-q,nCols)];
- pathMat[rc2index(q, k - q , nCols)] = AffineInsClose;
- }
- for (t = 1; t <= (int) k; t++) {
- scoreMat[rc2index(0, t + k , nCols)] = t * del;
- pathMat[rc2index(0, t + k , nCols)] = Left;
- }
-
-
- //
- // The recurrence relation here is a slight modification of the
- // standard affine gap alignment. Deletions are non-affine. Insertions
- // are affine with different scores for homopolymer insertions, and
- // an affine score for mixed insertions.
- //
-
-
- int matchScore, delScore;
- int hpInsExtendScore, hpInsOpenScore, insOpenScore, insExtendScore;
- int minHpInsScore, minInsScore;
- for (q = 1; q <= (int) qLen; q++) {
- for (t = q - k; t < (int) q + k + 1; t++) {
- if (t < 1) {
- continue;
- }
- if ((DNALength) t > tLen) {
- break;
- }
-
- VectorIndex upper = rc2index(q-1, k + t - q + 1, nCols);
- VectorIndex curIndex = rc2index(q, k + t - q, nCols);
-
- if (t < q + k)
- hpInsOpenScore = scoreMat[upper] + hpInsOpen;
- else
- hpInsOpenScore = INF_SCORE;
-
- //
- // The homopolymer insertion score is defined only when the previous nucleotide
- // is the same as the current, in which case the homopolymer insertion score
- // is used. If the current and previous nucleotide in the query are different,
- // the extension is not possible, and the best that can happen is a gap open.
- //
- if (q > 1 and qSeq[q-1] == qSeq[q-2]) {
- if (t < q + k)
- hpInsExtendScore = hpInsScoreMat[upper] + hpInsExtend;
- else
- hpInsExtendScore = INF_SCORE;
- }
- else {
- hpInsExtendScore = INF_SCORE;
- }
-
- //
- // Since this is only allowing insertions, this grid has only horizontal and
- // elevation arrows.
- //
-
- if (hpInsOpenScore < hpInsExtendScore) {
- hpInsPathMat[curIndex] = AffineHPInsOpen;
- minHpInsScore = hpInsOpenScore;
- }
- else {
- hpInsPathMat[curIndex] = AffineHPInsUp;
- minHpInsScore = hpInsExtendScore;
- }
-
- hpInsScoreMat[curIndex] = minHpInsScore;
- if (t < q + k) {
- insOpenScore = scoreMat[upper] + insOpen;
- insExtendScore = insScoreMat[upper] + insExtend;
- }
- else {
- insOpenScore = INF_SCORE;
- insExtendScore = INF_SCORE;
- }
-
- if (insOpenScore < insExtendScore) {
- insPathMat[curIndex] = AffineInsOpen;
- minInsScore = insOpenScore;
- }
- else {
- insPathMat[curIndex] = AffineInsUp;
- minInsScore = insExtendScore;
- }
- insScoreMat[curIndex] = minInsScore;
-
-
- // On left boundary of k-band.
- // do not allow deletions of t.
- if (t == q - k) {
- delScore = INF_SCORE;
- }
- else {
- // cur row = q
- // cur col = t - q
- // prev col therefore t - q - 1
- // and offset from diagonal is k + t - q - 1
- delScore = scoreMat[rc2index(q, k + t - q - 1, nCols)] + del;
- }
-
- // cur row = q
- // cur col = t - q
-
- // cur query index = q - 1
- // cur target index = t - 1
- // therefore match row (up) = q
- // match col (left, but since up shifted right) = t - q
- assert(rc2index(q - 1, k + t - q, nCols) < scoreMat.size());
- assert(t-1 >= 0);
- assert(q-1 >= 0);
- matchScore = scoreMat[rc2index(q - 1, k + t - q, nCols)] + matchMat[ThreeBit[qSeq.seq[q-1]]][ThreeBit[tSeq.seq[t-1]]];
-
- //
- // Possibly on right boundary of k-band, in which
- // case do not allow insertions from q.
-
- int minScore = MIN(matchScore, MIN(delScore, MIN(minInsScore, minHpInsScore)));
- curIndex = rc2index(q, k + t - q, nCols);
- assert(curIndex < scoreMat.size());
- scoreMat[curIndex] = minScore;
- if (minScore == matchScore) {
- pathMat[curIndex] = Diagonal;
- }
- else if (minScore == delScore) {
- pathMat[curIndex] = Left;
- }
- else if (minScore == minInsScore) {
- pathMat[curIndex] = AffineInsClose;
- }
- else {
- pathMat[curIndex] = AffineHPInsClose;
- }
- }
- }
- /*
- std::cout << "tracing back from: " << q << ", " << t << std::endl;
- std::cout << "match score: " << std::endl;
- PrintFlatMatrix(&scoreMat[0], qLen + 1, nCols, std::cout);
- std::cout << " path: " << std::endl;
- PrintFlatMatrix(pathMat, qLen + 1, nCols, std::cout);
- std::cout << "hp score: " << std::endl;
- PrintFlatMatrix(&hpInsScoreMat[0], qLen + 1, nCols, std::cout);
- std::cout << "hp path: " << std::endl;
- PrintFlatMatrix(hpInsPathMat, qLen + 1, nCols, std::cout);
- std::cout << "normal affine ins score: " << std::endl;
- PrintFlatMatrix(&insScoreMat[0], qLen + 1, nCols, std::cout);
- std::cout << "normal affine ins path: " << std::endl;
- PrintFlatMatrix(&insPathMat[0], qLen + 1, nCols, std::cout);
- */
- vector<Arrow> optAlignment;
- // First find the end position matrix.
-
- int minScoreTPos, minScore;
- int minScoreQPos;
- if (alignType == Global) {
- q = qLen ;
- t = k - ((int)qLen - (int)tLen);
- }
- else if (alignType == QueryFit) {
- q = qLen;
- minScoreTPos = max(q-k,1);
- DNALength index = rc2index(qLen, k + minScoreTPos - q, nCols);
- minScore = scoreMat[index];
- for (t = q - k; t < (int) q + k + 1; t++) {
- if (t < 1) { continue;}
- if (t > tLen) { break;}
- int index = rc2index(qLen,k + t - q,nCols);
- if (scoreMat[index] < minScore) {
- minScoreTPos = t;
- minScore = scoreMat[index ];
- }
- }
- t = k - ((int)qLen - minScoreTPos);
- }
- else if (alignType == TargetFit) {
- t = tLen;
-
- int qStart = max(0,min((int)qLen, (int)tLen) - max(0, k - max(((int)tLen) - ((int)qLen), 0)));
- int qEnd = min(qLen, tLen + k) + 1;
-
- minScoreQPos = qStart;
- int index = rc2index(minScoreQPos, k - (minScoreQPos - tLen), nCols);
- minScore = scoreMat[index];
- for (q = qStart; q < qEnd; q++) {
- // add to k since this is going up.
- index = rc2index(q, k + (q - tLen), nCols);
- if (scoreMat[index] < minScore) {
- minScoreQPos = q;
- minScore = scoreMat[index];
- }
- }
- q = minScoreQPos;
- t = (k+((int)q-(int)tLen));
- }
-
- int optScore = scoreMat[rc2index(q, t, nCols)];
- Arrow arrow;
- MatrixLabel curMatrix = Match;
-
-
- while ((q > 0) or
- (q == 0 and t > k)) {
- assert(t < 2*k+1);
- if (curMatrix == Match) {
- arrow = pathMat[rc2index(q,t, nCols)];
- if (arrow == Diagonal) {
- optAlignment.push_back(arrow);
- q--;
- }
- else if (arrow == Left) {
- optAlignment.push_back(arrow);
- t--;
- }
- //
- // The following two conditions change matrices
- // without changing coordinates, since the gap close
- // just changes state without adding to the alignment.
- //
- else if (arrow == AffineInsClose) {
- curMatrix = AffineIns;
- }
- else if (arrow == AffineHPInsClose) {
- curMatrix = AffineHPIns;
- }
- }
- else if (curMatrix == AffineHPIns) {
- //
- // The current
- arrow = hpInsPathMat[rc2index(q,t,nCols)];
- if (arrow == AffineHPInsOpen) {
- curMatrix = Match;
- }
- else if (arrow != AffineHPInsUp) {
- std::cout << "ERROR! Affine homopolymer insertion path matrix MUST only have UP or OPEN arrows." << std::endl;
- assert(0);
- }
- optAlignment.push_back(Up);
- q--;
- t++;
- }
- else if (curMatrix == AffineIns) {
- arrow = insPathMat[rc2index(q,t,nCols)];
- if (arrow == AffineInsOpen) {
- curMatrix = Match;
- }
- else if (arrow != AffineInsUp) {
- std::cout << "ERROR! Affine insertion path matrix MUST only have UP or OPEN arrows."<<std::endl;
- assert(0);
- }
- optAlignment.push_back(Up);
- q--;
- t++;
- }
- else {
- std::cout << "ERROR in affine local alignment, matrix is: " << curMatrix << std::endl;
- assert(0);
- }
- }
- // qSeq.Free();
- // tSeq.Free();
- std::reverse(optAlignment.begin(), optAlignment.end());
- alignment.ArrowPathToAlignment(optAlignment);
- return optScore;
-}
-
-
-#endif // _BLASR_AFFINE_KBAND_ALIGN_HPP_
diff --git a/libcpp/alignment/algorithms/alignment/AlignmentFormats.hpp b/libcpp/alignment/algorithms/alignment/AlignmentFormats.hpp
deleted file mode 100644
index b645b94..0000000
--- a/libcpp/alignment/algorithms/alignment/AlignmentFormats.hpp
+++ /dev/null
@@ -1,6 +0,0 @@
-#ifndef _BLASR_ALIGNMENT_FORMATS_HPP_
-#define _BLASR_ALIGNMENT_FORMATS_HPP_
-
-enum AlignmentPrintFormat { StickPrint, SummaryPrint, CompareXML, Vulgar, Interval, CompareSequencesParsable, SAM, BAM, NOFORMAT};
-
-#endif
diff --git a/libcpp/alignment/algorithms/alignment/AlignmentUtils.cpp b/libcpp/alignment/algorithms/alignment/AlignmentUtils.cpp
deleted file mode 100644
index 7912783..0000000
--- a/libcpp/alignment/algorithms/alignment/AlignmentUtils.cpp
+++ /dev/null
@@ -1,43 +0,0 @@
-#include <cassert>
-#include <vector>
-#include <stdint.h>
-#include <iostream>
-#include <ostream>
-#include <cstdlib>
-#include <fstream>
-#include "AlignmentUtils.hpp"
-
-using namespace blasr;
-
-int ComputeAlignmentScore(
- std::string &queryStr, std::string &textStr,
- int matchScores[5][5], int ins, int del) {
- DistanceMatrixScoreFunction<DNASequence, DNASequence> scoreFn(matchScores, ins, del);
- return ComputeAlignmentScore(queryStr, textStr, scoreFn);
-}
-
-int GetNumberWidth(unsigned int value) {
- // 0 has a width of 1.
- int width = 1;
- while (value / 10 > 0) {
- value = value / 10;
- ++width;
- }
- return width;
-}
-
-int ComputeDrift(Block &cur, Block &next) {
-
- int tGap = (next.tPos - cur.TEnd());
- int qGap = (next.qPos - cur.QEnd());
-
- int commonGap = 0;
-
- if (tGap > 0 and qGap > 0) {
- commonGap = abs(tGap - qGap);
- }
- tGap -= commonGap;
- qGap -= commonGap;
-
- return tGap - qGap;
-}
diff --git a/libcpp/alignment/algorithms/alignment/AlignmentUtils.hpp b/libcpp/alignment/algorithms/alignment/AlignmentUtils.hpp
deleted file mode 100644
index 0daa80f..0000000
--- a/libcpp/alignment/algorithms/alignment/AlignmentUtils.hpp
+++ /dev/null
@@ -1,139 +0,0 @@
-#ifndef _BLASR_ALIGNMENT_UTILS_HPP_
-#define _BLASR_ALIGNMENT_UTILS_HPP_
-
-#include <string>
-#include "DNASequence.hpp"
-#include "datastructures/alignment/Alignment.hpp"
-#include "algorithms/alignment/DistanceMatrixScoreFunction.hpp"
-
-enum AlignmentType {
- Local, // Standard Smith-Waterman
- Global, // Standard Needleman-Wuncsh
- QueryFit, // No gap penalties from query.
- TargetFit, // For when the query engulfs the target.
- Overlap, // No gap penalty at the beginning of
- // query, nor at the end of text **
- // not yet implemented for k-band **,
- FrontAnchored, // Require the alignment to align
- // pos 0,0 in the matrix
- EndAnchored, // Require the alignment to align
- // the pos m,n in the matrix
- // Score alignment types solely compute the score
- // of an alignment and do not store the actual
- // alignment itself. This is fast for filtering
- // potential alignments that may be re-aligned
- // later to store the actual alignment.
- Fit, // No gap penalties at the beginning nor ends of alignments.
- TSuffixQPrefix, // Same as overlap
- TPrefixQSuffix, // so that the order of the alignment does not have to be reversed
- ScoreGlobal,
- ScoreLocal,
- ScoreQueryFit,
- ScoreTargetFit,
- ScoreOverlap,
- ScoreFrontAnchored,
- ScoreEndAnchored,
- ScoreTSuffixQPrefix,
- ScoreTPrefixQSuffix,
- //
- // A LocalBoundaries alignment is in-between a
- // score-only and full-alignment. The full path
- // matrix is computed, but rather
- // than computing an alignment, simply the
- // (qStart, qLength), (tStart, tLength)
- // coordinates of the alignment are returned.
- //
- LocalBoundaries,
- //
- // A SignificanceLimited alignment is a banded
- // alignment that continues alignment until the
- // score drops below a certain threshold below
- // the maximum score.
- //
- SignificanceLimited
-};
-
-inline
-int ComputeAlignmentScore(
- std::string& queryStr, std::string& textStr,
- int matchScores[5][5], int ins, int del);
-
-template<typename T_ScoreFn>
-inline
-int ComputeAlignmentScore(
- std::string& queryStr, std::string& textStr,
- T_ScoreFn & scoreFn, bool useAffineScore = false);
-
-template<typename T_QuerySequence, typename T_TargetSequence, typename T_ScoreFn>
-int ComputeAlignmentScore(blasr::Alignment& alignment,
- T_QuerySequence& query,
- T_TargetSequence& text,
- T_ScoreFn& scoreFn,
- bool useAffinePenalty = false);
-
-template<typename T_QuerySequence, typename T_TargetSequence>
-int ComputeAlignmentScore(blasr::Alignment &alignment,
- T_QuerySequence &query,
- T_TargetSequence &text,
- int matchScores[5][5],
- int ins,
- int del);
-
-int GetNumberWidth(unsigned int value);
-
-template<typename T_Alignment>
-inline void PrintCompareSequencesAlignmentStats(T_Alignment &alignment, std::ostream &out);
-
-template<typename T_Alignment>
-inline int ReadCompareSequencesAlignmentStats(std::istream &in, T_Alignment &alignment);
-
-template<typename T_Alignment>
-inline int ReadCompSeqAlignment(std::istream &in, T_Alignment &alignment);
-
-/*
- * This should be changed to read any type of alignment, since templates are being
- * used.
- */
-inline void ReadCompSeqAlignments(std::string &compSeqAlignmentFileName, std::vector<blasr::CompSeqAlignment> &alignments);
-
-inline void PrintAlignmentStats(blasr::Alignment &alignment, std::ostream &out);
-
-template<typename T_QuerySequence, typename T_TargetSequence>
-void AppendGapCharacters(blasr::Gap &gap,
- T_QuerySequence &query, T_TargetSequence &text,
- DNALength &q, DNALength &t,
- char mismatchChar, char gapChar,
- std::string &textStr, std::string &alignStr, std::string &queryStr);
-
-template<typename T_Alignment, typename T_QuerySequence, typename T_TargetSequence>
-void CreateAlignmentStrings(T_Alignment &alignment,
- T_QuerySequence &query, T_TargetSequence &text,
- std::string &textStr, std::string &alignStr, std::string &queryStr, DNALength queryLength=0, DNALength textLength=0);
-
-template<typename T_Alignment, typename T_ScoreFn>
-void ComputeAlignmentStats(T_Alignment & alignment, Nucleotide* qSeq, Nucleotide * tSeq, T_ScoreFn & scoreFn, bool useAffineScore = false);
-
-template<typename T_Alignment>
-void ComputeAlignmentStats(T_Alignment &alignment, Nucleotide* qSeq, Nucleotide *tSeq, int matchMatrix[5][5], int ins, int del);
-
-template<typename T_Alignment>
-int ComputeDrift(T_Alignment &alignment);
-
-int ComputeDrift(blasr::Block &cur, blasr::Block &next);
-
-template<typename T_Alignment>
-void RemoveAlignmentPrefixGaps(T_Alignment &alignment);
-
-// QVsToCmpH5QVs converts the optional QVs read from a SAM file into something
-// that's ready to be written to the HDFArrays of a cmp.h5 file. This involves
-// two things: First, it needs to be converted from a std::string to a vector
-// of either chars or UChars. Second, it needs to have appropriate gap
-// characters inserted. The location of gaps if found using the byteAlignment.
-template<typename T>
-void QVsToCmpH5QVs(const std::string &fieldName, const std::string &qvs,
- const std::vector<unsigned char> &byteAlignment,
- bool isTag, std::vector<T> *gappedQVs);
-
-#include "AlignmentUtilsImpl.hpp"
-
-#endif // _BLASR_ALIGNMENT_UTILS_HPP_
diff --git a/libcpp/alignment/algorithms/alignment/AlignmentUtilsImpl.hpp b/libcpp/alignment/algorithms/alignment/AlignmentUtilsImpl.hpp
deleted file mode 100644
index 30f434b..0000000
--- a/libcpp/alignment/algorithms/alignment/AlignmentUtilsImpl.hpp
+++ /dev/null
@@ -1,548 +0,0 @@
-#ifndef _BLASR_ALIGNMENT_UTILS_IMPL_HPP_
-#define _BLASR_ALIGNMENT_UTILS_IMPL_HPP_
-
-#include <cassert>
-
-using namespace blasr;
-
-template<typename T_QuerySequence, typename T_TargetSequence, typename T_ScoreFn>
-int ComputeAlignmentScore(Alignment &alignment,
- T_QuerySequence &query,
- T_TargetSequence &text,
- T_ScoreFn &scoreFn,
- bool useAffinePenalty) {
- VectorIndex b, q, t, l, bi, gi;
- int alignmentScore = 0;
-
- for (b = 0; b < alignment.blocks.size(); b++ ) {
- for ((q = alignment.qPos + alignment.blocks[b].qPos,
- t = alignment.tPos + alignment.blocks[b].tPos,
- l = 0) ;
- l < alignment.blocks[b].length; q++, t++, l++) {
- alignmentScore += scoreFn.Match(text, t, query, q);
- }
- if (alignment.gaps.size() == alignment.blocks.size() + 1) {
- for (gi = 0; gi < alignment.gaps[b+1].size(); gi++) {
- if (alignment.gaps[b+1][gi].seq == Gap::Target) {
- if (useAffinePenalty) {
- alignmentScore += scoreFn.affineOpen + alignment.gaps[b+1][gi].length * scoreFn.affineExtend;
- }
- else {
- alignmentScore += alignment.gaps[b+1][gi].length * scoreFn.ins;
- }
- }
- else {
- if (useAffinePenalty) {
- alignmentScore += scoreFn.affineOpen + alignment.gaps[b+1][gi].length * scoreFn.affineExtend;
- }
- else {
- alignmentScore += alignment.gaps[b+1][gi].length * scoreFn.del;
- }
- }
- }
- }
- }
- return alignmentScore;
-}
-
-template<typename T_QuerySequence, typename T_TargetSequence>
-int ComputeAlignmentScore(blasr::Alignment &alignment,
- T_QuerySequence &query,
- T_TargetSequence &text,
- int matchScores[5][5],
- int ins,
- int del) {
- DistanceMatrixScoreFunction<DNASequence, DNASequence> scoreFn(matchScores, ins, del);
- return ComputeAlignmentScore(alignment, query, text, scoreFn);
-}
-
-template<typename T_ScoreFn>
-int ComputeAlignmentScore(std::string &queryStr, std::string &textStr, T_ScoreFn &scoreFn,
- bool useAffineScore) {
- if (queryStr.size() != textStr.size()) {
- std::cout << "Computing alignment score using invalid alignment string." << std::endl;
- std::cout << "Bailing out."<< std::endl;
- exit(1);
- }
- VectorIndex i;
- int score = 0;
- int alignStrLen = queryStr.size();
- for(i = 0; i < alignStrLen; i++) {
- if (queryStr[i] != '-' and
- textStr[i] != '-') {
- score += scoreFn.scoreMatrix[ThreeBit[(int)queryStr[i]]][ThreeBit[(int)textStr[i]]];
- }
- else {
- if (useAffineScore) {
- //
- // Compute affine gap scoring. For now this uses symmetric insertion/deletion penalties.
- //
- int gapEnd = i;
- while (gapEnd < queryStr.size() and gapEnd < textStr.size() and
- (queryStr[gapEnd] == '-' or textStr[gapEnd] == '-')) {
- ++gapEnd;
- }
- int gapLength = gapEnd - i;
- score += scoreFn.affineOpen + gapLength * scoreFn.affineExtend;
- //
- // Advance past gap -1, so that at the top of the for loop i
- // will be at the end of the gap.
- //
- i = gapEnd - 1;
- }
- else {
- //
- // Use non-affine gap scoring.
- //
- if (queryStr[i] == '-' and textStr[i] != '-') {
- score += scoreFn.del;
- }
- else if (queryStr[i] != '-' and textStr[i] == '-') {
- score += scoreFn.ins;
- }
- else {
- score += scoreFn.scoreMatrix[4][4];
- }
- }
- }
- }
- return score;
-}
-
-/*
- * This should be changed to read any type of alignment, since templates are being
- * used.
- */
-inline void ReadCompSeqAlignments(std::string &compSeqAlignmentFileName, std::vector<CompSeqAlignment> &alignments) {
- std::ifstream in;
- CrucialOpen(compSeqAlignmentFileName, in);
- CompSeqAlignment alignment;
- while (ReadCompSeqAlignment(in, alignment)) {
- alignments.push_back(alignment);
- }
-}
-
-inline void PrintAlignmentStats(Alignment &alignment, std::ostream &out) {
- out << " nMatch: " << alignment.nMatch << std::endl;
- out << " nMisMatch: " << alignment.nMismatch << std::endl;
- out << " nIns: " << alignment.nIns << std::endl;
- out << " nDel: " << alignment.nDel << std::endl;
- out << " %sim: " << alignment.pctSimilarity << std::endl;
- out << " Score: " << alignment.score << std::endl;
-}
-
-template<typename T_Alignment>
-inline void PrintCompareSequencesAlignmentStats(T_Alignment &alignment, std::ostream &out) {
- int lastBlock;
-
- lastBlock = alignment.blocks.size() -1;
-
- int qLength, tLength;
- if (lastBlock >= 0) {
- qLength = (alignment.blocks[lastBlock].qPos
- + alignment.blocks[lastBlock].length) ;
- tLength = (alignment.blocks[lastBlock].tPos
- + alignment.blocks[lastBlock].length);
- }
- else {
- qLength = tLength = 0;
- }
-
- //
- // First print the query
- //
- int alignmentQStart;
- if (lastBlock >= 0) {
- alignmentQStart = alignment.qPos + alignment.qAlignedSeqPos;
- }
- else {
- alignmentQStart = alignment.qAlignedSeqPos;
- }
- out << alignment.qName
- << " " << alignment.qLength
- << " " << alignmentQStart
- << " " << alignmentQStart + qLength;
-
- if (alignment.qStrand == 0) {
- out << " + ";
- }
- else {
- out << " - ";
- }
-
- int alignmentTStart;
- if (lastBlock >= 0) {
- alignmentTStart = alignment.tPos + alignment.tAlignedSeqPos;
- }
- else {
- alignmentTStart = 0;
- }
- out << " " << alignment.tName
- << " " << alignment.tLength;
- if (alignment.tStrand == 0) {
- out << " " << alignmentTStart
- << " " << alignmentTStart + tLength;
- out << " + ";
- }
- else {
- out << " " << alignment.tLength - (alignmentTStart + tLength)
- << " " << alignment.tLength - (alignmentTStart);
- out << " - ";
- }
-
- out << alignment.score
- << " " << alignment.nMatch
- << " " << alignment.nMismatch
- << " " << alignment.nIns
- << " " << alignment.nDel
- << " " << (int) alignment.mapQV
- << " ";
-}
-
-template<typename T_Alignment>
-inline int ReadCompareSequencesAlignmentStats(std::istream &in, T_Alignment &alignment) {
- int qEnd, tEnd;
- int qLength, tLength;
- char qStrand, tStrand;
- if (!(in >> alignment.qName )) return 0;
- if (!(in >> qLength)) return 0;
- if (!(in >> alignment.qPos)) return 0;
- if (!(in >> qEnd)) return 0;
- if (!(in >> qStrand)) return 0;
- if (!(in >> alignment.tName)) return 0;
- if (!(in >> tLength)) return 0;
- if (!(in >> alignment.tPos)) return 0;
- if (!(in >> tEnd)) return 0;
- if (!(in >> tStrand)) return 0;
- if (!(in >> alignment.score)) return 0;
- if (!(in >> alignment.nMatch)) return 0;
- if (!(in >> alignment.nMismatch)) return 0;
- if (!(in >> alignment.nIns)) return 0;
- if (!(in >> alignment.nDel)) return 0;
- return 1;
-}
-
-
-template<typename T_Alignment>
-inline int ReadCompSeqAlignment(std::istream &in, T_Alignment &alignment) {
- if (!ReadCompareSequencesAlignmentStats(in, alignment)) return 0;
- std::string alignStr;
- if (!(in >> alignment.qString)) return 0;
- if (!(in >> alignStr)) return 0;
- if (!(in >> alignment.tString)) return 0;
- std::string eol;
- std::getline(in, eol);
- return 1;
-}
-
-
-template<typename T_QuerySequence, typename T_TargetSequence>
-void AppendGapCharacters(Gap &gap,
- T_QuerySequence &query, T_TargetSequence &text,
- DNALength &q, DNALength &t,
- char mismatchChar, char gapChar,
- std::string &textStr, std::string &alignStr, std::string &queryStr) {
- int gp;
- for (gp = 0; gp < gap.length; gp++) {
- if (gap.seq == Gap::Query) {
- textStr.push_back(text[t]);
- alignStr.push_back(mismatchChar);
- queryStr.push_back(gapChar);
- t++;
- }
- else if (gap.seq == Gap::Target) {
- textStr.push_back(gapChar);
- alignStr.push_back(mismatchChar);
- queryStr.push_back(query[q]);
- q++;
- }
- }
-}
-
-template<typename T_Alignment, typename T_QuerySequence, typename T_TargetSequence>
-void CreateAlignmentStrings(T_Alignment &alignment,
- T_QuerySequence &query, T_TargetSequence &text,
- std::string &textStr, std::string &alignStr, std::string &queryStr,
- DNALength queryLength, DNALength textLength) {
- DNALength q = alignment.qPos;
- DNALength t = alignment.tPos;
- DNALength qPos, tPos;
- DNALength g;
- char mismatchChar = '*';
- char matchChar = '|';
- char gapChar = '-';
- char gapSeparationChar = ' ';
- if (alignment.blocks.size() == 0) {
- textStr = "";
- alignStr = "";
- queryStr = "";
- return;
- }
-
- if (alignment.gaps.size() == 0) {
- //
- // If there is no gap list, add the gaps as an offset here.
- //
- if (alignment.blocks[0].qPos > 0 or
- alignment.blocks[0].tPos > 0) {
- // commonGapLen should be the shorter gap.
- qPos = alignment.blocks[0].qPos;
- tPos = alignment.blocks[0].tPos;
- DNALength commonGapLen = qPos;
- if (commonGapLen > tPos) {
- commonGapLen = tPos;
- }
- for (g = 0; g < commonGapLen; g++ ) {
- textStr.push_back(text[t]);
- alignStr.push_back(mismatchChar);
- queryStr.push_back(query[q]);
- t++;
- q++;
- }
- tPos -= commonGapLen;
- qPos -= commonGapLen;
-
- //
- // one of tPos or qPos is now 0.
- // The other represents extra sequence
- // that should be output before starting the alignment
- DNALength p;
- for (p = 0; p < tPos; p++) {
- textStr.push_back(text[t]);
- alignStr.push_back(gapSeparationChar);
- queryStr.push_back(gapChar);
- t++;
- }
- for (p = 0; p < qPos; p++) {
- textStr.push_back(gapChar);
- alignStr.push_back(gapSeparationChar);
- queryStr.push_back(query[q]);
- q++;
- }
- }
- }
-
- //
- // Add gap characters if they are before the beginning of the alignment.
- // This shouldn't happen, but for some local alignments, it can.
- //
- DNALength b, bl, gi;
- if (alignment.gaps.size() > 0) {
- // The first gap is before the first block of characters.
- DNALength gi;
- for (gi = 0; gi < alignment.gaps[0].size(); gi++) {
- AppendGapCharacters(alignment.gaps[0][gi], query, text, q, t, mismatchChar, gapChar, textStr, alignStr, queryStr);
- }
- }
-
- for (b = 0; b < alignment.size() ; b++) {
- for (bl = 0; bl < alignment.blocks[b].length; bl++ ) {
- queryStr.push_back(query[q]);
- textStr.push_back(text[t]);
- assert(queryLength == 0 or q < queryLength);
- assert(textLength == 0 or t < textLength);
- if (TwoBit[query[q]] !=
- TwoBit[text[t]])
- alignStr.push_back(mismatchChar);
- else
- alignStr.push_back(matchChar);
- q++;
- t++;
- }
- //
- // There are no gaps to count after the last block, so
- // don't add the gapped characters for this.
- //
- if (alignment.blocks.size() == 0)
- continue;
- if (b == alignment.blocks.size() - 1) {
- continue;
- }
- if (alignment.gaps.size() > 0) {
- for (gi = 0; gi < alignment.gaps[b+1].size(); gi++) {
- AppendGapCharacters(alignment.gaps[b+1][gi], query, text, q, t, gapSeparationChar, gapChar, textStr, alignStr, queryStr);
- }
- }
- else {
-
-
- DNALength queryGapLen = (alignment.blocks[b+1].qPos -
- alignment.blocks[b].qPos - alignment.blocks[b].length);
- DNALength textGapLen = (alignment.blocks[b+1].tPos -
- alignment.blocks[b].tPos - alignment.blocks[b].length);
-
- if (queryGapLen > 0 or textGapLen > 0) {
- // commonGapLen should be the shorter gap.
- DNALength commonGapLen = queryGapLen;
- if (queryGapLen > textGapLen) {
- commonGapLen = textGapLen;
- }
- textGapLen -= commonGapLen;
- queryGapLen -= commonGapLen;
-
- for (g = 0; g < queryGapLen; g++, q++ ){
- textStr.push_back(gapChar);
- alignStr.push_back(gapSeparationChar);
- queryStr.push_back(query[q]);
- }
- for (g = 0; g < textGapLen; g++, t++ ){
- textStr.push_back(text[t]);
- alignStr.push_back(gapSeparationChar);
- queryStr.push_back(gapChar);
-
- }
-
- for (g = 0; g < commonGapLen; g++ ) {
- textStr.push_back(text[t]);
- alignStr.push_back(gapSeparationChar);
- queryStr.push_back(query[q]);
- t++;
- q++;
- }
- }
- }
- }
-}
-
-
-template<typename T_Alignment, typename T_ScoreFn>
-void ComputeAlignmentStats(T_Alignment & alignment, Nucleotide* qSeq, Nucleotide * tSeq, T_ScoreFn & scoreFn, bool useAffineScore) {
- int qp = 0, tp = 0;
- int nMatch = 0, nMismatch = 0, nIns =0, nDel = 0;
- float pctSimilarity;
- std::string textStr, alignStr, queryStr;
- CreateAlignmentStrings(alignment, qSeq, tSeq, textStr, alignStr, queryStr);
- int i;
- int alignLength = textStr.size();
-
- for (i = 0; i < alignLength; i++ ) {
- if ((textStr[i] != '-') and (queryStr[i] != '-')) {
- int ti = (int)textStr[i];
- int qi = (int)queryStr[i];
- if (ThreeBit[ti] == ThreeBit[qi]) {
- nMatch++;
- }
- else {
- nMismatch++;
- }
- tp++;
- qp++;
- }
- else if (textStr[i] == '-' and queryStr[i] != '-') {
- nIns++;
- qp++;
- }
- else if (queryStr[i] == '-' and textStr[i] != '-') {
- nDel++;
- tp++;
- }
- }
- if (tp + qp > 0) {
- if (textStr.size() + queryStr.size() > 0) {
- pctSimilarity = (nMatch*2.0) / (textStr.size() + queryStr.size()) * 100;
- }
- else {
- pctSimilarity = 0;
- }
- }
- else {
- pctSimilarity = 0;
- }
-
- alignment.score = ComputeAlignmentScore(queryStr, textStr, scoreFn);
- alignment.nMatch = nMatch;
- alignment.nMismatch = nMismatch;
- alignment.nDel = nDel;
- alignment.nIns = nIns;
- alignment.pctSimilarity = pctSimilarity;
-}
-
-template<typename T_Alignment>
-void ComputeAlignmentStats(T_Alignment &alignment, Nucleotide* qSeq, Nucleotide *tSeq, int matchMatrix[5][5], int ins, int del) {
- DistanceMatrixScoreFunction<DNASequence, DNASequence> scoreFn(matchMatrix, ins, del);
- ComputeAlignmentStats(alignment, qSeq, tSeq, scoreFn);
-}
-
-
-
-template<typename T_Alignment>
-int ComputeDrift(T_Alignment &alignment) {
- VectorIndex b;
- int qGap = 0, tGap = 0, commonGap = 0;
- int drift = 0;
- int maxDrift = 0;
- int driftBetweenBlocks;
- if (alignment.blocks.size() == 0)
- return 0;
- for (b = 0; b < alignment.blocks.size() - 1; b++) {
- driftBetweenBlocks = ComputeDrift(alignment.blocks[b], alignment.blocks[b+1]);
- drift += driftBetweenBlocks;
- if (abs(drift) > maxDrift)
- maxDrift = abs(drift);
- }
- return maxDrift;
-}
-
-template<typename T_Alignment>
-void RemoveAlignmentPrefixGaps(T_Alignment &alignment) {
- if (alignment.gaps.size() == 0) {
- return;
- }
-
- unsigned int g;
- int tStart = 0, qStart = 0;
- for (g = 0; g < alignment.gaps[0].size(); g++) {
- if (alignment.gaps[0][g].seq == Gap::Target) {
- qStart += alignment.gaps[0][g].length;
- }
- else if (alignment.gaps[0][g].seq == Gap::Query) {
- tStart += alignment.gaps[0][g].length;
- }
- }
- int b;
- int nBlocks;
- for (b = 0, nBlocks = alignment.blocks.size(); b < nBlocks; b++) {
- alignment.blocks[b].qPos -= qStart;
- alignment.blocks[b].tPos -= tStart;
- }
- alignment.gaps[0].clear();
- alignment.tPos += tStart;
- alignment.qPos += qStart;
-}
-
-template<typename T>
-void QVsToCmpH5QVs(const std::string &qvs,
- const std::vector<unsigned char> &byteAlignment,
- bool isTag,
- std::vector<T> *gappedQVs) {
- gappedQVs->clear();
-
- unsigned int qv_i = 0;
-
- // QVs and tags get different values at gaps in the read
- char tagGapChar = 'N';
- UChar qvGapChar = 255;
-
- for (int i=0; i<byteAlignment.size(); i++) {
- if (byteAlignment[i] >> 4 == 0) { //Look at upper bits to get query char
- if (isTag) {
- gappedQVs->push_back(tagGapChar);
- } else {
- gappedQVs->push_back(qvGapChar);
- }
- } else {
- if (isTag) {
- //std::cout << "Pushing back " << (T)qvs[qv_i] << " for tag " << qvs[qv_i] << std::endl;
- gappedQVs->push_back((T)qvs[qv_i]);
- } else {
- //std::cout << "Pushing back " << (T)qvs[qv_i] - FASTQSequence::charToQuality << " for QV " << qvs[qv_i] << std::endl;
- gappedQVs->push_back((T)qvs[qv_i] - FASTQSequence::charToQuality);
- }
-
- qv_i++;
- }
- }
-
- assert(gappedQVs->size() == byteAlignment.size());
-}
-#endif
diff --git a/libcpp/alignment/algorithms/alignment/BaseScoreFunction.cpp b/libcpp/alignment/algorithms/alignment/BaseScoreFunction.cpp
deleted file mode 100644
index 339b454..0000000
--- a/libcpp/alignment/algorithms/alignment/BaseScoreFunction.cpp
+++ /dev/null
@@ -1,11 +0,0 @@
-#include "BaseScoreFunction.hpp"
-
-BaseScoreFunction::BaseScoreFunction(int insP, int delP, int subPriorP,
- int delPriorP, int affineExtensionP, int affineOpenP) {
- ins = insP;
- del = delP;
- substitutionPrior = subPriorP;
- globalDeletionPrior = delPriorP;
- affineExtend = affineExtensionP;
- affineOpen = affineOpenP;
-}
diff --git a/libcpp/alignment/algorithms/alignment/BaseScoreFunction.hpp b/libcpp/alignment/algorithms/alignment/BaseScoreFunction.hpp
deleted file mode 100644
index 1d5c35c..0000000
--- a/libcpp/alignment/algorithms/alignment/BaseScoreFunction.hpp
+++ /dev/null
@@ -1,17 +0,0 @@
-#ifndef _BLASR_BASE_SCORE_FUNCTION_HPP_
-#define _BLASR_BASE_SCORE_FUNCTION_HPP_
-
-class BaseScoreFunction {
- public:
- int ins;
- int del;
- int substitutionPrior;
- int globalDeletionPrior;
- int affineExtend;
- int affineOpen;
-
- BaseScoreFunction(int insP = 0, int delP = 0, int subPriorP = 0,
- int delPriorP = 0, int affineExtensionP = 0, int affineOpenP = 0);
-};
-
-#endif // _BLASR_BASE_SCORE_FUNCTION_HPP_`
diff --git a/libcpp/alignment/algorithms/alignment/DistanceMatrixScoreFunction.hpp b/libcpp/alignment/algorithms/alignment/DistanceMatrixScoreFunction.hpp
deleted file mode 100644
index ed932ab..0000000
--- a/libcpp/alignment/algorithms/alignment/DistanceMatrixScoreFunction.hpp
+++ /dev/null
@@ -1,40 +0,0 @@
-#ifndef _BLASR_DISTANCE_MATRIX_SCORE_FUNCTION_HPP_
-#define _BLASR_DISTANCE_MATRIX_SCORE_FUNCTION_HPP_
-
-#include "BaseScoreFunction.hpp"
-#include "ScoreMatrices.hpp"
-
-template<typename T_RefSequence, typename T_QuerySequence>
-class DistanceMatrixScoreFunction : public BaseScoreFunction {
-public:
- int scoreMatrix[5][5];
- DistanceMatrixScoreFunction();
-
- DistanceMatrixScoreFunction(int scoreMatrixP[5][5], int insertionP, int deletionP);
-
- void InitializeScoreMatrix(int scoreMatrixP[5][5]);
-
- int Deletion(T_RefSequence &seq, DNALength pos, T_QuerySequence &querySeq, DNALength queryPos);
-
- int Insertion(T_RefSequence &seq, DNALength pos, T_QuerySequence &querySeq, DNALength queryPos);
-
- int Deletion(T_RefSequence &seq, DNALength pos);
-
- int Match(T_RefSequence &ref, DNALength refPos, T_QuerySequence &query, DNALength queryPos);
-
- //
- // Define the score function on dereferenced pointers for speed.
- //
- int Match(Nucleotide ref, Nucleotide query);
-
- int Insertion(T_QuerySequence &seq, DNALength pos);
-
- float NormalizedMatch(T_RefSequence &ref, DNALength refPos, T_QuerySequence &query, DNALength queryPos);
- float NormalizedInsertion(T_RefSequence &ref, DNALength refPos, T_QuerySequence &query, DNALength queryPos);
- float NormalizedDeletion(T_RefSequence &ref, DNALength refPos, T_QuerySequence &query, DNALength queryPos);
-
-};
-
-#include "DistanceMatrixScoreFunctionImpl.hpp"
-
-#endif // _BLASR_DISTANCE_MATRIX_SCORE_FUNCTION_HPP_
diff --git a/libcpp/alignment/algorithms/alignment/DistanceMatrixScoreFunctionImpl.hpp b/libcpp/alignment/algorithms/alignment/DistanceMatrixScoreFunctionImpl.hpp
deleted file mode 100644
index 97bacad..0000000
--- a/libcpp/alignment/algorithms/alignment/DistanceMatrixScoreFunctionImpl.hpp
+++ /dev/null
@@ -1,96 +0,0 @@
-#ifndef _BLASR_DISTANCE_MATRIX_SCORE_FUNCTION_IMPL_HPP_
-#define _BLASR_DISTANCE_MATRIX_SCORE_FUNCTION_IMPL_HPP_
-#include <string>
-#include <iostream>
-#include <stdint.h>
-#include <string>
-#include <cstring>
-#include <ostream>
-#include "Types.h"
-#include "NucConversion.hpp"
-#include "Enumerations.h"
-#include "DNASequence.hpp"
-#include "FASTASequence.hpp"
-#include "FASTQSequence.hpp"
-#include "DistanceMatrixScoreFunction.hpp"
-
-template<typename T_RefSequence, typename T_QuerySequence>
-void DistanceMatrixScoreFunction<T_RefSequence,T_QuerySequence>::InitializeScoreMatrix(int scoreMatrixP[5][5]) {
- int i, j;
- for (i = 0; i < 5; i++ ){
- for (j = 0; j < 5; j++ ){
- scoreMatrix[i][j] = scoreMatrixP[i][j];
- }
- }
-}
-
-template<typename T_RefSequence, typename T_QuerySequence>
-DistanceMatrixScoreFunction<T_RefSequence,T_QuerySequence>::DistanceMatrixScoreFunction() : BaseScoreFunction() {
-}
-
-template<typename T_RefSequence, typename T_QuerySequence>
-DistanceMatrixScoreFunction<T_RefSequence,T_QuerySequence>::DistanceMatrixScoreFunction(int scoreMatrixP[5][5], int insertionP, int deletionP) : BaseScoreFunction() {
- InitializeScoreMatrix(scoreMatrixP);
- ins = insertionP;
- del = deletionP;
-}
-
-template<typename T_RefSequence, typename T_QuerySequence>
-int DistanceMatrixScoreFunction<T_RefSequence,T_QuerySequence>::Deletion(
- T_RefSequence &seq, DNALength pos, T_QuerySequence &querySeq,
- DNALength queryPos) {
- return del;
-}
-
-template<typename T_RefSequence, typename T_QuerySequence>
-int DistanceMatrixScoreFunction<T_RefSequence,T_QuerySequence>::Insertion(
- T_RefSequence &seq, DNALength pos, T_QuerySequence &querySeq,
- DNALength queryPos) {
- return ins;
-}
-
-template<typename T_RefSequence, typename T_QuerySequence>
-int DistanceMatrixScoreFunction<T_RefSequence,T_QuerySequence>::Deletion(
- T_RefSequence &seq, DNALength pos) {
- return del;
-}
-
-
-template<typename T_RefSequence, typename T_QuerySequence>
-int DistanceMatrixScoreFunction<T_RefSequence,T_QuerySequence>::Match(
- T_RefSequence &ref, DNALength refPos, T_QuerySequence &query,
- DNALength queryPos) {
- return scoreMatrix[ThreeBit[ref[refPos]]][ThreeBit[query[queryPos]]];
-}
-
-//
-// Define the score function on dereferenced pointers for speed.
-//
-template<typename T_RefSequence, typename T_QuerySequence>
-int DistanceMatrixScoreFunction<T_RefSequence,T_QuerySequence>::Match(
- Nucleotide ref, Nucleotide query) {
- return scoreMatrix[ThreeBit[ref]][ThreeBit[query]];
-}
-
-template<typename T_RefSequence, typename T_QuerySequence>
-int DistanceMatrixScoreFunction<T_RefSequence,T_QuerySequence>::Insertion(
- T_QuerySequence &seq, DNALength pos) {
- return ins;
-}
-
-template<typename T_RefSequence, typename T_QuerySequence>
-float
-DistanceMatrixScoreFunction<T_RefSequence,T_QuerySequence>
-::NormalizedMatch(T_RefSequence &ref, DNALength refPos,
- T_QuerySequence &query, DNALength queryPos) {return 0;}
-
-template<typename T_RefSequence, typename T_QuerySequence>
-float DistanceMatrixScoreFunction<T_RefSequence,T_QuerySequence>
-::NormalizedInsertion(T_RefSequence &ref, DNALength refPos,
- T_QuerySequence &query, DNALength queryPos) {return 0;}
-
-template<typename T_RefSequence, typename T_QuerySequence>
-float DistanceMatrixScoreFunction<T_RefSequence,T_QuerySequence>::NormalizedDeletion(T_RefSequence &ref, DNALength refPos, T_QuerySequence &query, DNALength queryPos) {return 0;}
-
-
-#endif // _BLASR_DISTANCE_MATRIX_SCORE_FUNCTION_IMPL_HPP_
diff --git a/libcpp/alignment/algorithms/alignment/ExtendAlign.cpp b/libcpp/alignment/algorithms/alignment/ExtendAlign.cpp
deleted file mode 100644
index 1a17664..0000000
--- a/libcpp/alignment/algorithms/alignment/ExtendAlign.cpp
+++ /dev/null
@@ -1,79 +0,0 @@
-#include "ExtendAlign.hpp"
-
-RCToIndex::RCToIndex() {
- qStart = 0; tStart = 0;
- band = middleCol = nCols = 0;
-}
-
-int RCToIndex::operator()(int r, int c, int &index) {
- //
- // First do some error checking on the row and column to see if it
- // is within the band.
- //
- if (r < qStart) { return 0; }
- if (c < tStart) { return 0; }
- r -= qStart;
- c -= tStart;
- if (std::abs(r-c) > band) { return 0; } // outside band range.
- if (c < 0) { return 0; }
-
- if (middleCol - (r - c) >= nCols) { return 0; }
- index = (r*nCols) + (middleCol - (r - c));
- return 1;
-}
-
-int BaseIndex::QNotAtSeqBoundary(int q) {
- return q != queryAlignLength;
-}
-int BaseIndex::TNotAtSeqBoundary(int t) {
- return t != refAlignLength;
-}
-int BaseIndex::QAlignLength() {
- return queryAlignLength;
-}
-
-int BaseIndex::TAlignLength() {
- return refAlignLength;
-}
-
-
-int ForwardIndex::QuerySeqPos(int q) {
- return queryPos + q;
-}
-
-int ForwardIndex::RefSeqPos(int t) {
- return refPos + t;
-}
-
-int ForwardIndex::GetQueryStartPos(int startQ, int endQ) {
- return queryPos + startQ + 1;
-}
-
-int ForwardIndex::GetRefStartPos(int startT, int endT) {
- return refPos + startT + 1;
-}
-
-void ForwardIndex::OrderArrowVector(std::vector<Arrow> &mat) {
- reverse(mat.begin(), mat.end());
-}
-
-
-int ReverseIndex::QuerySeqPos(int q) {
- return queryPos - q;
-}
-
-int ReverseIndex::RefSeqPos(int t) {
- return refPos - t;
-}
-
-int ReverseIndex::GetQueryStartPos(int startQ, int endQ) {
- return queryPos - (endQ-1);
-}
-
-int ReverseIndex::GetRefStartPos(int startT, int endT) {
- return refPos - (endT-1);
-}
-
-void ReverseIndex::OrderArrowVector(std::vector<Arrow> &mat) {
-}
-
diff --git a/libcpp/alignment/algorithms/alignment/ExtendAlign.hpp b/libcpp/alignment/algorithms/alignment/ExtendAlign.hpp
deleted file mode 100644
index a5430bc..0000000
--- a/libcpp/alignment/algorithms/alignment/ExtendAlign.hpp
+++ /dev/null
@@ -1,416 +0,0 @@
-#ifndef _BLASR_EXTEND_ALIGN_HPP_
-#define _BLASR_EXTEND_ALIGN_HPP_
-
-#include <vector>
-#include <algorithm>
-#include "defs.h"
-#include "KBandAlign.hpp"
-#include "NucConversion.hpp"
-#include "matrix/FlatMatrix.hpp"
-#include "datastructures/alignment/Alignment.hpp"
-
-class RCToIndex {
-public:
- int qStart, tStart;
- int middleCol;
- int band;
- int nCols;
-
- RCToIndex();
-
- int operator()(int r, int c, int &index);
-};
-
-class BaseIndex {
-public:
- int queryPos, refPos;
- int queryAlignLength, refAlignLength;
-
- int QNotAtSeqBoundary(int q);
-
- int TNotAtSeqBoundary(int t);
-
- int QAlignLength();
-
- int TAlignLength();
-};
-
-class ForwardIndex : public BaseIndex {
-public:
-
- int QuerySeqPos(int q);
-
- int RefSeqPos(int t);
-
- int GetQueryStartPos(int startQ, int endQ);
-
- int GetRefStartPos(int startT, int endT);
-
- void OrderArrowVector(std::vector<Arrow> &mat);
-};
-
-
-class ReverseIndex : public BaseIndex {
-public:
-
- int QuerySeqPos(int q);
-
- int RefSeqPos(int t);
-
- int GetQueryStartPos(int startQ, int endQ);
-
- int GetRefStartPos(int startT, int endT);
-
- void OrderArrowVector(std::vector<Arrow> &mat);
-};
-
-template<typename T_Alignment,
- typename T_ScoreFn,
- typename T_QuerySeq,
- typename T_RefSeq,
- typename T_Index>
- int ExtendAlignment(T_QuerySeq &querySeq, int queryPos,
- T_RefSeq &refSeq, int refPos,
- int k,
- std::vector<int> &scoreMat,
- std::vector<Arrow> &pathMat,
- T_Alignment &alignment,
- T_ScoreFn &scoreFn,
- T_Index &index,
- int minExtendNBases=1, // Require that there
- // are more than one
- // base to align.
- int maxNDrops=2 // A drop is a row where
- // the alignment is
- // extended without
- // increasing the alignment
- // score. maxnDrops is the
- // maximum number of times
- // that one may have before
- // terminating the alignment
- //
- ) {
- //
- // Try extending an alignment in the forward direction as long the
- // maximum score that is extended is above a threshold above the
- // initial score. This dynamically grows the alignment matrices as
- // the alignment is extended (or the limits of the alignment
- // matrices since reusable buffers are used).
- //
-
- int nCols = 2 * k + 1 + 1; // 2*k is for search space, +1 is for the
- // middle band, and the last +1 is for the
- // boundary conditions at the beginning of
- // the array.
-
- RCToIndex rcToIndex;
- rcToIndex.band = k;
- rcToIndex.nCols = nCols;
- rcToIndex.middleCol = k+2-1;
-
- if (index.queryAlignLength < minExtendNBases or
- index.refAlignLength < minExtendNBases) {
- //
- // One of the sequences isn't long enough to even try to extend,
- // just bail with an empty alignment.
- //
- return 0;
- }
-
- //
- // Preallocate arrays to be at least k long. The full matrix may
- // not be loaded.
- //
- int matSize = nCols * (k+1);
- if (scoreMat.size() < nCols * (k+1)) {
- scoreMat.resize(nCols * (k+1));
- pathMat.resize(nCols * (k+1));
- }
-
- //
- // Initialize boundary conditions.
- //
-
- int q, t;
- // Initialize first column for insertions.
- int firstIndex;
- fill(scoreMat.begin(), scoreMat.begin() + matSize, 0);
- fill(pathMat.begin(), pathMat.begin() + matSize, NoArrow);
- rcToIndex(0, 0, firstIndex);
- scoreMat[firstIndex] = 0;
- pathMat[firstIndex] = NoArrow;
-
- // Initialize insertion penalties.
- t = 0;
- int i;
- int pi;
- for (q = 1; q <= k and index.QNotAtSeqBoundary(q-1); q++) {
- bool res = rcToIndex(q, t, i);
- assert(res);
- res = rcToIndex(q-1, t, pi);
- int qSeqPos = index.QuerySeqPos(q-1);
- scoreMat[i] = scoreMat[pi] + scoreFn.Insertion(querySeq, qSeqPos);
- pathMat[i] = Up;
- // cout << "initializing insertion gap penalty for " << q << " " << refPos-1 << " " << i << " " << scoreMat[i] << endl;
- }
-
-
- // Initialize the first row for deletions.
- q = 0;
-
- for (t = 1; t <= k and index.TNotAtSeqBoundary(t-1); t++) {
- bool res = rcToIndex(q, t, i);
- assert(res);
- int previ;
- res = rcToIndex(q,t-1,previ);
-
- int qSeqPos = index.QuerySeqPos(0);
- scoreMat[i] = scoreMat[previ] + scoreFn.Deletion(querySeq, qSeqPos);
- pathMat[i] = Left;
- // cout << "initializing deletion gap penalty for " << ((int)queryPos)-1 << " " << t << " " << i << " " << scoreMat[i] << endl;
- }
- /* PrintFlatMatrix(&scoreMat[0], k , nCols, cout);
- cout << endl;
- PrintFlatMatrix(&pathMat[0], k, nCols, cout);
- cout << endl;
- */
- int nDrops = 0;
- int prevRowMinScore = INF_INT;
- int globalMinScore = INF_INT;
- int globalMinScoreQPos = 0;
- int globalMinScoreTPos = 0;
-
- int curIndex = -1;
-
- int maxAlignLength = std::min(index.QAlignLength(), index.TAlignLength()) + maxNDrops;
-
- for (q = 1; (index.QNotAtSeqBoundary(q-1) and
- nDrops < maxNDrops and
- q < maxAlignLength);
- q++ ) {
-
- //
- // Grow the path and score matrices by another row if this has
- // extended beyond their current capacity.
- //
- if ((q+1) * nCols > scoreMat.size()) {
- scoreMat.resize((q+1)*nCols);
- pathMat.resize((q+1)*nCols);
- }
-
- //
- // Now score the latest row.
- //
- int curRowMinScore = INF_INT;
- int diagLength = q;
-
- int tStart = std::max((int) 1, ((int)diagLength) - k);
- int tEnd = std::min((int) (diagLength + k +1), index.TAlignLength() + 1 );
- int qSeqPos, tSeqPos;
- for (t = tStart; t < std::min(tEnd, maxAlignLength); t++) {
- int insIndex, delIndex, matchIndex;
-
- bool hasInsIndex = false, hasDelIndex = false, hasMatchIndex = false, hasCurIndex = false;
-
- hasCurIndex = rcToIndex(q, t, curIndex);
- assert(hasCurIndex);
-
- hasDelIndex = rcToIndex(q, t - 1, delIndex);
- hasInsIndex = rcToIndex(q - 1, t, insIndex);
- hasMatchIndex = rcToIndex(q-1, t-1, matchIndex);
-
- int insScore, delScore, matchScore;
- delScore = INF_INT;
- insScore = INF_INT;
- matchScore = INF_INT;
- // cout << "ins index: " << insIndex << " del: " << delIndex << " match index " << matchIndex << endl;
- qSeqPos = index.QuerySeqPos(q-1); // The offset is to allow for the boundary buffer.
- tSeqPos = index.RefSeqPos(t-1); // ditto.
- /* if (scoreMat[insIndex] == -1) {
- cout << "bleh" << endl;
- }
- if (scoreMat[matchIndex] == -1) {
- cout << "bleh" << endl;
- }
- if (scoreMat[delIndex] == -1) {
- cout << "bleh" << endl;
- }
-
- if (scoreFn.Insertion(refSeq, (DNALength) tSeqPos, querySeq, (DNALength) qSeqPos) == -1) {
- cout << "bleh" << endl;
- }
- if (scoreFn.Deletion(refSeq, (DNALength) tSeqPos, querySeq, (DNALength) qSeqPos) == -1) {
- cout << "ugh" << endl;
- }
- if ( scoreFn.Match(refSeq, (DNALength) tSeqPos, querySeq, (DNALength) qSeqPos) == -1) {
- cout <<" gah" << endl;
- }*/
-
- if (hasInsIndex) {
- insScore = scoreMat[insIndex] + scoreFn.Insertion(refSeq, (DNALength) tSeqPos, querySeq, (DNALength) qSeqPos);
- }
- if (hasDelIndex) {
- delScore = scoreMat[delIndex] + scoreFn.Deletion(refSeq, (DNALength) tSeqPos, querySeq, (DNALength) qSeqPos);
- }
- if (hasMatchIndex) {
- matchScore = scoreMat[matchIndex] + scoreFn.Match(refSeq, (DNALength) tSeqPos, querySeq, (DNALength) qSeqPos);
- }
- /* cout << "ins score: " << insScore << "[" << scoreMat[insIndex] << "] del score " << delScore
- << " [" << scoreMat[delIndex] << "] match score " << matchScore
- << " [" << scoreMat[matchIndex] << "] qchar " << (int) querySeq.seq[qSeqPos] << " tchar " << (int) refSeq.seq[tSeqPos] << endl;*/
- int minScore = std::min(matchScore, delScore);
- minScore = std::min(minScore, insScore);
- scoreMat[curIndex] = minScore;
- // cout << "extend: " << qSeqPos << " " << tSeqPos << " " << minScore << endl;
- if (minScore != INF_INT) {
- if (minScore == insScore) { pathMat[curIndex] = Up; }
- if (minScore == delScore) { pathMat[curIndex] = Left; }
- if (minScore == matchScore) { pathMat[curIndex] = Diagonal; }
- }
- else {
- pathMat[curIndex] = NoArrow;
- }
-
- assert(pathMat[curIndex] != NoArrow);
- if (minScore < curRowMinScore) {
- curRowMinScore = minScore;
- }
- int nRows = q+1;
- if (minScore < globalMinScore) {
- globalMinScore = minScore;
- globalMinScoreQPos = q;
- globalMinScoreTPos = t;
- }
-
- }
-
- if (curRowMinScore > prevRowMinScore) {
- nDrops++;
- }
- prevRowMinScore = curRowMinScore;
- }
-
- int nRows = q;
-
- q = globalMinScoreQPos;
- t = globalMinScoreTPos;
- std::vector<Arrow> optAlignment;
-
- rcToIndex(q,t,i);
- //
- // When the optimal score is on a cell with NoArrow, there is no
- // good alignment. Only try and trace an alignment out if the path
- // starts on a good alignment.
- //
- if (pathMat[i] != NoArrow) {
- while(q > 0 or t > 0) {
- int res;
- res = rcToIndex(q, t, i);
- assert(res != 0);
- Arrow arrow = pathMat[i];
-
- optAlignment.push_back(pathMat[i]);
- if (pathMat[i] == NoArrow) {
- assert(pathMat[i] != NoArrow);
- }
- if (arrow == Diagonal) {
- q--;
- t--;
- }
- else if (arrow == Left) {
- t--;
- }
- else if (arrow == Up) {
- q--;
- }
- }
- }
-
- index.OrderArrowVector(optAlignment);
- alignment.ArrowPathToAlignment(optAlignment);
- alignment.qPos = index.GetQueryStartPos(q, globalMinScoreQPos);
- alignment.tPos = index.GetRefStartPos(t, globalMinScoreTPos);
-
- return globalMinScore;
- }
-
-template<typename T_Alignment, typename T_ScoreFn, typename T_QuerySeq, typename T_RefSeq>
-int ExtendAlignmentForward(T_QuerySeq &querySeq, int queryPos,
- T_RefSeq &refSeq, int refPos,
- int k,
- std::vector<int> &scoreMat,
- std::vector<Arrow> &pathMat,
- T_Alignment &alignment,
- T_ScoreFn &scoreFn,
- int minExtendNBases=1, // Require that there
- // are more than one
- // base to align.
- int maxNDrops=2 // A drop is a row where
- // the alignment is
- // extended without
- // increasing the alignment
- // score. maxnDrops is the
- // maximum number of times
- // that one may have before
- // terminating the alignment
- //
- ) {
-
- ForwardIndex forwardIndex;
- forwardIndex.queryPos = queryPos;
- forwardIndex.refPos = refPos;
- //
- // The alignment does not include queryPos nor refPos.
- //
- forwardIndex.queryAlignLength = querySeq.length - queryPos;
- forwardIndex.refAlignLength = refSeq.length - refPos;
- int alignScore;
- alignScore= ExtendAlignment(querySeq, queryPos,
- refSeq, refPos,
- k,
- scoreMat, pathMat,
- alignment, scoreFn, forwardIndex, minExtendNBases, maxNDrops);
- alignment.qPos = queryPos;
- alignment.tPos = refPos;
- return alignScore;
-}
-
-template<typename T_Alignment, typename T_ScoreFn, typename T_QuerySeq, typename T_RefSeq>
-int ExtendAlignmentReverse(T_QuerySeq &querySeq, int queryPos,
- T_RefSeq &refSeq, int refPos,
- int k,
- std::vector<int> &scoreMat,
- std::vector<Arrow> &pathMat,
- T_Alignment &alignment,
- T_ScoreFn &scoreFn,
- int minExtendNBases=1, // Require that there
- // are more than one
- // base to align.
- int maxNDrops=2 // A drop is a row where
- // the alignment is
- // extended without
- // increasing the alignment
- // score. maxnDrops is the
- // maximum number of times
- // that one may have before
- // terminating the alignment
- //
- ) {
-
- ReverseIndex reverseIndex;
- reverseIndex.queryPos = queryPos-1;
- reverseIndex.refPos = refPos-1;
- reverseIndex.queryAlignLength = queryPos;
- reverseIndex.refAlignLength = refPos;
- int alignScore;
- alignScore = ExtendAlignment(querySeq, queryPos,
- refSeq, refPos,
- k,
- scoreMat, pathMat,
- alignment, scoreFn, reverseIndex, minExtendNBases, maxNDrops);
-
- return alignScore;
-
-}
-
-#endif // _BLASR_EXTEND_ALIGN_HPP_
diff --git a/libcpp/alignment/algorithms/alignment/FullQVAlign.hpp b/libcpp/alignment/algorithms/alignment/FullQVAlign.hpp
deleted file mode 100644
index a49395c..0000000
--- a/libcpp/alignment/algorithms/alignment/FullQVAlign.hpp
+++ /dev/null
@@ -1,132 +0,0 @@
-#ifndef _BLASR_FULL_QV_ALIGN_HPP_
-#define _BLASR_FULL_QV_ALIGN_HPP_
-
-#include "matrix/Matrix.hpp"
-#include "FASTQSequence.hpp"
-#include "FASTASequence.hpp"
-
-template<typename T_Query, typename T_Reference>
-double FullQVAlign(T_Query &query,
- T_Reference &target,
- Matrix<double> &alignProb) {
-
- alignProb.Resize(query.length + 1, target.length + 1);
- alignProb.Initialize(0);
-
- DNALength q, t;
-
- if (query.length == 0 or target.length == 0) { return 0; }
-
- // Initialize boundaries of ins/del/match probability matrices.
- q = 0;
- VectorIndex numCols = target.length + 1;
- VectorIndex numRows = query.length + 1;
- alignProb[0][0] = 1;
- for (t = 1; t < numCols; t++ ) {
- // cannot match to a gap
- alignProb[0][t] = log(target.GetInsertionQV(t-1)) + alignProb[0][t-1];
- }
-
- for (q = 1; q < numRows; q++) {
- alignProb[q][0] = log(query.GetInsertionQV(q-1)) + alignProb[q-1][0];
- }
-
- // Now compute probability of alignment with the Forward algorithm.
- for (q = 1; q < numRows; q++) {
- for (t = 1; t < numCols; t++) {
- // First compute p_ins[q,t] as transitions from match matrix
-
- double logMatchedPulseProb = 0;
- double logInsertedPulseProb = 0;
- double logDeletedPulseProb = 0;
-
-
- //
- // Use inefficient coding for now.
- //
-
- // Compute match, the bases are either the same, in which case
- // this is simply the product of the probabilities of the two
- // matches. Otherwise, either one of the pulses may be correct,
- // and the probability is the union of the two cases.
- //
-
- double matchedPulseProb;
-
- if (query.seq[q-1] == target.seq[t-1]) {
- matchedPulseProb = (1-query.GetSubstitutionQV(q-1)) * (1-target.GetSubstitutionQV(t-1));
- }
- else {
- matchedPulseProb = (query.GetSubstitutionQV(q-1)/3.0)*(1-target.GetSubstitutionQV(t-1)) +
- ((1-query.GetSubstitutionQV(q-1)))*(target.GetSubstitutionQV(t-1)/3.0);
- }
-
- matchedPulseProb = exp(alignProb[q-1][t-1])*matchedPulseProb;
- //
- // An insertion in the query can be either a normal extra base
- // in the query, or a deletion in the reference.
- //
- // logInsertedPulseProb = uery.GetInsertionQV(q-1)) + alignProb[q-1][t];
-
- double insertedPulseProb = 0;
- if (target.GetDeletionTag(t-1) != 'N') {
- //
- // The target has a pulse that was not strong enough to call a
- // real incorporation. For now assume that the weak pulse is
- // the previous nucleotide in the query. So the likelihood of
- // the weak pulse is influenced by the likelihood of the
- // previous nucleotide in the query.
- //
- // Also, we only consider the previous base to be a missed
- // weak pulse if the current base is a match.
- //
-
- if (q > 1) {
- insertedPulseProb =
- (target.GetPreBaseDeletionQV(t-1, query.seq[q-2]) *target.GetDeletionQV(t-1)
- + query.GetInsertionQV(q-1))
- * exp(alignProb[q-1][t]);
- }
- else {
- //
- // There can be no pre-base deletion tag here (could probably be an assert statement).
- //
- insertedPulseProb = query.GetInsertionQV(q-1) * exp(alignProb[q-1][t]);
- }
- }
- else {
- insertedPulseProb = (query.GetInsertionQV(q-1) + target.GetDeletionQV(t-1))*exp(alignProb[q-1][t]);
- }
-
- //
- // An insertion in the target may be either a normal extra base
- // in the target, or a deletion in the query.
- // logDeletedPulseProb = target.GetInsertionQV(t-1)) + alignProb[q][t-1];
- double deletedPulseProb = 0;
- if (query.GetDeletionTag(q-1) != 'N') {
- if (t > 1) {
- deletedPulseProb = (query.GetPreBaseDeletionQV(q-1, target.seq[t-2]) * query.GetDeletionQV(q-1)
- + target.GetInsertionQV(t-1))*exp(alignProb[q][t-1]);
- }
- else {
- // There was a dropped pulse before this position, but nothing to align it to.
- deletedPulseProb = target.GetInsertionQV(t-1) * exp(alignProb[q][t-1]);
- }
- }
- else {
- deletedPulseProb = (target.GetInsertionQV(t-1) + query.GetDeletionQV(q-1)) *exp(alignProb[q][t-1]);
- }
-
- // Determine the total probability of reaching this position.
- /* cout << "align prob " << q << " " << t << " " << logMatchedPulseProb << " "
- << logInsertedPulseProb << " " << logDeletedPulseProb << endl;*/
- alignProb[q][t] = log(matchedPulseProb + insertedPulseProb + deletedPulseProb);
- }
- }
- double fullAlignProb = alignProb[numRows-1][numCols-1];
- alignProb.Free();
- return fullAlignProb;
-}
-
-
-#endif // _BLASR_FULL_QV_ALIGN_HPP_
diff --git a/libcpp/alignment/algorithms/alignment/GraphPaper.hpp b/libcpp/alignment/algorithms/alignment/GraphPaper.hpp
deleted file mode 100644
index ddd1a4e..0000000
--- a/libcpp/alignment/algorithms/alignment/GraphPaper.hpp
+++ /dev/null
@@ -1,31 +0,0 @@
-#ifndef GRAPH_PAPER_HPP_
-#define GRAPH_PAPER_HPP_
-
-#include "datastructures/alignment/Path.h"
-#include "matrix/FlatMatrix.hpp"
-
-template<typename T_Point>
-bool SetBounds(vector<T_Point> &points,
- DNALength &minPos,
- DNALength &maxPos,
- int axis);
-
-inline int GetIndex(DNALength pos,
- DNALength minPos,
- DNALength maxPos,
- int nBins);
-
-template<typename T_Point>
-int GraphPaper(vector<T_Point> &points,
- int nRows, int nCols,
- FlatMatrix2D<int> &bins,
- FlatMatrix2D<int> &scoreMat,
- FlatMatrix2D<Arrow> &pathMat,
- vector<bool> &onOptPath);
-
-template<typename T_Point>
-void RemoveOffOpt(vector<T_Point> &points, vector<bool> &optPath);
-
-#include "GraphPaperImpl.hpp"
-
-#endif
diff --git a/libcpp/alignment/algorithms/alignment/GraphPaperImpl.hpp b/libcpp/alignment/algorithms/alignment/GraphPaperImpl.hpp
deleted file mode 100644
index c57d5a8..0000000
--- a/libcpp/alignment/algorithms/alignment/GraphPaperImpl.hpp
+++ /dev/null
@@ -1,175 +0,0 @@
-#ifndef GRAPH_PAPER_IMPL_HPP_
-#define GRAPH_PAPER_IMPL_HPP_
-
-template<typename T_Point>
-bool SetBounds(vector<T_Point> &points, DNALength &minPos, DNALength &maxPos, int axis) {
- int i;
- DNALength maxRow = 0;
- if (points.size() == 0) {
- return false;
- }
- else {
- if (axis == 0) {
- minPos = maxPos = points[0].GetX();
- }
- else {
- minPos = maxPos = points[0].GetY();
- }
- }
- for (i = 1; i < points.size(); i++) {
- DNALength curPos;
- if (axis == 0) {
- curPos = points[i].GetX();
- }
- else {
- curPos = points[i].GetY();
- }
- if (curPos < minPos) {
- minPos = curPos;
- }
- else if (curPos > maxPos) {
- maxPos = curPos;
- }
- }
-}
-
-
-inline int GetIndex(DNALength pos, DNALength minPos, DNALength maxPos, int nBins) {
- assert(maxPos != minPos);
- float diff = pos - minPos;
- float len = maxPos - minPos;
- float ratio = diff/len;
- return min((DNALength)(nBins-1),
- ((DNALength)(ratio * nBins)));
-}
-
-template<typename T_Point>
-int GraphPaper(vector<T_Point> &points,
- int nRows, int nCols,
- FlatMatrix2D<int> &bins,
- FlatMatrix2D<int> &scoreMat,
- FlatMatrix2D<Arrow> &pathMat,
- vector<bool> &onOptPath) {
-
- bins.Resize(nRows, nCols);
- bins.Fill(0);
- scoreMat.Resize(nRows+1, nCols+1);
- pathMat.Resize(nRows+1, nCols+1);
- scoreMat.Fill(0);
- pathMat.Fill(NoArrow);
- onOptPath.resize(points.size());
- fill(onOptPath.begin(), onOptPath.end(), false);
-
- DNALength xMin, xMax, yMin, yMax;
- SetBounds(points, xMin, xMax, 0);
- xMax++; // make half-open interval.
- SetBounds(points, yMin, yMax, 1);
- yMax++; // ditto.
-
- //
- // First set up the grid to optimize over.
- //
- int i;
- for (i = 0; i < points.size(); i++) {
- int rowIndex = GetIndex(points[i].GetX(), xMin, xMax, nRows);
- int colIndex = GetIndex(points[i].GetY(), yMin, yMax, nCols);
- bins[rowIndex][colIndex]+= points[i].length;
- }
-
- //
- // Now optimize using DP.
- //
-
- // First handle boundary strips
- int r, c;
- for (r = 1; r < nRows+1; r++) {
- scoreMat[r][0] = 0;
- pathMat[r][0] = Up;
- }
- for (c = 1; c < nCols+1; c++) {
- scoreMat[0][c] = 0;
- pathMat[0][c] = Left;
- }
- scoreMat[0][0] = 0;
- for (r = 1; r < nRows + 1; r++) {
- for (c = 1; c < nCols + 1; c++) {
- int diagScore, leftScore, upScore;
- diagScore = scoreMat[r-1][c-1];
- leftScore = scoreMat[r][c-1];
- upScore = scoreMat[r-1][c];
-
- int optScore;
- Arrow optDir;
- if (diagScore >= leftScore and
- diagScore >= upScore) {
- optScore = diagScore;
- optDir = Diagonal;
- }
- else if (leftScore >= diagScore and
- leftScore >= upScore) {
- optScore = leftScore;
- optDir = Left;
- }
- else {
- optScore = upScore;
- optDir = Up;
- }
-
- scoreMat[r][c] = optScore + bins[r-1][c-1];
- pathMat[r][c] = optDir;
- }
- }
-
- r = nRows; c = nCols;
- while (r > 0 or c > 0) {
- Arrow dir = pathMat[r][c];
- pathMat[r][c] = Star;
- if (dir == Diagonal) { r--; c--; }
- else if (dir == Left) { c--; }
- else if (dir == Up) { r--; }
- if (r == 0 and c == 0) { break; }
- }
-
- //
- // Now mark inclusion/exclusion from matrix.
- //
- int nOpt = 0;
- for (i = 0; i < points.size(); i++) {
- int rowIndex = GetIndex(points[i].GetX(), xMin, xMax, nRows);
- int colIndex = GetIndex(points[i].GetY(), yMin, yMax, nCols);
- if (pathMat[rowIndex+1][colIndex+1] == Star) {
- onOptPath[i] = true;
- }
- else if (pathMat[rowIndex][colIndex+1] == Star) {
- onOptPath[i] = true;
- }
- else if (rowIndex + 2 < nRows and pathMat[rowIndex+2][colIndex+1] == Star) {
- onOptPath[i] = true;
- }
- else if (pathMat[rowIndex+1][colIndex] == Star) {
- onOptPath[i] = true;
- }
- else if (colIndex < nCols + 2 and pathMat[rowIndex+1][colIndex+2] == Star) {
- onOptPath[i] = true;
- }
- if (onOptPath[i]) {
- ++nOpt;
- }
- }
- return nOpt;
-}
-
-
-template<typename T_Point>
-void RemoveOffOpt(vector<T_Point> &points, vector<bool> &optPath) {
- int i, c;
- for (i = 0, c = 0; i < points.size(); i++) {
- if (optPath[i]) {
- points[c] = points[i];
- c++;
- }
- }
- points.resize(c);
-}
-
-#endif
diff --git a/libcpp/alignment/algorithms/alignment/GuidedAlign.cpp b/libcpp/alignment/algorithms/alignment/GuidedAlign.cpp
deleted file mode 100644
index 2904720..0000000
--- a/libcpp/alignment/algorithms/alignment/GuidedAlign.cpp
+++ /dev/null
@@ -1,226 +0,0 @@
-#include "GuidedAlign.hpp"
-
-int GuideRow::GetRowLength() {
- return tPost + tPre + 1;
-}
-
-int GetBufferIndexFunctor::operator()(Guide &guide, int seqRow, int seqCol, int &index) {
- //
- // Whenever a previous index was found, just use the one in the array to the right
- //
- int prevIndex = -1;
- if (index != -1) {
- index++;
- return 1;
- }
-
- int row, col;
- row = seqRow + 1 - seqRowOffset;
- col = seqCol; // use the variable here for standardized naming.
- if (row < 0 or row > guideSize ) {
- return 0;
- }
- if (col <= guide[row].t and guide[row].t - col <= guide[row].tPre) {
- index = guide[row].matrixOffset - (guide[row].t - col);
- assert(prevIndex == -1 or prevIndex == index);
- return 1;
- }
- else if (col > guide[row].t and col - guide[row].t <= guide[row].tPost) {
- index = guide[row].matrixOffset + (col - guide[row].t);
- assert(prevIndex == -1 or prevIndex == index);
- return 1;
- }
- return 0;
-}
-
-int ComputeMatrixNElem(Guide &guide) {
- int totalSize = 0;
- int r;
- for (r = 0; r < guide.size(); r++) {
- totalSize += guide[r].GetRowLength();
- // cout << r << " " << totalSize << endl;
- assert(guide[r].GetRowLength() >= 0);
- }
- return totalSize;
-}
-
-void StoreMatrixOffsets(Guide &guide) {
- int curMatrixSize = 0;
- int r;
- for (r = 0; r < guide.size(); r++) {
- guide[r].matrixOffset = guide[r].tPre + curMatrixSize;
- curMatrixSize += guide[r].GetRowLength();
- }
-}
-
-float QVToLogPScale(char qv) {
- return qv/-10.0;
-}
-
-void QVToLogPScale(QualityValueVector<QualityValue> &qualVect, int phredVectLength, std::vector<float> &lnVect) {
- if (phredVectLength > lnVect.size()) {
- lnVect.resize(phredVectLength);
- }
- int i;
- for (i = 0; i < phredVectLength; i++) {
- lnVect[i] = qualVect[i]/-10.0; //log(qualVect.ToProbability(i));
- }
-}
-
-
-int AlignmentToGuide(Alignment &alignment, Guide &guide, int bandSize) {
- guide.clear();
- if (alignment.size() == 0) {
- // no blocks to make guide, exit.
- return 0;
- }
-
- int tStart, tEnd, qStart, qEnd;
- int firstBlock = 0;
- int lastBlock = alignment.size() - 1;
-
- tStart = alignment.blocks[firstBlock].tPos;
- tEnd = alignment.blocks[lastBlock].TEnd();
- qStart = alignment.blocks[firstBlock].qPos;
- qEnd = alignment.blocks[lastBlock].QEnd();
-
- int qAlignLength = qEnd - qStart;
-
- // Add one extra block for boundary conditions.
- guide.resize(qAlignLength+1);
-
- // Initilize the first (boundary condition) row.
- guide[0].t = tStart - 1;
- guide[0].q = qStart - 1;
- int drift = abs(tStart - qStart);
- if (drift > bandSize) {
- guide[0].tPost = drift;
- }
- else {
- guide[0].tPost = bandSize;
- }
- guide[0].tPre = 0;
-
- // The first row of the guide matches
- int q = 0;
- int t = 0;
- int guideIndex = 1;
- int b;
-
- for (b = 0; b < alignment.blocks.size(); b++) {
- //
- // First add the match stored in block b, each block is a
- // diagonal, so that makes life easy.
- //
- int bp;
-
- for (bp = 0; bp < alignment.blocks[b].length; bp++) {
- guide[guideIndex].t = alignment.blocks[b].tPos + bp;
- guide[guideIndex].q = alignment.blocks[b].qPos + bp;
- //
- // This complicated logic is to determine how far back the band
- // should stretch. The problem is that if the band stretches
- // back further than the previous row, it's possible for the
- // path matrix to go backwards into cells that should not be
- // touched.
- //
- int tDiff = guide[guideIndex].t - guide[guideIndex-1].t;
- if (bp == 0) {
- guide[guideIndex].tPre = guide[guideIndex].t -
- (guide[guideIndex-1].t - guide[guideIndex-1].tPre);
- guide[guideIndex].tPost = bandSize + abs(drift);
- }
- else {
- //
- // Within aligned blocks, align around the band size.
- //
- int fullLengthTPre = (guide[guideIndex].t -
- (guide[guideIndex-1].t -
- guide[guideIndex-1].tPre));
- guide[guideIndex].tPre = min(bandSize, fullLengthTPre);
- guide[guideIndex].tPost = min(MAX_BAND_SIZE, bandSize);
- //if (guide[guideIndex].tPre > 500 or guide[guideIndex].tPost > 500) {
- //cout << guideIndex << " " << guide[guideIndex].tPre << " " << guide[guideIndex].tPost << endl;
- //}
- //assert(guide[guideIndex].tPre >= 0);
- //assert(guide[guideIndex].tPost >= 0);
- }
- guideIndex++;
- }
-
- //
- // Now, widen k around regions where there is drift from the diagonal.
- //
-
-
- int diagonalLength;
- int qGap, tGap;
-
- if (b < alignment.blocks.size()-1) {
- qGap = alignment.blocks[b+1].qPos - alignment.blocks[b].QEnd();
- tGap = alignment.blocks[b+1].tPos - alignment.blocks[b].TEnd();
- //
- // Drift is how far from the diagonal the next block starts at.
- //
- drift = ComputeDrift(alignment.blocks[b], alignment.blocks[b+1]);
- //drift = min(drift, 100);
- diagonalLength = std::min(qGap, tGap);
-
- int diagPos;
- int qPos, tPos;
- int qEnd, tEnd;
-
- qPos = alignment.blocks[b].QEnd();
- tPos = alignment.blocks[b].TEnd();
-
- qEnd = alignment.blocks[b+1].qPos;
- tEnd = alignment.blocks[b+1].tPos;
-
- for (diagPos = 0; diagPos < diagonalLength; diagPos++, tPos++, qPos++) {
- guide[guideIndex].t = tPos;
- guide[guideIndex].q = qPos;
- guide[guideIndex].tPre = min(MAX_BAND_SIZE, (guide[guideIndex].t -
- (guide[guideIndex-1].t - guide[guideIndex-1].tPre)));
- guide[guideIndex].tPost = min(MAX_BAND_SIZE, bandSize + abs(drift));
-/* if (guide[guideIndex].tPre > 500 or guide[guideIndex].tPost > 500) {
- cout << guideIndex << " " << guide[guideIndex].tPre << " " << guide[guideIndex].tPost << endl;
- } */
- ++guideIndex;
- }
-
- //
- // If the query gap is shorter than target (there is a deletion
- // of the target), the guide must be extended down the side of
- // the gap. See the figure below.
- //
- // *****
- // **
- // * *
- // * *
- // * * // extend down from here.
- // * *
- // * *
- //
-
- while (qPos < qEnd) {
- guide[guideIndex].t = tPos;
- guide[guideIndex].q = qPos;
- // move q down.
- qPos++;
- // keep tPos fixed, the guide is straight down here.
- guide[guideIndex].tPre = min(MAX_BAND_SIZE, guide[guideIndex].t -
- (guide[guideIndex-1].t - guide[guideIndex-1].tPre)); //bandSize + abs(drift);
-
- guide[guideIndex].tPost = min(MAX_BAND_SIZE, bandSize + abs(drift));
- guideIndex++;
- }
- }
- }
- //int i;
- //for (i = 0; i < guide.size(); i++) {
- // guide[i].tPre = min(guide[i].tPre, 200);
- // guide[i].tPost = min(guide[i].tPost, 200);
- // }
- return 1; // signal ok.
-
-}
diff --git a/libcpp/alignment/algorithms/alignment/GuidedAlign.hpp b/libcpp/alignment/algorithms/alignment/GuidedAlign.hpp
deleted file mode 100644
index 3296a21..0000000
--- a/libcpp/alignment/algorithms/alignment/GuidedAlign.hpp
+++ /dev/null
@@ -1,600 +0,0 @@
-#ifndef _BLASR_GUIDE_ALIGNMENT_HPP_
-#define _BLASR_GUIDE_ALIGNMENT_HPP_
-
-#include <vector>
-#include <cmath>
-#include <limits.h>
-#include <ostream>
-#include "Types.h"
-#include "defs.h"
-#include "NucConversion.hpp"
-#include "DNASequence.hpp"
-#include "sdp/SDPFragment.hpp"
-#include "matrix/FlatMatrix.hpp"
-#include "datastructures/alignment/Alignment.hpp"
-#include "datastructures/anchoring/MatchPos.hpp"
-#include "matrix/Matrix.hpp"
-#include "tuples/TupleList.hpp"
-#include "tuples/TupleMetrics.hpp"
-#include "tuples/DNATuple.hpp"
-#include "utils/LogUtils.hpp"
-#include "utils/PhredUtils.hpp"
-#include "qvs/QualityValue.hpp"
-#include "qvs/QualityValueVector.hpp"
-#include "AlignmentUtils.hpp"
-#include "DistanceMatrixScoreFunction.hpp"
-#include "algorithms/alignment/SDPAlign.hpp"
-
-#define LOWEST_LOG_VALUE -700
-
-#define MAX_BAND_SIZE 250
-
-class GuideRow {
-public:
- int q, t;
- int tPre, tPost;
- unsigned int matrixOffset; // Where the center (q) is in the score
- // and path matrices.
- int GetRowLength();
-};
-
-typedef std::vector<GuideRow> Guide;
-
-class GetBufferIndexFunctor {
-// row + rowSeqOffset - 1 == seqRow
-// so, rowInSeq = -1, rowSeqOffset = 0 -> row = 0
-public:
- int seqRowOffset;
- int guideSize;
- int operator()(Guide &guide, int seqRow, int seqCol, int &index);
-};
-
-int ComputeMatrixNElem(Guide &guide);
-
-void StoreMatrixOffsets(Guide &guide);
-
-float QVToLogPScale(char qv);
-
-void QVToLogPScale(QualityValueVector<QualityValue> &qualVect, int phredVectLength, std::vector<float> &lnVect);
-
-int AlignmentToGuide(blasr::Alignment &alignment, Guide &guide, int bandSize);
-
-template<typename QSequence, typename TSequence, typename T_ScoreFn>
-int GuidedAlign(QSequence &origQSeq, TSequence &origTSeq, blasr::Alignment &guideAlignment,
- T_ScoreFn &scoreFn,
- int bandSize,
- blasr::Alignment &alignment,
- std::vector<int> &scoreMat,
- std::vector<Arrow> &pathMat,
- std::vector<double> &probMat,
- std::vector<double> &optPathProbMat,
- std::vector<float> &lnSubPValueVect,
- std::vector<float> &lnInsPValueVect,
- std::vector<float> &lnDelPValueVect,
- std::vector<float> &lnMatchPValueVect,
- AlignmentType alignType=Global,
- bool computeProb=false) {
-
- Guide guide;
- AlignmentToGuide(guideAlignment, guide, bandSize);
- StoreMatrixOffsets(guide);
- ComputeMatrixNElem(guide);
-
- //
- // Make a copy of the sequences that is guaranteed to be in 3-bit format for faster alignment.
- // (mabybe eventually reuse the qseq and tseq memory)
- //
- QSequence qSeq;
- TSequence tSeq;
- qSeq.Assign(origQSeq);
- tSeq.Assign(origTSeq);
-
- unsigned int matrixNElem = ComputeMatrixNElem(guide);
- assert(matrixNElem >= 0);
- StoreMatrixOffsets(guide);
-
- /*
- * The following code is useful to produce images of the dp-matrix.
- * Make sure the sequenences are less than 5kb each though.
-
- Matrix<float> probMatrix;
- probMatrix.Resize(qSeq.length, tSeq.length);
- probMatrix.Initialize(0);
- ofstream matrixOut;
- stringstream matrixOutNameStrm;
- matrixOutNameStrm << "probMatrix_"<< runIndex << ".dat";
- matrixOut.open(matrixOutNameStrm.str().c_str());
- */
-
- if (computeProb) {
- //
- // Convert phred scale to proper ln for faster manipulation later on.
- //
- QVToLogPScale(qSeq.substitutionQV, qSeq.length, lnSubPValueVect);
- QVToLogPScale(qSeq.insertionQV, qSeq.length, lnInsPValueVect);
- QVToLogPScale(qSeq.deletionQV, qSeq.length, lnDelPValueVect);
- if (lnMatchPValueVect.size() < qSeq.length) {
- lnMatchPValueVect.resize(qSeq.length);
- }
- //
- // Normalize probability vectors so that the probability of transition from each cell is 1.
- //
- unsigned int i;
- for (i = 0; i < qSeq.length; i++) {
- float subSum = LogSumOfTwo(lnSubPValueVect[i], QVToLogPScale(scoreFn.substitutionPrior)); // prior on substitution rate
- float denominator = LogSumOfThree(lnDelPValueVect[i], lnInsPValueVect[i], subSum);
- lnDelPValueVect[i] = lnDelPValueVect[i] - denominator;
- lnSubPValueVect[i] = lnSubPValueVect[i] - denominator;
- lnInsPValueVect[i] = lnInsPValueVect[i] - denominator;
- lnMatchPValueVect[i] = subSum - denominator;
- }
-
- }
-
-
-
- //
- // Make sure the alignments can fit in the reused buffers.
- //
-
- if (scoreMat.size() < matrixNElem) {
- scoreMat.resize(matrixNElem);
- pathMat.resize(matrixNElem);
- fill(scoreMat.begin(), scoreMat.end(), 0);
- fill(pathMat.begin(), pathMat.end(), NoArrow);
- }
- if (computeProb) {
- if (probMat.size() < matrixNElem) {
- probMat.resize(matrixNElem);
- optPathProbMat.resize(matrixNElem);
- }
- }
-
- //
- // Initialze matrices. Only initialize up to matrixNElem rather
- // than matrix.size() because the matrix.size() unnecessary space
- // may be allocated.
- //
-
- std::fill(scoreMat.begin(), scoreMat.begin() + matrixNElem, 0);
- std::fill(pathMat.begin(), pathMat.begin() + matrixNElem, NoArrow);
- if (computeProb) {
- std::fill(probMat.begin(), probMat.begin() + matrixNElem, 0);
- std::fill(optPathProbMat.begin(), optPathProbMat.begin() + matrixNElem, 0);
- }
- //
- // Initialize boundary conditions.
- //
- int q, t;
- int bufferIndex;
- // start alignemnt at the beginning of the guide, and align to the
- // end of the guide.
- if (guide.size() == 0) {
- qSeq.Free();
- tSeq.Free();
- return 0;
- }
- int qStart = guide[1].q;
- int tStart = guide[1].t;
- int qEnd = guide[guide.size()-1].q+1;
- int tEnd = guide[guide.size()-1].t+1;
-
- GetBufferIndexFunctor GetBufferIndex;
- GetBufferIndex.seqRowOffset = qStart;
- GetBufferIndex.guideSize = guide.size();
- int indicesAreValid, delIndexIsValid, insIndexIsValid;
- bufferIndex = -1;
- indicesAreValid = GetBufferIndex(guide, qStart-1, tStart-1, bufferIndex);
- assert(indicesAreValid);
- scoreMat[bufferIndex] = 0;
- pathMat[bufferIndex] = NoArrow;
- int matchIndex, insIndex, delIndex, curIndex;
-
- //
- // Initialize deletion row.
- //
- if (computeProb) {
- probMat[0] = optPathProbMat[0] = 0;
- }
- for (t = tStart; t < tStart + guide[0].tPost; t++) {
- curIndex=-1;
- indicesAreValid = GetBufferIndex(guide, qStart-1, t, curIndex);
- if (indicesAreValid == 0 ) {
- std::cout << "QSeq" << std::endl;
- (static_cast<DNASequence*>(&origQSeq))->PrintSeq(std::cout);
- std::cout << "TSeq" << std::endl;
- (static_cast<DNASequence*>(&origTSeq))->PrintSeq(std::cout);
- assert(0);
- }
- delIndex = -1;
- delIndexIsValid = GetBufferIndex(guide, qStart-1, t-1, delIndex);
-
- if (delIndexIsValid) {
- if (alignType == Global) {
- scoreMat[curIndex] = scoreMat[delIndex] + scoreFn.del;
- }
- else if (alignType == Local) {
- scoreMat[curIndex] = 0;
- }
- pathMat[curIndex] = Left;
- if (computeProb) {
- if (qSeq.qual.Empty() == false) {
- optPathProbMat[curIndex] = probMat[curIndex] = probMat[delIndex] + QVToLogPScale(scoreFn.globalDeletionPrior);
- }
- }
- }
- }
-
- //
- // Initialize stripe along the top of the grid.
- //
- for (q = qStart ; q < qStart + bandSize and q < qEnd; q++) {
- insIndex = -1;
- insIndexIsValid = GetBufferIndex(guide, q-1, tStart-1, // diagonal from t-start
- insIndex);
- curIndex = -1;
- indicesAreValid = GetBufferIndex(guide, q, tStart-1, curIndex);
-
- if (insIndexIsValid and indicesAreValid) {
- assert(insIndex >= 0);
- assert(curIndex >= 0);
- if (alignType == Global) {
- scoreMat[curIndex] = scoreMat[insIndex] + scoreFn.ins;
- }
- else {
- scoreMat[curIndex] = 0;
- }
- pathMat[curIndex] = Up;
- if (computeProb) {
- if (qSeq.qual.Empty() == false) {
- optPathProbMat[curIndex] = probMat[curIndex] = probMat[insIndex] + QVToLogPScale(scoreFn.Insertion(tSeq,(DNALength) 0, qSeq, (DNALength)q));
- }
- }
- }
- }
-
- int matchScore, insScore, delScore;
-
- for (q = qStart; q < qEnd; q++) {
- int qi = q - qStart + 1;
- int tp = guide[qi].t;
- curIndex = matchIndex = insIndex = delIndex = -1;
-
- //
- // Do some work that will help define when matchIndex and insIndex
- // may be used. Once delIndex is computed once, it is valid for
- // all t positions.
- //
- int prevRowTEnd = -1;
- if ( qi > 0) {
- //
- // Define the boundaries of the column which may access previously
- // computed cells with a match.
- //
- prevRowTEnd = guide[qi-1].t + guide[qi-1].tPost;
- }
-
- for (t = tp - guide[qi].tPre ; t < guide[qi].t + guide[qi].tPost +1; t++) {
-
-
- if (q < qStart + bandSize and t == tp - guide[qi].tPre - 1) {
- // On the boundary condition, don't access the 1st element;
- t++;
- continue;
- }
- // Make sure the index is not past the end of the sequence.
- if (t < -1) continue;
- if (t >= tEnd) continue;
-
- //
- // No cells are available to use for insertion cost
- // computation.
- //
- if (t > prevRowTEnd) {
- insIndex = -1;
- }
- if (t > prevRowTEnd + 1) {
- matchIndex = -1;
- }
-
- //
- // Find the indices in the buffer. Since the rows are of
- // different sizes, one can't just use offsets from the buffer
- // index.
- //
-
- if (GetBufferIndex(guide, q-1,t-1, matchIndex)) {
- assert(matchIndex >= 0);
- matchScore = scoreMat[matchIndex] + scoreFn.Match(tSeq, t, qSeq, q);
- }
- else {
- matchScore = INF_INT;
- }
-
- if (GetBufferIndex(guide, q-1, t, insIndex)) {
- assert(insIndex >= 0);
- insScore = scoreMat[insIndex] + scoreFn.Insertion(tSeq,(DNALength) t, qSeq, (DNALength)q);
- }
- else {
- insScore = INF_INT;
- }
- if (GetBufferIndex(guide, q, t-1, delIndex)) {
- assert(delIndex >= 0);
- delScore = scoreMat[delIndex] + scoreFn.Deletion(tSeq, (DNALength) t, qSeq, (DNALength)q);
- }
- else {
- delScore = INF_INT;
- }
-
- int minScore = MIN(matchScore, MIN(insScore, delScore));
- int result = GetBufferIndex(guide, q, t, curIndex);
- // This should only loop over valid cells.
- assert(result);
- assert(curIndex >= 0);
- scoreMat[curIndex] = minScore;
- if (minScore == INF_INT) {
- pathMat[curIndex] = NoArrow;
- if (computeProb) {
- probMat[curIndex] = 1;
- optPathProbMat[curIndex] = 0;
- }
- }
- else {
- assert(result == 1);
- if (minScore == matchScore) {
- pathMat[curIndex] = Diagonal;
- }
- else if (minScore == delScore) {
- pathMat[curIndex] = Left;
- }
- else {
- pathMat[curIndex] = Up;
- }
-
- float pMisMatch, pIns, pDel;
- // Assign these to anything over 1 to signal they are not assigned.
- pMisMatch = 2;
- pIns = 2;
- pDel = 2;
- if (computeProb) {
- if (matchScore != INF_INT) {
- pMisMatch = QVToLogPScale(scoreFn.NormalizedMatch(tSeq, t, qSeq, q));
- }
- if (insScore != INF_INT) {
- pIns = QVToLogPScale(scoreFn.NormalizedInsertion(tSeq, t, qSeq, q));
- }
- if (delScore != INF_INT) {
- pDel = QVToLogPScale(scoreFn.NormalizedDeletion(tSeq, t, qSeq, q));
- }
-
- if (qSeq.qual.Empty() == false) {
- if (matchScore != INF_INT and delScore != INF_INT and insScore != INF_INT) {
- probMat[curIndex] = LogSumOfThree(probMat[matchIndex] + pMisMatch,
- probMat[delIndex] + pDel,
- probMat[insIndex] + pIns);
- }
- else if (matchScore != INF_INT and delScore != INF_INT) {
- probMat[curIndex] = LogSumOfTwo(probMat[matchIndex] + pMisMatch,
- probMat[delIndex] + pDel);
- }
- else if (matchScore != INF_INT and insScore != INF_INT) {
- probMat[curIndex] = LogSumOfTwo(probMat[matchIndex] + pMisMatch,
- probMat[insIndex] + pIns);
- }
- else if (insScore != INF_INT and delScore != INF_INT) {
- probMat[curIndex] = LogSumOfTwo(probMat[delIndex] + pDel,
- probMat[insIndex] + pIns);
- }
- else if (matchScore != INF_INT) {
- probMat[curIndex] = probMat[matchIndex] + pMisMatch;
- }
- else if (delScore != INF_INT) {
- probMat[curIndex] = probMat[delIndex] + pDel;
- }
- else if (insScore != INF_INT) {
- probMat[curIndex] = probMat[insIndex] + pIns;
- }
- //
- // Not normalizing probabilities, but using value as if it
- // was a probability later on, so cap at 0 (= log 1).
- //
- if (probMat[curIndex] > 0) {
- probMat[curIndex] = 0;
- }
- assert(!std::isnan(probMat[curIndex]));
- }
- }
- }
- }
- }
- // Ok, for now just trace back from qend/tend
- q = qEnd-1;
- t = tEnd-1;
- std::vector<Arrow> optAlignment;
- int bufferIndexIsValid;
- while(q >= qStart or t >= tStart) {
- bufferIndex = -1;
- bufferIndexIsValid = GetBufferIndex(guide, q, t, bufferIndex);
- assert(bufferIndexIsValid);
- assert(bufferIndex >= 0);
- Arrow arrow;
- arrow = pathMat[bufferIndex];
- if (arrow == NoArrow) {
- tSeq.ToAscii();
- qSeq.ToAscii();
- unsigned int gi;
- for (gi = 0; gi < guide.size(); gi++) {
- std::cout << guide[gi].q << " " << guide[gi].t << " " << guide[gi].tPre << " " << guide[gi].tPost << std::endl;
- }
-
- std::cout << "qseq: "<< std::endl;
- (static_cast<DNASequence*>(&qSeq))->PrintSeq(std::cout);
- std::cout << "tseq: "<< std::endl;
- (static_cast<DNASequence*>(&tSeq))->PrintSeq(std::cout);
- std::cout << "ERROR, this path has gone awry at " << q << " " << t << " !" << std::endl;
- exit(1);
- }
- optAlignment.push_back(arrow);
- if (arrow == Diagonal) {
- q--;
- t--;
- }
- else if (arrow == Up) {
- q--;
- }
- else if (arrow == Left) {
- t--;
- }
- }
-
- alignment.nCells = ComputeMatrixNElem(guide);
- std::reverse(optAlignment.begin(), optAlignment.end());
- alignment.qPos = qStart;
- alignment.tPos = tStart;
- alignment.ArrowPathToAlignment(optAlignment);
- RemoveAlignmentPrefixGaps(alignment);
- int lastIndex = 0;
- tSeq.Free();
- qSeq.Free();
- lastIndex = -1;
- if (GetBufferIndex(guide, qEnd - 1, tEnd - 1, lastIndex)) {
- alignment.score = scoreMat[lastIndex];
- if (computeProb) {
- alignment.probScore = probMat[lastIndex];
- }
- return scoreMat[lastIndex];
- }
- else {
- return 0;
- }
-}
-
-template<typename QSequence, typename TSequence, typename T_ScoreFn> //, typename T_BufferCache>
-int GuidedAlign(QSequence &origQSeq, TSequence &origTSeq,
- T_ScoreFn &scoreFn,
- int bandSize,
- int sdpIns, int sdpDel, float sdpIndelRate,
- blasr::Alignment &alignment,
- AlignmentType alignType=Global,
- bool computeProb = false,
- int sdpTupleSize= 8) {
- blasr::Alignment sdpAlignment;
-
- int alignScore = SDPAlign(origQSeq, origTSeq,
- scoreFn, sdpTupleSize,
- sdpIns, sdpDel, sdpIndelRate,
- sdpAlignment); //, Local, false, false);
-
- int b;
- for (b = 0; b < sdpAlignment.blocks.size(); b++) {
- sdpAlignment.blocks[b].qPos += sdpAlignment.qPos;
- sdpAlignment.blocks[b].tPos += sdpAlignment.tPos;
- }
- sdpAlignment.tPos = 0;
- sdpAlignment.qPos = 0;
-
- return GuidedAlign(origQSeq, origTSeq, sdpAlignment, scoreFn, bandSize, alignment,
- // fill in optional parameters
- alignType, computeProb);
-
-}
-
-
-//
-// Use Case: No guide yet exists for this alignment, but using
-// buffers. Run SDP alignment first, then refine on the guide.
-//
-
-template<typename QSequence, typename TSequence, typename T_ScoreFn, typename T_BufferCache>
-int GuidedAlign(QSequence &origQSeq, TSequence &origTSeq,
- T_ScoreFn &scoreFn,
- int bandSize,
- int sdpIns, int sdpDel, float sdpIndelRate,
- T_BufferCache &buffers,
- blasr::Alignment &alignment,
- AlignmentType alignType=Global,
- bool computeProb = false,
- int sdpTupleSize= 8) {
-
- blasr::Alignment sdpAlignment;
-
- int alignScore = SDPAlign(origQSeq, origTSeq,
- scoreFn, sdpTupleSize,
- sdpIns, sdpDel, sdpIndelRate,
- sdpAlignment, buffers, Local, false, false);
-
- int b;
- for (b = 0; b < sdpAlignment.blocks.size(); b++) {
- sdpAlignment.blocks[b].qPos += sdpAlignment.qPos;
- sdpAlignment.blocks[b].tPos += sdpAlignment.tPos;
- }
- sdpAlignment.tPos = 0;
- sdpAlignment.qPos = 0;
-
- return GuidedAlign(origQSeq, origTSeq, sdpAlignment, scoreFn, bandSize, buffers, alignment,
- // fill in optional parameters
- alignType, computeProb);
-}
-
-//
-// Use case, guide exists, using buffers
-//
-template<typename QSequence, typename TSequence, typename T_ScoreFn, typename T_BufferCache>
-int GuidedAlign(QSequence &origQSeq, TSequence &origTSeq, blasr::Alignment &guideAlignment,
- T_ScoreFn &scoreFn,
- int bandSize,
- T_BufferCache &buffers,
- blasr::Alignment &alignment,
- AlignmentType alignType=Global,
- bool computeProb=false) {
- return GuidedAlign(origQSeq, origTSeq, guideAlignment, scoreFn, bandSize, alignment,
- buffers.scoreMat,
- buffers.pathMat,
- buffers.probMat,
- buffers.optPathProbMat,
- buffers.lnSubPValueMat,
- buffers.lnInsPValueMat,
- buffers.lnDelPValueMat,
- buffers.lnMatchPValueMat, alignType, computeProb);
-}
-
-//
-// Missing the use case for guide does not exist, and not using
-// buffers. This is just a very long function declaration, so it's
-// not worth writing until it is needed.
-//
-
-
-//
-// Use case, guide exists, but not using buffers.
-//
-template<typename QSequence, typename TSequence, typename T_ScoreFn>
-int GuidedAlign(QSequence &origQSeq, TSequence &origTSeq, blasr::Alignment &guideAlignment,
- T_ScoreFn &scoreFn,
- int bandSize,
- blasr::Alignment &alignment,
- AlignmentType alignType=Global,
- bool computeProb=false) {
-
- // Make synonyms for members of the buffers class for easier typing.
- std::vector<int> scoreMat;
- std::vector<Arrow> pathMat;
- std::vector<double> probMat;
- std::vector<double> optPathProbMat;
- std::vector<float> lnSubPValueVect;
- std::vector<float> lnInsPValueVect;
- std::vector<float> lnDelPValueVect;
- std::vector<float> lnMatchPValueVect;
-
- return GuidedAlign(origQSeq, origTSeq, guideAlignment, scoreFn, bandSize, alignment,
- scoreMat,
- pathMat,
- probMat,
- optPathProbMat,
- lnSubPValueVect,
- lnInsPValueVect,
- lnDelPValueVect,
- lnMatchPValueVect, alignType, computeProb);
-}
-
-#endif // _BLASR_GUIDE_ALIGNMENT_HPP_
diff --git a/libcpp/alignment/algorithms/alignment/IDSScoreFunction.cpp b/libcpp/alignment/algorithms/alignment/IDSScoreFunction.cpp
deleted file mode 100644
index cc40a5f..0000000
--- a/libcpp/alignment/algorithms/alignment/IDSScoreFunction.cpp
+++ /dev/null
@@ -1,158 +0,0 @@
-#include "IDSScoreFunction.hpp"
-
-float SumAsValidPhred(float v1, float v2, float v3) {
- float sum = 0;
- if (v1 > 0) {
- sum = std::pow(10,v1/-10.0);
- }
- if (v2 > 0) {
- sum += std::pow(10,v2/-10.0);
- }
- if (v3 > 0) {
- sum += std::pow(10,v3/-10.0);
- }
- return sum;
-}
-
-template<>
-int IDSScoreFunction<DNASequence,FASTQSequence>::Deletion(DNASequence &ref, DNALength refPos,
- FASTQSequence &query, DNALength queryPos) {
-
- if (query.deletionQV.Empty() == false and query.deletionTag != NULL) {
- if (query.deletionTag[queryPos] == 'N') {
- return globalDeletionPrior; //query.deletionQV[queryPos] ;
- }
- else {
- if (query.deletionTag[queryPos] == ref.seq[refPos]) {
- return query.deletionQV[queryPos];
- }
- else {
- return globalDeletionPrior;
- }
- }
- }
- else {
- return del;
- }
-}
-
-template<>
-int IDSScoreFunction<DNASequence, FASTQSequence>::Deletion(FASTQSequence &query, DNALength queryPos) {
- return query.deletionQV[queryPos];
-}
-
-
-template<>
-int IDSScoreFunction<DNASequence, DNASequence>::Deletion(DNASequence &query, DNALength pos) {
- return del; // For now there is no global deletion quality value.
-}
-
-template<>
-int IDSScoreFunction<DNASequence, FASTQSequence>::Insertion(DNASequence &refSeq, DNALength refPos,
- FASTQSequence &query, DNALength pos) {
- return query.insertionQV[pos] ;
-}
-
-template<>
-int IDSScoreFunction<DNASequence, FASTQSequence>::Insertion(FASTQSequence &query, DNALength pos) {
- return query.insertionQV[pos];
-}
-
-template<>
-int IDSScoreFunction<DNASequence, FASTQSequence>::Match(DNASequence &ref, DNALength refPos,
- FASTQSequence &query, DNALength queryPos) {
-
- if (query.seq[queryPos] == ref.seq[refPos]) {
- return 0;
- } else if (query.substitutionTag != NULL) {
- if (query.substitutionTag[queryPos] == ref.seq[refPos]) {
- return query.substitutionQV[queryPos];
- }
- }
- return substitutionPrior;
-}
-
-
-template<>
-float IDSScoreFunction<DNASequence, FASTQSequence>::NormalizedMatch(DNASequence &ref, DNALength refPos,
- FASTQSequence &query, DNALength queryPos) {
- /*
- * Return the match probability normalized such that the probability
- * of transitioning from refPos, queryPos is 1.
- */
-
- float matchScore = Match(ref, refPos, query, queryPos);
-
- float delScore = -1;
- if (refPos > 0) {
- delScore = Deletion(ref, refPos-1, query, queryPos);
- }
-
- float insScore = -1;
- if (queryPos > 0) {
- insScore = Insertion(ref, refPos, query, queryPos-1);
- }
-
- float sumScore = SumAsValidPhred(matchScore, delScore, insScore);
- if (sumScore > 0) {
- float numerator = std::pow(10, matchScore/-10.0);
- return -10*std::log10( numerator / sumScore);
- }
- else {
- return 0;
- }
-}
-
-
-
-template<>
-float IDSScoreFunction<DNASequence, FASTQSequence>::NormalizedInsertion(DNASequence &ref, DNALength refPos,
- FASTQSequence &query, DNALength queryPos) {
-
- float insScore = Insertion(ref, refPos, query, queryPos);
-
- float delScore = -1;
- float matchScore = -1;
- if (refPos < ref.length - 1) {
- matchScore = Match(ref, refPos + 1, query, queryPos);
- if (queryPos > 0) {
- delScore = Deletion(ref, refPos + 1, query, queryPos - 1);
- }
- }
-
- float sum = SumAsValidPhred(insScore, delScore, matchScore);
- if (sum > 0) {
- float numerator = std::pow(10,insScore/-10.0);
- return -10*std::log10( numerator / sum);
- }
- else {
- return 0;
- }
-}
-
-
-template<>
-float IDSScoreFunction<DNASequence, FASTQSequence>::NormalizedDeletion(DNASequence &ref, DNALength refPos,
- FASTQSequence &query, DNALength queryPos) {
-
- float delScore = Deletion(ref, refPos, query, queryPos);
-
- float matchScore = -1;
- float insScore = -1;
-
- if (queryPos < query.length - 1) {
- matchScore = Match(ref, refPos, query, queryPos + 1);
-
- if (refPos > 0) {
- insScore = Insertion(ref, refPos - 1, query, queryPos + 1);
- }
- }
- float sum = SumAsValidPhred(delScore, matchScore, insScore);
- if (sum > 0) {
- float numerator= std::pow(10, delScore/-10.0);
- return -10*std::log10( numerator / sum);
- }
- else {
- return 0;
- }
-}
diff --git a/libcpp/alignment/algorithms/alignment/IDSScoreFunction.hpp b/libcpp/alignment/algorithms/alignment/IDSScoreFunction.hpp
deleted file mode 100644
index 3b6b5e5..0000000
--- a/libcpp/alignment/algorithms/alignment/IDSScoreFunction.hpp
+++ /dev/null
@@ -1,109 +0,0 @@
-#ifndef _BLASR_IDS_SCORE_FUNCTION_HPP_
-#define _BLASR_IDS_SCORE_FUNCTION_HPP_
-
-#include <string>
-#include <cmath>
-#include "ScoreMatrices.hpp"
-#include "BaseScoreFunction.hpp"
-#include "FASTASequence.hpp"
-#include "FASTQSequence.hpp"
-#include "utils/LogUtils.hpp"
-
-float SumAsValidPhred(float v1, float v2, float v3);
-
-template<typename T_RefSequence, typename T_QuerySequence>
-class IDSScoreFunction : public BaseScoreFunction {
- public:
- int scoreMatrix[5][5];
-
- IDSScoreFunction(int scoreMatrixP[5][5], int insertionP, int deletionP, int globalInsertionPriorP,
- int globalDeletionPriorP) : BaseScoreFunction(insertionP, deletionP, globalInsertionPriorP, globalDeletionPriorP) {
- InitializeScoreMatrix(scoreMatrixP);
- }
-
-
- IDSScoreFunction() {
- substitutionPrior = 20;
- globalDeletionPrior = 13;
- }
-
- void InitializeScoreMatrix(int scoreMatrixP[5][5]) {
- int i, j;
- for (i = 0; i < 5; i++ ){
- for (j = 0; j < 5; j++ ){
- scoreMatrix[i][j] = scoreMatrixP[i][j];
- }
- }
- }
-
-
- int Deletion(T_QuerySequence &seq, DNALength pos) {
- std::cout << "IDS. For now, deletion must be specialized with FASTQ or FASTA Sequences. " << std::endl;
- exit(1);
- return 0;
- }
- int Deletion(T_RefSequence &refSeq, DNALength refPos, T_QuerySequence &querySeq, DNALength queryPos) {
- std::cout << "IDS. For now, this function must be specialized with either FASTQ or FASTA sequences"<<std::endl;
- exit(1);
- }
- int Match(T_RefSequence &ref, DNALength refPos, T_QuerySequence &query, DNALength queryPos) {
- std::cout << "IDS. For now, this function must be specialized with either FASTQ or FASTA sequences" << std::endl;
- return 0;
- exit(1);
- }
- int Insertion(T_RefSequence &refSeq, DNALength refPos, T_QuerySequence &querySeq, DNALength queryPos) {
- std::cout << "IDS. For now, this function must be specialized with either FASTQ or FASTA sequences"<<std::endl;
- exit(1);
- }
- int Insertion(T_QuerySequence &seq, DNALength pos) {
- std::cout << "IDS. For now, this function must be specialized with either FASTQ or FASTA sequences" << std::endl;
- return 0;
- exit(1);
- }
-
- float NormalizedMatch(T_RefSequence &ref, DNALength refPos, T_QuerySequence &query, DNALength queryPos);
- float NormalizedInsertion(T_RefSequence &ref, DNALength refPos, T_QuerySequence &query, DNALength queryPos);
- float NormalizedDeletion(T_RefSequence &ref, DNALength refPos, T_QuerySequence &query, DNALength queryPos);
-};
-
-/*
- * Define all specializations for a FASTA reference and FASTQSequence for the query, or FASTA sequence for query.
- */
-
-template<>
-int IDSScoreFunction<DNASequence,FASTQSequence>::Deletion(DNASequence &ref,
- DNALength refPos, FASTQSequence &query, DNALength queryPos);
-
-template<>
-int IDSScoreFunction<DNASequence, FASTQSequence>::Deletion(FASTQSequence &query,
- DNALength queryPos);
-
-template<>
-int IDSScoreFunction<DNASequence, DNASequence>::Deletion(DNASequence &query,
- DNALength pos);
-
-template<>
-int IDSScoreFunction<DNASequence, FASTQSequence>::Insertion(DNASequence &refSeq,
- DNALength refPos, FASTQSequence &query, DNALength pos);
-
-template<>
-int IDSScoreFunction<DNASequence, FASTQSequence>::Insertion(FASTQSequence &query,
- DNALength pos);
-
-template<>
-int IDSScoreFunction<DNASequence, FASTQSequence>::Match(DNASequence &ref,
- DNALength refPos, FASTQSequence &query, DNALength queryPos);
-
-template<>
-float IDSScoreFunction<DNASequence, FASTQSequence>::NormalizedMatch(
- DNASequence &ref, DNALength refPos, FASTQSequence &query, DNALength queryPos);
-
-template<>
-float IDSScoreFunction<DNASequence, FASTQSequence>::NormalizedInsertion(
- DNASequence &ref, DNALength refPos, FASTQSequence &query, DNALength queryPos);
-
-template<>
-float IDSScoreFunction<DNASequence, FASTQSequence>::NormalizedDeletion(
- DNASequence &ref, DNALength refPos, FASTQSequence &query, DNALength queryPos);
-
-#endif // _BLASR_IDS_SCORE_FUNCTION_HPP_
diff --git a/libcpp/alignment/algorithms/alignment/KBandAlign.cpp b/libcpp/alignment/algorithms/alignment/KBandAlign.cpp
deleted file mode 100644
index c25bb92..0000000
--- a/libcpp/alignment/algorithms/alignment/KBandAlign.cpp
+++ /dev/null
@@ -1,30 +0,0 @@
-#include "algorithms/alignment/KBandAlign.hpp"
-
-DefaultGuide::DefaultGuide() {}
-
-int DefaultGuide::operator()(int i) {
- return i;
-}
-
-void SetKBoundedLengths(DNALength tLength, DNALength qLength, DNALength k, DNALength &tLen, DNALength &qLen) {
- //
- // Determine how much of each read to align. If the query is
- // shorter than target - k, then it is impossible to align all the
- // way to the end of the target. Similar if the query is longer
- // than the target.
- //
- if (tLength < qLength) {
- tLen = tLength;
- qLen = MIN(qLength, tLength + k);
- }
- else if (qLength < tLength) {
- qLen = qLength;
- tLen = MIN(tLength, qLength + k);
- }
- else {
- // They are the same length, the diagonal will definitely fit the two.
- qLen = qLength;
- tLen = tLength;
- }
-}
-
diff --git a/libcpp/alignment/algorithms/alignment/KBandAlign.hpp b/libcpp/alignment/algorithms/alignment/KBandAlign.hpp
deleted file mode 100644
index 456c985..0000000
--- a/libcpp/alignment/algorithms/alignment/KBandAlign.hpp
+++ /dev/null
@@ -1,381 +0,0 @@
-#ifndef _BLASR_K_BAND_ALIGN_HPP_
-#define _BLASR_K_BAND_ALIGN_HPP_
-
-#include <algorithm>
-#include <vector>
-#include <limits.h>
-#include "defs.h"
-#include "AlignmentUtils.hpp"
-#include "NucConversion.hpp"
-#include "matrix/FlatMatrix.hpp"
-#include "datastructures/alignment/Alignment.hpp"
-#include "statistics/StatUtils.hpp"
-
-class DefaultGuide {
- public:
- DefaultGuide();
- int operator()(int i);
-};
-
-template<typename T_QuerySequence, typename T_TargetSequence, typename T_Alignment, typename T_ScoreFn>
-int KBandAlign(T_QuerySequence &pqSeq, T_TargetSequence &ptSeq,
- int matchMat[5][5], int ins, int del, DNALength k,
- std::vector<int> &scoreMat,
- std::vector<Arrow> & pathMat,
- T_Alignment &alignment,
- T_ScoreFn &scoreFn,
- AlignmentType alignType=Global,
- bool samplePaths=false) {
- return KBandAlign(pqSeq, ptSeq, matchMat, ins, del, k, scoreMat, pathMat, alignment, alignType, scoreFn, samplePaths);
-}
-
-void SetKBoundedLengths(DNALength tLength, DNALength qLength, DNALength k, DNALength &tLen, DNALength &qLen);
-
-template<typename T_Sequence>
-void CreateThreeBitSequence(T_Sequence &origSeq, T_Sequence &threeBitSeq) {
- //
- // Make a copy of the sequences that is guaranteed to be in 3-bit format.
- // This is 2 bits for A,C,T,and G, and an extra bit to signal masked sequence.
- //
-
- ResizeSequence(threeBitSeq, origSeq.length);
-
- VectorIndex i;
- for (i = 0; i < origSeq.length; i++ ) {
- threeBitSeq.seq[i] = ThreeBit[origSeq.seq[i]];
- }
-}
-
-
-template<typename T_QuerySequence, typename T_TargetSequence, typename T_Alignment, typename T_ScoreFn>
-int KBandAlign(T_QuerySequence &qSeq, T_TargetSequence &tSeq,
- int matchMat[5][5], int ins, int del, int k,
- std::vector<int> &scoreMat,
- std::vector<Arrow> &pathMat,
- T_Alignment &alignment,
- AlignmentType alignType,
- T_ScoreFn &scoreFn, bool samplePaths=false) {
-
- DNALength qLen, tLen;
- SetKBoundedLengths(tSeq.length, qSeq.length, k, tLen, qLen);
-
- //
- //
- // Allow for length up to diaonal + k + 1 for boundary.
- //
- // Allow for width:
- // diagonal (1)
- // up to k insertions (k)
- // up to k deletions (k)
- // boundary on left side of matrix (1)
- //
- DNALength nCols = 2*k + 1;
- DNALength totalMatSize = (qLen + 1) * nCols;
- alignment.nCells = totalMatSize;
- if (scoreMat.size() < totalMatSize) {
- scoreMat.resize(totalMatSize);
- pathMat.resize(totalMatSize);
- }
-
- //
- // Initialze matrices
- //
- std::fill(scoreMat.begin(), scoreMat.begin() + totalMatSize, 0);
- std::fill(pathMat.begin(), pathMat.begin() + totalMatSize, NoArrow);
-
- //
- // Initialize the boundaries of the score and path matrices.
- //
- int q, t;
-
- for (q = 1; q <= k && q < qLen + 1; q++) {
- scoreMat[rc2index(q, k - q, nCols)] = q * ins;
- pathMat[rc2index(q, k - q , nCols)] = Up;
- }
- if (alignType == Global) {
- for (t = 1; t <= k && t < tLen; t++) {
- scoreMat[rc2index(0, t + k , nCols)] = t * del;
- pathMat[rc2index(0, t + k , nCols)] = Left;
- }
- }
- if (alignType == QueryFit or alignType == Fit) {
- for (t = 1; t <= k & t < tLen; t++) {
- scoreMat[rc2index(0, t + k , nCols)] = 0;
- pathMat[rc2index(0, t + k , nCols)] = Left;
- }
- }
- if (alignType == TargetFit or alignType == Fit) {
- for (q = 1; q <= k & q < qLen; q++) {
- scoreMat[rc2index(q, 0, nCols)] = 0;
- pathMat[rc2index(q, 0, nCols)] = Up;
- }
- }
-
- //
- // Initialize the 0,0 position to be a match.
- //
- scoreMat[rc2index(0, k, nCols)] = 0;
- pathMat[rc2index(0, k, nCols)] = Diagonal;
-
- int matchScore, insScore, delScore;
-
- for (q = 1; q <= qLen; q++) {
- for (t = q - k; t < q + k + 1; t++) {
- if (t < 1)
- continue;
- if (t > tLen)
- continue;
-
- // On left boundary of k-band.
- // do not allow deletions of t.
- if (t == q - k) {
- delScore = INF_INT;
- }
- else {
- // cur row = q
- // cur col = t - q
- // prev col therefore t - q - 1
- // and offset from diagonal is k + t - q - 1
- delScore = scoreMat[rc2index(q, k + t - q - 1, nCols)] + scoreFn.Deletion(tSeq, (DNALength) t-1, qSeq, (DNALength)q-1);
- }
-
- // cur row = q
- // cur col = t - q
-
- // cur query index = q - 1
- // cur target index = t - 1
- // therefore match row (up) = q
- // match col (left, but since up shifted right) = t - q
- assert(rc2index(q - 1, k + t - q, nCols) < scoreMat.size());
- assert(t-1 >= 0);
- assert(q-1 >= 0);
- int tmpMatchScore = scoreFn.Match(tSeq, t-1, qSeq, q-1);
- matchScore = scoreMat[rc2index(q - 1, k + t - q, nCols)] + tmpMatchScore;
-
- //
- // Possibly on right boundary of k-band, in which
- // case do not allow insertions from q.
- if (t == q + k ) {
- insScore = INF_INT;
- }
- else {
- // cur row = q
- // cur col = t - q
- // therefore insertion col = t - q + 1
- insScore = scoreMat[rc2index(q-1, k + t - q+1, nCols)] + scoreFn.Insertion(tSeq, (DNALength) t-1, qSeq, q-1);
- }
-
- int minScore = MIN(matchScore, MIN(insScore, delScore));
- int curIndex = rc2index(q, k + t - q, nCols);
- assert(curIndex < scoreMat.size());
- scoreMat[curIndex] = minScore;
- int nEqual = 0;
- (matchScore == minScore ? nEqual++ : nEqual );
- (insScore == minScore ? nEqual++ : nEqual );
- (delScore == minScore ? nEqual++ : nEqual );
- if (samplePaths == false or nEqual == 1) {
- if (minScore == matchScore) {
- pathMat[curIndex] = Diagonal;
- }
- else if (minScore == delScore) {
- pathMat[curIndex] = Left;
- }
- else {
- pathMat[curIndex] = Up;
- }
- }
- else {
- //
- // When there are paths of equal score reaching
- //
- if (nEqual == 3) {
- int v = RandomInt(3);
- if (v == 0) { pathMat[curIndex] = Diagonal; }
- else if (v == 1) { pathMat[curIndex] = Left; }
- else if (v == 2) { pathMat[curIndex] = Up; }
- }
- else {
- assert(nEqual == 2);
- int v = RandomInt(2);
- if (matchScore == insScore) {
- if (v == 0) { pathMat[curIndex] = Diagonal; } else { pathMat[curIndex] = Up; }
- }
- else if (matchScore == delScore) {
- if (v == 0) { pathMat[curIndex] = Diagonal; } else { pathMat[curIndex] = Left; }
- }
- else if (delScore == insScore) {
- if (v == 0) { pathMat[curIndex] = Left; } else { pathMat[curIndex] = Up; }
- }
- else {
- std::cout << "ERROR, counted two values equal to the minimum but cannot find them." << std::endl;
- assert(0);
- }
- }
- alignment.nSampledPaths++;
- }
- }
- }
-
- //
- // Now create the alignment.
- //
-
- q = qLen ;
- t = k - (qLen - tLen);
-
- int globalMinScore;
- int minLastColScoreIndex, minLastRowScoreIndex;
- globalMinScore = scoreMat[rc2index(q,t,nCols)];
- int minLastColScore = globalMinScore, minLastRowScore = globalMinScore;
-
- if (alignType == QueryFit or alignType == Fit) {
- int q2,t2;
- q2 = qLen;
- t2 = k - (qLen - tLen);
- UInt qi, qend;
- bool minScoreSet = false;
- int minScoreIndex;
- for (t2 = q - k; t2 < q2 + k + 1; t2++) {
- if (t2 < 1)
- continue;
- if (t2 > tLen)
- continue;
- // std::cout << t2 << " " << tLen << " " << " " << scoreMat[rc2index(q2, k+t2-q,nCols)] << " " << minLastRowScore <<std::endl;
- if (minScoreSet == false or scoreMat[rc2index(q2, k+t2-q,nCols)] < minLastRowScore){
- minScoreSet = true;
- minLastRowScore = scoreMat[rc2index(q2,k+t2-q,nCols)];
- minLastRowScoreIndex = t2;
- }
- }
- if (minScoreSet) {
- t2 = k - (q - minLastRowScoreIndex);
- t = t2;
- q = q2;
- }
- }
- if (alignType == TargetFit or alignType == Fit) {
- // Fit the target inside the query wh
- int q2,t2;
- q2 = qLen;
- t2 = k - (qLen - tLen);
- bool minScoreSet = false;
- for (q2 = qLen; q2 >= tLen - k and q2 > 0; q2--) {
- int index = rc2index(q2, k+tLen-q2, nCols);
- if (minScoreSet == false or scoreMat[index] < minLastColScore) {
- minLastColScore = scoreMat[index];
- minScoreSet = true;
- minLastColScoreIndex = q2;
- }
- }
- if (alignType == Fit) {
- if (minLastColScore < minLastRowScore) {
- t = t2;
- q = minLastColScoreIndex;
- }
- }
- else if (alignType == TargetFit) {
- t = t2;
- q = minLastColScoreIndex;
- }
- }
-
- std::vector<Arrow> optAlignment;
- int optScore = scoreMat[rc2index(q, t, nCols)];
- Arrow arrow;
- /*
- PrintFlatMatrix(&pathMat[0], qLen + 1, nCols, debugOut);
- std::cout << std::endl;
- ofstream debugOut;
- stringstream debugOutName;
- debugOutName << "kband_" << kbandcounter << ".table";
- debugOut.open(debugOutName.str().c_str());
- PrintFlatMatrix(&scoreMat[0], qLen + 1, nCols, debugOut);
- kbandcounter++;
- */
- /*
- std::cout << std::endl;
- */
- //
- // Use some logic to deal with unsigned types. When t > k, t must
- // also be greater than 0, so it's not worth checking to see if it
- // hits a boundary.
- //
- if (alignType == Global or alignType == QueryFit) {
- while (q > 0 and (t < k ? (k - t != q) : true)) {
- arrow = pathMat[rc2index(q,t, nCols)];
- if (arrow == NoArrow) {
- break;
- }
- optAlignment.push_back(arrow);
- if (arrow == Diagonal) {
- q--;
- }
- else if (arrow == Up) {
- q--;
- t++;
- }
- else if (arrow == Left) {
- t--;
- }
- }
- }
- else if (alignType == Fit) {
- while (q > 0 and (t < k ? (k - t != q) : true) and ( q <= k ? k - q != t : true) ) {
- arrow = pathMat[rc2index(q,t, nCols)];
- if (arrow == NoArrow) {
- break;
- }
- optAlignment.push_back(arrow);
- if (arrow == Diagonal) {
- q--;
- }
- else if (arrow == Up) {
- q--;
- t++;
- }
- else if (arrow == Left) {
- t--;
- }
- }
- }
- else if (alignType == TargetFit) {
- while (q > 0 and ( q < k ? k - q != t : true) ) {
- arrow = pathMat[rc2index(q,t, nCols)];
- if (arrow == NoArrow) {
- break;
- }
- optAlignment.push_back(arrow);
- if (arrow == Diagonal) {
- q--;
- }
- else if (arrow == Up) {
- q--;
- t++;
- }
- else if (arrow == Left) {
- t--;
- }
- }
- }
-
- // remove the boundary condition.
- //optAlignment.pop_back();
- // qSeq.Free();
- // tSeq.Free();
- alignment.qPos = q;
-
- //
- // Use a little extra logic to deal with the unsignedness of indices.
- //
- if (t < k) {
- alignment.tPos = (k - t) - q;
- }
- else {
- alignment.tPos = (t - k) - q;
- }
- std::reverse(optAlignment.begin(), optAlignment.end());
- alignment.ArrowPathToAlignment(optAlignment);
- return optScore;
-}
-
-#endif // _BLASR_K_BAND_ALIGN_HPP_
diff --git a/libcpp/alignment/algorithms/alignment/OneGapAlignment.hpp b/libcpp/alignment/algorithms/alignment/OneGapAlignment.hpp
deleted file mode 100644
index 33405e6..0000000
--- a/libcpp/alignment/algorithms/alignment/OneGapAlignment.hpp
+++ /dev/null
@@ -1,374 +0,0 @@
-#ifndef _BLASR_ONEGAP_ALIGNMENT_HPP_
-#define _BLASR_ONEGAP_ALIGNMENT_HPP_
-
-#include <limits.h>
-#include "Types.h"
-#include "FASTQSequence.hpp"
-#include "matrix/FlatMatrix.hpp"
-#include "datastructures/alignment/Path.h"
-#include "datastructures/alignment/Alignment.hpp"
-
-/*
- Perform gapped alignment that aligns the entire query sequence to
- leftTarget, rightTarget, or between the two with a gap in between.
- The gap between leftTarget and rightTarget is an affine gap.
- */
-
-template<typename T_QuerySequence, typename T_RefSequence, typename T_ScoreFunction>
-int OneGapAlign(T_QuerySequence &query,
- T_RefSequence &leftTarget,
- T_RefSequence &rightTarget,
- DNALength distanceBetweenLeftAndRightTarget,
- T_ScoreFunction &scoreFn,
- Alignment &alignment,
- FlatMatrix2D<int> & scoreMat, FlatMatrix2D<Arrow> & pathMat,
- FlatMatrix2D<int> &affineScoreMat, FlatMatrix2D<Arrow> &affinePathMat) {
-
- /*
- Perform alignment that spans what is effectively two pairs of
- matrices. This is implemented as a single matrix, however paths
- may only transition through the boundary between the two through
- the affine portion of the matrices.
-
- leftTarget rightTarget
- affine |==============|
- | x------>x |
- | ^ | |
- |===|=======|==|
- | |
- regular |===|=+||===|=+|
- | x || | |
- | || v |
- |======||======|
-
-
-*/
-
-
- UInt nQueryRows, nLeftTargetCols, nRightTargetCols;
- UInt nTargetCols;
- nQueryRows = query.length + 1;
- nLeftTargetCols = leftTarget.length + 1;
- nRightTargetCols = rightTarget.length;
- nTargetCols = nLeftTargetCols + nRightTargetCols;
-
- //
- // Create the matrices
- //
- affineScoreMat.Grow(nQueryRows, nTargetCols);
- affinePathMat.Grow(nQueryRows, nTargetCols);
-
- scoreMat.Grow(nQueryRows, nTargetCols);
- pathMat.Grow(nQueryRows, nTargetCols);
-
- //
- // Initialize to undefined for debugging purposes.
- //
- affineScoreMat.Initialize(0);
- affinePathMat.Initialize(NoArrow);
-
- scoreMat.Initialize(0);
- pathMat.Initialize(NoArrow);
-
- // Initialize insertion and deletion strips
- UInt i, j;
- scoreMat[0][0] = 0;
- pathMat[0][0] = NoArrow;
- affineScoreMat[0][0] = 0;
- // always drop down to 0,0 at end of affine gap.
- affinePathMat[0][0] = AffineDelOpen;
- for (i = 1; i < nQueryRows; i++) {
- scoreMat[i][0] = scoreMat[i-1][0] + scoreFn.ins;
- pathMat[i][0] = Up;
- //
- // Affine gaps can only start here.
- //
- affineScoreMat[i][0] = scoreMat[i][0];
- affinePathMat[i][0] = AffineDelOpen;
- }
-
- for (j = 1; j < nTargetCols; j++) {
- scoreMat[0][j] = scoreMat[0][j-1] + scoreFn.del;
- pathMat[0][j] = Left;
- //
- // Allow free affine transition across first row.
- //
- affineScoreMat[0][j] = 0;
- affinePathMat[0][j] = Left;
- }
-
-
- // Now run the alignment.
- // i and j index over positions in the query/target sequences, or
- // [0,len(seq)). Since the score mat are of length len(seq) + 1,
- // the indices of the score matrices are [1, len(seq) + 1)
- for (i = 0; i < query.length; i++) {
-
- //
- // First align a row of the left target, allowing for transition
- // up to the big affine gap. No transitions down from affine gap
- // are allowed.
- //
- for (j = 0; j < leftTarget.length; j++) {
- //
- // First, assign the non-affine score.
- //
- int matchScore, insScore, delScore;
- // Remember mapping:
- // scoreMat[i+1][j+1] = position to fill
- // scoreMat[i+1][j] ==> back one column
- // scoreMat[i][j+1] ==> up one row.
- matchScore = scoreMat[i][j] + scoreFn.Match(leftTarget, j, query, i);
- insScore = scoreMat[i][j+1] + scoreFn.Insertion(leftTarget, j, query, i);
- delScore = scoreMat[i+1][j] + scoreFn.Deletion(leftTarget, j, query, i);
-
- int minScore = min(matchScore, min(insScore, delScore));
- scoreMat[i+1][j+1] = minScore;
-
-
- // set path.
- if (matchScore == minScore) {
- pathMat[i+1][j+1] = Diagonal;
- }
- else if (insScore == minScore) {
- pathMat[i+1][j+1] = Up;
- }
- else {
- assert(delScore == minScore);
- pathMat[i+1][j+1] = Left;
- }
-
- //
- // Next, assign the affine score
- //
- if (affineScoreMat[i+1][j] < scoreMat[i+1][j+1]) {
- affineScoreMat[i+1][j+1] = affineScoreMat[i+1][j];
- affinePathMat[i+1][j+1] = Left;
- }
- else {
- // Allow free gap open... maybe this will change.
- affineScoreMat[i+1][j+1] = scoreMat[i+1][j+1];
- affinePathMat[i+1][j+1] = AffineDelOpen;
- }
- }
-
- //
- // Now align the right target, allowing a jump over the divide.
- //
- int affineCloseScore;
- j = 0;
- //
- // A match here may only be preceded by an affine gap close.
- //
- int matchScore, delScore, insScore, minScore;
- matchScore = affineScoreMat[i][leftTarget.length] + scoreFn.Match(rightTarget, j, query, i);
- //
- // Cannot have a non-affine deletion here.
- delScore = INT_MAX;
- //
- // The insertion is a horizontal move, so that is all allowed.
- //
- insScore = scoreFn.Insertion(rightTarget, j, query, i - 1);
-
-
- minScore = min(matchScore, insScore);
- UInt targetCol = leftTarget.length;
-
- assert(scoreMat[i+1][targetCol+1] == 0);
- assert(pathMat[i+1][targetCol+1] == NoArrow);
- scoreMat[i+1][targetCol+1] = minScore;
-
- if (minScore == matchScore) {
- pathMat[i+1][targetCol+1] = AffineLongDelClose;
- }
- else {
- assert(minScore == insScore);
- pathMat[i+1][targetCol+1] = Up;
- }
-
- //
- // The affine matrix on the right side can only progress forward.
- //
- affineScoreMat[i+1][targetCol+1] = affineScoreMat[i+1][targetCol];
- affinePathMat[i+1][targetCol+1] = AffineLongDelLeft;
-
-
- for (j = 1; j < rightTarget.length; j++) {
- targetCol = leftTarget.length + j;
- matchScore = scoreMat[i][targetCol] + scoreFn.Match(rightTarget, j, query, i);
- insScore = scoreMat[i][targetCol+1] + scoreFn.Insertion(rightTarget, j, query, i);
- delScore = scoreMat[i+1][targetCol] + scoreFn.Deletion(rightTarget, j, query, i);
- affineCloseScore = affineScoreMat[i][targetCol] + scoreFn.Match(rightTarget, j, query, i);
-
- minScore = min(matchScore, min(insScore, min(delScore, affineCloseScore)));
-
- scoreMat[i+1][targetCol+1] = minScore;
- if (minScore == matchScore) {
- pathMat[i+1][targetCol+1] = Diagonal;
- }
- else if (minScore == insScore) {
- pathMat[i+1][targetCol+1] = Up;
- }
- else if (minScore == delScore) {
- pathMat[i+1][targetCol+1] = Left;
- }
- else {
- assert(minScore == affineCloseScore);
- pathMat[i+1][targetCol+1] = AffineLongDelClose;
- }
-
- //
- // As with before, the affine matrix on the right side can
- // only progress forward.
- //
- affineScoreMat[i+1][targetCol+1] = affineScoreMat[i+1][targetCol];
- affinePathMat[i+1][targetCol+1] = Left;
- } // done aligning right target
- } // done aligning full query
-
- //
- // Now build the alignment string
- //
- i = nQueryRows - 1;
- j = nTargetCols - 1;
- vector<Arrow> optAlignment;
-
- int REGULAR = 0;
- int AFFINE = 1;
-
- int curMatrix = REGULAR;
- Arrow arrow;
-
- /*
- cout << "score " << endl;
- PrintFlatMatrix(scoreMat.matrix, scoreMat.nRows, scoreMat.nCols, cout, 3);
- cout << "path " << endl;
- PrintFlatMatrix(pathMat.matrix, scoreMat.nRows, scoreMat.nCols, cout, 3);
- cout << "affine score " << endl;
- PrintFlatMatrix(affineScoreMat.matrix, scoreMat.nRows, scoreMat.nCols, cout, 3);
- cout << "affine path " << endl;
- PrintFlatMatrix(affinePathMat.matrix, scoreMat.nRows, scoreMat.nCols, cout, 3);
- */
- int optScore = scoreMat[i][j];
- while (i > 0 or j > 0 or curMatrix == AFFINE) {
- if (curMatrix == REGULAR) {
- arrow = pathMat[i][j];
- if (arrow == Diagonal) {
- optAlignment.push_back(arrow);
- i--;
- j--;
- }
- else if (arrow == Left) {
- optAlignment.push_back(arrow);
-
- j--;
- }
- else if (arrow == Up) {
- optAlignment.push_back(arrow);
- i--;
- }
- else if (arrow == AffineLongDelClose) {
- optAlignment.push_back(Left);
- j--;
- i--;
- curMatrix = AFFINE;
- }
- }
- else {
- // in affine matrix
- arrow = affinePathMat[i][j];
- if (arrow == Left or arrow == AffineLongDelLeft) {
- optAlignment.push_back(arrow);
- j--;
- }
- else if (arrow == AffineDelOpen) {
- //
- // no change in i nor j, and this does not result in an
- // arrow.
- // Drop down to the regular alignment matrix.
- //
- curMatrix = REGULAR;
- }
- }
- assert(arrow != NoArrow);
- //
- // Check for wrap around.
- //
- assert(i != UINT_MAX);
- assert(j != UINT_MAX);
- } // done tracing alignment path.
- std::reverse(optAlignment.begin(), optAlignment.end());
- alignment.LongGapArrowPathToAlignment(optAlignment, distanceBetweenLeftAndRightTarget);
- return optScore;
-}
-
-//
-// Create a version that does not need reusable mapping buffers.
-//
-
-template<typename T_QuerySequence, typename T_RefSequence, typename T_ScoreFunction>
-int OneGapAlign(T_QuerySequence &query,
- T_RefSequence &leftTarget,
- T_RefSequence &rightTarget,
- DNALength distanceBetweenLeftAndRightTarget,
- T_ScoreFunction &scoreFn,
- Alignment &alignment) {
-
- FlatMatrix2D<int> scoreMat;
- FlatMatrix2D<int> affineScoreMat;
- FlatMatrix2D<Arrow> pathMat;
- FlatMatrix2D<Arrow> affinePathMat;
-
-
- return OneGapAlign(query, leftTarget, rightTarget,
- distanceBetweenLeftAndRightTarget,
- scoreFn,
- alignment,
- scoreMat, pathMat,
- affineScoreMat, affinePathMat);
-}
-
-
-template<typename T_QuerySequence, typename T_RefSequence, typename T_ScoreFunction, typename T_BufferList>
-int OneGapAlign(T_QuerySequence &query,
- T_RefSequence &leftTarget,
- T_RefSequence &rightTarget,
- DNALength distanceBetweenLeftAndRightTarget,
- T_ScoreFunction &scoreFn,
- T_BufferList &buffers,
- Alignment &alignment) {
-
- return OneGapAlign(query, leftTarget, rightTarget, distanceBetweenLeftAndRightTarget, alignment,
- buffers.scoreMat, buffers.pathMat,
- buffers.affineScoreMat, buffers.affinePathMat);
-
-}
-
-template<typename T_QuerySequence, typename T_RefSequence, typename T_ScoreFunction, typename T_BufferList>
-int OneGapAlign(T_QuerySequence &query,
- T_RefSequence &reference,
- T_ScoreFunction &scoreFunction,
- T_BufferList &buffers,
- Alignment &alignment) {
-
- T_RefSequence leftReference, rightReference;
- UInt leftReferenceLength = min(reference.length, query.length);
- leftReference.ReferenceSubstring(reference, 0, leftReferenceLength);
-
- UInt rightReferenceLength = min(reference.length - leftReferenceLength, query.length);
- rightReference.ReferenceSubstring(reference, reference.length - rightReferenceLength, rightReferenceLength);
-
- DNALength distanceBetweenLeftAndRight = reference.length - rightReferenceLength - leftReferenceLength;
-
- assert(distanceBetweenLeftAndRight >= 0);
-
- return OneGapAlign(query,
- leftReference,
- rightReference,
- distanceBetweenLeftAndRight,
- scoreFunction, alignment);
-}
-
-
-
-#endif // _BLASR_ONEGAP_ALIGNMENT_HPP_
diff --git a/libcpp/alignment/algorithms/alignment/QualityValueScoreFunction.cpp b/libcpp/alignment/algorithms/alignment/QualityValueScoreFunction.cpp
deleted file mode 100644
index c73b49e..0000000
--- a/libcpp/alignment/algorithms/alignment/QualityValueScoreFunction.cpp
+++ /dev/null
@@ -1,90 +0,0 @@
-#include "QualityValueScoreFunction.hpp"
-
-int QualityScoreTypeNotSpecified(const std::string func) {
- std::cout << func << " must be specialized with FASTQ or "
- << "FASTA sequencecs." << std::endl;
- exit(1);
- return 0;
-}
-
-template<typename T_RefSequence, typename T_QuerySequence>
-int QualityValueScoreFunction<T_RefSequence, T_QuerySequence>::Deletion(
- T_RefSequence &seq, DNALength refPos, T_QuerySequence &querySeq,
- DNALength queryPos) {
- return QualityScoreTypeNotSpecified("Deletion");
-}
-
-template<typename T_RefSequence, typename T_QuerySequence>
-int QualityValueScoreFunction<T_RefSequence, T_QuerySequence>::Deletion(
- T_RefSequence &seq, DNALength pos) {
- return QualityScoreTypeNotSpecified("Deletion");
-}
-
-template<typename T_RefSequence, typename T_QuerySequence>
-int QualityValueScoreFunction<T_RefSequence, T_QuerySequence>::Match(
- T_RefSequence &ref, DNALength refPos, T_QuerySequence &query,
- DNALength queryPos) {
- return QualityScoreTypeNotSpecified("Match");
-}
-
-template<typename T_RefSequence, typename T_QuerySequence>
-int QualityValueScoreFunction<T_RefSequence, T_QuerySequence>::Insertion(
- T_RefSequence &ref, DNALength refPos, T_QuerySequence &seq,
- DNALength pos) {
- return QualityScoreTypeNotSpecified("Insertion");
-}
-
-template<typename T_RefSequence, typename T_QuerySequence>
-int QualityValueScoreFunction<T_RefSequence, T_QuerySequence>::Insertion(
- T_QuerySequence &seq, DNALength pos) {
- return QualityScoreTypeNotSpecified("Insertion");
-}
-
-/*
- * Define all specializations for a FASTA reference and FASTQSequence
- * for the query, or FASTA sequence for query.
- */
-template<>
-int QualityValueScoreFunction<FASTASequence, FASTQSequence>::Deletion(
- FASTASequence &ref, DNALength pos) {
- return del; // For now there is no global deletion quality value.
-}
-
-template<>
-int QualityValueScoreFunction<DNASequence, FASTQSequence>::Deletion(
- DNASequence &ref, DNALength pos) {
- return del; // For now there is no global deletion quality value.
-}
-
-template<>
-int QualityValueScoreFunction<DNASequence, FASTQSequence>::Deletion(
- DNASequence &seq, DNALength refPos, FASTQSequence &querySeq,
- DNALength queryPos) {
- return Deletion(seq, refPos);
-}
-
-template<>
-int QualityValueScoreFunction<DNASequence, FASTQSequence>::Insertion(
- FASTQSequence &query, DNALength pos) {
- // Positive value for quality value penalizes the alignment.
- return query.qual[pos];
-}
-
-template<>
-int QualityValueScoreFunction<DNASequence, FASTQSequence>::Insertion(
- DNASequence &ref, DNALength refPos, FASTQSequence &query,
- DNALength pos) {
- // Positive value for quality value penalizes the alignment.
- // return query.qual[pos];
- // return Insertion(query, pos);
- return ins;
-}
-
-template<>
-int QualityValueScoreFunction<DNASequence, FASTQSequence>::Match(
- DNASequence &ref, DNALength refPos, FASTQSequence &query,
- DNALength queryPos) {
- // Positive value for quality value penalizes the alignment.
- return (QVDistanceMatrix[ThreeBit[query.seq[queryPos]]][ThreeBit[ref.seq[refPos]]]
- * query.qual[queryPos]);
-}
diff --git a/libcpp/alignment/algorithms/alignment/QualityValueScoreFunction.hpp b/libcpp/alignment/algorithms/alignment/QualityValueScoreFunction.hpp
deleted file mode 100644
index 670b42f..0000000
--- a/libcpp/alignment/algorithms/alignment/QualityValueScoreFunction.hpp
+++ /dev/null
@@ -1,56 +0,0 @@
-#ifndef _BLASR_QUALITY_VALUE_SCORE_FUNCTION_HPP_
-#define _BLASR_QUALITY_VALUE_SCORE_FUNCTION_HPP_
-#include "FASTASequence.hpp"
-#include "FASTQSequence.hpp"
-#include "NucConversion.hpp"
-#include "ScoreMatrices.hpp"
-#include "BaseScoreFunction.hpp"
-
-template<typename T_RefSequence, typename T_QuerySequence>
-class QualityValueScoreFunction: public BaseScoreFunction{
-public:
- int Deletion(T_RefSequence &seq, DNALength refPos,
- T_QuerySequence &querySeq, DNALength queryPos);
- int Deletion(T_RefSequence &seq, DNALength pos);
-
- int Match(T_RefSequence &ref, DNALength refPos,
- T_QuerySequence &query, DNALength queryPos);
-
- int Insertion(T_RefSequence &ref, DNALength refPos,
- T_QuerySequence &seq, DNALength pos);
- int Insertion(T_QuerySequence &seq, DNALength pos);
-};
-
-
-//
-// Define all specializations for a FASTA reference and
-// FASTQSequence for the query, or FASTA sequence for query.
-//
-template<>
-int QualityValueScoreFunction<FASTASequence, FASTQSequence>::Deletion(
- FASTASequence &ref, DNALength pos);
-
-template<>
-int QualityValueScoreFunction<DNASequence, FASTQSequence>::Deletion(
- DNASequence &ref, DNALength pos);
-
-template<>
-int QualityValueScoreFunction<DNASequence, FASTQSequence>::Deletion(
- DNASequence &seq, DNALength refPos, FASTQSequence &querySeq,
- DNALength queryPos);
-
-template<>
-int QualityValueScoreFunction<DNASequence, FASTQSequence>::Insertion(
- FASTQSequence &query, DNALength pos);
-
-template<>
-int QualityValueScoreFunction<DNASequence, FASTQSequence>::Insertion(
- DNASequence &ref, DNALength refPos, FASTQSequence &query,
- DNALength pos);
-
-template<>
-int QualityValueScoreFunction<DNASequence, FASTQSequence>::Match(
- DNASequence &ref, DNALength refPos, FASTQSequence &query,
- DNALength queryPos);
-
-#endif
diff --git a/libcpp/alignment/algorithms/alignment/SDPAlign.hpp b/libcpp/alignment/algorithms/alignment/SDPAlign.hpp
deleted file mode 100644
index 14c3b23..0000000
--- a/libcpp/alignment/algorithms/alignment/SDPAlign.hpp
+++ /dev/null
@@ -1,64 +0,0 @@
-#ifndef _BLASR_SDP_ALIGN_HPP_
-#define _BLASR_SDP_ALIGN_HPP_
-
-#include "DNASequence.hpp"
-#include "tuples/TupleMatching.hpp"
-#include "sdp/SDPFragment.hpp"
-#include "FASTASequence.hpp"
-#include "FASTQSequence.hpp"
-#include "DistanceMatrixScoreFunction.hpp"
-
-#define SDP_DETAILED_WORD_SIZE 5
-#define SDP_PREFIX_LENGTH 50
-#define SDP_SUFFIX_LENGTH 50
-
-template<typename T_QuerySequence, typename T_TargetSequence, typename T_ScoreFn>
-int SDPAlign(T_QuerySequence &query, T_TargetSequence &target,
- T_ScoreFn &scoreFn, int wordSize,
- int sdpIns, int sdpDel, float indelRate,
- blasr::Alignment &alignment,
- AlignmentType alignType=Global,
- bool detailedAlignment=true,
- bool extendFrontByLocalAlignment=true,
- DNALength noRecurseUnder=10000,
- bool fastSDP=true,
- unsigned int minFragmentsToUseGraphPaper=100000);
-
-
-template<typename T_QuerySequence, typename T_TargetSequence, typename T_ScoreFn, typename T_BufferCache>
-int SDPAlign(T_QuerySequence &query, T_TargetSequence &target,
- T_ScoreFn &scoreFn, int wordSize,
- int sdpIns, int sdpDel, float indelRate,
- blasr::Alignment &alignment,
- T_BufferCache &buffers,
- AlignmentType alignType=Global,
- bool detailedAlignment=true,
- bool extendFrontByLocalAlignment=true,
- DNALength noRecurseUnder=10000,
- bool fastSDP=true,
- unsigned int minFragmentsToUseGraphPaper=100000);
-
-template<typename T_QuerySequence, typename T_TargetSequence, typename T_ScoreFn, typename T_TupleList>
-int SDPAlign(T_QuerySequence &query, T_TargetSequence &target,
- T_ScoreFn &scoreFn,
- int wordSize,
- int sdpIns, int sdpDel, float indelRate,
- blasr::Alignment &alignment,
- std::vector<Fragment> &fragmentSet,
- std::vector<Fragment> &prefixFragmentSet,
- std::vector<Fragment> &suffixFragmentSet,
- T_TupleList &targetTupleList,
- T_TupleList &targetPrefixTupleList,
- T_TupleList &targetSuffixTupleList,
- std::vector<int> &maxFragmentChain,
- // A few optinal parameters, should delete that last one.
- AlignmentType alignType=Global,
- bool detailedAlignment=true,
- bool extendFrontByLocalAlignment=true,
- DNALength noRecurseUnder=10000,
- bool fastSDP=true,
- unsigned int minFragmentsToUseGraphPaper=100000);
-
-#include "SDPAlignImpl.hpp"
-
-#endif // _BLASR_SDP_ALIGN_HPP_
diff --git a/libcpp/alignment/algorithms/alignment/SDPAlignImpl.hpp b/libcpp/alignment/algorithms/alignment/SDPAlignImpl.hpp
deleted file mode 100644
index 140b667..0000000
--- a/libcpp/alignment/algorithms/alignment/SDPAlignImpl.hpp
+++ /dev/null
@@ -1,614 +0,0 @@
-#ifndef _BLASR_SDP_ALIGN_IMPL_HPP_
-#define _BLASR_SDP_ALIGN_IMPL_HPP_
-
-#include <cstddef>
-#include <vector>
-#include <math.h>
-#include <cstdlib>
-#include <ostream>
-#include "Types.h"
-#include "defs.h"
-#include "utils.hpp"
-#include "Enumerations.h"
-#include "DNASequence.hpp"
-#include "matrix/FlatMatrix.hpp"
-#include "datastructures/alignment/Alignment.hpp"
-#include "sdp/SDPFragment.hpp"
-#include "GraphPaper.hpp"
-#include "AlignmentUtils.hpp"
-#include "SWAlign.hpp"
-#include "sdp/SparseDynamicProgramming.hpp"
-#include "SDPAlign.hpp"
-
-template<typename T_QuerySequence, typename T_TargetSequence, typename T_ScoreFn>
-int SDPAlign(T_QuerySequence &query, T_TargetSequence &target,
- T_ScoreFn &scoreFn, int wordSize,
- int sdpIns, int sdpDel, float indelRate,
- blasr::Alignment &alignment,
- AlignmentType alignType,
- bool detailedAlignment,
- bool extendFrontByLocalAlignment,
- DNALength noRecurseUnder,
- bool fastSDP,
- unsigned int minFragmentsToUseGraphPaper) {
- /*
- Since SDP Align uses a large list of buffers, but none are
- provided with this mechanism of calling SDPAlign, allocate the
- buffers on the stack.
- */
- std::vector<Fragment> fragmentSet, prefixFragmentSet, suffixFragmentSet;
- TupleList<PositionDNATuple> targetTupleList;
- TupleList<PositionDNATuple> targetPrefixTupleList;
- TupleList<PositionDNATuple> targetSuffixTupleList;
- std::vector<int> maxFragmentChain;
-
- return SDPAlign(query, target,
- scoreFn, wordSize,
- sdpIns, sdpDel, indelRate,
- alignment,
- fragmentSet, prefixFragmentSet, suffixFragmentSet,
- targetTupleList, targetPrefixTupleList, targetSuffixTupleList,
- maxFragmentChain,
- alignType,
- detailedAlignment,
- extendFrontByLocalAlignment,
- noRecurseUnder,
- minFragmentsToUseGraphPaper);
-}
-
-template<typename T_QuerySequence, typename T_TargetSequence, typename T_ScoreFn, typename T_BufferCache>
-int SDPAlign(T_QuerySequence &query, T_TargetSequence &target,
- T_ScoreFn &scoreFn, int wordSize,
- int sdpIns, int sdpDel, float indelRate,
- blasr::Alignment &alignment,
- T_BufferCache &buffers,
- AlignmentType alignType,
- bool detailedAlignment,
- bool extendFrontByLocalAlignment,
- DNALength noRecurseUnder,
- bool fastSDP,
- unsigned int minFragmentsToUseGraphPaper) {
-
- return SDPAlign(query, target, scoreFn, wordSize,
- sdpIns, sdpDel, indelRate,
- alignment,
- buffers.sdpFragmentSet,
- buffers.sdpPrefixFragmentSet,
- buffers.sdpSuffixFragmentSet,
- buffers.sdpCachedTargetTupleList,
- buffers.sdpCachedTargetPrefixTupleList,
- buffers.sdpCachedTargetSuffixTupleList,
- buffers.sdpCachedMaxFragmentChain,
- alignType, detailedAlignment,
- extendFrontByLocalAlignment, noRecurseUnder,
- fastSDP, minFragmentsToUseGraphPaper);
-}
-
-template<typename T_QuerySequence, typename T_TargetSequence, typename T_ScoreFn, typename T_TupleList>
-int SDPAlign(T_QuerySequence &query, T_TargetSequence &target,
- T_ScoreFn &scoreFn,
- int wordSize,
- int sdpIns, int sdpDel, float indelRate,
- blasr::Alignment &alignment,
- std::vector<Fragment> &fragmentSet,
- std::vector<Fragment> &prefixFragmentSet,
- std::vector<Fragment> &suffixFragmentSet,
- T_TupleList &targetTupleList,
- T_TupleList &targetPrefixTupleList,
- T_TupleList &targetSuffixTupleList,
- std::vector<int> &maxFragmentChain,
- // A few optinal parameters, should delete that last one.
- AlignmentType alignType,
- bool detailedAlignment,
- bool extendFrontByLocalAlignment,
- DNALength noRecurseUnder,
- bool fastSDP,
- unsigned int minFragmentsToUseGraphPaper) {
- // minFragmentsToUseGraphPaper: minimum number of fragments to
- // use Graph Paper for speed up.
-
- fragmentSet.clear();
- prefixFragmentSet.clear();
- suffixFragmentSet.clear();
- targetTupleList.clear();
- targetPrefixTupleList.clear();
- targetSuffixTupleList.clear();
- maxFragmentChain.clear();
-
- //
- // Collect a set of matching fragments between query and target.
- // Since this function is an inner-loop for alignment, anything to
- // speed it up will help. One way to speed it up is to re-use the
- // vectors that contain the sdp matches.
- //
-
- TupleMetrics tm, tmSmall;
- tm.Initialize(wordSize);
-
- int smallWordSize = (wordSize < SDP_DETAILED_WORD_SIZE ? wordSize : SDP_DETAILED_WORD_SIZE);
- tmSmall.Initialize(smallWordSize);
-
- //
- // Partition the read into a prefix, middle, and suffix. The prefix
- // and suffix are matched using a smaller word size allowing for
- // higher sensitivity at the ends of reads, which are more likely to
- // be misaligned.
- //
- int prefixLength, middleLength, suffixLength, middlePos, suffixPos; // prefix pos is 0
- prefixLength = min(target.length, (DNALength) SDP_PREFIX_LENGTH);
- suffixLength = min(target.length - prefixLength, (DNALength) SDP_SUFFIX_LENGTH);
- middleLength = target.length - prefixLength - suffixLength;
-
- DNASequence prefix, middle, suffix;
- DNASequence qPrefix, qMiddle, qSuffix;
- DNALength pos = 0;
- prefix.seq = &target.seq[pos];
- prefix.length = prefixLength;
- pos += prefixLength;
-
- // Align the entire query against the entire target to get alignments
- // in the middle.
- middlePos = 0;
- middle.seq = &target.seq[0];
- middle.length = target.length;
-
- pos += middleLength;
- suffixPos = pos; // while = prefixLength + middleLength
- suffix.seq = &target.seq[suffixPos];
- suffix.length = suffixLength;
-
- int qPrefixLength, qMiddleLength, qSuffixLength, qMiddlePos, qSuffixPos; // prefix pos is 0
- qPrefixLength = min(query.length, (DNALength) SDP_PREFIX_LENGTH);
- qSuffixLength = min(query.length - qPrefixLength, (DNALength) SDP_SUFFIX_LENGTH);
- qMiddleLength = query.length - qPrefixLength - qSuffixLength;
-
- pos = 0;
- qPrefix.seq = &query.seq[pos];
- qPrefix.length = qPrefixLength;
-
- // Align the entire query against the entire target to get alignments
- // in the middle.
- qMiddle.seq = &query.seq[0];
- qMiddle.length = query.length;
- qMiddlePos = pos += qPrefixLength;
-
- qSuffixPos = pos += qMiddleLength; // = qPrefixLength + qMiddleLength
- qSuffix.seq = &query.seq[qSuffixPos];
- qSuffix.length = qSuffixLength;
-
- fragmentSet.clear();
- SequenceToTupleList(prefix, tmSmall, targetPrefixTupleList);
- SequenceToTupleList(suffix, tmSmall, targetSuffixTupleList);
- SequenceToTupleList(middle, tm, targetTupleList);
-
- targetPrefixTupleList.Sort();
- targetSuffixTupleList.Sort();
- targetTupleList.Sort();
-
-
- //
- // Store in fragmentSet the tuples that match between the target
- // and query.
- //
- StoreMatchingPositions(qPrefix, tmSmall, targetPrefixTupleList, prefixFragmentSet);
- StoreMatchingPositions(qSuffix, tmSmall, targetSuffixTupleList, suffixFragmentSet);
- StoreMatchingPositions(qMiddle, tm, targetTupleList, fragmentSet);
-
- //
- // The method to store matching positions is not weight aware.
- // Store the weight here.
- //
- VectorIndex f;
-
- for (f = 0; f < suffixFragmentSet.size(); f++) {
- (suffixFragmentSet)[f].weight = tm.tupleSize;
- (suffixFragmentSet)[f].length = tmSmall.tupleSize;
- }
- for (f = 0; f < prefixFragmentSet.size(); f++) {
- (prefixFragmentSet)[f].weight = tm.tupleSize;
- (prefixFragmentSet)[f].length = tmSmall.tupleSize;
- }
- for (f = 0; f < fragmentSet.size(); f++) {
- (fragmentSet)[f].weight = tm.tupleSize;
- (fragmentSet)[f].length = tm.tupleSize;
- }
-
- //
- // Since different partitions of the read are matched, the locations
- // of the matches do not have the correct position because of the
- // offsets. Fix that here.
- for (f = 0; f < suffixFragmentSet.size(); f++) {
- (suffixFragmentSet)[f].x += qSuffixPos;
- (suffixFragmentSet)[f].y += suffixPos;
- }
-
- //
- // Collect all fragments into one.
- //
- fragmentSet.insert(fragmentSet.begin(), prefixFragmentSet.begin(), prefixFragmentSet.end());
- fragmentSet.insert(fragmentSet.end(), suffixFragmentSet.begin(), suffixFragmentSet.end());
-
- FlatMatrix2D<int> graphScoreMat;
- FlatMatrix2D<Arrow> graphPathMat;
- FlatMatrix2D<int> graphBins;
- int nOnOpt = fragmentSet.size();
- if (fragmentSet.size() > minFragmentsToUseGraphPaper and fastSDP) {
- int nCol = 50;
- vector<bool> onOptPath(fragmentSet.size(), false);
- nOnOpt = GraphPaper<Fragment>(fragmentSet, nCol, nCol,
- graphBins, graphScoreMat,
- graphPathMat, onOptPath);
- int prev = fragmentSet.size();
- RemoveOffOpt(fragmentSet, onOptPath);
- }
- graphScoreMat.Clear();
- graphPathMat.Clear();
- graphBins.Clear();
-
- //
- // Because there are fragments from multiple overlapping regions, remove
- // any fragments that have the same starting coordinate as a
- // previous fragment.
- //
- std::sort(fragmentSet.begin(), fragmentSet.end(), LexicographicFragmentSort<Fragment>());
- f = 0;
- int fCur = 0;
- while (f + 1 <= fragmentSet.size()) {
- fragmentSet[fCur] = fragmentSet[f];
- while (f < fragmentSet.size() and fragmentSet[fCur].x == fragmentSet[f].x and fragmentSet[fCur].y == fragmentSet[f].y) {
- f++;
- }
- fCur++;
- }
- fragmentSet.resize(fCur);
-
- if (fragmentSet.size() == 0) {
- //
- // This requires at least one seeded tuple to begin an alignment.
- //
- return 0;
- }
-
- //
- // Find the longest chain of anchors.
- //
- SDPLongestCommonSubsequence(query.length, fragmentSet, tm.tupleSize, sdpIns, sdpDel, scoreFn.scoreMatrix[0][0], maxFragmentChain, alignType);
-
- //
- // Now turn the max fragment chain into a real alignment.
- //
- int startF;
- blasr::Alignment chainAlignment;
- alignment.qPos = 0;
- alignment.tPos = 0;
- Block block;
- std::vector<int> fragScoreMat;
- std::vector<Arrow> fragPathMat;
-
- //
- // Patch the sdp fragments into an alignment, possibly breaking the
- // alignment if the gap between two fragments is too large.
- //
- for (f = 0; f < maxFragmentChain.size(); f++ ){
- startF = f;
- // Condense contiguous stretches.
- while(f < maxFragmentChain.size() - 1 and
- fragmentSet[maxFragmentChain[f]].x == fragmentSet[maxFragmentChain[f+1]].x - 1 and
- fragmentSet[maxFragmentChain[f]].y == fragmentSet[maxFragmentChain[f+1]].y - 1) {
- f++;
- }
-
- block.qPos = fragmentSet[maxFragmentChain[startF]].x;
- block.tPos = fragmentSet[maxFragmentChain[startF]].y;
-
- // Compute the block length as the difference between the starting
- // point of the current block and ending point of the last
- // overlapping block. This was previously calculated by adding
- // the number of merged blocks - 1 to the first block length.
- // When the block lengths are heterogenous, this does not work,
- // and it would be possible to have a block with a length that
- // extends past the end of a sequence. By taking the length as
- // the difference here, it ensures this will not happen.
- //
- block.length = fragmentSet[maxFragmentChain[f]].x + fragmentSet[maxFragmentChain[f]].length - fragmentSet[maxFragmentChain[startF]].x;
- chainAlignment.blocks.push_back(block);
- }
-
- //
- // It may be possible that in regions of low similarity, spurious matches fit into the LCS.
- // Assume that indels cause the matches to diverge from the diagonal on a random walk. If they
- // walk more than 3 standard deviations away from the diagonal, they are probably spurious.
- //
- unsigned int b;
- chainAlignment.qPos = 0;
- chainAlignment.tPos = 0;
-
- for (b = 0; b < chainAlignment.size()-1; b++){
- if (chainAlignment.blocks[b].qPos + chainAlignment.blocks[b].length > chainAlignment.blocks[b+1].qPos) {
- chainAlignment.blocks[b].length = (chainAlignment.blocks[b+1].qPos - chainAlignment.blocks[b].qPos);
- }
- if (chainAlignment.blocks[b].tPos + chainAlignment.blocks[b].length > chainAlignment.blocks[b+1].tPos) {
- chainAlignment.blocks[b].length = (chainAlignment.blocks[b+1].tPos - chainAlignment.blocks[b].tPos);
- }
- // the min indel rate between the two chain blocks is the difference in diagonals between the two sequences.
- int curDiag, nextDiag, diffDiag;
- curDiag = chainAlignment.blocks[b].tPos - chainAlignment.blocks[b].qPos;
- nextDiag = chainAlignment.blocks[b+1].tPos - chainAlignment.blocks[b+1].qPos;
- diffDiag = std::abs(curDiag - nextDiag);
-
- //
- // It is expected that the deviation is at least 1, so discount for this
- //
- diffDiag--;
- // compare the alignment distances.
- }
-
- std::vector<bool> blockIsGood;
- blockIsGood.resize(chainAlignment.size());
- fill(blockIsGood.begin(), blockIsGood.end(), true);
-
- //
- // The hack that allows anchors of different lengths at the front
- // and end of alignments (to increase sensitivity at the ends of
- // sequences) has the side effect that there may be blocks that have
- // zero length. This shouldn't happen, so to balance this out
- // remove blocks that have zero length.
- //
- bool badBlock;
- for (b = 0; b < chainAlignment.size(); b++){
- if (chainAlignment.blocks[b].length == 0) {
- blockIsGood[b] = false;
- }
- }
- for (b = 1; b < chainAlignment.size()-1; b++){
- // the min indel rate between the two chain blocks is the difference in diagonals between the two sequences.
- int prevDiag = abs(((int)chainAlignment.blocks[b].tPos - (int)chainAlignment.blocks[b].qPos) -
- ((int)chainAlignment.blocks[b-1].tPos - (int)chainAlignment.blocks[b-1].qPos));
-
- int prevDist = std::min(chainAlignment.blocks[b].tPos - chainAlignment.blocks[b-1].tPos,
- chainAlignment.blocks[b].qPos - chainAlignment.blocks[b-1].qPos);
-
- int nextDiag = abs(((int)chainAlignment.blocks[b+1].tPos - (int)chainAlignment.blocks[b+1].qPos) -
- ((int)chainAlignment.blocks[b].tPos - (int)chainAlignment.blocks[b].qPos));
-
- int nextDist = std::min(chainAlignment.blocks[b+1].tPos - chainAlignment.blocks[b].tPos,
- chainAlignment.blocks[b+1].qPos - chainAlignment.blocks[b].qPos);
-
- if (prevDist * indelRate < prevDiag and nextDist * indelRate < nextDiag) {
- blockIsGood[b] = false;
- }
- }
-
- for (b = chainAlignment.size(); b > 0; b--) {
- if (blockIsGood[b-1] == false) {
- chainAlignment.blocks.erase(chainAlignment.blocks.begin() + b-1);
- }
- }
-
- if (chainAlignment.blocks.size() > 0) {
- T_QuerySequence qFragment;
- T_TargetSequence tFragment;
- blasr::Alignment fragAlignment;
- unsigned int fb;
- if (alignType == Global) {
- //
- // For Global alignment, refine the alignment from the beginnings of the
- // sequences to the start of the first block.
- //
- if (chainAlignment.blocks[0].qPos > 0 and
- chainAlignment.blocks[0].tPos > 0) {
-
- qFragment.seq = &query.seq[0];
- qFragment.length = chainAlignment.blocks[0].qPos;
- tFragment.seq = &target.seq[0];
- tFragment.length = chainAlignment.blocks[0].tPos;
- for (fb = 0; fb < alignment.blocks.size(); fb++) {
- alignment.blocks.push_back(fragAlignment.blocks[b]);
- }
- }
- }
- else if (alignType == Local) {
- // Perform a front-anchored alignment to extend the alignment to
- // the beginning of the read.
- if (chainAlignment.blocks[0].qPos > 0 and
- chainAlignment.blocks[0].tPos > 0) {
- qFragment.seq = (Nucleotide*) &query.seq[0];
- qFragment.length = chainAlignment.blocks[0].qPos;
-
- tFragment.seq = (Nucleotide*) &target.seq[0];
- tFragment.length = chainAlignment.blocks[0].tPos;
- blasr::Alignment frontAlignment;
- int frontAlignmentScore;
- // Currently, there might be some space between the beginning
- // of the alignment and the beginning of the read. Run an
- // EndAnchored alignment that allows free gaps to the start of
- // where the alignment begins, but normal, ungapped alignment
- // otherwise.
- if (extendFrontByLocalAlignment) {
- if (noRecurseUnder == 0 or qFragment.length * tFragment.length < noRecurseUnder) {
- frontAlignmentScore =
- SWAlign(qFragment, tFragment, fragScoreMat, fragPathMat, frontAlignment, scoreFn, EndAnchored);
- } else {
- // cout << "running recursive sdp alignment. " << endl;
- vector<int> recurseFragmentChain;
- SDPAlign(qFragment, tFragment, scoreFn,
- std::max(wordSize/2, 5),
- sdpIns, sdpDel, indelRate,
- frontAlignment,
- fragmentSet,
- prefixFragmentSet,
- suffixFragmentSet,
- targetTupleList,
- targetPrefixTupleList,
- targetSuffixTupleList,
- recurseFragmentChain,
- alignType, detailedAlignment,
- extendFrontByLocalAlignment, 0);
- }
-
- unsigned int anchorBlock;
- for (anchorBlock = 0; anchorBlock < frontAlignment.blocks.size(); anchorBlock++) {
- //
- // The front alignment needs to be transformed to the
- // coordinate offsets that the chain alignment is in. This
- // is an alignment starting at position 0 in the target and
- // query. Currently, the front alignment is offset into the
- // sequences by frontAlignment.[q/t]Pos.
- //
- frontAlignment.blocks[anchorBlock].tPos += frontAlignment.tPos;
- frontAlignment.blocks[anchorBlock].qPos += frontAlignment.qPos;
- alignment.blocks.push_back(frontAlignment.blocks[anchorBlock]);
- }
- }
- }
- }
-
- //
- // The chain alignment blocks are not complete blocks, so they
- // must be appended to the true alignment and then patched up.
- //
- for (b = 0; b < chainAlignment.size() - 1; b++) {
- alignment.blocks.push_back(chainAlignment.blocks[b]);
- int alignScore;
-
- //
- // Do a detaied smith-waterman alignment between blocks, if this
- // is specified.
- fragAlignment.Clear();
- qFragment.Free();
- qFragment.ReferenceSubstring(query, chainAlignment.blocks[b].qPos + chainAlignment.blocks[b].length);
- qFragment.length = chainAlignment.blocks[b+1].qPos -
- (chainAlignment.blocks[b].qPos + chainAlignment.blocks[b].length);
-
- tFragment.seq = &(target.seq[chainAlignment.blocks[b].tPos + chainAlignment.blocks[b].length]);
- tFragment.length = (chainAlignment.blocks[b+1].tPos -
- (chainAlignment.blocks[b].tPos + chainAlignment.blocks[b].length));
-
- if (qFragment.length > 0 and
- tFragment.length > 0 and
- detailedAlignment == true) {
-
- if (noRecurseUnder == 0 or qFragment.length * tFragment.length < noRecurseUnder) {
- alignScore = SWAlign(qFragment, tFragment, fragScoreMat, fragPathMat, fragAlignment, scoreFn, Global);
- }
- else {
- // cout << "running recursive sdp alignment on " << qFragment.length * tFragment.length << endl;
- std::vector<int> recurseFragmentChain;
- SDPAlign(qFragment, tFragment, scoreFn,
- std::max(wordSize/2, 5),
- sdpIns, sdpDel, indelRate,
- fragAlignment,
- fragmentSet,
- prefixFragmentSet,
- suffixFragmentSet,
- targetTupleList,
- targetPrefixTupleList,
- targetSuffixTupleList,
- recurseFragmentChain,
- alignType, detailedAlignment, 0, 0);
- }
- fragAlignment.qPos = 0;
- fragAlignment.tPos = 0;
-
- int qOffset = chainAlignment.blocks[b].qPos + chainAlignment.blocks[b].length;
- int tOffset = chainAlignment.blocks[b].tPos + chainAlignment.blocks[b].length;
-
- for (fb = 0; fb < fragAlignment.blocks.size(); fb++) {
- fragAlignment.blocks[fb].qPos += qOffset;
- fragAlignment.blocks[fb].tPos += tOffset;
- alignment.blocks.push_back(fragAlignment.blocks[fb]);
- }
- }
- }
- int lastBlock = chainAlignment.blocks.size() - 1;
- if (alignType == Global or alignType == Local) {
- if (chainAlignment.size() > 0) {
- // Add the last block.
- alignment.blocks.push_back(chainAlignment.blocks[lastBlock]);
- if (alignType == Global and detailedAlignment == true) {
- //
- // When doing a global alignment, the sequence from the end of
- // the last block of the query should be aligned to the end of
- // the text.
- //
- qFragment.Free();
- qFragment.ReferenceSubstring(query, chainAlignment.blocks[lastBlock].qPos + chainAlignment.blocks[lastBlock].length,
- query.length -
- (chainAlignment.blocks[lastBlock].qPos + chainAlignment.blocks[lastBlock].length));
-
- tFragment.seq = &(target.seq[chainAlignment.blocks[lastBlock].tPos + chainAlignment.blocks[lastBlock].length]);
- tFragment.length = (target.length -
- (chainAlignment.blocks[lastBlock].tPos + chainAlignment.blocks[lastBlock].length));
- if (qFragment.length > 0 and
- tFragment.length > 0 ) {
-
- if (extendFrontByLocalAlignment) {
-
- fragAlignment.Clear();
- if (qFragment.length * tFragment.length > 10000) {
- // cout << "Cautin: slow alignment crossing! " << qFragment.length << " " << tFragment.length << endl;
- }
-
- if (noRecurseUnder == 0 or qFragment.length * tFragment.length < noRecurseUnder) {
- SWAlign(qFragment, tFragment, fragScoreMat, fragPathMat, fragAlignment, scoreFn, EndAnchored);
- }
- else {
- std::vector<int> recurseFragmentChain;
- SDPAlign(qFragment, tFragment, scoreFn,
- std::max(wordSize/2, 5),
- sdpIns, sdpDel, indelRate,
- fragAlignment,
- fragmentSet,
- prefixFragmentSet,
- suffixFragmentSet,
- targetTupleList,
- targetPrefixTupleList,
- targetSuffixTupleList,
- recurseFragmentChain,
- alignType, detailedAlignment, extendFrontByLocalAlignment, 0);
- }
-
-
-
- int qOffset = chainAlignment.blocks[lastBlock].qPos + chainAlignment.blocks[lastBlock].length;
- int tOffset = chainAlignment.blocks[lastBlock].tPos + chainAlignment.blocks[lastBlock].length;
- unsigned int fb;
- for (fb = 0; fb < fragAlignment.size(); fb++) {
- fragAlignment.blocks[fb].qPos += qOffset;
- fragAlignment.blocks[fb].tPos += tOffset;
- alignment.blocks.push_back(fragAlignment.blocks[fb]);
- }
- }
- }
- }
- }
- }
- }
-
- if (alignType == Local) {
- alignment.tPos = alignment.blocks[0].tPos;
- alignment.qPos = alignment.blocks[0].qPos;
- VectorIndex b;
- for (b = 0; b < alignment.blocks.size(); b++) {
- alignment.blocks[b].qPos -= alignment.qPos;
- alignment.blocks[b].tPos -= alignment.tPos;
- }
- }
- int alignmentScore;
- /* ofstream queryOut("query.fasta");
- FASTASequence tmp;
- ((DNASequence&)tmp).Copy(query);
- tmp.CopyTitle("query");
- tmp.PrintSeq(queryOut);
- queryOut.close();
- ofstream targetOut("target.fasta");
- ((DNASequence&)tmp).Copy(target);
- tmp.CopyTitle("target");
- tmp.PrintSeq(targetOut);
- targetOut.close();
- */
- alignmentScore = ComputeAlignmentScore(alignment, query, target, scoreFn);
- return alignmentScore;
-}
-
-#endif //_BLASR_SDP_ALIGN_IMPL_HPP_
diff --git a/libcpp/alignment/algorithms/alignment/SWAlign.hpp b/libcpp/alignment/algorithms/alignment/SWAlign.hpp
deleted file mode 100644
index a92b60b..0000000
--- a/libcpp/alignment/algorithms/alignment/SWAlign.hpp
+++ /dev/null
@@ -1,17 +0,0 @@
-#ifndef _BLASR_SW_ALIGN_HPP_
-#define _BLASR_SW_ALIGN_HPP_
-
-template<typename T_QuerySequence, typename T_TargetSequence, typename T_Alignment, typename T_ScoreFn>
-int SWAlign(T_QuerySequence &qSeq, T_TargetSequence &tSeq,
- std::vector<int> &scoreMat,
- std::vector<Arrow> &pathMat,
- T_Alignment &alignment,
- T_ScoreFn &scoreFn,
- AlignmentType alignType = Local,
- bool trustSequences = false,
- bool printMatrix = false
- );
-
-#include "SWAlignImpl.hpp"
-
-#endif // _BLASR_SW_ALIGN_HPP_
diff --git a/libcpp/alignment/algorithms/alignment/SWAlignImpl.hpp b/libcpp/alignment/algorithms/alignment/SWAlignImpl.hpp
deleted file mode 100644
index b30ec10..0000000
--- a/libcpp/alignment/algorithms/alignment/SWAlignImpl.hpp
+++ /dev/null
@@ -1,389 +0,0 @@
-#include <algorithm>
-#include <vector>
-#include <stdint.h>
-#include <iostream>
-#include <ostream>
-#include "Types.h"
-#include "defs.h"
-#include "DNASequence.hpp"
-#include "matrix/FlatMatrix.hpp"
-#include "datastructures/alignment/Path.h"
-#include "datastructures/alignment/AlignmentMap.hpp"
-#include "datastructures/alignment/AlignmentStats.hpp"
-#include "datastructures/alignment/Alignment.hpp"
-#include "AlignmentUtils.hpp"
-#include "SWAlign.hpp"
-
-template<typename T_QuerySequence, typename T_TargetSequence, typename T_Alignment, typename T_ScoreFn>
-int SWAlign(T_QuerySequence &qSeq, T_TargetSequence &tSeq,
- std::vector<int> &scoreMat,
- std::vector<Arrow> &pathMat,
- T_Alignment &alignment,
- T_ScoreFn &scoreFn,
- AlignmentType alignType,
- bool trustSequences,
- bool printMatrix
- ) {
- VectorIndex nRows = qSeq.length + 1;
- VectorIndex nCols = tSeq.length + 1;
-
- VectorIndex totalMatSize = nRows * nCols;
- if (scoreMat.size() < totalMatSize) {
- scoreMat.resize(totalMatSize);
- pathMat.resize(totalMatSize);
- }
-
-
- //
- // Initialze matrices
- std::fill(scoreMat.begin(), scoreMat.begin() + totalMatSize, 0);
- std::fill(pathMat.begin(), pathMat.begin() + totalMatSize, NoArrow);
-
- //
- // Initialize boundary conditions.
- //
- int r = 0, c = 0;
- if (alignType == Global or alignType == ScoreGlobal
- or alignType == FrontAnchored or alignType == ScoreFrontAnchored) {
- //
- // Global alignments penalize gaps at the beginning of both
- // sequences.
- //
- for (c = 0; c < (int) tSeq.length + 1; c++ ){
- scoreMat[rc2index(0, c, tSeq.length + 1)] = scoreFn.del * c;
- pathMat[rc2index(0, c, tSeq.length + 1)] = Left;
- }
-
- for (r = 0; r < (int) qSeq.length + 1; r++ ){
- scoreMat[rc2index(r,0, tSeq.length + 1)] = scoreFn.ins * r;
- pathMat[rc2index(r, 0, tSeq.length + 1)] = Up;
- }
- }
- else if (alignType == Local or alignType == ScoreLocal or alignType == LocalBoundaries
- // end anchoring requires free gap penalties at the
- // beginning of sequences.
- or alignType == EndAnchored or alignType == ScoreEndAnchored) {
- //
- // Local alignments may shave off the beginning of either read.
- // No penalties at the starts of reads.
- //
- for (c = 0; c < (int) tSeq.length + 1; c++ ){
- scoreMat[rc2index(0, c, tSeq.length + 1)] = 0;
- pathMat[rc2index(0, c, tSeq.length + 1)] = NoArrow;
- }
- for (r = 0; r < (int) qSeq.length + 1; r++ ){
- scoreMat[rc2index(r,0, tSeq.length + 1)] = 0;
- pathMat[rc2index(r, 0, tSeq.length + 1)] = NoArrow;
- }
- }
- else if (alignType == QueryFit or alignType == ScoreQueryFit) {
- //
- // Query fit allows free gaps at the beginning and end
- // of the target sequence.
- //
- for (c = 0; c < (int) tSeq.length + 1; c++ ){
- scoreMat[rc2index(0, c, tSeq.length + 1)] = 0;
- pathMat[rc2index(0, c, tSeq.length + 1)] = Left;
- }
- for (r = 0; r < (int) qSeq.length + 1; r++ ){
- scoreMat[rc2index(r,0, tSeq.length + 1)] = scoreFn.ins * r;
- pathMat[rc2index(r, 0, tSeq.length + 1)] = Up;
- }
- }
- else if (alignType == TargetFit or alignType == ScoreTargetFit) {
- //
- // Query fit allows free gaps at the beginning and end
- // of the target sequence.
- //
- for (c = 0; c < (int) tSeq.length + 1; c++ ){
- scoreMat[rc2index(0, c, tSeq.length + 1)] = scoreFn.del * c;
- pathMat[rc2index(0, c, tSeq.length + 1)] = Left;
- }
- for (r = 0; r < (int) qSeq.length + 1; r++ ){
- scoreMat[rc2index(r,0, tSeq.length + 1)] = 0;
- pathMat[rc2index(r, 0, tSeq.length + 1)] = Up;
- }
- }
- else if (alignType == Overlap or alignType == ScoreOverlap or
- alignType == TSuffixQPrefix or alignType == ScoreTSuffixQPrefix) {
- //
- // Overlap alignments allow a gap at the beginning of the
- // query, and at the end of the target.
- //
- for (r = 0; r < (int) qSeq.length + 1; r++ ){
- scoreMat[rc2index(r,0, tSeq.length + 1)] = scoreFn.ins*r;
- pathMat[rc2index(r, 0, tSeq.length + 1)] = Up;
- }
- for (c = 0; c < (int) tSeq.length + 1; c++ ){
- scoreMat[rc2index(0, c, tSeq.length + 1)] = 0;
- pathMat[rc2index(0, c, tSeq.length + 1)] = Left;
- }
- }
- else if (alignType == TPrefixQSuffix or alignType == ScoreTPrefixQSuffix) {
- //
- // Overlap alignments allow a gap at the beginning of the
- // query, and at the end of the target.
- //
- for (c = 0; c < (int) tSeq.length + 1; c++ ){
- scoreMat[rc2index(0, c, tSeq.length + 1)] = scoreFn.del * c;
- pathMat[rc2index(0, c, tSeq.length + 1)] = Left;
- }
- for (r = 0; r < (int) qSeq.length + 1; r++ ){
- scoreMat[rc2index(r,0, tSeq.length + 1)] = 0;
- pathMat[rc2index(r, 0, tSeq.length + 1)] = Up;
- }
- }
-
- pathMat[0] = Diagonal;
-
- int match, qGap, tGap;
-
- //
- // Begin matrix pointers after the
- int *matchScorePtr = &scoreMat[0];
- int *gapQScorePtr = &scoreMat[1];
- int *gapTScorePtr = &scoreMat[tSeq.length + 1 ];
- int *curScorePtr = &scoreMat[tSeq.length + 2 ];
- Arrow *optPathPtr = &pathMat[tSeq.length + 2];
- int minScore;
-
- int localMinScore = 0;
- int localMinRow = 0;
- int localMinCol = 0;
- for (r = 0; r < (int) qSeq.length; r++ ){
- for (c = 0; c < (int) tSeq.length; c++ ) {
- //
- // r+1, c+1 is the current row /col in the score and path mat.
- //
-
- //match = matchMat[TwoBit[qSeq.seq[r]]][TwoBit[tSeq.seq[c]]] + *matchScorePtr;
- // qGap = *gapQScorePtr + gap;
- // tGap = *gapTScorePtr + gap;
- match = scoreFn.Match(tSeq, c, qSeq, r) + scoreMat[rc2index(r,c,nCols)];
- qGap = scoreMat[rc2index(r,c+1, nCols)] + scoreFn.Insertion(tSeq, r+1, qSeq, c);
- tGap = scoreMat[rc2index(r+1,c, nCols)] + scoreFn.Deletion(tSeq, r, qSeq, c+1);
- minScore = MIN(match, MIN(qGap, tGap));
- if (minScore < localMinScore) {
- localMinScore = minScore;
- localMinRow = r;
- localMinCol = c;
- }
-
- if (minScore > 0 and
- (alignType == Local or alignType == ScoreLocal or
- alignType == LocalBoundaries or
- alignType == EndAnchored or alignType == ScoreEndAnchored )) {
- *curScorePtr = 0;
- *optPathPtr = NoArrow;
- }
- // This staement will get easier when the alignTypes are bitfields.
- // Not sure why this explicitly checks all conditions.
- else if (alignType == Local or alignType == Global or
- alignType == QueryFit or alignType == Overlap or
- alignType == TargetFit or alignType == ScoreTargetFit or
- alignType == ScoreLocal or alignType == ScoreGlobal or
- alignType == ScoreQueryFit or alignType == ScoreOverlap or
- alignType == FrontAnchored or alignType == ScoreFrontAnchored or
- alignType == EndAnchored or alignType == ScoreEndAnchored or
- alignType == LocalBoundaries or
- alignType == TPrefixQSuffix or alignType == ScoreTPrefixQSuffix or
- alignType == TSuffixQPrefix or alignType == ScoreTSuffixQPrefix ) {
- *curScorePtr = minScore;
- // scoreMat[rc2index(r+1,c+1, tl)] = minScore;
- if (minScore == match) {
- *optPathPtr = Diagonal;
- //pathMat[rc2index(r+1,c+1,tl)] = Diagonal;
- }
- else if (minScore == qGap) {
- *optPathPtr = Up;
- //pathMat[rc2index(r+1,c+1, tl)] = Up;
- }
- else if (minScore == tGap) {
- *optPathPtr = Left;
- //pathMat[rc2index(r+1,c+1, tl)] = Left;
- }
- }
- ++matchScorePtr;
- ++gapTScorePtr;
- ++gapQScorePtr;
- ++curScorePtr;
- ++optPathPtr;
- }
- // Done processing a row.
- // This leaves the pointers starting at the first column in the next row
- // which is a boundary column. Advance one more.
- //
- ++matchScorePtr;
- ++gapTScorePtr;
- ++gapQScorePtr;
- ++curScorePtr;
- ++optPathPtr;
- }
- //
- // Now trace back in the pairwise alignment.
- //
-
- // The location of the trace back depends on the type of alignment that is done.
- int minRow = 0, minCol = 0;
- if (alignType == Global or alignType == ScoreGlobal or
- alignType == EndAnchored or alignType == ScoreEndAnchored ) {
- // start at bottom right of matrix.
- r = qSeq.length;
- c = tSeq.length;
- minRow = r;
- minCol = c;
- }
- else if (alignType == Local or alignType == ScoreLocal or
- alignType == FrontAnchored or alignType == ScoreFrontAnchored or
- alignType == LocalBoundaries) {
- // start at cell that gives the highest score.
- r = localMinRow;
- c = localMinCol;
- minRow = r;
- minCol = c;
- }
- else if (alignType == QueryFit or alignType == Overlap or
- alignType == ScoreQueryFit or alignType == ScoreOverlap) {
- // Start at the point at the end of the target that gives the highest score, but has the
- // end query sequence alignment.
-
- r = nRows-1;
- int minScore = scoreMat[rc2index(nRows-1, 1, nCols)];
- minCol = 1;
- for (c = 2; c < (int) nCols; c++ ) {
- if (scoreMat[rc2index(nRows-1, c, nCols)] < minScore) {
- minScore = scoreMat[rc2index(nRows-1, c, nCols)];
- minCol = c;
- }
- }
- c = minCol;
- minRow = nRows - 1;
- }
- else if (alignType == TargetFit or alignType == ScoreTargetFit) {
- // Start at the point at the end of the target that gives the highest score, but has the
- // end query sequence alignment.
-
- //
- // Always trace back from the end of the target.
- //
- minCol = nCols-1;
- c = nCols-1;
- r = 0;
- int minScore = scoreMat[rc2index(1, nCols-1, nCols)];
- for (r = 2; r < (int) nRows; r++ ) {
- if (scoreMat[rc2index(r, nCols-1, nCols)] < minScore) {
- minScore = scoreMat[rc2index(r, nCols-1, nCols)];
- minRow = r;
- }
- }
- // store where to trace back from in the query.
- r = minRow;
- }
- else if (alignType == TSuffixQPrefix or alignType == ScoreTSuffixQPrefix) {
- // Start at the point at the end of the target that gives the highest score, but has the
- // end query sequence alignment.
- c = nCols - 1;
- r = 1;
-
- int minScore = scoreMat[rc2index(1, nCols-1, nCols)];
- minRow = 1;
- for (r = 2; r < (int) nRows; r++) {
- if (scoreMat[rc2index(r, nCols-1, nCols)] < minScore) {
- minScore = scoreMat[rc2index(r, nCols-1, nCols)];
- minRow = r;
- }
- }
- r = minRow;
- minCol = nCols - 1;
- }
- else if (alignType == TPrefixQSuffix or alignType == ScoreTPrefixQSuffix) {
- r = nRows-1;
- int minScore = scoreMat[rc2index(nRows-1, 1, nCols)];
- minCol = 1;
- for (c = 2; c < (int) nCols; c++ ) {
- if (scoreMat[rc2index(nRows-1, c, nCols)] < minScore) {
- minScore = scoreMat[rc2index(nRows-1, c, nCols)];
- minCol = c;
- }
- }
- c = minCol;
- minRow = nRows - 1;
- }
- /*
- PrintFlatMatrix(&scoreMat[0], nRows, nCols, cout);
- PrintFlatMatrix(&pathMat[0], nRows,nCols, cout);
- */
- if (alignType != ScoreGlobal and
- alignType != ScoreLocal and
- alignType != ScoreQueryFit and
- alignType != ScoreOverlap and
- alignType != ScoreTPrefixQSuffix and
- alignType != ScoreTSuffixQPrefix) {
- std::vector<Arrow> optAlignment;
- Arrow arrow;
- while (((alignType == Global or alignType == FrontAnchored ) and (r > 0 or c > 0)) or // global alignment stops at top corner
- ((alignType == QueryFit or
- alignType == Overlap or
- alignType == TSuffixQPrefix) and r > 0) or
- ((alignType == TPrefixQSuffix) and c > 0) or
- (alignType == TargetFit and c > 0) or
- // local alignment stops at top corner -or- when new local alignment started.
- ((alignType == Local or alignType == EndAnchored or alignType == LocalBoundaries)
- and r > 0 and c > 0 and pathMat[r*nCols+c] != NoArrow)
- ) {
- arrow = pathMat[rc2index(r, c, nCols)];
-
- //
- // When the alignment type is localBoundaries, it is not necessary to store
- // the actual alignment. Only the starting positions and lengts will be stored.
- //
- if (alignType != LocalBoundaries) {
- optAlignment.push_back(arrow);
- }
- if (arrow == Diagonal) {
- r--;
- c--;
- }
- else if (arrow == Up) {
- r--;
- }
- else if (arrow == Left) {
- c--;
- }
- }
- // remove the boundary condition that is added for global alignment.
- if (alignType == LocalBoundaries and alignType != Local and alignType != EndAnchored and optAlignment.size() > 0)
- optAlignment.pop_back();
- if (optAlignment.size() > 1)
- std::reverse(optAlignment.begin(), optAlignment.end());
- if (optAlignment.size() > 0)
- alignment.ArrowPathToAlignment(optAlignment);
-
- //
- // If running a local alignment, the alignment does not
- // explicityly encode the gaps at the beginning and ending of the
- // alignment. These are stored in the qPos and tPos fields.
- //
- if (alignType == TSuffixQPrefix or alignType == TPrefixQSuffix) {
- alignment.qPos = r;
- alignment.tPos = c;
- }
- else if (alignType == Local or alignType == EndAnchored or alignType == LocalBoundaries) {
- alignment.qPos = r;
- alignment.tPos = c;
- alignment.qLength = localMinRow - alignment.qPos + 1;
- alignment.tLength = localMinCol - alignment.tPos + 1;
- }
- else if (alignType == QueryFit or alignType == TargetFit) {
- alignment.qPos = r;
- alignment.tPos = c;
- }
-
- }
- if (printMatrix) {
- PrintFlatMatrix( &scoreMat[0], qSeq.length + 1, tSeq.length + 1, std::cout);
- std::cout << std::endl;
- PrintFlatMatrix( &pathMat[0], qSeq.length + 1, tSeq.length + 1, std::cout);
- }
- return scoreMat[rc2index(minRow, minCol, nCols)];
-}
diff --git a/libcpp/alignment/algorithms/alignment/ScoreMatrices.cpp b/libcpp/alignment/algorithms/alignment/ScoreMatrices.cpp
deleted file mode 100644
index 5aa06cc..0000000
--- a/libcpp/alignment/algorithms/alignment/ScoreMatrices.cpp
+++ /dev/null
@@ -1,58 +0,0 @@
-#include "ScoreMatrices.hpp"
-
-int QVDistanceMatrix[5][5] = {
- {-1, 1, 1, 1, 1},
- {1, -1, 1, 1, 1},
- {1, 1, -1, 1, 1},
- {1, 1, 1, -1, 1},
- {1, 1, 1, 1, 1}
-};
-
-int EditDistanceMatrix[5][5] = {
- {0, 1, 1, 1, 1},
- {1, 0, 1, 1, 1},
- {1, 1, 0, 1, 1},
- {1, 1, 1, 0, 1},
- {1, 1, 1, 1, 1}
-};
-
-int SMRTDistanceMatrix[5][5] = {
- {-5, 6, 6, 6, 6},
- {6, -5, 6, 6, 6},
- {6, 6, -5, 6, 6},
- {6, 6, 6, -5, 6},
- {6, 6, 6, 6, 0}
-};
-
-int SMRTLogProbMatrix[5][5] = {
- {0, 15, 15, 15, 15},
- {15, 0, 15, 15, 15},
- {15, 15, 0, 15, 15},
- {15, 15, 15, 0, 15},
- {15, 15, 15, 15, 0},
-};
-
-int LowMutationMatrix[5][5] = {
- {0, 5, 5, 5, 5},
- {5, 0, 5, 5, 5},
- {5, 5, 0, 5, 5},
- {5, 5, 5, 0, 5},
- {5, 5, 5, 5, 5}
-};
-
-int LocalAlignLowMutationMatrix[5][5] = {
- {-2, 5, 5, 5, 5},
- {5, -2, 5, 5, 5},
- {5, 5, -2, 5, 5},
- {5, 5, 5, -2, 5},
- {5, 5, 5, 5, 5}
-};
-
-int CrossMatchMatrix[5][5] = {
- {-1, 2, 2, 2, 2},
- {2, -1, 2, 2, 2},
- {2, 2, -1, 2, 2},
- {2, 2, 2, -1, 2},
- {2, 2, 2, 2, 2}
-};
-
diff --git a/libcpp/alignment/algorithms/alignment/ScoreMatrices.hpp b/libcpp/alignment/algorithms/alignment/ScoreMatrices.hpp
deleted file mode 100644
index e948cf6..0000000
--- a/libcpp/alignment/algorithms/alignment/ScoreMatrices.hpp
+++ /dev/null
@@ -1,18 +0,0 @@
-#ifndef _BLASR_SCORE_MATRICES_HPP_
-#define _BLASR_SCORE_MATRICES_HPP_
-
-extern int QVDistanceMatrix[5][5];
-
-extern int EditDistanceMatrix[5][5];
-
-extern int SMRTDistanceMatrix[5][5];
-
-extern int SMRTLogProbMatrix[5][5];
-
-extern int LowMutationMatrix[5][5];
-
-extern int LocalAlignLowMutationMatrix[5][5];
-
-extern int CrossMatchMatrix[5][5];
-
-#endif // _BLASR_SCORE_MATRICES_HPP_
diff --git a/libcpp/alignment/algorithms/alignment/StringToScoreMatrix.cpp b/libcpp/alignment/algorithms/alignment/StringToScoreMatrix.cpp
deleted file mode 100644
index ea48abe..0000000
--- a/libcpp/alignment/algorithms/alignment/StringToScoreMatrix.cpp
+++ /dev/null
@@ -1,26 +0,0 @@
-#include "StringToScoreMatrix.hpp"
-
-bool StringToScoreMatrix(std::string &str, int matrix[5][5]) {
- std::stringstream strm(str);
- std::vector<int> values;
- while(strm) {
- int val;
- if ((strm >> val)) {
- values.push_back(val);
- }
- }
- if (values.size() != 25) {
- return 0;
- }
- else {
- int i,j;
- int index = 0;
- for (i = 0; i < 5; i++) {
- for (j = 0; j < 5; j++) {
- matrix[i][j] = values[index];
- ++index;
- }
- }
- return true;
- }
-}
diff --git a/libcpp/alignment/algorithms/alignment/StringToScoreMatrix.hpp b/libcpp/alignment/algorithms/alignment/StringToScoreMatrix.hpp
deleted file mode 100644
index b1f415c..0000000
--- a/libcpp/alignment/algorithms/alignment/StringToScoreMatrix.hpp
+++ /dev/null
@@ -1,9 +0,0 @@
-#ifndef _BLASR_STRING_TO_SCORE_MATRIX_HPP_
-#define _BLASR_STRING_TO_SCORE_MATRIX_HPP_
-
-#include <string>
-#include <sstream>
-#include <vector>
-
-bool StringToScoreMatrix(std::string &str, int matrix[5][5]);
-#endif
diff --git a/libcpp/alignment/algorithms/alignment/sdp/FragmentSort.hpp b/libcpp/alignment/algorithms/alignment/sdp/FragmentSort.hpp
deleted file mode 100644
index f665833..0000000
--- a/libcpp/alignment/algorithms/alignment/sdp/FragmentSort.hpp
+++ /dev/null
@@ -1,19 +0,0 @@
-#ifndef _BLASR_FRAGMENT_SORT_HPP_
-#define _BLASR_FRAGMENT_SORT_HPP_
-
-
-template<typename T_Fragment>
-class LexicographicFragmentSort {
-public:
- int operator()(const T_Fragment &a, const T_Fragment &b) const;
-};
-
-template<typename T_Fragment>
-class LexicographicFragmentSortByY {
-public:
- int operator()(const T_Fragment &a, const T_Fragment &b) const;
-};
-
-#include "FragmentSortImpl.hpp"
-
-#endif // _BLASR_FRAGMENT_SORT_HPP_
diff --git a/libcpp/alignment/algorithms/alignment/sdp/FragmentSortImpl.hpp b/libcpp/alignment/algorithms/alignment/sdp/FragmentSortImpl.hpp
deleted file mode 100644
index b9a3aa8..0000000
--- a/libcpp/alignment/algorithms/alignment/sdp/FragmentSortImpl.hpp
+++ /dev/null
@@ -1,16 +0,0 @@
-#include "FragmentSort.hpp"
-
-template<typename T_Fragment>
-int
-LexicographicFragmentSort<T_Fragment>::operator()
- (const T_Fragment &a, const T_Fragment &b) const {
- return a.LessThanXY(b);
-}
-
-template<typename T_Fragment>
-int
-LexicographicFragmentSortByY<T_Fragment>::operator()
- (const T_Fragment &a, const T_Fragment &b) const {
- return a.LessThanYX(b);
-}
-
diff --git a/libcpp/alignment/algorithms/alignment/sdp/NonoverlappingSparseDynamicProgramming.h b/libcpp/alignment/algorithms/alignment/sdp/NonoverlappingSparseDynamicProgramming.h
deleted file mode 100644
index 148c16d..0000000
--- a/libcpp/alignment/algorithms/alignment/sdp/NonoverlappingSparseDynamicProgramming.h
+++ /dev/null
@@ -1,193 +0,0 @@
-#ifndef NONOVERLAPPING_SPARSE_DYNAMIC_PROGRAMMING_H_
-#define NONOVERLAPPING_SPARSE_DYNAMIC_PROGRAMMING_H_
-
-/*
- *
- * Compute the subset of fragmentSet of largest weight that is not overlapping.
- *
- */
-#include "FragmentSort.h"
-#include "SDPSet.h"
-#include "SDPFragment.h"
-#include "SDPColumn.h"
-#include "../AlignmentUtils.h"
-#include "../../../datastructures/alignment/Alignment.h"
-
-
-template<typename T_Fragment>
-int SDPHeaviestSubsequence(int queryLength,
- vector<T_Fragment> &fragmentSet,
- int indel, int match,
- vector<int> &maxFragmentChain,
- AlignmentType alignType=Global) {
-
- maxFragmentChain.clear();
-
- if (fragmentSet.size() < 1)
- return 0;
-
- std::sort(fragmentSet.begin(), fragmentSet.end(), LexicographicFragmentSort<T_Fragment>());
-
- SDPSet<SDPColumn> activeSet;
-
- int sweepX;
- int trailRow;
- int fSweep;
- int fi;
- for (fi = 0; fi < fragmentSet.size(); fi++) {
- fragmentSet[fi].index = fi;
- }
-
- sweepX = fragmentSet[0].x;
-
- fSweep = 0;
- int maxChainLength = 0;
- int maxChainFragment = -1;
- int minFragmentCost, minFragmentIndex;
- minFragmentCost = INF_INT;
- minFragmentIndex = -1;
- for (sweepX = 0; sweepX < queryLength; sweepX++) {
- //
- // For each fragment ending in sweepX, attempt to compute its cost
- // by looking for the best previous match.
- //
- int fSweepStart = fSweep;
- while (fSweep < fragmentSet.size() and
- fragmentSet[fSweep].x == sweepX) {
-
- //
- // Compute the cost of every fragment in the sweep.
- //
- int cp = INF_INT, cl = INF_INT, ca = INF_INT;
- SDPColumn curCol, predCol;
- curCol.col = fragmentSet[fSweep].y;
- //
- // Search preceeding fragments.
- //
-
- //
- // Compute the cost of fragment_f
- int foundPrev = 0;
- T_Fragment fragStartPoint;
- fragStartPoint.x = fragmentSet[fSweep].x - fragmentSet[fSweep].GetLength();
- fragStartPoint.y = fragmentSet[fSweep].y - fragmentSet[fSweep].GetLength();
- T_Fragment predFrag;
-
- int predFragScore;
-
- if (activeSet.Predecessor(fragStartPoint, predFrag)) {
- //
- // predCol points to the fragment with greatest value less than curCol.
- //
- predFragScore = fragmentSet[predCol.optFragment].cost +
- abs((fragmentSet[fSweep].x - fragmentSet[fSweep].y)
- - (fragmentSet[predCol.optFragment].x - fragmentSet[predCol.optFragment].y)) * indel;
- foundPrev = 1;
- }
-
- //
- // Now assign the score for the fragment. When doing a local alignment
- // start a new chain if the score is not good.
-
- if (foundPrev and
- (alignType == Global or
- (alignType == Local and predFragScore < 0))) {
- fragmentSet[fSweep].chainPrev = predCol.optFragment;
- fragmentSet[fSweep].cost = predFragScore - fragmentSet[fSweep].weight;
- fragmentSet[fSweep].chainLength = fragmentSet[fragmentSet[fSweep].chainPrev].chainLength + 1;
- }
- else {
- fragmentSet[fSweep].chainPrev = -1;
- fragmentSet[fSweep].cost = fragmentSet[fSweep].GetLength() * match - fragmentSet[fSweep].weight;
- fragmentSet[fSweep].chainLength = 1;
- }
-
- if (minFragmentCost > fragmentSet[fSweep].cost) {
- minFragmentCost = fragmentSet[fSweep].cost;
- minFragmentIndex = fSweep;
- // maxChainLength = fragmentSet[fSweep].chainLength;
- }
-
- if (fragmentSet[fSweep].chainLength > maxChainLength) {
- maxChainLength = fragmentSet[fSweep].chainLength;
- maxChainFragment = fSweep;
- }
-
- fSweep++;
- }
-
- //
- // Each column must contain the highest scoring hit in that column.
- //
- fSweep = fSweepStart;
- while (fSweep < fragmentSet.size() and
- fragmentSet[fSweep].x == sweepX) {
- //
- // These elements are removed from the sweep set since they are done being processed.
- // If they are the lowest cost in the value, update activeSet
- //
- SDPColumn col;
- int storeCol = 0;
- col.col = fragmentSet[fSweep].y;
-
- if (activeSet.Member(col)) {
- if (fragmentSet[col.optFragment].cost < fragmentSet[fSweep].cost) {
- storeCol = 1;
- }
- }
- else {
- storeCol = 1;
- }
- if (storeCol) {
- col.col = fragmentSet[fSweep].y;
- col.optFragment = fSweep;
- //
- // Insert new column or replace col with a more optimal one.
- //
- activeSet.Insert(col);
-
- //
- // The invariant structure of the activeSet is that
- // after inserting a fragment of score S at column col,
- // the score of all columns greater than 'col' in col set
- // must be less than col.
- //
- // To preserve this invariant, when an element is inserted
- // at 'col', look to columns greater. As long as any columns
- // have scores that are greater than col, remove them.
- // Once a column col_next has been found that has a score less than S
- // by the structure of the loop invariant, all columns greater than col_next
- // are guaranteed to have lower score than S, so we can continue searching
- // through this loop.
- //
- // Since fragments are processed at most once, this remains O(M).
-
- SDPColumn successorCol = col;
-
- while (activeSet.Successor(col, successorCol) and
- fragmentSet[successorCol.optFragment].cost > fragmentSet[fSweep].cost) {
- activeSet.Delete(successorCol);
- }
- }
-
- //
- // Now remove this fragment, it is at the end of the sweep line.
- //
- int deleted;
- deleted = activeSet.Delete(fragmentSet[fSweep]);
- assert(deleted);
- ++fSweep;
- }
- }
- if (alignType == Local) {
- maxChainFragment = minFragmentIndex;
- }
- while (maxChainFragment != -1) {
- maxFragmentChain.push_back(maxChainFragment);
- maxChainFragment = fragmentSet[maxChainFragment].chainPrev;
- }
- std::reverse(maxFragmentChain.begin(), maxFragmentChain.end());
- return maxFragmentChain.size();
-}
-
-#endif
diff --git a/libcpp/alignment/algorithms/alignment/sdp/SDPColumn.hpp b/libcpp/alignment/algorithms/alignment/sdp/SDPColumn.hpp
deleted file mode 100644
index 6ae674e..0000000
--- a/libcpp/alignment/algorithms/alignment/sdp/SDPColumn.hpp
+++ /dev/null
@@ -1,23 +0,0 @@
-#ifndef _BLASR_SDP_COLUMN_HPP_
-#define _BLASR_SDP_COLUMN_HPP_
-
-class SDPColumn {
- public:
- int col;
- int optFragment;
- SDPColumn() : col(0), optFragment(0) {}
- int operator<(const SDPColumn & rhs) const {
- return col < rhs.col;
- }
- int operator<(const int y) const {
- return col < y;
- }
- int operator==(const SDPColumn &rhs) const {
- return col == rhs.col;
- }
- int operator>(const SDPColumn &rhs) const {
- return (!(*this < rhs) && !(*this == rhs));
- }
-};
-
-#endif // _BLASR_SDP_COLUMN_HPP_
diff --git a/libcpp/alignment/algorithms/alignment/sdp/SDPFragment.cpp b/libcpp/alignment/algorithms/alignment/sdp/SDPFragment.cpp
deleted file mode 100644
index 861144e..0000000
--- a/libcpp/alignment/algorithms/alignment/sdp/SDPFragment.cpp
+++ /dev/null
@@ -1,27 +0,0 @@
-#include "SDPFragment.hpp"
-
-int Fragment::operator>(const Fragment &f) const {
- return (!(*this < f) && !(*this == f));
-}
-int Fragment::GetLength() {
- return length;
-}
-void Fragment::SetLength(int _length) {
- length = _length;
-}
-
-bool Fragment::SetAbove(int a) {
- above = a;
- return true;
-}
-
-bool Fragment::GetAbove(int & a) {
- if (above >= 0) {
- a = above;
- return true;
- } else {
- a = -1;
- return false;
- }
-}
-
diff --git a/libcpp/alignment/algorithms/alignment/sdp/SDPFragment.hpp b/libcpp/alignment/algorithms/alignment/sdp/SDPFragment.hpp
deleted file mode 100644
index 23b0e1c..0000000
--- a/libcpp/alignment/algorithms/alignment/sdp/SDPFragment.hpp
+++ /dev/null
@@ -1,132 +0,0 @@
-#ifndef _BLASR_SDP_FRAGMENT_HPP_
-#define _BLASR_SDP_FRAGMENT_HPP_
-
-class Fragment {
-public:
- unsigned int x;
- unsigned int y;
- unsigned int weight;
- unsigned int length;
- int index;
- int chainPrev;
- int cost;
- int above;
- unsigned int chainLength;
-
- inline Fragment(unsigned int px, unsigned int py, int pweight=0);
-
- inline Fragment();
-
- unsigned int GetX() const {return x;}
-
- unsigned int GetY() const {return y;}
-
- bool SetAbove(int a);
- bool GetAbove(int & a);
-
- inline int LessThanXY(const Fragment &f) const;
-
- inline int LessThanYX(const Fragment &f) const;
-
- inline int operator<(const Fragment &f) const;
-
- inline Fragment& operator=(const Fragment &rhs);
-
- inline int operator==(const Fragment &f) const;
-
- int operator>(const Fragment &f) const;
-
- int GetLength();
-
- void SetLength(int _length);
-};
-
-inline Fragment::Fragment(unsigned int px, unsigned int py, int pweight) {
- x = px;
- y = py;
- weight = pweight;
- length = index = 0;
- chainPrev = cost = chainLength = 0;
- above = -1;
-}
-
-//
-// Provide default constructor that will
-// give bad results if members are not properly initialized
-// later on.
-//
-inline Fragment::Fragment() {
- x = -1;
- y = -1;
- weight = length = index = 0;
- chainPrev = cost = chainLength = 0;
- above = -1;
-}
-
-inline int Fragment::LessThanXY(const Fragment &f) const {
- if (x == f.x) {
- if (y == f.y) {
- if (length == f.length) return 0;
- else return length < f.length;
- } else return y < f.y;
- } else return x < f.x;
- /*
- if (x < f.x)
- return 1;
- else if (x == f.x)
- return y < f.y;
- else
- return 0;
- */
-}
-
-inline int Fragment::LessThanYX(const Fragment &f) const {
- if (y == f.y) {
- if (x == f.x) {
- if (length == f.length) return 0;
- else return length < f.length;
- } else return x < f.x;
- } else return y < f.y;
- /*
- if (y < f.y)
- return 1;
- else if (y == f.y)
- return x < f.x;
- else
- return 0;
- */
-}
-
-inline Fragment& Fragment::operator=(const Fragment &rhs) {
- x = rhs.x;
- y = rhs.y;
- index = rhs.index;
- cost = rhs.cost;
- weight = rhs.weight;
- length = rhs.length;
- chainLength = rhs.chainLength;
- chainPrev = rhs.chainPrev;
- above = rhs.above;
- return *this;
-}
-
-inline int Fragment::operator==(const Fragment &f) const {
- return (x == f.x and y == f.y);
-}
-
-inline int Fragment::operator<(const Fragment &f) const {
- //
- // Sort fragments by diagonal:
- //
- int diag, fDiag;
- diag = (y - x);
- fDiag = f.y - f.x;
- if (diag < fDiag)
- return 1;
- else if (diag == fDiag)
- return (x < f.x);
- else
- return 0;
-}
-
-#endif // _BLASR_SDP_FRAGMENT_HPP_
diff --git a/libcpp/alignment/algorithms/alignment/sdp/SDPSet.hpp b/libcpp/alignment/algorithms/alignment/sdp/SDPSet.hpp
deleted file mode 100644
index 866dbfb..0000000
--- a/libcpp/alignment/algorithms/alignment/sdp/SDPSet.hpp
+++ /dev/null
@@ -1,52 +0,0 @@
-#ifndef _BLASR_SDP_SET_HPP_
-#define _BLASR_SDP_SET_HPP_
-
-
-/*
- A SDPSet is a collection of types T that have strict ordering
- defined. It supports ways to query for points immediately less or
- immediately greater than another value.
-*/
-
-template<typename T>
-class SDPSet {
-private:
- typedef std::set<T> Tree;
- typename SDPSet<T>::Tree tree;
-public:
- int size();
-
- /*
- * Remove a fragment f if it exists.
- */
- int Delete(T &f);
-
- /*
- * Insert a fresh copy of f into the set. If a copy
- * already exists, replace it with this one.
- */
- inline VectorIndex Insert(T &f);
-
- /*
- Returns true if there is a value such that value == f
- */
- int Member(T &f);
-
- int Min(T &f);
-
- /*
- * Given f, set succ to be the first value greater than f.
- * Return 1 if such a value exists, 0 otherwise.
- */
- int Successor(T &f, T &succ);
-
- /*
- * Given f, set pred to the first value less than f.
- * Returns 1 if such a value exists, 0 otherwise.
- */
- int Predecessor(T &f, T &pred);
-};
-
-#include "SDPSetImpl.hpp"
-
-#endif // _BLASR_SDP_SET_HPP_
diff --git a/libcpp/alignment/algorithms/alignment/sdp/SDPSetImpl.hpp b/libcpp/alignment/algorithms/alignment/sdp/SDPSetImpl.hpp
deleted file mode 100644
index 6dbe709..0000000
--- a/libcpp/alignment/algorithms/alignment/sdp/SDPSetImpl.hpp
+++ /dev/null
@@ -1,113 +0,0 @@
-#include <stdint.h>
-#include <set>
-#include "Types.h"
-#include "SDPSet.hpp"
-
-template<typename T>
-int SDPSet<T>::size() {
- return tree.size();
-}
-
-/*
- * Remove a fragment f if it exists.
- */
-template<typename T>
-int SDPSet<T>::Delete(T &f) {
- typename std::set<T>::iterator it = tree.find(f);
- if (it != tree.end() and (*it) == f) {
- tree.erase(f);
- return 1;
- }
- return 0;
-}
-/*
- * Insert a fresh copy of f into the set. If a copy
- * already exists, replace it with this one.
- */
-template<typename T>
-inline VectorIndex SDPSet<T>::Insert(T &f) {
- typename SDPSet<T>::Tree::iterator it = tree.find(f);
- if (it != tree.end())
- tree.erase(it);
- tree.insert(f);
- return tree.size();
-}
-/*
- Returns true if there is a value such that value == f
- */
-
-template<typename T>
-int SDPSet<T>::Member(T &f) {
- typename SDPSet<T>::Tree::iterator it = tree.find(f);
- if (it != tree.end()) {
- f = *it;
- return 1;
- }
- return 0;
-}
-
-template<typename T>
-int SDPSet<T>::Min(T &f) {
- if (tree.size() == 0) {
- return 0;
- }
- else {
- f = *(tree.begin());
- }
-}
-
-/*
- * Given f, set succ to be the first value greater than f.
- * Return 1 if such a value exists, 0 otherwise.
- */
-template<typename T>
-int SDPSet<T>::Successor(T &f, T &succ) {
-
- //
- // Set succ to the first value > f, if such a value exists.
- //
- if (tree.size() < 2) {
- return 0;
- }
- typename Tree::iterator it = tree.upper_bound(f);
-
- if (it == tree.end())
- return 0;
-
- succ = *it;
- return 1;
-}
-
-/*
- * Given f, set pred to the first value less than f.
- * Returns 1 if such a value exists, 0 otherwise.
- */
-template<typename T>
-int SDPSet<T>::Predecessor(T &f, T &pred) {
- //
- // Set pred equal to the largest value <= f.
- // Return 1 if such a value exists, 0 otherwise.
- //
- if (tree.size() == 0)
- return 0;
-
- typename Tree::iterator it = tree.find(f);
-
- if (it != tree.end()) {
- pred = *it;
- return 1;
- }
-
- it = tree.lower_bound(f);
- if (it != tree.begin())
- --it;
-
- if (f < *it) {
- // No elements less than f exist.
- return 0;
- }
- else {
- pred = *it;
- return 1;
- }
-}
diff --git a/libcpp/alignment/algorithms/alignment/sdp/SparseDynamicProgramming.cpp b/libcpp/alignment/algorithms/alignment/sdp/SparseDynamicProgramming.cpp
deleted file mode 100644
index 9325491..0000000
--- a/libcpp/alignment/algorithms/alignment/sdp/SparseDynamicProgramming.cpp
+++ /dev/null
@@ -1,18 +0,0 @@
-#include "SparseDynamicProgramming.hpp"
-
-int IndelPenalty(int x1, int y1, int x2, int y2, int insertion, int deletion) {
- int drift, driftPenalty;
- drift = (x1 - y1) - (x2 - y2);
- if (drift > 0) {
- driftPenalty = drift * insertion;
- }
- else if (drift < 0) {
- driftPenalty = -drift * deletion;
- }
- else {
- driftPenalty = 0;
- }
- return driftPenalty;
-}
-
-
diff --git a/libcpp/alignment/algorithms/alignment/sdp/SparseDynamicProgramming.hpp b/libcpp/alignment/algorithms/alignment/sdp/SparseDynamicProgramming.hpp
deleted file mode 100644
index 8f42113..0000000
--- a/libcpp/alignment/algorithms/alignment/sdp/SparseDynamicProgramming.hpp
+++ /dev/null
@@ -1,37 +0,0 @@
-#ifndef SPARSE_DYNAMIC_PROGRAMMING_H_
-#define SPARSE_DYNAMIC_PROGRAMMING_H_
-
-#include <vector>
-#include <string>
-#include "Types.h"
-#include "defs.h"
-#include "DNASequence.hpp"
-#include "datastructures/alignment/Alignment.hpp"
-#include "algorithms/alignment/AlignmentUtils.hpp"
-
-/*******************************************************************************
- * Sparse dynamic programming implementation of Longest Common Subsequence
- *
- * Implementation of method described in Baker and Giancarlo, Journal of
- * Algorithms 42, 231-254, 2002.
- *
- * 5/7/09 -- Modified to incorporate different linear cost functions, and
- * local alignments.
- *
- ******************************************************************************/
-
-int IndelPenalty(int x1, int y1, int x2, int y2, int insertion, int deletion);
-
-template<typename T_Fragment>
-void StoreAbove(std::vector<T_Fragment> &fragmentSet, DNALength fragmentLength);
-
-template<typename T_Fragment>
-int SDPLongestCommonSubsequence(DNALength queryLength,
- std::vector<T_Fragment> &fragmentSet,
- DNALength fragmentLength,
- int insertion, int deletion, int match,
- std::vector<int> &maxFragmentChain, AlignmentType alignType=Global);
-
-#include "SparseDynamicProgrammingImpl.hpp"
-
-#endif
diff --git a/libcpp/alignment/algorithms/alignment/sdp/SparseDynamicProgrammingImpl.hpp b/libcpp/alignment/algorithms/alignment/sdp/SparseDynamicProgrammingImpl.hpp
deleted file mode 100644
index a227c70..0000000
--- a/libcpp/alignment/algorithms/alignment/sdp/SparseDynamicProgrammingImpl.hpp
+++ /dev/null
@@ -1,266 +0,0 @@
-#ifndef SPARSE_DYNAMIC_PROGRAMMING_IMPL_HPP_
-#define SPARSE_DYNAMIC_PROGRAMMING_IMPL_HPP_
-
-#include <stdlib.h>
-#include <stdint.h>
-#include <algorithm>
-#include <cassert>
-#include <set>
-#include <limits.h>
-#include <ostream>
-#include "SDPSet.hpp"
-#include "SDPFragment.hpp"
-#include "SDPColumn.hpp"
-#include "FragmentSort.hpp"
-
-template<typename T_Fragment>
-void StoreAbove(std::vector<T_Fragment> &fragmentSet, DNALength fragmentLength) {
- std::sort(fragmentSet.begin(), fragmentSet.end(), LexicographicFragmentSortByY<T_Fragment>());
- int i;
- for (i = 1; i < fragmentSet.size(); i++) {
- if (fragmentSet[i-1].x <= fragmentSet[i].x
- and fragmentSet[i-1].x + fragmentSet[i-1].length > fragmentSet[i].x
- and fragmentSet[i-1].y < fragmentSet[i].y) {
- fragmentSet[i].SetAbove(fragmentSet[i-1].index);
- }
- }
- // Place back in original order.
- std::sort(fragmentSet.begin(), fragmentSet.end(), LexicographicFragmentSort<T_Fragment>());
-}
-
-template<typename T_Fragment>
-int SDPLongestCommonSubsequence(DNALength queryLength,
- std::vector<T_Fragment> &fragmentSet,
- DNALength fragmentLength,
- int insertion, int deletion, int match,
- std::vector<int> &maxFragmentChain, AlignmentType alignType) {
-
- maxFragmentChain.clear();
- if (fragmentSet.size() < 1)
- return 0;
-
- std::sort(fragmentSet.begin(), fragmentSet.end(), LexicographicFragmentSort<T_Fragment>());
-
- SDPSet<Fragment> sweepSet;
- SDPSet<SDPColumn> colSet;
-
- unsigned int sweepRow;
- unsigned int trailRow;
- VectorIndex fSweep, fTrail;
- VectorIndex fi;
- for (fi = 0; fi < fragmentSet.size(); fi++) {
- fragmentSet[fi].index = fi;
- }
-
- StoreAbove(fragmentSet, fragmentLength);
- sweepRow = fragmentSet[0].x;
- Fragment pred, succ;
- fSweep = 0;
- fTrail = 0;
- unsigned int maxChainLength = 0;
- int maxChainFragment = -1;
- int minFragmentCost, minFragmentIndex;
- minFragmentCost = INF_INT;
- minFragmentIndex = -1;
- for (; sweepRow < queryLength + fragmentLength; sweepRow++) {
- //
- // Add all elements on the sweep row to the sweep set. Note that when
- // fSweep is past query.length.
- int startF = fSweep;
- int fragmentSetSize = fragmentSet.size();
- while (fSweep < fragmentSetSize and
- fragmentSet[fSweep].x == sweepRow) {
-
- //
- // Compute the cost of every fragment in the sweep.
- //
- int cp = INF_INT, cl = INF_INT, ca = INF_INT;
- SDPColumn curCol, predCol;
- curCol.col = fragmentSet[fSweep].y;
- //
- // Search preceeding fragments.
- //
- //
- // Compute the cost of fragment_f
- int foundPrev = 0;
- int drift, driftPenalty;
- if (colSet.Predecessor(curCol, predCol)) {
- //
- // predCol points to the fragment with greatest value less than curCol.
- //
- // Baker and Giancarlo LCS cost
- driftPenalty = IndelPenalty(fragmentSet[fSweep].x, fragmentSet[fSweep].y,
- fragmentSet[predCol.optFragment].x,
- fragmentSet[predCol.optFragment].y,
- insertion, deletion);
- cp = fragmentSet[predCol.optFragment].cost + driftPenalty;
- foundPrev = 1;
- }
-
- // Search overlapping fragments.
- if (sweepSet.Predecessor(fragmentSet[fSweep], pred)) {
- //
- // Baker and Giancarlo LCS cost
- // Cost with insertion and deletion penalty.
- //
- cl = pred.cost +
- MIN((int)(fragmentLength - (fragmentSet[fSweep].y - pred.y)) * match, 0) +
- IndelPenalty(fragmentSet[fSweep].x, fragmentSet[fSweep].y,
- pred.x, pred.y, insertion, deletion);
- foundPrev = 1;
- }
-
- int aboveIndex;
- if (fragmentSet[fSweep].GetAbove(aboveIndex)) {
- // Baker and Giancarlo LCS cost
- ca = fragmentSet[aboveIndex].cost +
- (fragmentLength - (int)(fragmentSet[fSweep].y - fragmentSet[aboveIndex].y)) * match +
- IndelPenalty(fragmentSet[fSweep].x, fragmentSet[fSweep].y,
- fragmentSet[aboveIndex].x,
- fragmentSet[aboveIndex].y,
- insertion, deletion);
- foundPrev = 1;
- }
-
- //
- // Now compute the minimum of all these.
- //
- int minCost;
- minCost = MIN(cp, MIN(cl, ca));
-
- //
- // If doing a global alignment, chain is always extended. If local, the chain may not be.
- //
- if (foundPrev and
- (alignType == Global or
- (alignType == Local and minCost < 0))) {
- fragmentSet[fSweep].cost = minCost - fragmentSet[fSweep].weight;
- if (minCost == cp) {
- fragmentSet[fSweep].chainPrev = predCol.optFragment;
- }
- else if (minCost == cl) {
- fragmentSet[fSweep].chainPrev = pred.index;
- }
- else if (minCost == ca) {
- fragmentSet[fSweep].chainPrev = aboveIndex;
- }
- assert(fragmentSet[fSweep].chainPrev >= 0 and
- fragmentSet[fSweep].chainPrev < (int)fragmentSet.size());
- fragmentSet[fSweep].chainLength = fragmentSet[fragmentSet[fSweep].chainPrev].chainLength + 1;
- }
- else {
- if (alignType == Global) {
- fragmentSet[fSweep].chainPrev = (int) -1;
- fragmentSet[fSweep].cost = (fragmentSet[fSweep].x + fragmentSet[fSweep].y) * deletion +
- fragmentLength * match - fragmentSet[fSweep].weight;
- fragmentSet[fSweep].chainLength = 1;
- }
- else if (alignType == Local) {
- fragmentSet[fSweep].chainPrev = (int) -1;
- fragmentSet[fSweep].cost = fragmentLength * match - fragmentSet[fSweep].weight;
- fragmentSet[fSweep].chainLength = 1;
- }
- }
-
- if (minFragmentCost > fragmentSet[fSweep].cost) {
- minFragmentCost = fragmentSet[fSweep].cost;
- minFragmentIndex = fSweep;
- // maxChainLength = fragmentSet[fSweep].chainLength;
- }
-
- if (fragmentSet[fSweep].chainLength > maxChainLength) {
- maxChainLength = fragmentSet[fSweep].chainLength;
- maxChainFragment = fSweep;
- }
-
- // Done computing the optimal score for this fragment.
- fSweep++;
- }
-
- //
- // Insert all fragments in the sweep set
- //
- fSweep = startF;
- while (fSweep < fragmentSetSize and
- fragmentSet[fSweep].x == sweepRow) {
- // cout << "inserting sweep set with index" << fragmentSet[fSweep].index << endl;
- sweepSet.Insert(fragmentSet[fSweep]);
- ++fSweep;
- }
-
- // Remove elements from the sweep set that are too far back.
- if (sweepRow >= fragmentLength + 1) {
- trailRow = sweepRow - fragmentLength - 1;
- while (fTrail < fragmentSetSize and
- fragmentSet[fTrail].x == trailRow) {
- //
- // These elements are removed from the sweep set since they are done being processed.
- // If they are the lowest cost in the value, update colSet
- //
- SDPColumn col;
- int storeCol = 0;
- col.col = fragmentSet[fTrail].y;
-
- if (colSet.Member(col)) {
- if (fragmentSet[col.optFragment].cost < fragmentSet[fTrail].cost) {
- storeCol = 1;
- }
- }
- else {
- storeCol = 1;
- }
- if (storeCol) {
- col.col = fragmentSet[fTrail].y;
- col.optFragment = fTrail;
- //
- // Insert new column or replace col with a more optimal one.
- //
- colSet.Insert(col);
-
- //
- // The invariant structure of the colSet is that
- // after inserting a fragment of score S at column col,
- // the score of all columns greater than 'col' in col set
- // must be less than col.
- //
- // To preserve this invariant, when an element is inserted
- // at 'col', look to columns greater. As long as any columns
- // have scores that are greater than col, remove them.
- // Once a column col_next has been found that has a score less than S
- // by the structure of the loop invariant, all columns greater than col_next
- // are guaranteed to have lower score than S, so we can continue searching
- // through this loop.
- //
- // Since fragments are processed at most once, this remains O(M).
-
- SDPColumn successorCol = col;
-
- while (colSet.Successor(col, successorCol) and
- fragmentSet[successorCol.optFragment].cost > fragmentSet[fTrail].cost) {
- colSet.Delete(successorCol);
- }
- }
-
- //
- // Now remove this fragment, it is at the end of the sweep line.
- //
- int deleted;
- deleted = sweepSet.Delete(fragmentSet[fTrail]);
- assert(deleted);
-
- ++fTrail;
- }
- }
- }
- if (alignType == Local) {
- maxChainFragment = minFragmentIndex;
- }
- while (maxChainFragment != -1) {
- maxFragmentChain.push_back(maxChainFragment);
- maxChainFragment = fragmentSet[maxChainFragment].chainPrev;
- }
- std::reverse(maxFragmentChain.begin(), maxFragmentChain.end());
- return maxFragmentChain.size();
-}
-
-#endif // __SPARSE_DYNAMIC_PROGRAMMING_IMPL_HPP_
diff --git a/libcpp/alignment/algorithms/alignment/sdp/VariableLengthSDPFragment.h b/libcpp/alignment/algorithms/alignment/sdp/VariableLengthSDPFragment.h
deleted file mode 100644
index 618b25e..0000000
--- a/libcpp/alignment/algorithms/alignment/sdp/VariableLengthSDPFragment.h
+++ /dev/null
@@ -1,51 +0,0 @@
-#ifndef VARIABLE_LENGTH_SDP_FRAGMENT_H_
-#define VARIABLE_LENGTH_SDP_FRAGMENT_H_
-#include "SDPFragment.h"
-
-class ChainedFragment : public Fragment {
- int score;
- ChainedFragment *chainPrev;
- public:
- ChainedFragment():Fragment() {
- score = 0;
- chainPrev = NULL;
- }
-
- int SetScore(int _score) {
- return (score = _score);
- }
-
- int GetScore() {
- return score;
- }
-
- ChainedFragment *SetChainPrev(ChainedFragment *_chainPrev) {
- return (chainPrev = _chainPrev);
- }
-
- ChainedFragment *GetChainPrev() {
- return chainPrev;
- }
-
- int LessThan(const ChainedFragment &f) const {
- //
- // Order fragments by endpoint.
- //
- if (x == f.GetX()) {
- return (y < f.GetY());
- }
- else {
- return x < f.GetX();
- }
- }
-
- int operator<(const ChainedFragment &f) const {
- //
- // Sort fragments by x then y.
- //
- return LessThan(f);
- }
-};
-
-
-#endif
diff --git a/libcpp/alignment/algorithms/anchoring/BWTSearch.cpp b/libcpp/alignment/algorithms/anchoring/BWTSearch.cpp
deleted file mode 100644
index 16ea57c..0000000
--- a/libcpp/alignment/algorithms/anchoring/BWTSearch.cpp
+++ /dev/null
@@ -1,85 +0,0 @@
-#include "algorithms/anchoring/BWTSearch.hpp"
-
-int MapReadToGenome(BWT & bwt,
- FASTASequence & seq,
- DNALength subreadStart, DNALength subreadEnd,
- std::vector<ChainedMatchPos> &matchPosList,
- AnchorParameters & params, int &numBasesAnchored,
- std::vector<DNALength> & spv,
- std::vector<DNALength> & epv) {
-
- FASTASequence prefix;
- numBasesAnchored = 0;
- if (subreadEnd - subreadStart < params.minMatchLength) {
- return 0;
- }
- else {
- DNALength p;
- prefix.seq = seq.seq;
- for (p = subreadStart + params.minMatchLength;
- p < subreadEnd; p++) {
- //
- // Try reusing the vectors between calls - not thread
- // safe replace function call with one that has access
- // to a buffer class.
- //
- spv.clear(); epv.clear();
- prefix.length = p;
- bwt.Count(prefix, spv, epv);
-
- DNALength matchLength = spv.size();
- //
- // Keep going without subtracting from zero if there
- // are no hits.
- //
- if (spv.size() == 0) {
- continue;
- }
-
- DNALength i;
- std::vector<DNALength> matches;
- while (matchLength >= params.minMatchLength) {
- i = matchLength - 1;
-
- if (matchLength > 0 and epv[i] >= spv[i]) {
- //
- // Add the positions of the matches here.
- //
- matches.clear();
- if (epv[i] - spv[i] + 1 < params.maxAnchorsPerPosition) {
- numBasesAnchored++;
- bwt.Locate(spv[i], epv[i], matches);
- }
- break;
- }
- matchLength--;
- }
-
- // Convert from genome positions to tuples
- DNALength m;
- for (m = 0; m < matches.size(); m++ ) {
- // This if statement is a workaround for a bug
- // that is allowing short matches
- if (matches[m] >= matchLength) {
- matchPosList.push_back(ChainedMatchPos(
- matches[m] - matchLength,
- p-matchLength, matchLength ,
- matches.size()));
- }
- }
- }
- }
- return matchPosList.size();
-}
-
-int MapReadToGenome(BWT & bwt,
- FASTASequence & seq,
- DNALength start, DNALength end,
- std::vector<ChainedMatchPos> & matchPosList,
- AnchorParameters & params, int &numBasesAnchored) {
- std::vector<DNALength> spv,epv;
-
- return MapReadToGenome(bwt, seq, start, end, matchPosList,
- params, numBasesAnchored, spv, epv);
-}
-
diff --git a/libcpp/alignment/algorithms/anchoring/BWTSearch.hpp b/libcpp/alignment/algorithms/anchoring/BWTSearch.hpp
deleted file mode 100644
index e3e0366..0000000
--- a/libcpp/alignment/algorithms/anchoring/BWTSearch.hpp
+++ /dev/null
@@ -1,35 +0,0 @@
-#ifndef _BLASR_BWT_SEARCH_HPP_
-#define _BLASR_BWT_SEARCH_HPP_
-
-#include <vector>
-#include "FASTASequence.hpp"
-#include "bwt/BWT.hpp"
-#include "datastructures/anchoring/MatchPos.hpp"
-#include "datastructures/anchoring/AnchorParameters.hpp"
-
-int MapReadToGenome(BWT & bwt,
- FASTASequence & seq,
- DNALength subreadStart, DNALength subreadEnd,
- std::vector<ChainedMatchPos> &matchPosList,
- AnchorParameters & params, int &numBasesAnchored,
- std::vector<DNALength> & spv,
- std::vector<DNALength> & epv);
-
-
-int MapReadToGenome(BWT & bwt,
- FASTASequence & seq,
- DNALength start, DNALength end,
- std::vector<ChainedMatchPos> & matchPosList,
- AnchorParameters & params, int &numBasesAnchored);
-
-
-template<typename T_MappingBuffers>
-int MapReadToGenome(BWT & bwt,
- FASTASequence & seq,
- std::vector<ChainedMatchPos> &matchPosList,
- AnchorParameters & params, int & numBasesAnchored,
- T_MappingBuffers & mappingBuffers);
-
-#include "algorithms/anchoring/BWTSearchImpl.hpp"
-
-#endif
diff --git a/libcpp/alignment/algorithms/anchoring/BWTSearchImpl.hpp b/libcpp/alignment/algorithms/anchoring/BWTSearchImpl.hpp
deleted file mode 100644
index ec71552..0000000
--- a/libcpp/alignment/algorithms/anchoring/BWTSearchImpl.hpp
+++ /dev/null
@@ -1,14 +0,0 @@
-#ifndef _BLASR_BWT_SEARCH_IMPL_HPP_
-#define _BLASR_BWT_SEARCH_IMPL_HPP_
-
-template<typename T_MappingBuffers>
-int MapReadToGenome(BWT & bwt,
- FASTASequence & seq,
- std::vector<ChainedMatchPos> &matchPosList,
- AnchorParameters & params, int & numBasesAnchored,
- T_MappingBuffers & mappingBuffers) {
- return MapReadToGenome(bwt, seq, matchPosList, params,
- numBasesAnchored, mappingBuffers.spv, mappingBuffers.epv);
-}
-
-#endif
diff --git a/libcpp/alignment/algorithms/anchoring/BasicEndpoint.hpp b/libcpp/alignment/algorithms/anchoring/BasicEndpoint.hpp
deleted file mode 100644
index 28ffaae..0000000
--- a/libcpp/alignment/algorithms/anchoring/BasicEndpoint.hpp
+++ /dev/null
@@ -1,50 +0,0 @@
-#ifndef _BLASR_BASIC_ENDPOINT_HPP_
-#define _BLASR_BASIC_ENDPOINT_HPP_
-
-#include "Types.h"
-#include "algorithms/anchoring/Coordinate.hpp"
-//
-// An endpoint is one of the ends of a fragment, where
-// a fragment is an exact match between two genomes.
-// So, a fragment is a 2D object that has a position and length,
-// and an endpoint is 1D, where it just has a position.
-// A fragment may be associated with a score that is the score
-// of the fragment in a maximum scoring chain. When finding a
-// maximum scoring chain using priority search trees, one must
-// be able to set the score of a fragment when indexing solely
-// a point.
-//
-
-enum WhichEnd {Start, End};
-typedef UInt KeyType;
-
-template<typename T_ScoredFragment>
-class BasicEndpoint {
-private:
- Coordinate p;
- WhichEnd side;
- T_ScoredFragment *fragmentPtr;
-
-public:
- class LessThan {
- public:
- int operator()(const BasicEndpoint<T_ScoredFragment> & lhs, const BasicEndpoint<T_ScoredFragment> & rhs) const {
- return lhs.p < rhs.p;
- }
- };
- BasicEndpoint();
- WhichEnd GetSide();
- void FragmentPtrToStart(T_ScoredFragment* fragment);
- void FragmentPtrToEnd(T_ScoredFragment* fragment);
- int GetScore();
- int SetScore(int score);
- T_ScoredFragment* SetScoredReference(T_ScoredFragment* _fragmentPtr);
- int operator<(const BasicEndpoint &rhs) const;
- KeyType GetKey();
- T_ScoredFragment* GetFragmentPtr();
- void SetChainPrev(T_ScoredFragment* prevChainFragment);
-};
-
-#include "algorithms/anchoring/BasicEndpointImpl.hpp"
-
-#endif
diff --git a/libcpp/alignment/algorithms/anchoring/BasicEndpointImpl.hpp b/libcpp/alignment/algorithms/anchoring/BasicEndpointImpl.hpp
deleted file mode 100644
index dd61377..0000000
--- a/libcpp/alignment/algorithms/anchoring/BasicEndpointImpl.hpp
+++ /dev/null
@@ -1,78 +0,0 @@
-#ifndef _BLASR_BASIC_ENDPOINT_IMPL_HPP_
-#define _BLASR_BASIC_ENDPOINT_IMPL_HPP_
-
-#include "algorithms/anchoring/BasicEndpoint.hpp"
-/*
- An endpoint is one of the ends of a fragment, where
- a fragment is an exact match between two genomes.
- So, a fragment is a 2D object that has a position and length,
- and an endpoint is 1D, where it just has a position.
- A fragment may be associated with a score that is the score
- of the fragment in a maximum scoring chain. When finding a
- maximum scoring chain using priority search trees, one must
- be able to set the score of a fragment when indexing solely
- a point.
-*/
-
-template<typename T_ScoredFragment>
-BasicEndpoint<T_ScoredFragment>::
-BasicEndpoint(){}
-
-template<typename T_ScoredFragment>
-WhichEnd BasicEndpoint<T_ScoredFragment>::
-GetSide() {return side;}
-
-template<typename T_ScoredFragment>
-void BasicEndpoint<T_ScoredFragment>::
-FragmentPtrToStart(T_ScoredFragment *fragment) {
- p.SetX(fragment->GetX());
- p.SetY(fragment->GetY());
- side = Start;
- fragmentPtr = fragment;
-}
-
-template<typename T_ScoredFragment>
-void BasicEndpoint<T_ScoredFragment>::FragmentPtrToEnd(
- T_ScoredFragment *fragment) {
- p.SetX(fragment->GetX() + fragment->GetLength());
- p.SetY(fragment->GetY() + fragment->GetLength());
- side = End;
- fragmentPtr = fragment;
-}
-
-template<typename T_ScoredFragment>
-int BasicEndpoint<T_ScoredFragment>::GetScore() {
- return fragmentPtr->GetScore();
-}
-
-template<typename T_ScoredFragment>
-int BasicEndpoint<T_ScoredFragment>::SetScore(int score) {
- return (fragmentPtr->SetScore(score));
-}
-
-template<typename T_ScoredFragment>
-T_ScoredFragment* BasicEndpoint<T_ScoredFragment>::
-SetScoredReference(
- T_ScoredFragment *_fragmentPtr) {
- return (fragmentPtr = _fragmentPtr);
-}
-
-template<typename T_ScoredFragment>
-int BasicEndpoint<T_ScoredFragment>::
-operator<(const BasicEndpoint &rhs) const {return p < rhs.p;}
-
-template<typename T_ScoredFragment>
-KeyType BasicEndpoint<T_ScoredFragment>::
-GetKey() {return p.GetY();}
-
-template<typename T_ScoredFragment>
-T_ScoredFragment* BasicEndpoint<T_ScoredFragment>::
-GetFragmentPtr() {return fragmentPtr;}
-
-template<typename T_ScoredFragment>
-void BasicEndpoint<T_ScoredFragment>::
-SetChainPrev(T_ScoredFragment* prevChainFragment) {
- fragmentPtr->SetChainPrev(prevChainFragment);
-}
-
-#endif
diff --git a/libcpp/alignment/algorithms/anchoring/ClusterProbability.cpp b/libcpp/alignment/algorithms/anchoring/ClusterProbability.cpp
deleted file mode 100644
index 0dc61dc..0000000
--- a/libcpp/alignment/algorithms/anchoring/ClusterProbability.cpp
+++ /dev/null
@@ -1,45 +0,0 @@
-#include "algorithms/anchoring/ClusterProbability.hpp"
-#include <cassert>
-#include <math.h>
-
-float ComputeAnchorProbability(float pMatch, int minAnchorLength) {
- assert(minAnchorLength >= 0);
- assert(pMatch < 1.00001 and pMatch > 0);
-
- int i;
- float totalProbability = 0.0;
- float pMisMatch = 1 - pMatch;
- for (i = 0; i < minAnchorLength; i++) {
- totalProbability += pMatch * pMisMatch;
- pMatch *= pMatch;
- }
- return 1 - totalProbability;
-}
-
-
-float ComputeExpectedAnchorLength(float pMatch, int minAnchorLength,
- float pAnchor) {
- int i = 0;
- for (i = 0; i < minAnchorLength; i++) {
- pMatch *= pMatch;
- }
- float pMismatch = 1 - pMatch;
- float pValueEpsilon = 0.000000001;
- float expAnchorLength = 0;
-
- while(pMatch*pMismatch > pValueEpsilon) {
- expAnchorLength += i * pMatch*pMismatch/pAnchor;
- pMatch *= pMatch;
- }
- return expAnchorLength;
-}
-
-
-float AnchorBasesPerRead(int readLength, float pAnchor) {
- return pAnchor * readLength;
-}
-
-float AnchorBasesPerReadSigma(float expAnchorBasesPerRead) {
- // Assume exponential distribution:
- return sqrt(expAnchorBasesPerRead);
-}
diff --git a/libcpp/alignment/algorithms/anchoring/ClusterProbability.hpp b/libcpp/alignment/algorithms/anchoring/ClusterProbability.hpp
deleted file mode 100644
index 23d4e4e..0000000
--- a/libcpp/alignment/algorithms/anchoring/ClusterProbability.hpp
+++ /dev/null
@@ -1,13 +0,0 @@
-#ifndef _BLASR_CLUSTER_PROBABILITY_HPP_
-#define _BLASR_CLUSTER_PROBABILITY_HPP_
-
-float ComputeAnchorProbability(float pMatch, int minAnchorLength);
-
-float ComputeExpectedAnchorLength(float pMatch, int minAnchorLength,
- float pAnchor);
-
-float AnchorBasesPerRead(int readLength, float pAnchor);
-
-float AnchorBasesPerReadSigma(float expAnchorBasesPerRead);
-
-#endif
diff --git a/libcpp/alignment/algorithms/anchoring/Coordinate.cpp b/libcpp/alignment/algorithms/anchoring/Coordinate.cpp
deleted file mode 100644
index 9e6f624..0000000
--- a/libcpp/alignment/algorithms/anchoring/Coordinate.cpp
+++ /dev/null
@@ -1,12 +0,0 @@
-#include "algorithms/anchoring/Coordinate.hpp"
-
-
-int Coordinate::operator<=(const Coordinate &rhs) const {
- return (*this < rhs) or (x == rhs.x && y == rhs.y);
-}
-
-int Coordinate::Equals(const Coordinate &rhs) const {
- return (x == rhs.GetX() and y == rhs.GetY());
-}
-
-
diff --git a/libcpp/alignment/algorithms/anchoring/Coordinate.hpp b/libcpp/alignment/algorithms/anchoring/Coordinate.hpp
deleted file mode 100644
index 1e86e29..0000000
--- a/libcpp/alignment/algorithms/anchoring/Coordinate.hpp
+++ /dev/null
@@ -1,45 +0,0 @@
-#ifndef _BLASR_COORDINATE_HPP_
-#define _BLASR_COORDINATE_HPP_
-
-#include "Types.h"
-
-class Coordinate {
-private:
- UInt x;
- UInt y;
-public:
- inline UInt GetX() const;
- inline UInt GetY() const;
- inline UInt SetX(UInt _x);
- inline UInt SetY(UInt _y);
- inline int operator<(const Coordinate &rhs) const;
- int operator<=(const Coordinate &rhs) const;
- int Equals(const Coordinate &rhs) const;
- //
- // Synonym for Equals.
- //
- inline int operator==(const Coordinate &rhs) const;
- inline Coordinate &operator=(const Coordinate &rhs);
-};
-
-inline UInt Coordinate::GetX() const {return x;}
-inline UInt Coordinate::GetY() const {return y;}
-
-inline UInt Coordinate::SetX(UInt _x) {return (x = _x);}
-inline UInt Coordinate::SetY(UInt _y) {return (y = _y);}
-
-inline int Coordinate::operator<(const Coordinate &rhs) const {
- if (x == rhs.GetX()) return y < rhs.GetY();
- else return x < rhs.GetX();
-}
-
-inline int Coordinate::operator==(const Coordinate &rhs) const {
- return this->Equals(rhs);
-}
-
-inline Coordinate& Coordinate::operator=(const Coordinate &rhs) {
- this->x = rhs.x;
- this->y = rhs.y;
- return *this;
-}
-#endif
diff --git a/libcpp/alignment/algorithms/anchoring/FindMaxInterval.cpp b/libcpp/alignment/algorithms/anchoring/FindMaxInterval.cpp
deleted file mode 100644
index cc9ca5b..0000000
--- a/libcpp/alignment/algorithms/anchoring/FindMaxInterval.cpp
+++ /dev/null
@@ -1,23 +0,0 @@
-#include "algorithms/anchoring/FindMaxInterval.hpp"
-
-unsigned int NumRemainingBases(DNALength curPos, DNALength intervalLength) {
- if (curPos > intervalLength) {
- return 0;
- }
- else {
- return intervalLength - curPos;
- }
-}
-
-IntervalSearchParameters::IntervalSearchParameters() {
- advanceHalf = false;
- globalChainType = 0;
- maxPValue = log(0.1);
- aboveCategoryPValue = 0;
- warp = true;
- fastMaxInterval = false;
- aggressiveIntervalCut = false;
- verbosity = 0;
- ddPValueThreshold = -500;
-}
-
diff --git a/libcpp/alignment/algorithms/anchoring/FindMaxInterval.hpp b/libcpp/alignment/algorithms/anchoring/FindMaxInterval.hpp
deleted file mode 100644
index 3f64505..0000000
--- a/libcpp/alignment/algorithms/anchoring/FindMaxInterval.hpp
+++ /dev/null
@@ -1,175 +0,0 @@
-#ifndef _BLASR_FIND_MAX_INTERVAL_HPP_
-#define _BLASR_FIND_MAX_INTERVAL_HPP_
-
-#include <semaphore.h>
-#include <math.h>
-#include <fstream>
-#include <iostream>
-#include "algorithms/anchoring/LongestIncreasingSubsequence.hpp"
-#include "algorithms/anchoring/GlobalChain.hpp"
-#include "algorithms/anchoring/BasicEndpoint.hpp"
-#include "datastructures/anchoring/WeightedInterval.hpp"
-#include "datastructures/anchoring/MatchPos.hpp"
-#include "datastructures/anchoring/ClusterList.hpp"
-#include "statistics/VarianceAccumulator.hpp"
-
-unsigned int NumRemainingBases(DNALength curPos, DNALength intervalLength);
-
-class IntervalSearchParameters {
-public:
- bool advanceHalf;
- int globalChainType;
- float maxPValue;
- float aboveCategoryPValue;
- bool warp;
- bool fastMaxInterval;
- bool aggressiveIntervalCut;
- int verbosity;
- float ddPValueThreshold;
- IntervalSearchParameters();
-};
-
-
-template<typename T_Sequence, typename T_AnchorList>
-class DefaultWeightFunction {
-public:
- float operator()(T_Sequence &text, T_Sequence &read,
- T_AnchorList matchPosList);
-};
-
-
-template<typename T_Pos>
-class MatchPosQueryOrderFunctor {
-public:
- int operator()(T_Pos &pos);
-};
-
-
-template<typename T_MatchList>
-void PrintLIS(T_MatchList &matchList, DNALength curPos,
- DNALength curGenomePos, DNALength nextGenomePos, DNALength clp,
- DNALength cle);
-
-template<typename T_MatchList, typename T_SequenceDB>
-void FilterMatchesAsLIMSTemplateSquare(T_MatchList &matches,
- DNALength queryLength, DNALength limsTemplateLength,
- T_SequenceDB &seqDB);
-
-template<typename T_MatchList, typename T_SequenceBoundaryDB>
-void AdvanceIndexToPastInterval(T_MatchList &pos, DNALength nPos,
- DNALength intervalLength, DNALength contigLength,
- T_SequenceBoundaryDB &SeqBoundary,
- DNALength startIndex, DNALength startIntervalBoundary,
- DNALength &index, DNALength &indexIntervalBoundary);
-
-template<typename T_MatchList>
-int RemoveZeroLengthAnchors(T_MatchList &matchList);
-
-template<typename T_MatchList>
-int RemoveOverlappingAnchors(T_MatchList &matchList);
-
-template<typename T_MatchList>
-int SumAnchors(T_MatchList &pos, int start, int end);
-
-template<typename T_MatchList,
- typename T_SequenceBoundaryDB>
-void StoreLargestIntervals(
- T_MatchList &pos,
- // End search for intervals at boundary positions
- // stored in seqBoundaries
- T_SequenceBoundaryDB & ContigStartPos,
- // parameters
- // How many values to search through for a max set.
- DNALength intervalLength,
- // How many sets to keep track of
- int minSize,
- vector<DNALength> &start,
- vector<DNALength> &end);
-
-template<typename T_MatchList,
- typename T_PValueFunction,
- typename T_WeightFunction,
- typename T_SequenceBoundaryDB,
- typename T_ReferenceSequence,
- typename T_Sequence>
-int FindMaxIncreasingInterval(
- // Input
- // readDir is used to indicate if the interval that is being stored is
- // in the forward or reverse strand. This is important later when
- // refining alignments so that the correct sequence is aligned back
- // to the reference.
- int readDir,
- T_MatchList &pos,
- // How many values to search through for a max set.
- DNALength intervalLength,
- // How many sets to keep track of
- VectorIndex nBest,
- // End search for intervals at boundary positions
- // stored in seqBoundaries
- T_SequenceBoundaryDB & ContigStartPos,
- // First rand intervals by their p-value
- T_PValueFunction &MatchPValueFunction,
- // When ranking intervals, sum over weights determined by MatchWeightFunction
- T_WeightFunction &MatchWeightFunction,
- // Output.
- // The increasing interval coordinates,
- // in order by queue weight.
- WeightedIntervalSet &intervalQueue,
- T_ReferenceSequence &reference,
- T_Sequence &query,
- IntervalSearchParameters ¶ms,
- std::vector<BasicEndpoint<ChainedMatchPos> > *chainEndpointBuffer,
- ClusterList &clusterList,
- VarianceAccumulator<float> &accumPValue,
- VarianceAccumulator<float> &accumWeight,
- VarianceAccumulator<float> &accumNumAnchorBases,
- const char *titlePtr=NULL);
-
-template<typename T_MatchList,
- typename T_PValueFunction,
- typename T_WeightFunction,
- typename T_SequenceBoundaryDB,
- typename T_ReferenceSequence,
- typename T_Sequence>
-int FastFindMaxIncreasingInterval(
- int readDir,
- T_MatchList &pos,
- DNALength intervalLength,
- VectorIndex nBest,
- T_SequenceBoundaryDB & ContigStartPos,
- T_PValueFunction &MatchPValueFunction,
- T_WeightFunction &MatchWeightFunction,
- WeightedIntervalSet &intervalQueue,
- T_ReferenceSequence &reference,
- T_Sequence &query,
- IntervalSearchParameters ¶ms,
- std::vector<BasicEndpoint<ChainedMatchPos> > *chainEndpointBuffer,
- ClusterList &clusterList,
- VarianceAccumulator<float> &accumPValue,
- VarianceAccumulator<float> &accumWeight);
-
-template<typename T_MatchList,
- typename T_PValueFunction,
- typename T_WeightFunction,
- typename T_SequenceBoundaryDB,
- typename T_ReferenceSequence,
- typename T_Sequence>
-int ExhaustiveFindMaxIncreasingInterval(
- int readDir,
- T_MatchList &pos,
- DNALength intervalLength,
- VectorIndex nBest,
- T_SequenceBoundaryDB & ContigStartPos,
- T_PValueFunction &MatchPValueFunction,
- T_WeightFunction &MatchWeightFunction,
- WeightedIntervalSet &intervalQueue,
- T_ReferenceSequence &reference,
- T_Sequence &query,
- IntervalSearchParameters ¶ms,
- std::vector<BasicEndpoint<ChainedMatchPos> > *chainEndpointBuffer,
- ClusterList &clusterList,
- VarianceAccumulator<float> &accumPValue,
- VarianceAccumulator<float> &accumWeight);
-
-#include "algorithms/anchoring/FindMaxIntervalImpl.hpp"
-#endif
diff --git a/libcpp/alignment/algorithms/anchoring/FindMaxIntervalImpl.hpp b/libcpp/alignment/algorithms/anchoring/FindMaxIntervalImpl.hpp
deleted file mode 100644
index 65b2922..0000000
--- a/libcpp/alignment/algorithms/anchoring/FindMaxIntervalImpl.hpp
+++ /dev/null
@@ -1,945 +0,0 @@
-#ifndef _BLASR_FIND_MAX_INTERVAL_IMPL_HPP_
-#define _BLASR_FIND_MAX_INTERVAL_IMPL_HPP_
-
-template<typename T_Sequence, typename T_AnchorList>
-float DefaultWeightFunction<T_Sequence, T_AnchorList>::operator() (
- T_Sequence &text, T_Sequence &read, T_AnchorList matchPosList) {
- int i;
- float weight = 0;
- for (i = 0; i < matchPosList.size(); i++) {
- weight += matchPosList[i].weight();
- }
- return weight;
-}
-
-template<typename T_Pos>
-int MatchPosQueryOrderFunctor<T_Pos>::operator()(T_Pos &pos) {
- return pos.q;
-}
-
-template<typename T_MatchList>
-void PrintLIS(T_MatchList &matchList, DNALength curPos,
- DNALength curGenomePos, DNALength nextGenomePos,
- DNALength clp, DNALength cle) {
- int i;
- cout << curPos << " " << curGenomePos << " "
- << nextGenomePos << " " << clp << " " << cle << endl;
- for (i = 0; i < matchList.size(); i++) {
- cout.width(8);
- cout << matchList[i].l << " ";
- }
- cout << endl;
- for (i = 0; i < matchList.size(); i++) {
- cout.width(8);
- cout << matchList[i].q << " ";
- }
- cout << endl;
- for (i = 0; i < matchList.size(); i++) {
- cout.width(8);
- cout << matchList[i].t << " ";
- }
- cout << endl << endl;
-}
-
-
-template<typename T_MatchList, typename T_SequenceDB>
-void FilterMatchesAsLIMSTemplateSquare(T_MatchList &matches,
- DNALength queryLength, DNALength limsTemplateLength,
- T_SequenceDB &seqDB) {
- int seqIndex;
- //
- // Make sure there is sequence coordinate information.
- //
- if (seqDB.nSeqPos == 0) {
- return;
- }
- int matchIndex = 0;
- for (seqIndex = 1; seqIndex < seqDB.nSeqPos; seqIndex++) {
- DNALength refLength = seqDB.seqStartPos[seqIndex] -
- seqDB.seqStartPos[seqIndex - 1];
- // account for indel error.
- refLength = queryLength * 1.15 + limsTemplateLength;
-
- //
- // Flag matches that are beyond the (rough) square with the length
- // of the query for removal.
- //
- while (matchIndex < matches.size() and
- matches[matchIndex].t < seqDB.seqStartPos[seqIndex]) {
- if (matches[matchIndex].t > seqDB.seqStartPos[seqIndex-1]
- + refLength) {
- matches[matchIndex].l = 0;
- }
- matchIndex++;
- }
- int curMatchIndex = 0;
- matchIndex = 0;
- for (matchIndex = 0; matchIndex < matches.size(); matchIndex++) {
- if (matches[matchIndex].l != 0) {
- matches[curMatchIndex] = matches[matchIndex];
- curMatchIndex++;
- }
- }
- matches.resize(curMatchIndex);
- }
-}
-
-template<typename T_MatchList, typename T_SequenceBoundaryDB>
-void AdvanceIndexToPastInterval(T_MatchList &pos, DNALength nPos,
- DNALength intervalLength, DNALength contigLength,
- T_SequenceBoundaryDB &SeqBoundary,
- DNALength startIndex, DNALength startIntervalBoundary,
- DNALength &index, DNALength &indexIntervalBoundary) {
- if (index >= pos.size()) {
- return;
- }
- indexIntervalBoundary = SeqBoundary(pos[index].t);
- DNALength boundaryIndex = SeqBoundary.GetIndex(pos[index].t);
- DNALength nextBoundary = SeqBoundary.GetStartPos(boundaryIndex + 1);
- while (// index is not past the end of the genome
- index < nPos and
- //
- // Stop when the index goes too far ahead.
- //
- pos[index].t - pos[startIndex].t <= intervalLength and
- //
- // Still searching in the current contig.
- //
- indexIntervalBoundary == startIntervalBoundary) {
- index++;
- if (index < nPos) {
- indexIntervalBoundary = SeqBoundary(pos[index].t);
- }
- }
-}
-
-
-template<typename T_MatchList>
-int RemoveZeroLengthAnchors(T_MatchList &matchList) {
- int origSize = matchList.size();
- int cur = 0, m;
- for (m = 0; m < matchList.size(); m++) {
- if (matchList[m].l > 0) {
- matchList[cur] = matchList[m];
- cur++;
- }
- }
- matchList.resize(cur);
- return origSize - cur;
-}
-
-template<typename T_MatchList>
-int RemoveOverlappingAnchors(T_MatchList &matchList) {
- int cur = 0;
- int m;
- int n;
- for (m = matchList.size(); m > 0; m--) {
- n = m - 1;
- //
- // Skip past repeats in the query.
- while (n > 0 and matchList[n].t == matchList[m].t) {
- n--;
- }
-
- bool mergeFound = false;
- int ni = n;
- while (mergeFound == false and
- n > 0 and
- matchList[n].t == matchList[ni].t) {
- if (matchList[n].q < matchList[m].q and
- matchList[n].t < matchList[m].t and
- matchList[n].l + matchList[n].q >=
- matchList[m].l + matchList[m].q and
- matchList[n].l + matchList[n].t >=
- matchList[m].l + matchList[m].t) {
- matchList[m].l = 0;
- mergeFound = true;
- }
- n--;
- }
- }
- int numRemoved = RemoveZeroLengthAnchors(matchList);
- return numRemoved;
-}
-
-template<typename T_MatchList>
-int SumAnchors(T_MatchList &pos, int start, int end) {
- int sum = 0;
- int i;
- for (i = start; i < end; i++) {
- sum += pos[i].l;
- }
- return sum;
-}
-
-template<typename T_MatchList,
- typename T_SequenceBoundaryDB>
-void StoreLargestIntervals(
- T_MatchList &pos,
- // End search for intervals at boundary positions
- // stored in seqBoundaries
- T_SequenceBoundaryDB & ContigStartPos,
- // parameters
- // How many values to search through for a max set.
- DNALength intervalLength,
- // How many sets to keep track of
- int minSize,
- vector<DNALength> &start,
- vector<DNALength> &end) {
-
- if (pos.size() == 0) {
- return;
- }
- //
- // Search for clusters of intervals within the pos array within
- // pos[cur...next). The value of 'next' should be the first anchor
- // outside the possible range to cluster, or the end of the anchor list.
- VectorIndex cur = 0;
- VectorIndex nPos = pos.size();
- VectorIndex next = cur + 1;
- DNALength curBoundary = 0, nextBoundary = 0;
- DNALength contigLength = ContigStartPos.Length(pos[cur].t);
- DNALength endOfCurrentInterval = curBoundary + contigLength;
-
- curBoundary = ContigStartPos(pos[cur].t);
- nextBoundary = ContigStartPos(pos[next].t);
-
- //
- // Advance next until the anchor is outside the interval that
- // statrts at 'cur', and is inside the same contig that the anchor
- // at cur is in.
- //
-
- DNALength curIntervalLength = NumRemainingBases(pos[cur].q, intervalLength);
-
- AdvanceIndexToPastInterval(pos, nPos, intervalLength, contigLength, ContigStartPos,
- cur, curBoundary, next, nextBoundary);
-
- DNALength prevStart = cur, prevEnd = next ;
- int prevSize = next - cur;
- DNALength maxStart = cur, maxEnd = next;
- int maxSize = SumAnchors(pos, cur, next);
- int curSize = maxSize;
- bool onFirst = true;
- if (curSize > minSize) {
- start.push_back(cur);
- end.push_back(next);
- }
- while ( cur < nPos ) {
- //
- // This interval overlaps with a possible max start
- //
-
- if (pos[cur].t >= pos[maxStart].t and maxEnd > 0 and pos[cur].t < pos[maxEnd-1].t) {
- if (curSize > maxSize) {
- maxSize = curSize;
- maxStart = cur;
- maxEnd = next;
- }
- }
- else {
- if (maxSize > minSize) {
- start.push_back(maxStart);
- end.push_back(maxEnd);
- }
- maxStart = cur;
- maxEnd = next;
- maxSize = curSize;
- }
-
- //
- // Done scoring current interval. At this point the range
- // pos[cur...next) has been searched for a max increasing
- // interval. Find a new range that will possibly yield a new
- // maximum interval.
- // There are a few cases to consider:
- //
- //
- // genome |---+----+------------+------+-----------------------|
- // anchors cur cur+1 next next+1
- //
- // Case 1. The range on the target pos[ cur+1 ... next].t is a
- // valid interval (it is roughly the length of the read). In this
- // case increase cur and next by 1, and search this range.
- //
- // genome |---+----+------------+------+-----------------------|
- // cur cur+1 next next+1
- // read interval ====================
- //
- // Case 2. The range on the target pos[cur+1 ... next] is not a
- // valid interval, and it is much longer than the length of the
- // read. This implies that it is impossible to increase the score
- // of the read by including both
- //
- // genome |---+----+--------------------------------+-----+---|
- // cur cur+1 next next+1
- // read interval ====================
- //
- // Advance the interval until it includes the next anchor
- //
- // genome |---+----+------------------+-------------+-----+---|
- // cur cur+1 cur+n next next+1
- // read interval ====================
- //
-
- // First advance pointer in anchor list. If this advances to the
- // end, done and no need for further logic checking (break now).
-
-
- //
- // If the next position is not within the same contig as the current,
- // advance the current to the next since it is impossible to find
- // any more intervals in the current pos.
- //
- bool recountInterval = false;
- if (curBoundary != nextBoundary) {
- cur = next;
- curBoundary = nextBoundary;
-
- //
- // Start the search for the first interval in the next contig
- // just after the current position.
- //
- if (next < nPos) {
- next = cur + 1;
- }
- }
- else {
-
- //
- // The next interval is in the same contig as the current interval.
- // Make sure not to double count the current interval.
- //
-
- curSize -= pos[cur].l;
-
- cur++;
- if (cur >= nPos)
- break;
-
- //
- // Advance the next to outside this interval.
- //
- curSize += pos[next].l;
- if (pos[next].t - pos[cur].t > intervalLength) {
- if (maxSize > minSize) {
- start.push_back(maxStart);
- end.push_back(maxEnd);
- }
-
- cur = next;
- recountInterval = true;
- maxSize = 0;
- }
- next++;
- }
-
- if (next > nPos) {
- //
- // Searched last interval, done.
- //
- break;
- }
-
- //
- // Next has advanced. Check what contig it is in.
- //
- if (next < nPos) {
- nextBoundary = ContigStartPos(pos[next].t);
- //
- // Advance next to the maximum position within this contig that is
- // just after where the interval starting at cur is, or the first
- // position in the next contig.
- //
- int prevNext = next;
- AdvanceIndexToPastInterval(pos, nPos, intervalLength, contigLength, ContigStartPos,
- cur, curBoundary, next, nextBoundary);
- if (prevNext != next or recountInterval) {
- curSize = SumAnchors(pos, cur, next);
- }
- }
-
- // if next >= nPos, the boundary stays the same.
-
- //
- // When searching multiple contigs, it is important to know the
- // boundary of the contig that this anchor is in so that clusters
- // do not span multiple contigs. Find the (right hand side)
- // boundary of the current contig.
- //
-
- curBoundary = ContigStartPos(pos[cur].t);
- contigLength = ContigStartPos.Length(pos[cur].t);
-
- //
- // Previously tried to advance half. This is being removed since
- // proper heuristics are making it not necessary to use.
- //
- }
- if (curSize > minSize) {
- start.push_back(maxStart);
- end.push_back(maxEnd);
- }
-}
-
-template<typename T_MatchList,
- typename T_PValueFunction,
- typename T_WeightFunction,
- typename T_SequenceBoundaryDB,
- typename T_ReferenceSequence,
- typename T_Sequence>
-int FindMaxIncreasingInterval(
- // Input
- // readDir is used to indicate if the interval that is being stored is
- // in the forward or reverse strand. This is important later when
- // refining alignments so that the correct sequence is aligned back
- // to the reference.
- int readDir,
- T_MatchList &pos,
- // How many values to search through for a max set.
- DNALength intervalLength,
- // How many sets to keep track of
- VectorIndex nBest,
- // End search for intervals at boundary positions
- // stored in seqBoundaries
- T_SequenceBoundaryDB & ContigStartPos,
- // First rand intervals by their p-value
- T_PValueFunction &MatchPValueFunction,
- // When ranking intervals, sum over weights determined by
- // MatchWeightFunction
- T_WeightFunction &MatchWeightFunction,
- // Output.
- // The increasing interval coordinates,
- // in order by queue weight.
- WeightedIntervalSet &intervalQueue,
- T_ReferenceSequence &reference,
- T_Sequence &query,
- IntervalSearchParameters ¶ms,
- vector<BasicEndpoint<ChainedMatchPos> > *chainEndpointBuffer,
- ClusterList &clusterList,
- VarianceAccumulator<float> &accumPValue,
- VarianceAccumulator<float> &accumWeight,
- VarianceAccumulator<float> &accumNumAnchorBases,
- const char *titlePtr) {
-
- int maxLISSize = 0;
- if (params.fastMaxInterval) {
- maxLISSize = FastFindMaxIncreasingInterval(
- readDir, pos, intervalLength,
- nBest, ContigStartPos,
- MatchPValueFunction, MatchWeightFunction,
- intervalQueue, reference, query,
- params, chainEndpointBuffer, clusterList,
- accumPValue, accumWeight);
- } else {
- maxLISSize = ExhaustiveFindMaxIncreasingInterval(
- readDir, pos, intervalLength,
- nBest, ContigStartPos,
- MatchPValueFunction, MatchWeightFunction,
- intervalQueue, reference, query,
- params, chainEndpointBuffer, clusterList,
- accumPValue, accumWeight);
- }
-
- if (params.aggressiveIntervalCut and intervalQueue.size() >= 3) {
- // aggressiveIntervalCut mode:
- // only pick up the most promising intervals if we can classify
- // intervals into 'promising' and 'non-promising' clusters.
- WeightedIntervalSet::iterator it = intervalQueue.begin();
- int sz = intervalQueue.size();
- vector<float> pValues, ddPValues;
- pValues.resize(sz);
- ddPValues.resize(sz);
- float sumPValue = 0;
- int i = 0;
- for(; it != intervalQueue.end(); i++,it++) {
- sumPValue += (*it).pValue;
- pValues[i] = (*it).pValue;
- }
- //We will attemp to divide intervals into two clusters, promising
- //and non-promising.
- float prevSumPValue = pValues[0];
- // ddPValue[i], where i in [1...n-2] is the difference of
- // (1) (mean pvalue of [0...i-1] minus pvalue[i])
- // and
- // (2) (pvalue[i] minus mean pvalue of [i+1...n-1])
- // pValues are all negative, the lower the better.
- // if ddPValue is negative, interval i is closer to cluster [i+1...n-1],
- // otherwise, interval i is closer to cluster [0..i-1].
- it = intervalQueue.begin();
- it ++; //both it and i should point to the second interval in intervalQueue.
- for(i = 1; i < sz - 1; i++,it++) {
- ddPValues[i] = (prevSumPValue / i) +
- (sumPValue - prevSumPValue - pValues[i]) / (sz - i - 1) -
- 2 * pValues[i];
- if (ddPValues[i] <= params.ddPValueThreshold) {
- // PValue of interval i is much closer to cluster [i+1...n-1] than
- // to cluster [0...i-1]. Mean pValue of cluster [0..i-1]
- // minus mean pvalue of cluster [i+1...n-1] < 2 * -500
- break;
- }
- prevSumPValue += pValues[i];
- }
- if (it != intervalQueue.end()) {
- // Erase intervals in the non-promising cluster.
- intervalQueue.erase(it, intervalQueue.end());
- // Recompute accumPValue, accmWeight, clusterList;
- accumPValue.Reset();
- accumWeight.Reset();
- clusterList.Clear();
- for(it = intervalQueue.begin(); it != intervalQueue.end(); it++) {
- accumPValue.Append((*it).pValue);
- accumWeight.Append((*it).size);
- clusterList.Store((*it).totalAnchorSize, (*it).start, (*it).end, (*it).nAnchors);
- }
- }
- }
- return maxLISSize;
-}
-
-template<typename T_MatchList,
- typename T_PValueFunction,
- typename T_WeightFunction,
- typename T_SequenceBoundaryDB,
- typename T_ReferenceSequence,
- typename T_Sequence>
-int FastFindMaxIncreasingInterval(
- // Input
- // readDir is used to indicate if the interval that is being stored is in the forward
- // or reverse strand. This is important later when refining alignments so that the
- // correct sequene is aligned back to the reference.
- int readDir,
- T_MatchList &pos,
- // How many values to search through for a max set.
- DNALength intervalLength,
- // How many sets to keep track of
- VectorIndex nBest,
- // End search for intervals at boundary positions
- // stored in seqBoundaries
- T_SequenceBoundaryDB & ContigStartPos,
- // First rand intervals by their p-value
- T_PValueFunction &MatchPValueFunction,
- // When ranking intervals, sum over weights determined by MatchWeightFunction
- T_WeightFunction &MatchWeightFunction,
- // Output.
- // The increasing interval coordinates,
- // in order by queue weight.
- WeightedIntervalSet &intervalQueue,
- T_ReferenceSequence &reference,
- T_Sequence &query,
- IntervalSearchParameters ¶ms,
- vector<BasicEndpoint<ChainedMatchPos> > *chainEndpointBuffer,
- ClusterList &clusterList,
- VarianceAccumulator<float> &accumPValue,
- VarianceAccumulator<float> &accumWeight) {
-
- WeightedIntervalSet sdpiq;
- VectorIndex cur = 0;
- VectorIndex nPos = pos.size();
- vector<VectorIndex> lisIndices;
- //
- // Initialize the first interval.
- //
- if (pos.size() == 0) {
- return 0;
- }
-
- int lisSize;
- float lisWeight;
- float lisPValue;
- T_MatchList lis;
- float neginf = -1.0/0.0;
- int noOvpLisSize = 0;
- int noOvpLisNBases = 0;
-
- //
- // Search for clusters of intervals within the pos array within
- // pos[cur...next). The value of 'next' should be the first anchor
- // outside the possible range to cluster, or the end of the anchor list.
-
- VectorIndex next = cur + 1;
- DNALength curBoundary = 0, nextBoundary = 0;
- DNALength contigLength = ContigStartPos.Length(pos[cur].t);
- DNALength endOfCurrentInterval = curBoundary + contigLength;
-
- vector<UInt> scores, prevOpt;
- vector<DNALength> start, end;
-
- StoreLargestIntervals(pos, ContigStartPos, intervalLength, 30, start, end);
-
- VectorIndex i;
- VectorIndex posi;
- int maxLISSize = 0;
-
- for (posi = 0; posi < start.size(); posi++) {
- lis.clear();
- lisIndices.clear();
- cur = start[posi];
- next = end[posi];
- if (next - cur == 1) {
- //
- // Just one match in this interval, don't invoke call to global chain since it is given.
- //
- lisSize = 0;
- lisIndices.push_back(0);
- }
- else {
- //
- // Find the largest set of increasing intervals that do not overlap.
- //
- if (params.globalChainType == 0) {
- lisSize = GlobalChain<ChainedMatchPos, BasicEndpoint<ChainedMatchPos> >(pos, cur, next,
- lisIndices, chainEndpointBuffer);
- }
- else {
- //
- // A different call that allows for indel penalties.
- //
- lisSize = RestrictedGlobalChain(&pos[cur],next - cur, 0.1, lisIndices, scores, prevOpt);
- }
- }
-
- // Maybe this should become a function?
- for (i = 0; i < lisIndices.size(); i++) {
- lis.push_back(pos[lisIndices[i]+cur]);
- }
-
- //
- // Compute pvalue of this match.
- //
- if (lis.size() > 0) {
- lisPValue = MatchPValueFunction.ComputePValue(lis, noOvpLisNBases, noOvpLisSize);
- }
- else {
- lisPValue = 0;
- }
-
- if (lisSize > maxLISSize) {
- maxLISSize = lisSize;
- }
-
- //
- // Insert the interval into the interval queue maintaining only the
- // top 'nBest' intervals.
- //
- WeightedIntervalSet::iterator lastIt = intervalQueue.begin();
- MatchWeight lisWeight = MatchWeightFunction(lis);
- VectorIndex lisEnd = lis.size() - 1;
-
- accumPValue.Append(lisPValue);
- accumWeight.Append(lisWeight);
-
- if (lisPValue < params.maxPValue and lisSize > 0) {
- WeightedInterval weightedInterval(lisWeight, noOvpLisSize, noOvpLisNBases,
- lis[0].t, lis[lisEnd].t + lis[lisEnd].GetLength(),
- readDir, lisPValue,
- lis[0].q, lis[lisEnd].q + lis[lisEnd].GetLength(),
- lis);
- intervalQueue.insert(weightedInterval);
- if (weightedInterval.isOverlapping == false) {
- clusterList.Store((float)noOvpLisNBases, lis[0].t, lis[lis.size()-1].t, noOvpLisSize);
- }
- if (params.verbosity > 1) {
- cout << "Weighted Interval to insert:"<< endl << weightedInterval << endl;
- cout << "Interval Queue:"<< endl << intervalQueue << endl;
- }
- }
- }
- return maxLISSize;
-}
-
-template<typename T_MatchList,
- typename T_PValueFunction,
- typename T_WeightFunction,
- typename T_SequenceBoundaryDB,
- typename T_ReferenceSequence,
- typename T_Sequence>
-int ExhaustiveFindMaxIncreasingInterval(
- // Input
- // readDir is used to indicate if the interval that is being stored is in the forward
- // or reverse strand. This is important later when refining alignments so that the
- // correct sequene is aligned back to the reference.
- int readDir,
- T_MatchList &pos,
- // How many values to search through for a max set.
- DNALength intervalLength,
- // How many sets to keep track of
- VectorIndex nBest,
- // End search for intervals at boundary positions
- // stored in seqBoundaries
- T_SequenceBoundaryDB & ContigStartPos,
- // First rand intervals by their p-value
- T_PValueFunction &MatchPValueFunction,
- // When ranking intervals, sum over weights determined by MatchWeightFunction
- T_WeightFunction &MatchWeightFunction,
- // Output.
- // The increasing interval coordinates,
- // in order by queue weight.
- WeightedIntervalSet &intervalQueue,
- T_ReferenceSequence &reference,
- T_Sequence &query,
- IntervalSearchParameters ¶ms,
- vector<BasicEndpoint<ChainedMatchPos> > *chainEndpointBuffer,
- ClusterList &clusterList,
- VarianceAccumulator<float> &accumPValue,
- VarianceAccumulator<float> &accumWeight) {
-
- WeightedIntervalSet sdpiq;
- VectorIndex cur = 0;
- VectorIndex nPos = pos.size();
- //
- // Initialize the first interval.
- //
- if (pos.size() == 0) {
- return 0;
- }
-
- int lisSize;
- float lisWeight;
- float lisPValue;
- T_MatchList lis;
- float neginf = -1.0/0.0;
- int noOvpLisSize = 0;
- int noOvpLisNBases = 0;
-
- //
- // Search for clusters of intervals within the pos array within
- // pos[cur...next). The value of 'next' should be the first anchor
- // outside the possible range to cluster, or the end of the anchor list.
-
- VectorIndex next = cur + 1;
- DNALength curBoundary = 0, nextBoundary = 0;
- DNALength contigLength = ContigStartPos.Length(pos[cur].t);
- DNALength endOfCurrentInterval = curBoundary + contigLength;
-
-
- curBoundary = ContigStartPos(pos[cur].t);
- nextBoundary = ContigStartPos(pos[next].t);
- vector<UInt> scores, prevOpt;
-
- //
- // Advance next until the anchor is outside the interval that
- // statrts at 'cur', and is inside the same contig that the anchor
- // at cur is in.
- //
-
- DNALength curIntervalLength = NumRemainingBases(pos[cur].q, intervalLength);
-
- AdvanceIndexToPastInterval(pos, nPos, intervalLength, contigLength, ContigStartPos,
- cur, curBoundary, next, nextBoundary);
-
-
- vector<VectorIndex> lisIndices;
- VectorIndex i;
-
- //
- // Do some preprocessing. If the number of anchors considered for this hit is 1,
- // the global chain is this sole ancor. Don't bother calling GlobalChain
- // since it allocates and deallocates extra memory.
- //
-
- int maxLISSize = 0;
-
- //
- // Search intervals until cur reaches the end of the list of
- // anchors.
- //
- while ( cur < nPos ) {
- //
- // Search the local interval for a LIS larger than a previous LIS.
- //
- lis.clear();
- lisIndices.clear();
-
- if (next - cur == 1) {
- //
- // Just one match in this interval, don't invoke call to global chain since it is given.
- //
- lisSize = 1;
- lisIndices.push_back(0);
- }
- else {
- //
- // Find the largest set of increasing intervals that do not overlap.
- //
- if (params.globalChainType == 0) {
- lisSize = GlobalChain<ChainedMatchPos, BasicEndpoint<ChainedMatchPos> >(pos, cur, next,
- lisIndices, chainEndpointBuffer);
- }
- else {
- //
- // A different call that allows for indel penalties.
- //
- lisSize = RestrictedGlobalChain(&pos[cur],next - cur, 0.1, lisIndices, scores, prevOpt);
- }
- }
-
- // Maybe this should become a function?
- for (i = 0; i < lisIndices.size(); i++) { lis.push_back(pos[lisIndices[i]+cur]); }
-
-
- //
- // Compute pvalue of this match.
- //
- lisPValue = MatchPValueFunction.ComputePValue(lis, noOvpLisNBases, noOvpLisSize);
-
- if (lisSize > maxLISSize) {
- maxLISSize = lisSize;
- }
-
- //
- // Insert the interval into the interval queue maintaining only the
- // top 'nBest' intervals.
- //
-
- WeightedIntervalSet::iterator lastIt = intervalQueue.begin();
- MatchWeight lisWeight = MatchWeightFunction(lis);
- VectorIndex lisEnd = lis.size() - 1;
-
- accumPValue.Append(lisPValue);
- accumWeight.Append(lisWeight);
-
- if (lisPValue < params.maxPValue and lisSize > 0) {
- WeightedInterval weightedInterval(lisWeight, noOvpLisSize, noOvpLisNBases,
- lis[0].t, lis[lisEnd].t + lis[lisEnd].GetLength(),
- readDir, lisPValue,
- lis[0].q, lis[lisEnd].q + lis[lisEnd].GetLength(),
- lis);
- intervalQueue.insert(weightedInterval);
- if (weightedInterval.isOverlapping == false) {
- clusterList.Store((float)noOvpLisNBases, lis[0].t, lis[lis.size()-1].t, noOvpLisSize);
- }
- if (params.verbosity > 1) {
- cout << "Weighted Interval to insert:"<< endl << weightedInterval << endl;
- cout << "Interval Queue:"<< endl << intervalQueue << endl;
- }
- }
-
- //
- // Done scoring current interval. At this point the range
- // pos[cur...next) has been searched for a max increasing
- // interval. Find a new range that will possibly yield a new
- // maximum interval.
- // There are a few cases to consider:
- //
- //
- //genome |---+----+------------+------+-----------------------|
- // anchors cur cur+1 next next+1
- //
- // Case 1. The range on the target pos[ cur+1 ... next].t is a
- // valid interval (it is roughly the length of the read). In this
- // case increase cur and next by 1, and search this range.
- //
- // genome |---+----+------------+------+-----------------------|
- // cur cur+1 next next+1
- // read interval ====================
- //
- // Case 2. The range on the target pos[cur+1 ... next] is not a
- // valid interval, and it is much longer than the length of the
- // read. This implies that it is impossible to increase the score
- // of the read by including both
- //
- // genome |---+----+--------------------------------+-----+---|
- // cur cur+1 next next+1
- // read interval ====================
- //
- // Advance the interval until it includes the next anchor
- //
- // genome |---+----+------------------+-------------+-----+---|
- // cur cur+1 cur+n next next+1
- // read interval ====================
- //
-
- // First advance pointer in anchor list. If this advances to the
- // end, done and no need for further logic checking (break now).
-
-
- //
- // If the next position is not within the same contig as the current,
- // advance the current to the next since it is impossible to find
- // any more intervals in the current pos.
- //
- if (curBoundary != nextBoundary) {
- cur = next;
- curBoundary = nextBoundary;
-
- //
- // Start the search for the first interval in the next contig
- // just after the current position.
- //
- if (next < nPos) {
- next = cur + 1;
- }
- }
- else {
- cur++;
- if (cur >= nPos)
- break;
-
- //
- // Look for need to advance the interval within the same
- // contig. If the start of the next match is well past the
- // length of this read, keep moving forward matches until it is
- // possible to include the next interval in the matches for
- // this read.
- //
- if (params.warp) {
- while (cur < next and
- next < nPos and
- pos[next].t - pos[cur].t >= intervalLength) {
- //
- // It is impossible to increase the max interval weight any more
- // using pos[cur] when pos[next] is too far away from
- // pos[cur]. This is because the same set of anchors are used
- // when clustering pos[cur+1] ... pos[next] as
- // pos[cur] ... pos[next].
- // Advance cur until pos[cur] is close enough to matter again.
- cur++;
- }
- }
- //
- // Advance the next to outside this interval.
- next++;
- }
-
- if (next > nPos) {
- //
- // Searched last interval, done.
- //
- break;
- }
-
- //
- // Next has advanced. Check what contig it is in.
- //
- if (next < nPos) {
- nextBoundary = ContigStartPos(pos[next].t);
- //
- // Advance next to the maximum position within this contig that is
- // just after where the interval starting at cur is, or the first
- // position in the next contig.
- //
- AdvanceIndexToPastInterval(pos, nPos, intervalLength, contigLength, ContigStartPos,
- cur, curBoundary, next, nextBoundary);
- }
- // if next >= nPos, the boundary stays the same.
- //
- // When searching multiple contigs, it is important to know the
- // boundary of the contig that this anchor is in so that clusters
- // do not span multiple contigs. Find the (right hand side)
- // boundary of the current contig.
- //
-
- curBoundary = ContigStartPos(pos[cur].t);
- contigLength = ContigStartPos.Length(pos[cur].t);
-
- //
- // Previously tried to advance half. This is being removed since
- // proper heuristics are making it not necessary to use.
- //
- }
-
- return maxLISSize;
-}
-
-#endif
diff --git a/libcpp/alignment/algorithms/anchoring/GlobalChain.hpp b/libcpp/alignment/algorithms/anchoring/GlobalChain.hpp
deleted file mode 100644
index b3565ec..0000000
--- a/libcpp/alignment/algorithms/anchoring/GlobalChain.hpp
+++ /dev/null
@@ -1,37 +0,0 @@
-#ifndef _BLASR_GLOBAL_CHAIN_HPP_
-#define _BLASR_GLOBAL_CHAIN_HPP_
-
-#include <vector>
-#include "Types.h"
-#include "DNASequence.hpp"
-#include "algorithms/anchoring/PrioritySearchTree.hpp"
-
-template<typename T_Fragment, typename T_Endpoint>
-void FragmentSetToEndpoints(T_Fragment* fragments, int nFragments,
- std::vector<T_Endpoint> &endpoints);
-
-template<typename T_Fragment>
-UInt RestrictedGlobalChain(T_Fragment *fragments,
- DNALength nFragments, float maxIndelRate,
- std::vector<VectorIndex>& optFragmentChainIndices,
- std::vector<UInt>& scores, std::vector<UInt>& prevOpt);
-
-template<typename T_Fragment, typename T_Endpoint>
-int GlobalChain( T_Fragment *fragments,
- DNALength nFragments,
- std::vector<VectorIndex> &optFragmentChainIndices,
- std::vector<T_Endpoint> *bufEndpointsPtr = NULL);
-
-template<typename T_Fragment, typename T_Endpoint>
-int GlobalChain(std::vector<T_Fragment> &fragments,
- std::vector<VectorIndex> &optFragmentChainIndices);
-
-template<typename T_Fragment, typename T_Endpoint>
-int GlobalChain(std::vector<T_Fragment> &fragments,
- DNALength start, DNALength end,
- std::vector<VectorIndex> &optFragmentChainIndices,
- std::vector<T_Endpoint> *bufEndpointsPtr = NULL);
-
-#include "algorithms/anchoring/GlobalChainImpl.hpp"
-
-#endif
diff --git a/libcpp/alignment/algorithms/anchoring/GlobalChainImpl.hpp b/libcpp/alignment/algorithms/anchoring/GlobalChainImpl.hpp
deleted file mode 100644
index 49c7788..0000000
--- a/libcpp/alignment/algorithms/anchoring/GlobalChainImpl.hpp
+++ /dev/null
@@ -1,225 +0,0 @@
-#ifndef _BLASR_GLOBAL_CHAIN_IMPL_HPP_
-#define _BLASR_GLOBAL_CHAIN_IMPL_HPP_
-
-#include <algorithm>
-#include "Types.h"
-#include "DNASequence.hpp"
-#include "algorithms/anchoring/PrioritySearchTree.hpp"
-
-using namespace std;
-
-template<typename T_Fragment,typename T_Endpoint>
-void FragmentSetToEndpoints(T_Fragment* fragments,
- int nFragments, std::vector<T_Endpoint>& endpoints) {
-
- endpoints.resize(nFragments*2);
- int i;
- int ep = 0;
- for (i = 0; i < nFragments; i++) {
- endpoints[ep].FragmentPtrToStart(&fragments[i]);
- ep++;
- endpoints[ep].FragmentPtrToEnd(&fragments[i]);
- ep++;
- }
-}
-
-
-template<typename T_Fragment>
-UInt RestrictedGlobalChain(T_Fragment *fragments,
- DNALength nFragments,
- float maxIndelRate,
- vector<VectorIndex> &optFragmentChainIndices,
- vector<UInt> &scores,
- vector<UInt> &prevOpt) {
- // assume fragments are sorted by t
-
- UInt f1, f2;
- scores.resize(nFragments);
- prevOpt.resize(nFragments);
- std::fill(scores.begin(), scores.end(), 0);
-
- UInt globalOptScore = 0;
- UInt globalOptIndex = 0;
- for (f1 = 0; f1 < nFragments; f1++) {
- prevOpt[f1] = f1;
- scores[f1] = 1;
- }
-
- for (f1 = 0; f1 < nFragments - 1; f1++) {
- UInt maxF1Score = 0;
- UInt maxF1Prev = f1;
- for (f2 = f1+1; f2 < nFragments; f2++ ){
- //
- // Check to see if the fragments may be connected within the
- // expected indel rate.
- //
- if (fragments[f2].GetQ() > fragments[f1].GetQ() + fragments[f1].GetW()
- and
- fragments[f2].GetT() > fragments[f1].GetT() + fragments[f1].GetW()) {
- //
- // Compute drift from diagonal.
- //
- UInt tDiff, qDiff;
- tDiff = fragments[f2].GetT() - (fragments[f1].GetT() + fragments[f1].GetW());
- qDiff = fragments[f2].GetQ() - (fragments[f1].GetQ() + fragments[f1].GetW());
- UInt tIns, qIns;
- tIns = qIns = 0;
- UInt maxDiff = max(tDiff, qDiff);
- UInt minDiff = min(tDiff, qDiff);
- if (maxDiff - minDiff < minDiff*maxIndelRate) {
- //
- // The fragment is sufficiently close to the diagonal to
- // consider it as a chain.
- //
- if (scores[f2] < scores[f1] + 1) {
- scores[f2] = scores[f1] + 1;
- prevOpt[f2] = f1;
- if (scores[f2] > globalOptScore) {
- globalOptScore = scores[f2];
- globalOptIndex = f2;
- }
- }
- }
- }
- }
- }
- UInt index = globalOptIndex;
- UInt prevIndex;
- while(index != prevOpt[index]) {
- optFragmentChainIndices.push_back(index);
- assert(optFragmentChainIndices.size() < nFragments);
- prevIndex = index;
- index = prevOpt[index];
- // Make sure there was no problem with backtracking.
- assert(index < nFragments);
- assert(index <= prevOpt[prevIndex]);
- }
- optFragmentChainIndices.push_back(index);
- std::reverse(optFragmentChainIndices.begin(), optFragmentChainIndices.end());
- return optFragmentChainIndices.size();
-}
-
-
-template<typename T_Fragment, typename T_Endpoint>
-int GlobalChain(T_Fragment *fragments,
- DNALength nFragments,
- vector<VectorIndex> & optFragmentChainIndices,
- vector<T_Endpoint> * bufEndpointsPtr) {
-
- //
- // Initialize the fragment score to be the length of each fragment.
- //
- if (nFragments == 0) {
- return 0;
- }
-
- DNALength f;
- for (f = 0; f < nFragments; f++) {
- fragments[f].SetScore(fragments[f].GetLength());
- }
-
- //
- // Add the start/end points of each fragment. This allows separate
- // scoring of start points and activation of endpoints.
- //
- vector<T_Endpoint> endpoints;
- vector<T_Endpoint> *endpointsPtr;
- if (bufEndpointsPtr != NULL) {
- endpointsPtr = bufEndpointsPtr;
- }
- else {
- endpointsPtr = &endpoints;
- }
-
-
- FragmentSetToEndpoints<T_Fragment, T_Endpoint>(fragments,
- nFragments, *endpointsPtr);
-
- //
- // The Starting points of all the fragmements are in order,
- // but not necessarily all of the end endpoints, so
- // the list must be resorted.
- //
- std::sort(endpointsPtr->begin(), endpointsPtr->end(),
- typename T_Endpoint::LessThan());
-
- PrioritySearchTree<T_Endpoint> pst;
-
- pst.CreateTree(*endpointsPtr);
-
- VectorIndex p;
- VectorIndex maxScoringEndpoint = 0;
- bool maxScoringEndpointFound = false;
-
- for (p = 0; p < endpointsPtr->size(); p++) {
- if ((*endpointsPtr)[p].GetSide() == Start) {
- int maxPointIndex;
- if (pst.FindIndexOfMaxPoint((*endpointsPtr), (*endpointsPtr)[p].GetKey(), maxPointIndex)) {
- (*endpointsPtr)[p].SetChainPrev((*endpointsPtr)[maxPointIndex].GetFragmentPtr());
- (*endpointsPtr)[p].SetScore((*endpointsPtr)[maxPointIndex].GetScore() + (*endpointsPtr)[p].GetScore());
- }
- else {
- (*endpointsPtr)[p].SetChainPrev(NULL);
- }
- } else {
- assert((*endpointsPtr)[p].GetSide() == End);
- //
- // The score of the fragment should be already set. So simply activate
- // it here (make the point be visible in a search).
- //
- pst.Activate((*endpointsPtr), p);
- if (maxScoringEndpointFound == false or
- (*endpointsPtr)[maxScoringEndpoint].GetScore() < (*endpointsPtr)[p].GetScore()) {
- maxScoringEndpoint = p;
- maxScoringEndpointFound = true;
- }
- }
- }
-
- //
- // Now compute the chain of optimum fragments
- //
- T_Fragment *optFragmentPtr;
- if (maxScoringEndpointFound == false) {
- //
- // Null case, no endpoints have been processed.
- //
- return 0;
- }
-
- optFragmentPtr = (*endpointsPtr)[maxScoringEndpoint].GetFragmentPtr();
- unsigned int numIter = 0;
- while (optFragmentPtr != NULL) {
- optFragmentChainIndices.push_back((int) (optFragmentPtr - &fragments[0]));
- optFragmentPtr = optFragmentPtr->GetChainPrev();
- //
- // Do a sanity check to make sure this loop is finite -- the optimal
- // fragment chain should never contain more fragments than what are
- // input.
- //
- assert(numIter < nFragments);
- ++numIter;
- }
- reverse(optFragmentChainIndices.begin(), optFragmentChainIndices.end());
- return optFragmentChainIndices.size();
-
-}
-
-
-template<typename T_Fragment, typename T_Endpoint>
-int GlobalChain(vector<T_Fragment> &fragments,
- vector<VectorIndex> &optFragmentChainIndices) {
- return GlobalChain<T_Fragment, T_Endpoint>(&fragments[0],
- fragments.size(), optFragmentChainIndices);
-}
-
-template<typename T_Fragment, typename T_Endpoint>
-int GlobalChain(vector<T_Fragment> &fragments,
- DNALength start, DNALength end,
- vector<VectorIndex> &optFragmentChainIndices,
- vector<T_Endpoint> *bufEndpointsPtr) {
- return GlobalChain<T_Fragment, T_Endpoint>(&fragments[start],
- end - start, optFragmentChainIndices, bufEndpointsPtr);
-}
-
-#endif
diff --git a/libcpp/alignment/algorithms/anchoring/LISPValue.hpp b/libcpp/alignment/algorithms/anchoring/LISPValue.hpp
deleted file mode 100644
index 1a0e9ab..0000000
--- a/libcpp/alignment/algorithms/anchoring/LISPValue.hpp
+++ /dev/null
@@ -1,24 +0,0 @@
-#ifndef _BLASR_LISPVALUE_HPP_
-#define _BLASR_LISPVALUE_HPP_
-
-#include <math.h>
-#include "datastructures/anchoring/MatchPos.hpp"
-#include "tuples/TupleCountTable.hpp"
-#include "algorithms/anchoring/ScoreAnchors.hpp"
-
-template<typename T_MatchPos>
-void StoreNonOverlappingIndices(std::vector<T_MatchPos> &lis,
- std::vector<T_MatchPos> &noOvpLis);
-
-template<typename T_TextSequence,
- typename T_Sequence,
- typename T_MatchPos,
- typename T_Tuple>
-float ComputeLISPValue(std::vector<T_MatchPos> &lis,
- T_TextSequence &text, T_Sequence &read,
- TupleMetrics &tm, TupleCountTable<T_TextSequence, T_Tuple> &ct,
- int &lisNBases, int &lisSize );
-
-#include "algorithms/anchoring/LISPValueImpl.hpp"
-
-#endif
diff --git a/libcpp/alignment/algorithms/anchoring/LISPValueImpl.hpp b/libcpp/alignment/algorithms/anchoring/LISPValueImpl.hpp
deleted file mode 100644
index 613381c..0000000
--- a/libcpp/alignment/algorithms/anchoring/LISPValueImpl.hpp
+++ /dev/null
@@ -1,165 +0,0 @@
-#ifndef _BLASR_LISP_VALUE_IMPL_HPP_
-#define _BLASR_LISP_VALUE_IMPL_HPP_
-
-template<typename T_MatchPos>
-void StoreNonOverlappingIndices(std::vector<T_MatchPos> &lis,
- std::vector<T_MatchPos> &noOvpLis) {
- unsigned int i;
-
- //
- // Greedily add lis matches according to weight. A match may be added
- // as long as it does not overlap with any other matches.
- //
-
- // do nothing on empty lists
- if (lis.empty()) return;
-
- //
- // First build a list of matches sorted by weight.
- SortMatchPosListByWeight(lis);
-
- //
- // The first match is guaranteed to not overlap.
- noOvpLis.push_back(lis[0]);
-
- //
- // Nothing is overlapping, and everything is sorted when there is
- // just one value.
- if (lis.size() == 1) return;
-
- //
- // Next, add matches as long as they do not overlap.
- for (i = 1; i < lis.size(); i++ ){
- VectorIndex j;
- int lts = lis[i].t;
- int lte = lis[i].t + lis[i].GetLength();
- int lqs = lis[i].q;
- int lqe = lis[i].q + lis[i].GetLength();
-
- int ovpFound = 0;
- for (j =0; j < noOvpLis.size(); j++ ){
- int tIntvStart = noOvpLis[j].t;
- int tIntvEnd = noOvpLis[j].t + noOvpLis[j].GetLength();
- int qIntvStart = noOvpLis[j].q;
- int qIntvEnd = noOvpLis[j].q + noOvpLis[j].GetLength();
- if ((lts >= tIntvStart and lts < tIntvEnd) or
- (lte > tIntvStart and lte <= tIntvEnd) or
- (lqs >= qIntvStart and lqs < qIntvEnd) or
- (lqe > qIntvStart and lqe <= qIntvEnd)) {
- ovpFound = 1;
- break;
- }
- }
- if (!ovpFound) {
- noOvpLis.push_back(lis[i]);
- }
- }
-
- //
- // Now, the matches are found in order of size, but they need to
- // be stored in order of text.
- //
- SortMatchPosList(noOvpLis);
-
- //
- // The match pos list was sorted in order of weight.
- // Just in case it causes problems down the line, re-sort it
- // according to query pos.
- //
- lis = noOvpLis;
- SortMatchPosList(lis);
-}
-
-
-template<typename T_TextSequence,
- typename T_Sequence,
- typename T_MatchPos,
- typename T_Tuple>
-float ComputeLISPValue(std::vector<T_MatchPos> &lis,
- T_TextSequence &text, T_Sequence &read,
- TupleMetrics &tm, TupleCountTable<T_TextSequence, T_Tuple> &ct,
- int &lisNBases, int &lisSize ) {
- //
- // First, find a subset of the lis that has non-overlapping matches.
- //
- int i;
- lisNBases = 0;
- for (i = 0; i < lis.size(); i++) {
- lisNBases += lis[i].l;
- }
- lisSize = lis.size();
-
- float neginf = -1.0/0.0;
- float inf = 1.0/0.0;
-
- if (lis.size() == 1) {
- //
- // When just one LIS is found, the pvalue of the match is just the
- // pvalue of getting a single hit with one read, which we estimate
- // as the pvalue of at least one hit.
- //
- float matchProb;
- //
- // Weight the single match based on how frequently it appears in
- // the genome.
- if (POneOrMoreMatches<T_TextSequence>(text, lis[0].t,
- lis[0].GetLength(), tm, ct, matchProb)) {
- return matchProb;
- }
- else {
- // return non-significant match value.
- return 1;
- }
- }
- else {
- //
- // There is more than one non overlapping match. This evokes a
- // totally different probability metric on LIS values. Rather
- // than computing the probability of a single match, compute
- // the probability of seeing several matches in a row.
- //
- VectorIndex i;
- float pChain = 0; // In other words, pChain = log(1)
- //
- // prob of chain starts out as prob of first match.
- //
- if (POneOrMoreMatches(text, lis[0].t, lis[0].GetLength(),
- tm, ct, pChain)) {
- //
- // Next, for each match, compute the expected probability of
- // having to wait at most tGap time for a match. Since this
- // has screened for anchors that are not overlapping,
- // consider the events to be independent, and therefore
- // the probabilities multiply.
- //
- for (i = 1; i < lis.size(); i++ ){
-
- int tupleMatchCount;
- //
- // Find out how many times this word appears in the genome.
- //
- int approxNumMatches;
- //
- // Assume all hits are uniformly distributed across the
- // genome. qLambda is the frequency of seeing hit i in the
- // genome.
- //
- float qLambda;
- int tGap;
- int qGap;
- qLambda = lis[i].GetMultiplicity() / (1.0*text.length);
-
- // Now compute the probability of the chain. Since the
- // matches are uniformly distributed across the genome, the
- // waiting time between matches is exponentially distributed.
- pChain = pChain + log(qLambda);
- }
- return pChain;
- }
- else {
- return 1;
- }
- }
-}
-
-#endif
diff --git a/libcpp/alignment/algorithms/anchoring/LISPValueWeightor.hpp b/libcpp/alignment/algorithms/anchoring/LISPValueWeightor.hpp
deleted file mode 100644
index 85213ff..0000000
--- a/libcpp/alignment/algorithms/anchoring/LISPValueWeightor.hpp
+++ /dev/null
@@ -1,52 +0,0 @@
-#ifndef _BLASR_LISPVALUE_WEIGHTOR_HPP_
-#define _BLASR_LISPVALUE_WEIGHTOR_HPP_
-
-#include "algorithms/anchoring/LISPValue.hpp"
-#include "tuples/TupleMetrics.hpp"
-
-template<typename T_RefSequence, typename T_MatchList>
-class LISSumOfLogPWeightor {
-public:
- DNALength genomeLength;
- LISSumOfLogPWeightor(T_RefSequence &targetGenome);
- float ComputePValue(T_MatchList &matchList,
- int &noOvpLisNBases, int &noOvpLisSize);
- float operator()(T_MatchList &matchList);
-};
-
-
-template<typename T_RefSequence, typename T_Tuple, typename T_MatchList>
-class LISSMatchFrequencyPValueWeightor {
-public:
- T_RefSequence target;
- LISSMatchFrequencyPValueWeightor(T_RefSequence &_target);
- float ComputePValue(T_MatchList &lis,
- int &noOvpLisNBases, int &noOvpLisSize);
- float operator() (T_MatchList &lis);
-};
-
-
-template<typename T_RefSequence, typename T_Tuple, typename T_MatchList>
-class LISPValueWeightor {
-public:
- //
- // All of these must be initialized prior to
- // computing weights (running the functor).
- //
- FASTASequence query;
- T_RefSequence target;
- TupleMetrics tm;
- TupleCountTable<T_RefSequence, T_Tuple> *ct;
-
- LISPValueWeightor(FASTASequence &_query, T_RefSequence &_target,
- TupleMetrics _tm, TupleCountTable<T_RefSequence, T_Tuple> *_ct);
-
- float ComputePValue(T_MatchList &matchList, int &noOvpLisNBases,
- int &noOvpLisSize);
-
- float operator()(T_MatchList &matchList);
-};
-
-#include "algorithms/anchoring/LISPValueWeightorImpl.hpp"
-
-#endif
diff --git a/libcpp/alignment/algorithms/anchoring/LISPValueWeightorImpl.hpp b/libcpp/alignment/algorithms/anchoring/LISPValueWeightorImpl.hpp
deleted file mode 100644
index 2e06940..0000000
--- a/libcpp/alignment/algorithms/anchoring/LISPValueWeightorImpl.hpp
+++ /dev/null
@@ -1,112 +0,0 @@
-#ifndef _BLASR_LISPVALUE_WEIGHTOR_IMPL_HPP_
-#define _BLASR_LISPVALUE_WEIGHTOR_IMPL_HPP_
-
-#include "algorithms/anchoring/LISPValue.hpp"
-#include "tuples/TupleMetrics.hpp"
-
-template<typename T_RefSequence, typename T_MatchList>
-LISSumOfLogPWeightor<T_RefSequence, T_MatchList>::LISSumOfLogPWeightor(
- T_RefSequence &targetGenome) {
- genomeLength = targetGenome.length;
-}
-
-template<typename T_RefSequence, typename T_MatchList>
-float LISSumOfLogPWeightor<T_RefSequence, T_MatchList>::ComputePValue(
- T_MatchList &matchList, int &noOvpLisNBases, int &noOvpLisSize) {
- float pMatch = 0;
- int i;
- T_MatchList noOvpLis;
- StoreNonOverlappingIndices(matchList, noOvpLis);
- noOvpLisSize = noOvpLis.size();
- noOvpLisNBases = 0;
- for (i = 0; i < noOvpLis.size(); i++) {
- noOvpLisNBases += noOvpLis[i].l;
- }
- for (i = 0; i < noOvpLis.size(); i++ ) {
- pMatch += -1 * ((int)noOvpLis[i].l);
- // log(matchList[i].GetMultiplicity() / (1.0*genomeLength));
- }
- noOvpLisNBases = 0;
- for (i = 0; i < matchList.size(); i++) {
- noOvpLisNBases += matchList[i].l;
- }
- return pMatch;
-}
-
-
-template<typename T_RefSequence, typename T_MatchList>
-float LISSumOfLogPWeightor<T_RefSequence, T_MatchList>::operator()(
- T_MatchList &matchList) {
- int temp;
- return ComputePValue(matchList, temp, temp);
-}
-
-
-template<typename T_RefSequence, typename T_Tuple, typename T_MatchList>
-LISSMatchFrequencyPValueWeightor<T_RefSequence, T_Tuple, T_MatchList>::LISSMatchFrequencyPValueWeightor(
- T_RefSequence &_target) {
- target.seq = _target.seq;
- target.length = _target.length;
-}
-
-
-template<typename T_RefSequence, typename T_Tuple, typename T_MatchList>
-float LISSMatchFrequencyPValueWeightor<T_RefSequence, T_Tuple, T_MatchList>::ComputePValue(
- T_MatchList &lis, int &noOvpLisNBases, int &noOvpLisSize) {
- T_MatchList noOvpLis;
- StoreNonOverlappingIndices(lis, noOvpLis);
- noOvpLisSize = noOvpLis.size();
- int i;
- noOvpLisNBases = 0;
- for (i = 0; i < noOvpLis.size(); i++) {
- noOvpLisNBases += noOvpLis[i].l;
- }
- if (noOvpLis.size() == 0){
- return 1;
- }
-
- float pMatch = 0;
- for (i = 0; i < noOvpLis.size(); i++ ) {
- assert(noOvpLis[i].GetMultiplicity() > 0);
- pMatch += log((1.0*noOvpLis[i].GetMultiplicity()) / target.length) * noOvpLis[i].l;
- }
- return pMatch;
-}
-
-
-template<typename T_RefSequence, typename T_Tuple, typename T_MatchList>
-float LISSMatchFrequencyPValueWeightor<T_RefSequence, T_Tuple, T_MatchList>::operator() (
- T_MatchList &lis) {
- int noOvpLisSize = 0;
- return ComputePValue(lis, noOvpLisSize, noOvpLisSize);
-}
-
-
-template<typename T_RefSequence, typename T_Tuple, typename T_MatchList>
-LISPValueWeightor<T_RefSequence, T_Tuple, T_MatchList>::LISPValueWeightor(
- FASTASequence &_query, T_RefSequence &_target, TupleMetrics _tm,
- TupleCountTable<T_RefSequence, T_Tuple> *_ct) {
- query.seq = _query.seq;
- query.length = _query.length;
- target.seq = _target.seq;
- target.length = _target.length;
- ct = _ct;
- tm = _tm;
-}
-
-
-template<typename T_RefSequence, typename T_Tuple, typename T_MatchList>
-float LISPValueWeightor<T_RefSequence, T_Tuple, T_MatchList>::ComputePValue(
- T_MatchList &matchList, int &noOvpLisNBases, int &noOvpLisSize) {
- return ComputeLISPValue(matchList, target, query, tm, *ct,
- noOvpLisNBases, noOvpLisSize);
-}
-
-
-template<typename T_RefSequence, typename T_Tuple, typename T_MatchList>
-float LISPValueWeightor<T_RefSequence, T_Tuple, T_MatchList>::operator()(
- T_MatchList &matchList){
- int noOvpLisSize = 0, noOvpLisNBases = 0;
- return ComputeLISPValue(matchList, target, query, tm, *ct, noOvpLisNBases, noOvpLisSize);
-}
-#endif
diff --git a/libcpp/alignment/algorithms/anchoring/LISQValueWeightor.hpp b/libcpp/alignment/algorithms/anchoring/LISQValueWeightor.hpp
deleted file mode 100644
index fd537ca..0000000
--- a/libcpp/alignment/algorithms/anchoring/LISQValueWeightor.hpp
+++ /dev/null
@@ -1,35 +0,0 @@
-#ifndef _BLASR_LIS_QVALUE_WEIGHTOR_HPP_
-#define _BLASR_LIS_QVALUE_WEIGHTOR_HPP_
-
-#include "qvs/QualityValue.hpp"
-#include "DNASequence.hpp"
-#include "FASTQSequence.hpp"
-
-template<typename T_MatchList, typename T_Sequence>
-class LISQValueWeightor {
-public:
- T_Sequence *seq;
- float operator()(const T_MatchList &matchList);
-};
-
-template<typename T_MatchList, typename T_Sequence>
-float LISQValueWeightor<T_MatchList, T_Sequence>::operator() (
- const T_MatchList &matchList) {
- float totalQ;
- DNALength nBases;
- VectorIndex i;
- totalQ = 0.0;
- nBases = 0;
- for (i = 0; i < matchList.size(); i++) {
- DNALength mp;
- for (mp = matchList[i].q; mp < matchList[i].q + matchList[i].w; mp++) {
- totalQ += (*seq).qual[mp];
- }
- nBases += matchList[i].w;
- }
- if (nBases > 0) {
- return totalQ / nBases;
- }
-}
-
-#endif
diff --git a/libcpp/alignment/algorithms/anchoring/LISSizeWeightor.hpp b/libcpp/alignment/algorithms/anchoring/LISSizeWeightor.hpp
deleted file mode 100644
index fa71bd0..0000000
--- a/libcpp/alignment/algorithms/anchoring/LISSizeWeightor.hpp
+++ /dev/null
@@ -1,14 +0,0 @@
-#ifndef _BLASR_LIS_SIZE_WEIGHTOR_HPP_
-#define _BLASR_LIS_SIZE_WEIGHTOR_HPP_
-
-#include "Types.h"
-
-template<typename T_MatchList>
-class LISSizeWeightor {
-public:
- MatchWeight operator()(T_MatchList &matchList);
-};
-
-#include "algorithms/anchoring/LISSizeWeightorImpl.hpp"
-
-#endif
diff --git a/libcpp/alignment/algorithms/anchoring/LISSizeWeightorImpl.hpp b/libcpp/alignment/algorithms/anchoring/LISSizeWeightorImpl.hpp
deleted file mode 100644
index ff778f5..0000000
--- a/libcpp/alignment/algorithms/anchoring/LISSizeWeightorImpl.hpp
+++ /dev/null
@@ -1,13 +0,0 @@
-#ifndef _BLASR_LISSIZE_WEIGHTOR_IMPL_HPP_
-#define _BLASR_LISSIZE_WEIGHTOR_IMPL_HPP_
-template<typename T_MatchList>
-MatchWeight LISSizeWeightor<T_MatchList>:: operator()(
- T_MatchList &matchList) {
- MatchWeight size = 0;
- VectorIndex i;
- for (i = 0; i < matchList.size(); i++) {
- size += matchList[i].GetLength();
- }
- return size;
-}
-#endif
diff --git a/libcpp/alignment/algorithms/anchoring/LongestIncreasingSubsequence.hpp b/libcpp/alignment/algorithms/anchoring/LongestIncreasingSubsequence.hpp
deleted file mode 100644
index ef8c920..0000000
--- a/libcpp/alignment/algorithms/anchoring/LongestIncreasingSubsequence.hpp
+++ /dev/null
@@ -1,31 +0,0 @@
-#ifndef _BLASR_LONGEST_INCREASING_SUBSEQUENCE_HPP_
-#define _BLASR_LONGEST_INCREASING_SUBSEQUENCE_HPP_
-
-#include <assert.h>
-#include <vector>
-#include <iostream>
-#include <algorithm>
-
-using namespace std;
-
-template<typename T>
-class RawValue {
- int operator()(T &t) {
- return t;
- }
-};
-
-template<typename T, typename F_IntValue>
-int BinarySearch(T *x, vector<int> &m, int i, int lenM, F_IntValue IntValue);
-
-template<typename T, typename F_IntValue >
-int LongestIncreasingSubset(T *x, int xLength, vector<int> &subsetIndices,
- vector<int> &m, vector<int> &p, F_IntValue IntValue,
- int start=0, int end = -1);
-
-template<typename T, typename F_IntValue>
-int LongestIncreasingSubset(T*x, int& xLength, vector<int> &subsetIndices);
-
-#include "algorithms/anchoring/LongestIncreasingSubsequenceImpl.hpp"
-
-#endif
diff --git a/libcpp/alignment/algorithms/anchoring/LongestIncreasingSubsequenceImpl.hpp b/libcpp/alignment/algorithms/anchoring/LongestIncreasingSubsequenceImpl.hpp
deleted file mode 100644
index acda550..0000000
--- a/libcpp/alignment/algorithms/anchoring/LongestIncreasingSubsequenceImpl.hpp
+++ /dev/null
@@ -1,135 +0,0 @@
-#ifndef _BLASR_LONGEST_INCREASING_SUBSEQUENCE_IMPL_HPP_
-#define _BLASR_LONGEST_INCREASING_SUBSEQUENCE_IMPL_HPP_
-
-using namespace std;
-
-template<typename T, typename F_IntValue>
-int BinarySearch(T *x, vector<int> &m, int i, int lenM, F_IntValue IntValue) {
- //
- // Binary search for the largest
- // j ≤ L such that X[M[j]] < X[i]
- // (or set j = 0 if no such value exists)
- //
-
- //
- // In English: Find the longest subsequence ending
- // at some value less than X[i]. That
- // way, X[i] can increase this subsequence by 1.
- //
- int low = 0, high = lenM, cur;
- cur = (high + low) / 2;
- assert(cur < m.size());
-
- while (low < high) {
- if (high == 1) {
- assert(cur == 0);
- return cur;
- }
- // The highest value is between cur and high.
- if (IntValue(x[m[cur]]) < IntValue(x[i])) {
- low = cur + 1;
- }
- else {
- // x[m[cur]] is above x[i], so the highest valid value is
- // strictly below cur
- high = cur;
- }
- cur = (low + high) / 2;
- }
-
- // cur is either the last spot where x[m[cur]] < x[i], or
- // the first spot where x[m[cur]] > x[i];
- // Typically x[m[cur]] must be less than x[i], except on the first
- // call to this, in which case x[m[cur]] == x[i] == the first element
- // in the array.
- if (cur == 0) {
- return cur;
- }
- else {
- return cur - 1;
- }
-}
-
-
-template<typename T, typename F_IntValue >
-int LongestIncreasingSubset(T *x, int xLength, vector<int> &subsetIndices,
- vector<int> &m, vector<int> &p, F_IntValue IntValue,
- int start, int end) {
-
- //
- // m[i] is the index of the LIS of length i+1
- //
- m.resize(xLength+1);
- if (xLength == 0)
- return 0;
- m[0] = -1;
-
- p.resize(xLength);
- int i;
-
- int maxM;
- // On the first iteration m[0] should be set to 0.
- int lenM = 1;
- int mi;
-
- for (i = 0; i < xLength; i++) {
- //
- // Find the index of the longest increasing subsequence ending
- // before x[i]
- //
- maxM = BinarySearch<T,F_IntValue>(x, m, i, lenM);
-
- //
- // p is the list of back pointers.
- // Create a reference for where the previous longest increasing
- // subsequence that x[i] is part of.
- //
-
- p[i] = m[maxM];
-
- //
- // If this creates a LIS longer than any previously known one,
- // add this to maxM.
- //
- if (maxM + 1 >= lenM) {
- assert(maxM+1 < m.size());
- m[maxM+1] = i;
- if (maxM + 1>= lenM) {
- // assume that lenM is never more than 2 greater than maxM.
- lenM++;
- }
- }
- //
- // Otherwise, x[i] cannot create a longer LIS, BUT, if
- // it is less than the current element that ends a LIS of length maxM,
- // it bumps that element out from the slot of ending the LIS with
- // length maxM.
- //
- else if (IntValue(x[i]) < IntValue(x[m[maxM+1]])) {
- m[maxM+1] = i;
- }
- }
-
- //
- // Trace back;
- //
- int lisLen = lenM-1;
- int lisCur = m[lisLen];
- for (i = 0 ; i < lisLen and lisCur != -1; i++) {
- subsetIndices.push_back(lisCur);
- lisCur = p[lisCur];
- }
- std::reverse(subsetIndices.begin(), subsetIndices.end());
-
- return lenM - 1;
-}
-
-template<typename T, typename F_IntValue>
-int LongestIncreasingSubset(T*x, int& xLength, vector<int> &subsetIndices) {
- vector<int> p;
- vector<int> m;
- return LongestIncreasingSubset(x, xLength, subsetIndices, m, p);
-}
-
-
-#endif
diff --git a/libcpp/alignment/algorithms/anchoring/MapBySuffixArray.hpp b/libcpp/alignment/algorithms/anchoring/MapBySuffixArray.hpp
deleted file mode 100644
index ce8ac39..0000000
--- a/libcpp/alignment/algorithms/anchoring/MapBySuffixArray.hpp
+++ /dev/null
@@ -1,44 +0,0 @@
-#ifndef _BLASR_MAP_BY_SUFFIX_ARRAY_HPP_
-#define _BLASR_MAP_BY_SUFFIX_ARRAY_HPP_
-
-#include <algorithm>
-#include "suffixarray/SuffixArray.hpp"
-#include "datastructures/anchoring/MatchPos.hpp"
-#include "datastructures/anchoring/AnchorParameters.hpp"
-#include "algorithms/alignment/SWAlign.hpp"
-#include "algorithms/alignment/ScoreMatrices.hpp"
-
-/*
- * Parameters:
- * Eventually this should be strongly typed, since this is specific to
- * suffix array searching on DNASequence read/genome types.
- * reference - should be of type DNASequence
- * sa - shuld be of type SuffixArray
- * read - may be of any DNASequence subclass.
- * tupleSize - The length of the keyword used to speed up searching.
- * Out:
- * matchLow - The starting point in the suffix array for the LCP
- * match for the read at pos p.
- * matchHigh -The same array but for the upper bound.
- * saMatchLength - The length of the lcp.
- */
-template<typename T_SuffixArray,
- typename T_RefSequence,
- typename T_Sequence>
-int LocateAnchorBoundsInSuffixArray(T_RefSequence &reference,
- T_SuffixArray &sa, T_Sequence &read, unsigned int minPrefixMatchLength,
- std::vector<DNALength> &matchLow, std::vector<DNALength> &matchHigh,
- std::vector<DNALength> &matchLength, AnchorParameters ¶ms);
-
-template<typename T_SuffixArray,
- typename T_RefSequence,
- typename T_Sequence,
- typename T_MatchPos>
-int MapReadToGenome(T_RefSequence &reference,
- T_SuffixArray &sa, T_Sequence &read,
- unsigned int minPrefixMatchLength,
- vector<T_MatchPos> &matchPosList,
- AnchorParameters &anchorParameters);
-
-#include "algorithms/anchoring/MapBySuffixArrayImpl.hpp"
-#endif
diff --git a/libcpp/alignment/algorithms/anchoring/MapBySuffixArrayImpl.hpp b/libcpp/alignment/algorithms/anchoring/MapBySuffixArrayImpl.hpp
deleted file mode 100644
index 6cbac02..0000000
--- a/libcpp/alignment/algorithms/anchoring/MapBySuffixArrayImpl.hpp
+++ /dev/null
@@ -1,315 +0,0 @@
-#ifndef _BLASR_MAP_BY_SUFFIX_ARRAY_IMPL_HPP_
-#define _BLASR_MAP_BY_SUFFIX_ARRAY_IMPL_HPP_
-#include "defs.h"
-#include "algorithms/anchoring/MapBySuffixArray.hpp"
-
-/*
- * Parameters:
- * Eventually this should be strongly typed, since this is specific to
- * suffix array searching on DNASequence read/genome types.
- * reference - should be of type DNASequence
- * sa - shuld be of type SuffixArray
- * read - may be of any DNASequence subclass.
- * tupleSize - The length of the keyword used to speed up searching.
- * Out:
- * matchLow - The starting point in the suffix array for the LCP
- * match for the read at pos p.
- * matchHigh -The same array but for the upper bound.
- * saMatchLength - The length of the lcp.
- */
-template<typename T_SuffixArray,
- typename T_RefSequence,
- typename T_Sequence>
-int LocateAnchorBoundsInSuffixArray(T_RefSequence &reference,
- T_SuffixArray &sa, T_Sequence &read, unsigned int minPrefixMatchLength,
- std::vector<DNALength> &matchLow, std::vector<DNALength> &matchHigh,
- std::vector<DNALength> &matchLength, AnchorParameters ¶ms) {
-
- //
- // Make sure there is enough of this read to map. Since searches
- // are keyed off of 'minPrefixMatchLength' matches, don't search
- // anything shorter than that.
- //
- if (minPrefixMatchLength > 0 and
- read.subreadEnd - read.subreadStart < minPrefixMatchLength) {
- return 0;
- }
-
- DNALength p, m;
- DNALength alignEnd;
- DNALength matchEnd = read.subreadEnd - minPrefixMatchLength + 1;
- DNALength numSearchedPositions = matchEnd - read.subreadStart;
-
- matchLength.resize(numSearchedPositions);
- matchLow.resize(numSearchedPositions);
- matchHigh.resize(numSearchedPositions);
-
- std::fill(matchLength.begin(), matchLength.end(), 0);
- std::fill(matchLow.begin(), matchLow.end(), 0);
- std::fill(matchHigh.begin(), matchHigh.end(), 0);
- vector<SAIndex> lowMatchBound, highMatchBound;
-
- for (m = 0, p = read.subreadStart; p < matchEnd; p++, m++) {
- DNALength lcpLow, lcpHigh, lcpLength;
- lowMatchBound.clear(); highMatchBound.clear();
- lcpLow = 0;
- lcpHigh = 0;
- lcpLength = sa.StoreLCPBounds(reference.seq, reference.length,
- &read.seq[p], matchEnd - p,
- params.useLookupTable,
- params.maxLCPLength,
- //
- // Store the positions in the SA
- // that are searched.
- //
- lowMatchBound, highMatchBound,
- params.stopMappingOnceUnique);
-
- //
- // Possibly print the lcp bounds for debugging
- //
- if (params.lcpBoundsOutPtr != NULL) {
- for (int i = 0; i < lowMatchBound.size(); i++) {
- *params.lcpBoundsOutPtr <<
- (highMatchBound[i] - lowMatchBound[i]);
- if (i < lowMatchBound.size() - 1) {
- *params.lcpBoundsOutPtr << " ";
- }
- }
- *params.lcpBoundsOutPtr << endl;
- }
-
- //
- // Default to no match.
- //
- matchLow[m] = matchHigh[m] = matchLength[m] = 0;
-
- //
- // If anything was found in the suffix array:
- //
- if (lowMatchBound.size() > 0) {
- //
- // First expand the search bounds until at least
- // one match is found.
- //
- int lcpSearchLength = lowMatchBound.size();
- bool extendedForward = false;
- while (lcpSearchLength > 0 and
- lowMatchBound[lcpSearchLength - 1] ==
- highMatchBound[lcpSearchLength - 1]) {
- lcpSearchLength--;
- lcpLength--;
- }
- matchLow[m] = lowMatchBound[lcpSearchLength - 1];
- matchHigh[m] = highMatchBound[lcpSearchLength - 1];
- matchLength[m] = minPrefixMatchLength + lcpSearchLength;
-
- //
- // Next, apply some heuristics to the anchor generation.
- //
- // 1.1 If the suffix array match is unique, try and extend that
- // match as long as possible to ease global chaining later on.
- //
- // 1.2 If the suffix array match is unique, but cannot be
- // extended, it probably ends in an error. Back the search up
- // by 1.
- //
- // 2.1 If the suffix array match is not unique, return the
- // default matches, or expand the search to include more
- // matches.
- //
-
- //
- // Check to see if the match was unique.
- //
- if (matchLow[m] + 1 == matchHigh[m]) {
- //
- // If the match is unique, extend for as long as possible.
- //
- lcpLength = minPrefixMatchLength + lcpSearchLength;
- long refPos = sa.index[matchLow[m]] + lcpLength;
- long queryPos = p + lcpLength;
- bool extensionWasPossible = false;
-
- while (refPos + 1 < reference.length and
- queryPos + 1 < read.length and
- reference.seq[refPos + 1] == read.seq[queryPos + 1] and
- (params.maxLCPLength == 0 or
- lcpLength < params.maxLCPLength)) {
- refPos++;
- queryPos++;
- lcpLength++;
- extensionWasPossible = true;
- }
-
- if (extensionWasPossible) {
- //
- // Was able to extend match far into the genome, store that.
- //
- matchLength[m] = lcpLength;
- }
- else if (extensionWasPossible == false) {
- //
- // No extension was possible, indicating that this match
- // ends at an error. To be safe, expand search by up to
- // 1.
- //
- if (lcpSearchLength > 1) {
- lcpSearchLength = lcpSearchLength - 1;
- }
- matchLow[m] = lowMatchBound[lcpSearchLength-1];
- matchHigh[m] = highMatchBound[lcpSearchLength-1];
- matchLength[m] = minPrefixMatchLength + lcpSearchLength;
- }
- }
- else {
- //
- // The match is not unique. Store a possibly expanded search.
- //
- int numBacktrack = params.expand;
- if (lcpSearchLength > params.expand) {
- lcpSearchLength -= params.expand;
- }
- else {
- assert(lowMatchBound.size() > 0);
- lcpSearchLength = 1;
- }
-
- //
- // There are multiple matches for this position.
- //
- matchLow[m] = lowMatchBound[lcpSearchLength - 1];
- matchHigh[m] = highMatchBound[lcpSearchLength - 1];
- matchLength[m] = minPrefixMatchLength + lcpSearchLength;
- }
- }
- else {
- //
- // The match is shorter than what the search is supposed to
- // expand to. In order to avoid expanding to before the end
- // of the match list, do not set any match.
- //
- matchLow[m] = 0;
- matchHigh[m] = 0;
- matchLength[m] = 0;
- }
-
- //
- // Possibly advance a bunch of steps.
- //
- if (params.advanceExactMatches) {
- int tmp = (int)lcpLength - (int)params.expand
- - params.advanceExactMatches;
- int advance = MAX(tmp, 0);
- p += advance;
- m += advance;
- }
- }
- return 1;
-}
-
-
-template<typename T_SuffixArray,
- typename T_RefSequence,
- typename T_Sequence,
- typename T_MatchPos>
-int MapReadToGenome(T_RefSequence &reference,
- T_SuffixArray &sa, T_Sequence &read,
- unsigned int minPrefixMatchLength,
- vector<T_MatchPos> &matchPosList,
- AnchorParameters &anchorParameters) {
-
- vector<DNALength> matchLow, matchHigh, matchLength;
-
- int minMatchLen = anchorParameters.minMatchLength;
- if (read.subreadEnd - read.subreadStart < minMatchLen) {
- matchPosList.clear();
- return 0;
- }
-
- LocateAnchorBoundsInSuffixArray(reference, sa, read,
- minPrefixMatchLength, matchLow, matchHigh, matchLength,
- anchorParameters);
-
- //
- // Try evaluating some contexts.
- //
- DNALength pos;
- DNALength mappedLength = matchLow.size();
- assert(matchLow.size() == matchHigh.size());
-
- DNASequence evalQrySeq, evalRefSeq;
- vector<Arrow> pathMat;
- vector<int> scoreMat;
- Alignment alignment;
-
- //
- // Do some filtering on the matches looking for overlapping matches
- // if there are any.
- //
- if (anchorParameters.removeEncompassedMatches) {
- vector<bool> removed;
- removed.resize(read.length);
- std::fill(removed.begin(), removed.end(), false);
- int i;
- int nRemoved = 0;
- for (i = 0; i < read.length-1; i++) {
- if (matchLength[i] == matchLength[i+1]+1) {
- removed[i+1] = true;
- }
- }
- for (i = 1; i < matchLength.size(); i++) {
- if (removed[i]) {
- matchLength[i] = matchLow[i] = matchHigh[i] = 0;
- }
- }
- }
- //
- // Now add
- //
- DNALength endOfMapping;
- DNALength trim = MAX(minMatchLen + 1, sa.lookupPrefixLength + 1);
- if (read.subreadEnd < trim) {
- endOfMapping = 0;
- }
- else {
- endOfMapping = read.subreadEnd - trim;
- }
-
- for (pos = read.subreadStart; pos < endOfMapping; pos++) {
- int matchIndex = pos - read.subreadStart;
- assert(matchIndex < matchHigh.size());
- if (matchHigh[matchIndex] - matchLow[matchIndex] <=
- anchorParameters.maxAnchorsPerPosition) {
- DNALength mp;
- for (mp = matchLow[matchIndex]; mp < matchHigh[matchIndex]; mp++) {
- if (matchLength[matchIndex] < minMatchLen) {
- continue;
- }
-
- //
- // By default, add all anchors.
- //
- if (matchLength[matchIndex] + pos > read.length) {
- //
- // When doing branching, it's possible that a deletion
- // branch finds an anchor that goes past the end of a
- // read. When that is the case, trim back the anchor
- // match since this confuses downstream assertions.
- //
- matchLength[matchIndex] = read.length - pos;
- }
- assert(sa.index[mp] + matchLength[matchIndex]
- <= reference.length);
-
- matchPosList.push_back(ChainedMatchPos(sa.index[mp], pos,
- matchLength[matchIndex],
- matchHigh[matchIndex] - matchLow[matchIndex]));
- }
- }
- }
-
- return matchPosList.size();
-}
-
-#endif
diff --git a/libcpp/alignment/algorithms/anchoring/PrioritySearchTree.hpp b/libcpp/alignment/algorithms/anchoring/PrioritySearchTree.hpp
deleted file mode 100644
index e9f4c69..0000000
--- a/libcpp/alignment/algorithms/anchoring/PrioritySearchTree.hpp
+++ /dev/null
@@ -1,69 +0,0 @@
-#ifndef _BLASR_PRIORITY_SEARCH_TREE_HPP_
-#define _BLASR_PRIORITY_SEARCH_TREE_HPP_
-
-#include <vector>
-#include "algorithms/anchoring/BasicEndpoint.hpp"
-
-/*
- * Define a priority search tree on a point that implements
- * the following interface:
- *
- * int T_point::GetIndex()
- * - Return the index of the point in a list of points.
- * int T_point::GetKey()
- * - Return the key value that the points are sorted by (x-value in a 2D query)
- * int T_point::GetValue()
- * - Return the value of a point.
- * int T_point::SetValue(int value)
- * - sets the value of a point.
- *
- * This class implements a query FindMax(key), which returns
- * the index of the point with greatest value of all points with key [0...key).
- *
- *
- */
-template<typename T_Point>
-class PSTVertex {
-public:
- unsigned int leftChildIndex;
- unsigned int rightChildIndex;
- unsigned int isALeaf;
- KeyType medianKey;
- KeyType maxKey;
- unsigned int pointIndex;
- int maxScoreNode;
- PSTVertex();
-};
-
-template<typename T_Point>
-class PrioritySearchTree {
-private:
- std::vector<PSTVertex<T_Point> > tree;
- std::vector<PSTVertex<T_Point> > * treePtr;
- int GetMedianIndex(int start, int end);
-
- inline KeyType CreateTree(std::vector<T_Point> &points,
- int start, int end, unsigned int &iterativeIndex);
-
- int FindIndexOfMaxPoint(int curVertexIndex, std::vector<T_Point> &points,
- KeyType maxKey, int &maxPointValue,
- int &maxPointIndex);
-
-public:
- PrioritySearchTree();
-
- void CreateTree(std::vector<T_Point> &points,
- std::vector<PSTVertex<T_Point> > *bufTreePtr=NULL);
-
- int FindPoint(KeyType pointKey,
- int curVertexIndex, int &pointVertexIndex);
-
- void Activate(std::vector<T_Point> &points, int pointIndex);
-
- int FindIndexOfMaxPoint(std::vector<T_Point> &points,
- KeyType maxPointKey, int &maxPointIndex);
-};
-
-#include "algorithms/anchoring/PrioritySearchTreeImpl.hpp"
-
-#endif
diff --git a/libcpp/alignment/algorithms/anchoring/PrioritySearchTreeImpl.hpp b/libcpp/alignment/algorithms/anchoring/PrioritySearchTreeImpl.hpp
deleted file mode 100644
index baa5b5b..0000000
--- a/libcpp/alignment/algorithms/anchoring/PrioritySearchTreeImpl.hpp
+++ /dev/null
@@ -1,296 +0,0 @@
-#ifndef _BLASR_PRIORITY_SEARCH_TREE_IMPL_HPP_
-#define _BLASR_PRIORITY_SEARCH_TREE_IMPL_HPP_
-
-/*
- * Define a priority search tree on a point that implements
- * the following interface:
- *
- * int T_point::GetIndex()
- * - Return the index of the point in a list of points.
- * int T_point::GetKey()
- * - Return the key value that the points are sorted by (x-value in a 2D query)
- * int T_point::GetValue()
- * - Return the value of a point.
- * int T_point::SetValue(int value)
- * - sets the value of a point.
- *
- * This class implements a query FindMax(key), which returns
- * the index of the point with greatest value of all points with key [0...key).
- *
- *
- */
-template<typename T_Point>
-PSTVertex<T_Point>::PSTVertex() {
- isALeaf = 0;
- leftChildIndex = 0;
- rightChildIndex = 0;
- maxScoreNode = -1;
- maxKey = 0;
- medianKey = 0;
- pointIndex = 0;
-}
-
-
-template<typename T_Point>
-PrioritySearchTree<T_Point>::PrioritySearchTree() {treePtr = NULL;}
-
-template<typename T_Point>
-int PrioritySearchTree<T_Point>::
-GetMedianIndex(int start, int end) {
- return (end + start) / 2;
-}
-
-template<typename T_Point>
-inline
-KeyType PrioritySearchTree<T_Point>::
-CreateTree(std::vector<T_Point> &points,
- int start, int end, unsigned int &iterativeIndex) {
- assert(iterativeIndex < (*treePtr).size());
-
- //
- // Look to see if this vertex is the parent of a leaf
- // -- when there are only two points below.
- //
- int medianIndex = GetMedianIndex(start, end);
- int curVertexIndex = iterativeIndex;
- (*treePtr)[curVertexIndex].medianKey = points[medianIndex].GetKey();
-
- if (end == start) {
- // No children for this node, done.
- (*treePtr)[curVertexIndex].pointIndex = start;
- return (*treePtr)[curVertexIndex].medianKey;
- }
-
- //
- // Check to see if the current
- // node is a leaf node. No recursion on this node.
- //
- if (end - start == 1) {
- (*treePtr)[curVertexIndex].isALeaf = 1;
- (*treePtr)[curVertexIndex].medianKey = points[start].GetKey();
- (*treePtr)[curVertexIndex].pointIndex = start;
- //
- // Return the key of this vertex. The parent
- // will know what to do with it. If this is
- // a left child, the parent will use the key to
- // distinguish what is on the left side of the branches.
- // If it is the right side of a (*treePtr), it is ignored.
- //
- return (*treePtr)[curVertexIndex].medianKey;
- }
- else {
- //
- // This vertex contains at least two children, so it is not
- // a leaf. Recurse assigning leaves.
- //
- (*treePtr)[curVertexIndex].isALeaf = 0;
- (*treePtr)[curVertexIndex].leftChildIndex = ++iterativeIndex;
- KeyType leftTreeKey, rightTreeKey;
- leftTreeKey = CreateTree(points, start, medianIndex, iterativeIndex);
-
- //
- // The leftTreeKey separates the branches BELOW this vertex.
- //
- (*treePtr)[curVertexIndex].medianKey = leftTreeKey;
-
- (*treePtr)[curVertexIndex].rightChildIndex = ++iterativeIndex;
- rightTreeKey = CreateTree(points, medianIndex, end, iterativeIndex);
- //
- // The rightTreeKey will separate the parent's left tree from the right.
- //
- (*treePtr)[curVertexIndex].maxKey = rightTreeKey;
- return rightTreeKey;
- }
-}
-
-template<typename T_Point>
-int PrioritySearchTree<T_Point>::
-FindIndexOfMaxPoint(int curVertexIndex, std::vector<T_Point> &points,
- KeyType maxKey, int &maxPointValue,
- int &maxPointIndex) {
- //
- // Attempt to find the leaf vertex beneath this vertex that has
- // the largest score, with a key less than max key.
- //
- // On return:
- // Return 1 if a value is assigned to maxPointValue, 0 otherwise.
- // If a value is assigned to maxPointValue, this sets:
- // maxPointValue is the score of the maximum point.
- // maxPointIndex the index of the point in 'points' that has
- // the maximum score.
- //
-
- //
- // The vertex at curVertexIndex has a max score node beneath it,
- // if it has been initialized. If the maxScoreNode has a key less
- // than the current maxKey, then we know the maximum value is
- // contained beneath this vertex, AND that its key is within the
- // range in the rage maximum query.
- // That means that there is no need to continue the search below here.
- //
- if ((*treePtr)[curVertexIndex].maxScoreNode == -1) {
- return 0;
- }
- T_Point thisPoint = points[(*treePtr)[curVertexIndex].maxScoreNode];
- if (thisPoint.GetKey() < maxKey) {
- if (thisPoint.GetScore() >= maxPointValue) {
- maxPointValue = thisPoint.GetScore();
- maxPointIndex = (*treePtr)[curVertexIndex].maxScoreNode;
- return 1;
- }
- else {
- return 0;
- }
- }
- //
- // Otherwise, the maximum scoring node beneath this node has a
- // key greater than the max key. That means that the search must
- // continue for the maximum value node with a key less than 'maxKey'.
- //
- // The search has two cases:
- // First, if the median key of this node is greater than the maxKey,
- // all keys on the right side of the tree are greater than maxKey,
- // so do not search there.
- //
- // If the median key of this node si less than maxKey, there may
- // be a node on the left or right child of the current node with
- // a maximum key. Search both to the left and right.
- //
- else {
- if (!(*treePtr)[curVertexIndex].isALeaf) {
- if (maxKey <= (*treePtr)[curVertexIndex].medianKey) {
- return FindIndexOfMaxPoint(
- (*treePtr)[curVertexIndex].leftChildIndex,
- points, maxKey, maxPointValue, maxPointIndex);
- }
- else {
- int foundValueLeft, foundValueRight;
- foundValueLeft = FindIndexOfMaxPoint(
- (*treePtr)[curVertexIndex].leftChildIndex,
- points, maxKey, maxPointValue, maxPointIndex);
-
- foundValueRight = FindIndexOfMaxPoint(
- (*treePtr)[curVertexIndex].rightChildIndex,
- points, maxKey, maxPointValue, maxPointIndex);
- return (foundValueLeft or foundValueRight);
- }
- }
- else {
- //
- // The current node is a leaf node, but due to the condition
- // from before, its key is greater than or equal to the max key,
- // therefore its score cannot be used for the maximum score.
- // Returning 0 here signifies that this search-branch did not
- // turn up any candidates for
- // the maximum scoring node.
- return 0;
- }
- }
-}
-
-
-template<typename T_Point>
-void PrioritySearchTree<T_Point>::
-CreateTree(std::vector<T_Point> &points,
- std::vector< PSTVertex<T_Point> >* bufTreePtr) {
- //
- // Precondition: points is sorted according to key.
- //
- //
- // The tree is a binary tree containing all the points. The
- // perfectly balanced tree is of maximum size points.size()-1,
- // so go ahead and preallocate that now.
- //
- if (bufTreePtr != NULL) {
- treePtr = bufTreePtr;
- }
- else {
- treePtr = &tree;
- }
- treePtr->resize((points.size() * 2) - 1);
- unsigned int curVertexIndex = 0;
- CreateTree(points, 0, points.size(), curVertexIndex);
-}
-
-
-//
-// Implement the tree as an array of interior nodes.
-// Since there is already space allocated for the
-//
-template<typename T_Point>
-int PrioritySearchTree<T_Point>::
-FindPoint(KeyType pointKey,
- int curVertexIndex, int &pointVertexIndex) {
-
- if ((*treePtr)[curVertexIndex].isALeaf) {
- pointVertexIndex = curVertexIndex;
- return (*treePtr)[curVertexIndex].medianKey == pointKey;
- }
- else {
- if (pointKey <= (*treePtr)[curVertexIndex].medianKey) {
- return FindPoint(pointKey,
- (*treePtr)[curVertexIndex].leftChildIndex,
- pointVertexIndex);
- }
- else {
- return FindPoint(pointKey,
- (*treePtr)[curVertexIndex].rightChildIndex,
- pointVertexIndex);
- }
- }
-}
-
-
-template<typename T_Point>
-void PrioritySearchTree<T_Point>::
-Activate(std::vector<T_Point> &points, int pointIndex) {
-
- int pointScore = points[pointIndex].GetScore();
- // Now, update the pMax scores in the (*treePtr).
-
- int curVertexIndex = 0;
- KeyType pointKey = points[pointIndex].GetKey();
- unsigned int itIndex = 0;
- while (pointIndex != -1 and
- (*treePtr)[curVertexIndex].isALeaf == 0) {
- assert(itIndex < (*treePtr).size());
- int nodeIndex = (*treePtr)[curVertexIndex].maxScoreNode;
- if (nodeIndex == -1 or
- points[nodeIndex].GetScore() < pointScore) {
- (*treePtr)[curVertexIndex].maxScoreNode = pointIndex;
- pointIndex = nodeIndex;
- }
-
- if (pointKey <= (*treePtr)[curVertexIndex].medianKey) {
- curVertexIndex = (*treePtr)[curVertexIndex].leftChildIndex;
- }
- else {
- curVertexIndex = (*treePtr)[curVertexIndex].rightChildIndex;
- }
-
- // Keep track of the number of times this loop is executed... an
- // infinite loop will bomb.
- ++itIndex;
- }
-}
-
-template<typename T_Point>
-int PrioritySearchTree<T_Point>::
-FindIndexOfMaxPoint(std::vector<T_Point> &points,
- KeyType maxPointKey, int &maxPointIndex) {
-
- // start at the root
- int curVertexIndex = 0;
- if ((*treePtr)[curVertexIndex].maxScoreNode == -1) {
- //
- // This case can only be hit if none of the points have been
- // activated.
- //
- return 0;
- }
- int maxPointValue = 0;
- return FindIndexOfMaxPoint(0, points, maxPointKey,
- maxPointValue, maxPointIndex);
-}
-
-#endif
diff --git a/libcpp/alignment/algorithms/anchoring/ScoreAnchors.hpp b/libcpp/alignment/algorithms/anchoring/ScoreAnchors.hpp
deleted file mode 100644
index 5d11504..0000000
--- a/libcpp/alignment/algorithms/anchoring/ScoreAnchors.hpp
+++ /dev/null
@@ -1,46 +0,0 @@
-#ifndef _BLASR_SCORE_ANCHORS_HPP_
-#define _BLASR_SCORE_ANCHORS_HPP_
-
-#include <math.h>
-#include "tuples/TupleCountTable.hpp"
-#include "tuples/DNATuple.hpp"
-#include "tuples/TupleMetrics.hpp"
-#include "statistics/cdfs.hpp"
-#include "statistics/pdfs.hpp"
-
-template<typename TSequence, typename T_Tuple>
-int GetTupleCount(TSequence &seq, DNALength startPos,
- TupleMetrics &tm, TupleCountTable<TSequence, T_Tuple> &ct,
- int &count);
-
-template<typename TSequence, typename T_Tuple>
-int PMatch(TSequence &seq, DNALength startPos, DNALength length,
- TupleMetrics &tm, TupleCountTable<TSequence, T_Tuple> &ct,
- float &pMatch);
-
-template<typename TSequence, typename T_Tuple>
-int POneOrMoreMatches(TSequence &seq, DNALength startPos,
- DNALength length, TupleMetrics &tm,
- TupleCountTable<TSequence, T_Tuple> &ct,
- float &pValue);
-
-template<typename TSequence, typename T_Tuple>
-int SumRightShiftMarginalTupleCounts(TupleMetrics &tm,
- TupleCountTable<TSequence, T_Tuple> &ct, T_Tuple curTuple,
- int nextNuc, int &nextSeqCount);
-
-template<typename TSequence, typename T_Tuple>
-int ComputeTotalTupleCount(TupleMetrics &tm,
- TupleCountTable<TSequence, T_Tuple> &ct, TSequence &seq,
- int start=0, int end=-1);
-
-template<typename TSequence, typename T_Tuple>
-int ComputeAverageTupleCount(TupleMetrics &tm,
- TupleCountTable<TSequence, T_Tuple> &ct, TSequence &seq);
-
-inline
-int ComputeExpectedFirstWaitingTime(float lambda);
-
-#include "ScoreAnchorsImpl.hpp"
-
-#endif
diff --git a/libcpp/alignment/algorithms/anchoring/ScoreAnchorsImpl.hpp b/libcpp/alignment/algorithms/anchoring/ScoreAnchorsImpl.hpp
deleted file mode 100644
index 2debcbf..0000000
--- a/libcpp/alignment/algorithms/anchoring/ScoreAnchorsImpl.hpp
+++ /dev/null
@@ -1,179 +0,0 @@
-#ifndef _BLASR_SCORE_ANCHOR_IMPL_HPP_
-#define _BLASR_SCORE_ANCHOR_IMPL_HPP_
-
-template<typename TSequence, typename T_Tuple>
-int GetTupleCount(TSequence &seq, DNALength startPos,
- TupleMetrics &tm, TupleCountTable<TSequence, T_Tuple> &ct,
- int &count) {
-
- T_Tuple tuple;
- if (tuple.FromStringLR(&seq.seq[startPos], tm)) {
- count = ct.countTable[tuple.ToLongIndex()];
- return 1;
- }
- else {
- return 0;
- }
-}
-
-
-template<typename TSequence, typename T_Tuple>
-int PMatch(TSequence &seq, DNALength startPos, DNALength length,
- TupleMetrics &tm, TupleCountTable<TSequence, T_Tuple> &ct,
- float &pMatch){
- int tupleCount;
- T_Tuple tuple, curTuple;
- //
- // Compute the probability of a match of length 'length'
- // in the genome using a k-th order Markov model of the genome.
- // Other than that there is no spatial constraint on a match.
- // This means that if the length of seq is k, and that sequence
- // of length k exists in the genome, then the probability of a
- // match is 1.
- pMatch = 1;
- if (GetTupleCount(seq, startPos, tm, ct, tupleCount)) {
- if (tupleCount == 0) return 0;
- int i;
- //
- // Compute the frequency of the following tuple, and compare this
- // to the frequencies of all 4 possible tuples that are next.
- //
- curTuple.FromStringLR(&seq.seq[startPos], tm);
- if (length < tm.tupleSize) {
- // the match is shorter than the tuples used to model the
- // genome sequence composition. Don't try and compute a p-value
- // for it -- assume that you will always find a match of this
- // length.
- //
- pMatch = 0;
- return 1;
- }
- for (i = 1; i < length - tm.tupleSize; i++) {
- //
- // now add on the log counts for the transitions.
- //
- if (tuple.FromStringLR(&seq.seq[i+startPos], tm) == 0) {
- return 0;
- }
- int nextTupleCount = 0;
- int rightMarCount = SumRightShiftMarginalTupleCounts(tm, ct,
- tuple, TwoBit[seq.GetNuc(startPos+i+tm.tupleSize-1)],
- nextTupleCount);
- //
- // tuple counts are not defined for N's.
- //
- if (TwoBit[seq.GetNuc(startPos + i+tm.tupleSize)] > 3) {
- return 0;
- }
-
- if (nextTupleCount == 0) {
- //
- // There is no background distribution available for this
- // sequence context, therefore no way to evaluate p-value.
- //
- return 0;
- }
- pMatch += log((nextTupleCount / (1.0*rightMarCount)));
- curTuple.tuple = tuple.tuple;
- }
- //
- // Done computing the probability of an extension. Now compute the probability
- // of the match. There are nMatches of the initial seed. We assume that each has
- // an equal probability of matching.
- //
- return 1;
- }
- else {
- return 0;
- }
-}
-
-
-template<typename TSequence, typename T_Tuple>
-int POneOrMoreMatches(TSequence &seq, DNALength startPos,
- DNALength length, TupleMetrics &tm,
- TupleCountTable<TSequence, T_Tuple> &ct,
- float &pValue){
- int nMatches;
- float pMatch = 1;
- //
- // Compute the probability that the sequence matches ANY spot
- // in the reference for at least 'length' bases.
- //
- PMatch(seq, startPos, length, tm, ct, pMatch);
- pValue = pMatch;
- return 1;
-}
-
-
-template<typename TSequence, typename T_Tuple>
-int SumRightShiftMarginalTupleCounts(TupleMetrics &tm,
- TupleCountTable<TSequence, T_Tuple> &ct, T_Tuple curTuple,
- int nextNuc, int &nextSeqCount) {
- int totalCount = 0;
- int rightMarCount = 0;
- long i;
- T_Tuple altMask;
- altMask.tuple = 3L;
- altMask.tuple = ~altMask.tuple;
- for (i = 0; i < 4; i++ ) {
- T_Tuple alt = curTuple;
- // next.ShiftLeft(tm, 2);
- alt.tuple = alt.tuple & altMask.tuple;
- alt.tuple += i;
- // next.Append(i,2L);
- long countedTuple = alt.ToLongIndex();
- rightMarCount = ct.countTable[countedTuple];
- totalCount += rightMarCount;
- if (i == nextNuc) {
- nextSeqCount = rightMarCount;
- }
- }
- return totalCount;
-}
-
-
-template<typename TSequence, typename T_Tuple>
-int ComputeTotalTupleCount(TupleMetrics &tm,
- TupleCountTable<TSequence, T_Tuple> &ct, TSequence &seq,
- int start, int end) {
- if (end == -1) {
- end = seq.length;
- }
- int nTuples = end - tm.tupleSize + 1;
- if (nTuples == 0 ){
- return 0;
- }
- int totalCount = 0;
- T_Tuple tuple;
- int i;
- for (i = 0; i < nTuples; i++) {
- tuple.FromStringLR(&seq.seq[i], tm);
- totalCount += ct.countTable[tuple.ToLongIndex()];
- }
- return totalCount;
-}
-
-
-template<typename TSequence, typename T_Tuple>
-int ComputeAverageTupleCount(TupleMetrics &tm,
- TupleCountTable<TSequence, T_Tuple> &ct, TSequence &seq) {
- int i;
- int nTuples = seq.length - tm.tupleSize + 1;
- if (nTuples == 0 ){
- return 0;
- }
- int totalCount = ComputeTotalTupleCount(tm, ct, seq);
- return totalCount / nTuples;
-}
-
-
-inline
-int ComputeExpectedFirstWaitingTime(float lambda) {
- // The first waiting time of a Poisson process is
- // exponentially distributed. The mean of an exponentially
- // distributed variable with parameter lambda is 1/lambda.
- return (1/lambda);
-}
-
-#endif
diff --git a/libcpp/alignment/algorithms/compare/CompareStrings.hpp b/libcpp/alignment/algorithms/compare/CompareStrings.hpp
deleted file mode 100644
index 18170c7..0000000
--- a/libcpp/alignment/algorithms/compare/CompareStrings.hpp
+++ /dev/null
@@ -1,81 +0,0 @@
-#ifndef _BLASR_COMPARE_STRINGS_HPP_
-#define _BLASR_COMPARE_STRINGS_HPP_
-
-template<typename T>
-class DefaultCompareStrings {
-public:
-
- static int Compare(T lhs, T rhs) {
- return ThreeBit[lhs] - ThreeBit[rhs];
- }
-
- static int Compare(T *lhs, T *rhs, int length) {
- int i;
- int res;
- i = 0;
- T *lhsptr;
- T *rhsptr;
- lhsptr = lhs;
- rhsptr = rhs;
- char *lhsend = lhs + length;
- res = 0;
- while (lhsptr != lhsend and res == 0) {
- res = ThreeBit[*lhsptr] - ThreeBit[*rhsptr];
- ++lhsptr;
- ++rhsptr;
- }
- return res;
- }
-
- static int Equal(T a, T b) {
- //
- // Compare single characters.
- //
- return a == b;
- }
- static int LessThan(T *a, int aLen, T *b, int bLen) {
- int minabLen = MIN(aLen, bLen);
- if (minabLen <= 0)
- return 0;
-
- int cmpRes = memcmp((void*) a, (void*) b, minabLen);
- if (cmpRes < 0) {
- return 1;
- }
- else {
- return 0;
- }
- }
-
- static int LessThanEqual(T *a, int aLen, T *b, int bLen) {
- int minabLen = MIN(aLen, bLen);
- if (minabLen <= 0)
- return 1;
- int cmpRes = memcmp((void*) a, (void*)b, minabLen);
- if (cmpRes <= 0) {
- return 1;
- }
- else {
- return 0;
- }
- }
-
- static int Equal(T* a, int aLen, T *b, int bLen) {
- int minabLen = MIN(aLen, bLen);
- if (minabLen < 0)
- return 0;
- if (minabLen == 0)
- return 1;
-
- int cmpRes = memcmp((void*) a, (void*)b, minabLen);
- if (cmpRes == 0 and aLen <= bLen) {
- return 1;
- }
- else {
- return 0;
- }
- }
-};
-
-
-#endif // _BLASR_COMPARE_STRINGS_HPP_
diff --git a/libcpp/alignment/algorithms/sorting/DifferenceCovers.cpp b/libcpp/alignment/algorithms/sorting/DifferenceCovers.cpp
deleted file mode 100644
index 09a4be7..0000000
--- a/libcpp/alignment/algorithms/sorting/DifferenceCovers.cpp
+++ /dev/null
@@ -1,15 +0,0 @@
-#include <cstring>
-#include "DifferenceCovers.hpp"
-
-int InitializeDifferenceCover(int diffCoverSize, UInt &diffCoverLength, UInt *&diffCover) {
- UInt index;
- for (index = 0; index < N_COVERS; index++) {
- if (diffCovers[index][0] == diffCoverSize) {
- diffCoverLength = diffCovers[index][1];
- diffCover = new UInt[diffCoverLength];
- memcpy(diffCover, &diffCovers[index][2], sizeof(UInt)*diffCoverLength);
- return 1;
- }
- }
- return 0;
-}
diff --git a/libcpp/alignment/algorithms/sorting/DifferenceCovers.hpp b/libcpp/alignment/algorithms/sorting/DifferenceCovers.hpp
deleted file mode 100644
index 3ed502a..0000000
--- a/libcpp/alignment/algorithms/sorting/DifferenceCovers.hpp
+++ /dev/null
@@ -1,16 +0,0 @@
-#ifndef _BLASR_DIFFERENCE_COVERS_HPP_
-#define _BLASR_DIFFERENCE_COVERS_HPP_
-
-#include "Types.h"
-
-#define N_COVERS 5
-const UInt diffCovers[N_COVERS][60] = {
- {7, 3, 1, 2, 4, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
- {32, 7, 1, 2, 3, 4, 8,12,20, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
- {64, 9, 1, 2, 3, 6,15,17,35,43,60, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
- {111,12, 1, 2, 3, 6,13,28,37,39,45,53,66,94, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
- {2281, 58, 0, 1,2,3,4,5,6,7,8,9,19,38,57,76,95,114,133,152,171,190,229,268,307,346,385,424,463,502,541,580,619,658,697,736,775,814,853,892,931,951,971,991,1011,1031,1051,1071,1091,1111,1131,1132,1133,1134,1135,1136,1137,1138,1139, 1140}};
-
-int InitializeDifferenceCover(int diffCoverSize, UInt &diffCoverLength, UInt *&diffCover);
-
-#endif // _BLASR_DIFFERENCE_COVERS_HPP_
diff --git a/libcpp/alignment/algorithms/sorting/Karkkainen.hpp b/libcpp/alignment/algorithms/sorting/Karkkainen.hpp
deleted file mode 100644
index a02f70a..0000000
--- a/libcpp/alignment/algorithms/sorting/Karkkainen.hpp
+++ /dev/null
@@ -1,134 +0,0 @@
-#ifndef ALGORITHMS_SORTING_KARKKAINEN_HPP_
-#define ALGORITHMS_SORTING_KARKKAINEN_HPP_
-
-#include "DNASequence.hpp"
-
-inline bool
-leq(DNALength a1, DNALength a2, DNALength b1, DNALength b2) // lexicographic order
-{
- return(a1 < b1 || a1 == b1 && a2 <= b2);
-} // for pairs
-
-inline bool
-leq(DNALength a1, DNALength a2, DNALength a3, DNALength b1, DNALength b2, DNALength b3)
-{
- return(a1 < b1 || a1 == b1 && leq(a2, a3, b2, b3));
-} // and triples
-
-// stably sort a[0..n-1] to b[0..n-1] with keys in 0..K from r
-template<typename T_R>
-void radixPass(DNALength* a, DNALength* b, T_R* r, DNALength n, DNALength K)
-{ // count occurrences
- DNALength* c = new DNALength[K + 1]; // counter array
- for (DNALength i = 0; i <= K; i++)
- c[i] = 0; // reset counters
-
- for (DNALength i = 0; i < n; i++)
- c[r[a[i]]]++; // count occurrences
-
- for (DNALength i = 0, sum = 0; i <= K; i++) { // exclusive prefix sums
- DNALength t = c[i]; c[i] = sum; sum += t;
- }
-
- for (DNALength i = 0; i < n; i++)
- b[c[r[a[i]]]++] = a[i]; // sort
-
- delete [] c;
-}
-
-// find the suffix array SA of T[0..n-1] in {1..K}^n
-// require T[n]=T[n+1]=T[n+2]=0, n>=2
-template<typename T_T>
-void KarkkainenBuildSuffixArray(T_T* T, DNALength* SA, DNALength n, int K)
-{
- DNALength n0=(n+2)/3, n1=(n+1)/3, n2=n/3, n02=n0+n2;
- DNALength* R = new DNALength[n02 + 3];
- R[n02] = R[n02+1] = R[n02+2]=0;
-
- DNALength* SA12 = new DNALength[n02 + 3];
- SA12[n02]=SA12[n02+1]=SA12[n02+2]=0;
-
- DNALength* R0 = new DNALength[n0];
- DNALength* SA0 = new DNALength[n0];
-
- //******* Step 0: Construct sample ********
- // generate positions of mod 1 and mod 2 suffixes
- // the "+(n0-n1)" adds a dummy mod 1 suffix if n%3 == 1
- for(DNALength i=0; i < n02+3; i++) {
- R[i] = 0;
- }
-
- for (DNALength i=0, j=0; i < n+(n0-n1); i++)
- if (i%3 != 0)
- R[j++] = i;
-
- //******* Step 1: Sort sample suffixes ********
- // lsb radix sort the mod 1 and mod 2 triples
- radixPass(R , SA12, T+2, n02, K);
- radixPass(SA12, R, T+1, n02, K);
- radixPass(R , SA12, T , n02, K);
-
- // find lexicographic names of triples and
- // write them to correct places in R
- int name = 0, c0 = -1, c1 = -1, c2 = -1;
- for (DNALength i = 0; i < n02; i++) {
- if (T[SA12[i]] != c0 || T[SA12[i]+1] != c1 || T[SA12[i]+2] != c2) {
- name++; c0 = T[SA12[i]]; c1 = T[SA12[i]+1]; c2 = T[SA12[i]+2];
- }
- if (SA12[i] % 3 == 1) {
- R[SA12[i]/3] = name;
- } // write to R1
- else {
- R[SA12[i]/3 + n0] = name;
- } // write to R2
- }
-
- // recurse if names are not yet unique
- if (name < n02) {
- KarkkainenBuildSuffixArray<DNALength>(R, SA12, n02, name);
-
- // store unique names in R using the suffix array
- for (DNALength i = 0; i < n02; i++)
- R[SA12[i]] = i + 1;
- } else {// generate the suffix array of R directly
- for (DNALength i = 0; i < n02; i++)
- SA12[R[i] - 1] = i;
- }
-
- //******* Step 2: Sort nonsample suffixes ********
- // stably sort the mod 0 suffixes from SA12 by their first character
- for (DNALength i=0, j=0; i < n02; i++)
- if (SA12[i] < n0)
- R0[j++] = 3*SA12[i];
-
- radixPass(R0, SA0, T, n0, K);
-
- //******* Step 3: Merge ********
- // merge sorted SA0 suffixes and sorted SA12 suffixes
- for (DNALength p=0, t=n0-n1, k=0; k < n; k++) {
-
-#define GetI() (SA12[t] < n0 ? SA12[t] * 3 + 1 : (SA12[t] - n0) * 3 + 2)
-
- DNALength i = GetI(); // pos of current offset 12 suffix
- DNALength j = SA0[p]; // pos of current offset 0 suffix
- if (SA12[t] < n0 ? // different compares for mod 1 and mod 2 suffixes
- leq(T[i], R[SA12[t] + n0], T[j], R[j/3]) :
- leq(T[i],T[i+1],R[SA12[t]-n0+1], T[j],T[j+1],R[j/3+n0]))
- { // suffix from SA12 is smaller
- SA[k] = i; t++;
- if (t == n02) // done --- only SA0 suffixes left
- for (k++; p < n0; p++, k++)
- SA[k] = SA0[p];
- } else { // suffix from SA0 is smaller
- SA[k] = j; p++;
- if (p == n0) // done --- only SA12 suffixes left
- for (k++; t < n02; t++, k++)
- SA[k] = GetI();
- }
- }
- delete [] R;
- delete [] SA12;
- delete [] SA0;
- delete [] R0;
-}
-#endif
diff --git a/libcpp/alignment/algorithms/sorting/LightweightSuffixArray.cpp b/libcpp/alignment/algorithms/sorting/LightweightSuffixArray.cpp
deleted file mode 100644
index eb0e607..0000000
--- a/libcpp/alignment/algorithms/sorting/LightweightSuffixArray.cpp
+++ /dev/null
@@ -1,405 +0,0 @@
-#include "LightweightSuffixArray.hpp"
-
-UInt DiffMod(UInt a, UInt b, UInt d) {
- if (b > a) {
- return (d - ((b - a) % d))%d;
- }
- else {
- return (a - b) % d;
- }
-}
-
-void BuildDiffCoverReverseLookup(UInt diffCover[], UInt diffCoverLength,
- UInt reverseDiffCover[] // of size diffCoverSize
- ){
- UInt i;
- for (i = 0; i < diffCoverLength; i++ ){
- reverseDiffCover[diffCover[i]] = i;
- }
-}
-
-UInt DiffCoverFindH(UInt diffCover[], UInt diffCoverLength, UInt diffCoverSize, UInt textSize) {
- UInt h;
- for (h = 0; h < diffCoverSize; h++) {
- UInt rem = textSize % diffCoverSize ;
- if (rem == 0) return 0;
- if ((h < diffCoverSize -1 and (diffCover[h] <= rem and rem < diffCover[h+1])) or
- (h == diffCoverSize-1 and (diffCover[h] <= rem and rem < diffCoverSize))) {
- return h;
- }
- }
- return h;
-}
-
-
-UInt DiffCoverMu::compute(UInt i, UInt j) {
- return textSize/diffCoverSize * i + std::min(i,h+1) + j;
-}
-UInt DiffCoverMu::operator()(const UInt k) {
- //
- // k is from 0 .. n (size of string)
- //
- UInt di = k % diffCoverSize;
- UInt j = k / diffCoverSize;
- UInt i = diffCoverReverseLookup[di];
- // return (textSize/diffCoverSize)*i + min(i,h) + j;
- // return (textSize/diffCoverSize)*i + i + j;
- UInt itemsInBucket;
- // return min(i,h)*(1 + textSize / diffCoverSize) + (i > h ? i - h : 0)*(textSize/diffCoverSize) + j;
- return (textSize/diffCoverSize) * i + std::min(i,h+1) + j;
-}
-
-DiffCoverMu::DiffCoverMu() {
- diffCoverLength = diffCoverSize = textSize = h = 0;
- diffCoverReverseLookup = diffCover = NULL;
-}
-
-DiffCoverMu::~DiffCoverMu() {
- if (diffCoverReverseLookup !=NULL)
- delete[] diffCoverReverseLookup;
-}
-
-void DiffCoverMu::Initialize(UInt diffCoverP[], UInt diffCoverLengthP, UInt diffCoverSizeP, UInt textSizeP) {
- diffCoverReverseLookup = new UInt[diffCoverSizeP];
- diffCoverLength = diffCoverLengthP;
- textSize = textSizeP;
- diffCoverSize = diffCoverSizeP;
- diffCover = diffCoverP;
- UInt i;
- for (i = 0; i < diffCoverSize; i++ ) {
- diffCoverReverseLookup[i] = 9999999;
- }
- BuildDiffCoverReverseLookup(diffCoverP, diffCoverLength, diffCoverReverseLookup);
- h = DiffCoverFindH(diffCoverP, diffCoverLength, diffCoverSize, textSize);
-}
-
-void BuildDiffCoverLookup(UInt diffCover[], UInt diffCoverLength, UInt v, UInt diffCoverLookup[]) {
- UInt h;
- // Initialize with sentinal that shows a value has not been set (for small problems);
- for (h = 0; h < v; h++) {
- diffCoverLookup[h] = 99999999;
- }
- for (h = 0; h < v; h++) {
- //
- // For now, fill table via exhaustive search.
- //
- UInt hd;
- for (hd = 0; hd < diffCoverLength; hd++) {
- UInt dcm = (diffCover[hd] + h ) % v;
- UInt hdi;
- for (hdi = 0; hdi < diffCoverLength; hdi++ ){
- if (dcm == diffCover[hdi])
- break;
- }
- if (hdi < diffCoverLength) {
- diffCoverLookup[h] = diffCover[hd];
- break;
- }
- }
- }
-}
-
-void DiffCoverDelta::Initialize(UInt diffCoverP[], UInt diffCoverLengthP, UInt diffCoverSizeP) {
- diffCoverLookup = new UInt[diffCoverSizeP];
- diffCoverSize = diffCoverSizeP;
- BuildDiffCoverLookup(diffCoverP, diffCoverLengthP, diffCoverSizeP, diffCoverLookup);
-}
-
-UInt DiffCoverDelta::operator()(UInt i, UInt j) {
- return DiffMod(diffCoverLookup[DiffMod(j,i,diffCoverSize)],i,diffCoverSize);
-}
-
-DiffCoverDelta::~DiffCoverDelta() {
- if (diffCoverLookup) {
- delete [] diffCoverLookup;
- diffCoverLookup = NULL;
- }
-}
-
-
-UInt NCompareSuffices(unsigned char text[], UInt a, UInt b, UInt n) {
- // not sure how to make lower amortized cost of the comparison.
- return(strncmp((const char*) &text[a], (const char*)&text[b], n));
-}
-
-UInt ComputeDSetSize(UInt diffCover, UInt diffCoverLength, UInt diffCoverSize, UInt textSize) {
- UInt div = textSize / diffCoverSize + 1;
- UInt rem = textSize % diffCoverSize;
- return div*diffCoverSize + rem;
-}
-
-void ComputeSufVNaming(UInt diffCover[], UInt diffCoverLength, UInt diffCoverN, UInt textSize, UInt lexNaming[],
- DiffCoverMu &mu,
- UInt sufVNaming[]) {
- UInt nDiffCover = textSize / diffCoverN + 1;
- UInt cover;
- UInt d;
- UInt diffCoverIndex;
- UInt ln = 0;
- for (cover = 0; cover < nDiffCover; cover++) {
- for (d = 0; d < diffCoverLength; d++) {
- diffCoverIndex = cover * diffCoverN + diffCover[d];
- sufVNaming[mu(diffCoverIndex)] = lexNaming[ln];
- ln++;
- }
- }
-}
-
-UInt IndexToDiffCoverIndex(UInt index, UInt diffCoverlookup[], UInt diffCoverSize, UInt diffCoverLength ){
- UInt diff = index / diffCoverSize;
- UInt offset = index % diffCoverSize;
- return diff*diffCoverLength + diffCoverlookup[offset];
-}
-
-void DiffCoverComputeLOrder(UInt sufVNaming[], UInt sufVNamingLength, UInt maxVNaming, UInt textLength,
- DiffCoverMu &mu,
- UInt lOrder[]) {
- //
- // the sufvnaming now contains the
- UInt i, di;
- UInt nDiffCover = textLength / mu.diffCoverSize + 1;
- UInt dci;
- for (i = 0; i < sufVNamingLength; i++ ) {
- lOrder[i] = 0;
- }
-
- for (dci = 0; dci < nDiffCover; dci++ ) {
- for (di = 0; di < mu.diffCoverLength; di++ ){
- i = dci*mu.diffCoverSize + mu.diffCover[di];
- if (i >= textLength) {
- break;
- }
- UInt dsetIndex = IndexToDiffCoverIndex(i, mu.diffCoverReverseLookup, mu.diffCoverSize, mu.diffCoverLength);
- UInt mui = mu(i);
- lOrder[mui] = sufVNaming[dsetIndex] + 1;
- }
- }
- lOrder[sufVNamingLength] = 0;
- //
- // The result of the sufsort function is to store the inverse suffix
- // array in the first parameter.
- //
-
- LarssonSuffixSort<UInt> sufsorter;
- sufsorter.INDEX_MAX = maxVNaming + 2;
- sufsorter(lOrder, sufVNaming, sufVNamingLength, maxVNaming+2, 0);
- for (i = 0; i < sufVNamingLength; i++) {
- assert(lOrder[i] > 0);
- lOrder[i]--;
- }
-}
-
-
-
-/*
- * Build the lex naming of the v-ordered suffices.
- *
- * Input: textVOrder - the v-ordering of a subset of the text.
- * textSize - the size of the v-order set.
- * diffCover - the diff cover used, and it's length
- * diffCoverLength
- * diffCoverSize - the size of the diff cover.
- * Output: lexNaming: the lex-naming of the v-order suffices. The
- * names are implemented as unsigned integers.
- * Returns: the largest value of the lex-ordering.
- */
-UInt DiffCoverBuildLexNaming( unsigned char text[], UInt textSize,
- UInt textVOrder[],
- UInt dSetSize, UInt diffCover[], UInt diffCoverLength, UInt diffCoverSize,
- UInt diffCoverLookup[],
- UInt lexNaming[]) {
- UInt nCovers = textSize / diffCoverSize + 1;
- UInt cover = 0;
- UInt d;
- UInt vOrder = 0;
- UInt prevCoverIndex, coverIndex;
- UInt lexOrder = 0;
- UInt lexIndex = 0;
- //
- // Make sure there is something to do here.
- //
- if (dSetSize == 0)
- return 0;
- UInt dcindex;
- dcindex = IndexToDiffCoverIndex(textVOrder[0], diffCoverLookup, diffCoverSize, diffCoverLength);
- lexNaming[dcindex] = 0;
- for (d = 1; d < dSetSize; d++) {
- if (NCompareSuffices(text, textVOrder[d-1], textVOrder[d], diffCoverSize) != 0) {
- lexOrder++;
- }
- dcindex = IndexToDiffCoverIndex(textVOrder[d], diffCoverLookup, diffCoverSize, diffCoverLength);
- lexNaming[dcindex] = lexOrder;
- }
- return lexOrder;
-}
-
-int DiffCoverCompareSuffices::operator()(UInt a, UInt b) {
- UInt aDCIndex, bDCIndex;
- UInt dab = (*delta)(a,b);
- aDCIndex = IndexToDiffCoverIndex(a + dab, diffCoverReverseLookup, diffCoverSize, diffCoverLength);
- bDCIndex = IndexToDiffCoverIndex(b + dab, diffCoverReverseLookup, diffCoverSize, diffCoverLength);
- return (lOrder[aDCIndex] < lOrder[bDCIndex]);
-}
-
-bool LightweightSuffixSort(unsigned char text[], UInt textLength, UInt *index, int diffCoverSize) {
- //
- // index is an array of length textLength that contains all
- // suffices.
- //
-
- //
- // Phase 0. Compute delta function for difference cover.
- //
-
- // For now, use a very small hard wired diff cover for testing
- UInt *diffCover;
- UInt diffCoverLength;
- if (InitializeDifferenceCover(diffCoverSize, diffCoverLength, diffCover) == 0) {
- std::cout << "ERROR! There is no difference cover of size " << diffCoverSize << " that is precomputed." << std::endl;
- exit(1);
- }
-
- DiffCoverDelta delta;
-
- delta.Initialize(diffCover, diffCoverLength, diffCoverSize);
-
- //
- // Phase 1. Sort suffices whose starting position modulo v is in D.
- //
-
- // The set d is given by
- // Step 1.1 v-sort D-sample suffices
- UInt dIndex = 0; // index in D-sample
- UInt tIndex = 0; // index in text
- UInt nDiffCover;
- nDiffCover = textLength / diffCoverSize + 1;
- UInt coverIndex;
- UInt d;
- bool done = false;
-
- for (coverIndex = 0; coverIndex < nDiffCover and done == false; coverIndex++) {
- for (d = 0; d < diffCoverLength and done == false; d++) {
- tIndex = coverIndex * diffCoverSize + diffCover[d];
- if (tIndex >= textLength) {
- done = true;
- break;
- }
- index[dIndex] = tIndex;
- dIndex++;
- }
- }
- UInt dSetSize = dIndex;
- std::cerr << "Sorting " << diffCoverSize << "-prefixes of the genome." << std::endl;
- MediankeyBoundedQuicksort(text, index, dIndex, 0, dSetSize, 0, diffCoverSize);
- UInt i;
-
- //
- // Step 1.2 Compute l^v(i) for all i \in D_n by traversing the
- // D-sample suffixes in lexicographic order and construct s^\prime
- // by setting s^\prime[\mu(i)] = l^v(i)
- //
- UInt *lexVNaming;
- lexVNaming = new UInt[dSetSize+1];
- if (lexVNaming == NULL) {
- std::cout << "Could not initialize welterweight order structure." << std::endl;
- exit(1);
- }
- DiffCoverMu mu;
- mu.Initialize(diffCover, diffCoverLength, diffCoverSize, textLength);
- UInt largestLexName;
- std::cerr << "Enumerating " << diffCoverSize << "-prefixes." << std::endl;
- largestLexName = DiffCoverBuildLexNaming(text, textLength,
- index, dSetSize, diffCover, diffCoverLength, diffCoverSize,
- mu.diffCoverReverseLookup, lexVNaming);
- //
- // Step 1.3 Compute ISA' of lex-order.
- //
-
- UInt *lexOrder;
- //
- // lexVNaming is allocated space. The suffix sorting needs an
- // auxiliary array. Since the index is not being used right now,
- // use that as the extra space.
- //
- UInt t;
- UInt dci,di;
- for (dci = 0; dci < nDiffCover; dci++) {
- for (di = 0 ; di < diffCoverLength; di++) {
- i = dci*diffCoverSize + diffCover[di];
- if (i > textLength) {
- break;
- }
- mu.compute(di, dci);
- }
- }
-
- UInt *tmpLexOrder = index;
- DiffCoverComputeLOrder(lexVNaming, dSetSize, largestLexName, textLength, mu, tmpLexOrder);
- lexOrder = lexVNaming;
-
- nDiffCover = textLength / diffCoverSize + 1;
-
- for (dci = 0; dci < nDiffCover; dci++) {
- for (di = 0 ; di < diffCoverLength; di++) {
- i = dci*diffCoverSize + diffCover[di];
- if (i >= textLength) {
- break;
- }
- UInt lexOrderIndex = mu(i);
- UInt diffCoverIndex = IndexToDiffCoverIndex(i, mu.diffCoverReverseLookup, diffCoverSize, diffCoverLength);
- lexOrder[diffCoverIndex] = tmpLexOrder[lexOrderIndex];
- }
- }
-
- //
- // Phase 2. Construct SA by exploiting the fact that for any i,j\in
- // [0,n-v], the relative order of the suffixes starting at
- // i+\delta(,j) and j+\delta(i,j) is already known.
- //
- std::cerr << "Sorting suffices." << std::endl;
- // Step 2.1 v-order suffices using multikey quicksort
- for (i = 0; i < textLength; i++ ){
- index[i] = i;
- }
- MediankeyBoundedQuicksort(text, index, textLength, 0, textLength, 0, diffCoverSize);
-
- // Step 2.2. For each group of suffixes that remains unsorted
- // (shares a prefix of length diffCoverSize, complete the sorting
- // with a comparison based on the sorting algorithm using
- // l(i+\delta(i,j)) nad l(j+\delta(i,j)) as keys when comparing
- // suffixes S_i and S_j.
- //
- DiffCoverCompareSuffices lOrderComparator;
- lOrderComparator.lOrder = lexOrder;
- lOrderComparator.delta = δ
- lOrderComparator.diffCoverSize = diffCoverSize;
- lOrderComparator.diffCoverLength=diffCoverLength;
- lOrderComparator.diffCoverReverseLookup = mu.diffCoverReverseLookup;
- UInt setBegin, setEnd;
- setBegin = setEnd = 0;
- std::cerr << "Sorting buckets." << std::endl;
- int percentDone = 0;
- int curPercentage = 0;
- while(setBegin < textLength) {
- setEnd = setBegin;
- percentDone = (int)(((1.0*setBegin) / textLength) * 100);
- if ( percentDone > curPercentage) {
- std::cerr << " " << percentDone << "% of buckets sorted." << std::endl;
- curPercentage = percentDone;
- }
- while(setEnd < textLength and
- NCompareSuffices(text, index[setBegin], index[setEnd], diffCoverSize) == 0) {
- setEnd++;
- }
- std::sort(&index[setBegin], &index[setEnd], lOrderComparator);
- setBegin = setEnd;
- }
-
- // diffCover was allocated in DifferenceCovers.cpp ->
- // InitializeDifferenceCover(...). Deallocate it.
- if (diffCover) {delete [] diffCover; diffCover = NULL;}
- if (lexVNaming) {delete [] lexVNaming; lexVNaming = NULL;}
- return true;
- // DONE!!!!!
-
-}
diff --git a/libcpp/alignment/algorithms/sorting/LightweightSuffixArray.hpp b/libcpp/alignment/algorithms/sorting/LightweightSuffixArray.hpp
deleted file mode 100644
index e312671..0000000
--- a/libcpp/alignment/algorithms/sorting/LightweightSuffixArray.hpp
+++ /dev/null
@@ -1,103 +0,0 @@
-#ifndef ALGORITHMS_SORTING_LIGHTWEIGHT_SUFFIX_ARRAY_H_
-#define ALGORITHMS_SORTING_LIGHTWEIGHT_SUFFIX_ARRAY_H_
-
-#include <algorithm>
-#include "qsufsort.hpp"
-#include "MultikeyQuicksort.hpp"
-#include "DifferenceCovers.hpp"
-#include "Types.h"
-
-/*
- * a - b potentially may not fit into a signed type. Use some logic
- * to get around that.
- */
-
-UInt DiffMod(UInt a, UInt b, UInt d);
-
-void BuildDiffCoverReverseLookup(UInt diffCover[], UInt diffCoverLength,
- UInt reverseDiffCover[] // of size diffCoverSize
- );
-
-UInt DiffCoverFindH(UInt diffCover[], UInt diffCoverLength, UInt diffCoverSize, UInt textSize);
-
-class DiffCoverMu {
-public:
- UInt *diffCoverReverseLookup;
- UInt diffCoverLength;
- UInt diffCoverSize;
- UInt textSize;
- UInt h;
- UInt *diffCover;
-
- UInt compute(UInt i, UInt j);
-
- UInt operator()(const UInt k);
-
- DiffCoverMu();
-
- ~DiffCoverMu();
-
- void Initialize(UInt diffCoverP[], UInt diffCoverLengthP, UInt diffCoverSizeP, UInt textSizeP);
-
-};
-
-void BuildDiffCoverLookup(UInt diffCover[], UInt diffCoverLength, UInt v, UInt diffCoverLookup[]);
-
-class DiffCoverDelta {
-public:
- UInt *diffCoverLookup;
- UInt diffCoverSize;
-
- void Initialize(UInt diffCoverP[], UInt diffCoverLengthP, UInt diffCoverSizeP);
-
- UInt operator()(UInt i, UInt j);
-
- ~DiffCoverDelta();
-};
-
-
-
-UInt NCompareSuffices(unsigned char text[], UInt a, UInt b, UInt n);
-
-UInt ComputeDSetSize(UInt diffCover, UInt diffCoverLength, UInt diffCoverSize, UInt textSize);
-
-void ComputeSufVNaming(UInt diffCover[], UInt diffCoverLength, UInt diffCoverN, UInt textSize, UInt lexNaming[],
- DiffCoverMu &mu,
- UInt sufVNaming[]);
-
-UInt IndexToDiffCoverIndex(UInt index, UInt diffCoverlookup[], UInt diffCoverSize, UInt diffCoverLength );
-
-void DiffCoverComputeLOrder(UInt sufVNaming[], UInt sufVNamingLength, UInt maxVNaming, UInt textLength, DiffCoverMu &mu, UInt lOrder[]);
-
-
-/*
- * Build the lex naming of the v-ordered suffices.
- *
- * Input: textVOrder - the v-ordering of a subset of the text.
- * textSize - the size of the v-order set.
- * diffCover - the diff cover used, and it's length
- * diffCoverLength
- * diffCoverSize - the size of the diff cover.
- * Output: lexNaming: the lex-naming of the v-order suffices. The
- * names are implemented as unsigned integers.
- * Returns: the largest value of the lex-ordering.
- */
-UInt DiffCoverBuildLexNaming( unsigned char text[], UInt textSize,
- UInt textVOrder[],
- UInt dSetSize, UInt diffCover[], UInt diffCoverLength, UInt diffCoverSize,
- UInt diffCoverLookup[],
- UInt lexNaming[]);
-
-class DiffCoverCompareSuffices {
-public:
- UInt *lOrder;
- DiffCoverDelta *delta;
- UInt diffCoverSize;
- UInt diffCoverLength;
- UInt *diffCoverReverseLookup;
- int operator()(UInt a, UInt b);
-};
-
-bool LightweightSuffixSort(unsigned char text[], UInt textLength, UInt *index, int diffCoverSize);
-
-#endif
diff --git a/libcpp/alignment/algorithms/sorting/MultikeyQuicksort.cpp b/libcpp/alignment/algorithms/sorting/MultikeyQuicksort.cpp
deleted file mode 100644
index 40936ee..0000000
--- a/libcpp/alignment/algorithms/sorting/MultikeyQuicksort.cpp
+++ /dev/null
@@ -1,197 +0,0 @@
-#include <cassert>
-#include "MultikeyQuicksort.hpp"
-
-void UIntSwap(unsigned int &a, unsigned int &b) {
- //
- // There probably is an SSE for this.
- //
- unsigned int tmp = a;
- a = b; b = tmp;
-}
-
-void VecSwap( UInt i, UInt j, UInt n, UInt index[]) {
- UInt ni;
- for (ni = 0; ni < n; ni++) {
- UIntSwap(index[i], index[j]);
- i++; j++;
- }
-}
-
-unsigned char ComputeMedianValue(unsigned char text[], UInt index[], int length,
- UInt low, UInt high, int offset, UInt maxPossible, UInt *freq ) {
- /*
- * Compute the median value of positions at suffix+offset across all
- * suffices from [low,high).
- */
-
- int f;
- for (f = 0; f< maxPossible+1; f++) {
- freq[f] = 0;
- }
-
- UInt pos;
- UInt maxValue = 0;
- int val;
- // return text[index[(high+low)/2]+offset];
- // Compute frequencies of nucleotides (+N), packed into 3-bit representation.
- for (pos = low; pos < high; pos++) {
- // if (index[pos] + offset < length) {
- // val = ThreeBit[text[index[pos] + offset]];
- val = text[index[pos]+offset];
- if (val > maxValue) {
- maxValue = val;
- }
- freq[val]++;
- // }
- }
- UInt medianBound = (high - low)/2;
- int i;
- int runningTotal = 0;
-
- for(i =1; i<= maxValue; i++ ){
- runningTotal = freq[i] + runningTotal;
- if (runningTotal >= medianBound) {
- return i;
- }
- }
- return maxValue;
-}
-
-UInt FindFirstOf(unsigned char text[], UInt index[], UInt length,
- UInt low, UInt high, int offset, Nucleotide nuc) {
- UInt p;
- for (p = low; p < high and text[index[p]+offset] != nuc; p++);
- return p;
-}
-
-inline
-void SwapIndices(UInt &a, UInt &b) {
- UInt temp = a;
- a = b;
- b = temp;
-}
-
-/*
- UInt min(UInt a, UInt b) {
- return (a < b) ? a : b;
- }
- */
-void TransformSequenceForSorting(unsigned char text[], UInt textLength, int bound) {
- UInt i;
- for (i = 0; i < textLength; i++) {
- text[i] = ThreeBit[text[i]] + 1;
- }
- for (i = textLength; i < textLength+bound;i++) {
- text[i] = 0;
- }
-}
-
-void TransformBackSequence(Nucleotide text[], UInt textLength) {
- UInt i;
- for (i = 0; i < textLength; i++) {
- text[i]--;
- text[i] = ThreeBitToAscii[text[i]];
- }
-}
-
-
-/*
- * depth: the current depth of how much is sorted.
- * bound: how far to sort.
- */
-void MediankeyBoundedQuicksort(unsigned char text[], UInt index[], UInt length,
- UInt low, UInt high, int depth, int bound, UInt maxChar, UInt *freq) {
-
- if (high - low <= 1)
- return;
- if (depth > bound)
- return;
-
- bool deleteFreq = false;
- if (freq == NULL) {
- UInt ci;
- maxChar = 0;
- for (ci = low; ci < high; ci++) {
- UInt c = text[index[ci]+depth];
- if ( c > maxChar) {
- maxChar = c;
- }
- }
- freq = new UInt[maxChar+1];
- deleteFreq = true;
- }
-
- Nucleotide medianChar = ComputeMedianValue(text, index, length, low, high, depth, maxChar, freq );
- UInt medianCharPos = FindFirstOf(text, index, length, low, high, depth, medianChar);
- UInt medLeft, lastLeft;
- UInt medRight, lastRight;
-
- //
- // Pack the median characters into the sides of the array.
- //
- SwapIndices(index[low], index[medianCharPos]);
-
- medLeft = lastLeft = low+1;
- medRight = lastRight = high-1;
-
- for(;;) {
- Nucleotide nuc;
- while(lastLeft <= lastRight and (nuc = text[index[lastLeft]+depth]) <= medianChar) {
- if (nuc == medianChar) {
- SwapIndices(index[medLeft], index[lastLeft]);
- medLeft++;
- }
- lastLeft++;
- }
-
- while(lastLeft <= lastRight and (nuc = text[index[lastRight]+depth]) >= medianChar) {
- if (nuc == medianChar) {
- SwapIndices(index[medRight], index[lastRight]);
- medRight--;
- }
- lastRight--;
- }
- if (lastLeft > lastRight) {
- // done with median sort.
- break;
- }
- //
- // Otherwise, this ends with an index at the left out of order
- // from the right
- assert(text[index[lastLeft]+depth] > text[index[lastRight]+depth]);
- SwapIndices(index[lastLeft], index[lastRight]);
- }
-
- //
- // Now join the indices of the median charactes in the middle of the
- // array.
- //
- // move left outside to middle
- UInt swapLeftLength = std::min(medLeft - low, lastLeft - medLeft);
- VecSwap(low, lastLeft - swapLeftLength, swapLeftLength, index);
- // move right outside to middle
- UInt swapRightLength = std::min(high - medRight - 1, medRight - lastRight);
- VecSwap(lastRight+1, high-swapRightLength, swapRightLength, index);
-
- UInt medianStartIndex = low + lastLeft - medLeft;
- UInt medianEndIndex = lastRight + (high - medRight);
-
- // Sort the suffices with keys lower than the median.
- // Since these may contain multiple keys that are less than the
- // median, the same depth is used.
- MediankeyBoundedQuicksort(text, index, length,
- low,
- medianStartIndex,
- depth, bound, maxChar,freq);
- if (medianEndIndex - medianStartIndex > 1) {
- MediankeyBoundedQuicksort(text, index, length,
- medianStartIndex, medianEndIndex, depth+1, bound, maxChar, freq);
- }
-
- MediankeyBoundedQuicksort(text, index, length,
- medianEndIndex,
- high,
- depth, bound, maxChar, freq);
-
- if (deleteFreq) {delete [] freq; freq = NULL;}
-}
diff --git a/libcpp/alignment/algorithms/sorting/MultikeyQuicksort.hpp b/libcpp/alignment/algorithms/sorting/MultikeyQuicksort.hpp
deleted file mode 100644
index c09a10b..0000000
--- a/libcpp/alignment/algorithms/sorting/MultikeyQuicksort.hpp
+++ /dev/null
@@ -1,48 +0,0 @@
-#ifndef _BLASR_MULTIKEY_QUICKSORT_HPP_
-#define _BLASR_MULTIKEY_QUICKSORT_HPP_
-
-/*
- * This is an implementation of MultiKey Quicksort, or ssort1 from
- * Bentley and Sedgewick, Fast Algorithms for Sorting and Searching
- * Strings, Proc. 8th Annual ACM-SIAM Symposium on Discrete Algorithms
- * (SODA), pages 360-369, January 1997.
- *
- * The implementation here sorts lists of indices into an array of
- * substrings rather than the substrings themselves (for use in suffix
- * array generation). Furthermore, it is made to be sse-alizeable to
- * speed up sorts on modern architectures.
- */
-
-#include <limits.h>
-#include <vector>
-#include <algorithm>
-#include "NucConversion.hpp"
-#include "FASTASequence.hpp"
-#include "Types.h"
-
-typedef unsigned int UInt;
-
-void UIntSwap(unsigned int &a, unsigned int &b);
-
-void VecSwap( UInt i, UInt j, UInt n, UInt index[]);
-
-unsigned char ComputeMedianValue(unsigned char text[], UInt index[], int length,
- UInt low, UInt high, int offset, UInt maxPossible, UInt *freq );
-
-UInt FindFirstOf(unsigned char text[], UInt index[], UInt length,
- UInt low, UInt high, int offset, Nucleotide nuc);
-
-void SwapIndices(UInt &a, UInt &b);
-
-void TransformSequenceForSorting(unsigned char text[], UInt textLength, int bound);
-
-void TransformBackSequence(Nucleotide text[], UInt textLength);
-
-/*
- * depth: the current depth of how much is sorted.
- * bound: how far to sort.
- */
-void MediankeyBoundedQuicksort(unsigned char text[], UInt index[], UInt length,
- UInt low, UInt high, int depth, int bound, UInt maxChar= 0, UInt *freq=NULL);
-
-#endif // _BLASR_MULTIKEY_QUICKSORT_HPP_
diff --git a/libcpp/alignment/algorithms/sorting/qsufsort.cpp b/libcpp/alignment/algorithms/sorting/qsufsort.cpp
deleted file mode 100644
index aa23e85..0000000
--- a/libcpp/alignment/algorithms/sorting/qsufsort.cpp
+++ /dev/null
@@ -1,302 +0,0 @@
-/* qsufsort.c
- Copyright 1999, N. Jesper Larsson, all rights reserved.
-
- This file contains an implementation of the algorithm presented in "Faster
- Suffix Sorting" by N. Jesper Larsson (jesper at cs.lth.se) and Kunihiko
- Sadakane (sada at is.s.u-tokyo.ac.jp).
-
- This software may be used freely for any purpose. However, when distributed,
- the original source must be clearly stated, and, when the source code is
- distributed, the copyright notice must be retained and any alterations in
- the code must be clearly marked. No warranty is given regarding the quality
- of this software.*/
-
-#include <limits.h>
-
-static int *I, /* group array, ultimately suffix array.*/
- *V, /* inverse array, ultimately inverse of I.*/
- r, /* number of symbols aggregated by transform.*/
- h; /* length of already-sorted prefixes.*/
-
-#define KEY(p) (V[*(p)+(h)])
-#define SWAP(p, q) (tmp=*(p), *(p)=*(q), *(q)=tmp)
-#define MED3(a, b, c) (KEY(a)<KEY(b) ? \
- (KEY(b)<KEY(c) ? (b) : KEY(a)<KEY(c) ? (c) : (a)) \
- : (KEY(b)>KEY(c) ? (b) : KEY(a)>KEY(c) ? (c) : (a)))
-
-/* Subroutine for select_sort_split and sort_split. Sets group numbers for a
- group whose lowest position in I is pl and highest position is pm.*/
-
-static void update_group(int *pl, int *pm)
-{
- int g;
-
- g=pm-I; /* group number.*/
- V[*pl]=g; /* update group number of first position.*/
- if (pl==pm)
- *pl=-1; /* one element, sorted group.*/
- else
- do /* more than one element, unsorted group.*/
- V[*++pl]=g; /* update group numbers.*/
- while (pl<pm);
-}
-
-/* Quadratic sorting method to use for small subarrays. To be able to update
- group numbers consistently, a variant of selection sorting is used.*/
-
-static void select_sort_split(int *p, int n) {
- int *pa, *pb, *pi, *pn;
- int f, v, tmp;
-
- pa=p; /* pa is start of group being picked out.*/
- pn=p+n-1; /* pn is last position of subarray.*/
- while (pa<pn) {
- for (pi=pb=pa+1, f=KEY(pa); pi<=pn; ++pi)
- if ((v=KEY(pi))<f) {
- f=v; /* f is smallest key found.*/
- SWAP(pi, pa); /* place smallest element at beginning.*/
- pb=pa+1; /* pb is position for elements equal to f.*/
- } else if (v==f) { /* if equal to smallest key.*/
- SWAP(pi, pb); /* place next to other smallest elements.*/
- ++pb;
- }
- update_group(pa, pb-1); /* update group values for new group.*/
- pa=pb; /* continue sorting rest of the subarray.*/
- }
- if (pa==pn) { /* check if last part is single element.*/
- V[*pa]=pa-I;
- *pa=-1; /* sorted group.*/
- }
-}
-
-/* Subroutine for sort_split, algorithm by Bentley & McIlroy.*/
-
-static int choose_pivot(int *p, int n) {
- int *pl, *pm, *pn;
- int s;
-
- pm=p+(n>>1); /* small arrays, middle element.*/
- if (n>7) {
- pl=p;
- pn=p+n-1;
- if (n>40) { /* big arrays, pseudomedian of 9.*/
- s=n>>3;
- pl=MED3(pl, pl+s, pl+s+s);
- pm=MED3(pm-s, pm, pm+s);
- pn=MED3(pn-s-s, pn-s, pn);
- }
- pm=MED3(pl, pm, pn); /* midsize arrays, median of 3.*/
- }
- return KEY(pm);
-}
-
-/* Sorting routine called for each unsorted group. Sorts the array of integers
- (suffix numbers) of length n starting at p. The algorithm is a ternary-split
- quicksort taken from Bentley & McIlroy, "Engineering a Sort Function",
- Software -- Practice and Experience 23(11), 1249-1265 (November 1993). This
- function is based on Program 7.*/
-
-static void sort_split(int *p, int n)
-{
- int *pa, *pb, *pc, *pd, *pl, *pm, *pn;
- int f, v, s, t, tmp;
-
- if (n<7) { /* multi-selection sort smallest arrays.*/
- select_sort_split(p, n);
- return;
- }
-
- v=choose_pivot(p, n);
- pa=pb=p;
- pc=pd=p+n-1;
- while (1) { /* split-end partition.*/
- while (pb<=pc && (f=KEY(pb))<=v) {
- if (f==v) {
- SWAP(pa, pb);
- ++pa;
- }
- ++pb;
- }
- while (pc>=pb && (f=KEY(pc))>=v) {
- if (f==v) {
- SWAP(pc, pd);
- --pd;
- }
- --pc;
- }
- if (pb>pc)
- break;
- SWAP(pb, pc);
- ++pb;
- --pc;
- }
- pn=p+n;
- if ((s=pa-p)>(t=pb-pa))
- s=t;
- for (pl=p, pm=pb-s; s; --s, ++pl, ++pm)
- SWAP(pl, pm);
- if ((s=pd-pc)>(t=pn-pd-1))
- s=t;
- for (pl=pb, pm=pn-s; s; --s, ++pl, ++pm)
- SWAP(pl, pm);
-
- s=pb-pa;
- t=pd-pc;
- if (s>0)
- sort_split(p, s);
- update_group(p+s, p+n-t-1);
- if (t>0)
- sort_split(p+n-t, t);
-}
-
-/* Bucketsort for first iteration.
-
-Input: x[0...n-1] holds integers in the range 1...k-1, all of which appear
-at least once. x[n] is 0. (This is the corresponding output of transform.) k
-must be at most n+1. p is array of size n+1 whose contents are disregarded.
-
-Output: x is V and p is I after the initial sorting stage of the refined
-suffix sorting algorithm.*/
-
-static void bucketsort(int *x, int *p, int n, int k)
-{
- int *pi, i, c, d, g;
-
- for (pi=p; pi<p+k; ++pi)
- *pi=-1; /* mark linked lists empty.*/
- for (i=0; i<=n; ++i) {
- x[i]=p[c=x[i]]; /* insert in linked list.*/
- p[c]=i;
- }
- for (pi=p+k-1, i=n; pi>=p; --pi) {
- d=x[c=*pi]; /* c is position, d is next in list.*/
- x[c]=g=i; /* last position equals group number.*/
- if (d>=0) { /* if more than one element in group.*/
- p[i--]=c; /* p is permutation for the sorted x.*/
- do {
- d=x[c=d]; /* next in linked list.*/
- x[c]=g; /* group number in x.*/
- p[i--]=c; /* permutation in p.*/
- } while (d>=0);
- } else
- p[i--]=-1; /* one element, sorted group.*/
- }
-}
-
-/* Transforms the alphabet of x by attempting to aggregate several symbols into
- one, while preserving the suffix order of x. The alphabet may also be
- compacted, so that x on output comprises all integers of the new alphabet
- with no skipped numbers.
-
-Input: x is an array of size n+1 whose first n elements are positive
-integers in the range l...k-1. p is array of size n+1, used for temporary
-storage. q controls aggregation and compaction by defining the maximum value
-for any symbol during transformation: q must be at least k-l; if q<=n,
-compaction is guaranteed; if k-l>n, compaction is never done; if q is
-INT_MAX, the maximum number of symbols are aggregated into one.
-
-Output: Returns an integer j in the range 1...q representing the size of the
-new alphabet. If j<=n+1, the alphabet is compacted. The global variable r is
-set to the number of old symbols grouped into one. Only x[n] is 0.*/
-
-static int transform(int *x, int *p, int n, int k, int l, int q)
-{
- int b, c, d, e, i, j, m, s;
- int *pi, *pj;
-
- for (s=0, i=k-l; i; i>>=1)
- ++s; /* s is number of bits in old symbol.*/
- e=INT_MAX>>s; /* e is for overflow checking.*/
- for (b=d=r=0; r<n && d<=e && (c=d<<s|(k-l))<=q; ++r) {
- b=b<<s|(x[r]-l+1); /* b is start of x in chunk alphabet.*/
- d=c; /* d is max symbol in chunk alphabet.*/
- }
- m=(1<<(r-1)*s)-1; /* m masks off top old symbol from chunk.*/
- x[n]=l-1; /* emulate zero terminator.*/
- if (d<=n) { /* if bucketing possible, compact alphabet.*/
- for (pi=p; pi<=p+d; ++pi)
- *pi=0; /* zero transformation table.*/
- for (pi=x+r, c=b; pi<=x+n; ++pi) {
- p[c]=1; /* mark used chunk symbol.*/
- c=(c&m)<<s|(*pi-l+1); /* shift in next old symbol in chunk.*/
- }
- for (i=1; i<r; ++i) { /* handle last r-1 positions.*/
- p[c]=1; /* mark used chunk symbol.*/
- c=(c&m)<<s; /* shift in next old symbol in chunk.*/
- }
- for (pi=p, j=1; pi<=p+d; ++pi)
- if (*pi)
- *pi=j++; /* j is new alphabet size.*/
- for (pi=x, pj=x+r, c=b; pj<=x+n; ++pi, ++pj) {
- *pi=p[c]; /* transform to new alphabet.*/
- c=(c&m)<<s|(*pj-l+1); /* shift in next old symbol in chunk.*/
- }
- while (pi<x+n) { /* handle last r-1 positions.*/
- *pi++=p[c]; /* transform to new alphabet.*/
- c=(c&m)<<s; /* shift right-end zero in chunk.*/
- }
- } else { /* bucketing not possible, don't compact.*/
- for (pi=x, pj=x+r, c=b; pj<=x+n; ++pi, ++pj) {
- *pi=c; /* transform to new alphabet.*/
- c=(c&m)<<s|(*pj-l+1); /* shift in next old symbol in chunk.*/
- }
- while (pi<x+n) { /* handle last r-1 positions.*/
- *pi++=c; /* transform to new alphabet.*/
- c=(c&m)<<s; /* shift right-end zero in chunk.*/
- }
- j=d+1; /* new alphabet size.*/
- }
- x[n]=0; /* end-of-string symbol is zero.*/
- return j; /* return new alphabet size.*/
-}
-
-/* Makes suffix array p of x. x becomes inverse of p. p and x are both of size
- n+1. Contents of x[0...n-1] are integers in the range l...k-1. Original
- contents of x[n] is disregarded, the n-th symbol being regarded as
- end-of-string smaller than all other symbols.*/
-
-void suffixsort(int *x, int *p, int n, int k, int l)
-{
- int *pi, *pk;
- int i, j, s, sl;
-
- V=x; /* set global values.*/
- I=p;
-
- if (n>=k-l) { /* if bucketing possible,*/
- j=transform(V, I, n, k, l, n);
- bucketsort(V, I, n, j); /* bucketsort on first r positions.*/
- } else {
- transform(V, I, n, k, l, INT_MAX);
- for (i=0; i<=n; ++i)
- I[i]=i; /* initialize I with suffix numbers.*/
- h=0;
- sort_split(I, n+1); /* quicksort on first r positions.*/
- }
- h=r; /* number of symbols aggregated by transform.*/
-
- while (*I>=-n) {
- pi=I; /* pi is first position of group.*/
- sl=0; /* sl is negated length of sorted groups.*/
- do {
- if ((s=*pi)<0) {
- pi-=s; /* skip over sorted group.*/
- sl+=s; /* add negated length to sl.*/
- } else {
- if (sl) {
- *(pi+sl)=sl; /* combine sorted groups before pi.*/
- sl=0;
- }
- pk=I+V[s]+1; /* pk-1 is last position of unsorted group.*/
- sort_split(pi, pk-pi);
- pi=pk; /* next group.*/
- }
- } while (pi<=I+n);
- if (sl) /* if the array ends with a sorted group.*/
- *(pi+sl)=sl; /* combine sorted groups at end of I.*/
- h=2*h; /* double sorted-depth.*/
- }
-
- for (i=0; i<=n; ++i) /* reconstruct suffix array from inverse.*/
- I[V[i]]=i;
-}
diff --git a/libcpp/alignment/algorithms/sorting/qsufsort.hpp b/libcpp/alignment/algorithms/sorting/qsufsort.hpp
deleted file mode 100644
index 5525fe4..0000000
--- a/libcpp/alignment/algorithms/sorting/qsufsort.hpp
+++ /dev/null
@@ -1,376 +0,0 @@
-#ifndef _BLASR_QSUFSORT_HPP_
-#define _BLASR_QSUFSORT_HPP_
-#include <assert.h>
-
-void suffixsort(int *x, int *p, int n, int k, int l);
-
-
-/* qsufsort.c
- Copyright 1999, N. Jesper Larsson, all rights reserved.
-
- This file contains an implementation of the algorithm presented in "Faster
- Suffix Sorting" by N. Jesper Larsson (jesper at cs.lth.se) and Kunihiko
- Sadakane (sada at is.s.u-tokyo.ac.jp).
-
- This software may be used freely for any purpose. However, when distributed,
- the original source must be clearly stated, and, when the source code is
- distributed, the copyright notice must be retained and any alterations in
- the code must be clearly marked. No warranty is given regarding the quality
- of this software.*/
-
-#include <limits.h>
-
-#define KEY(p) (V[*(p)+(h)])
-
-
-#define MED3(a, b, c) (KEY(a)<KEY(b) ? \
- (KEY(b)<KEY(c) ? (b) : KEY(a)<KEY(c) ? (c) : (a)) \
- : (KEY(b)>KEY(c) ? (b) : KEY(a)>KEY(c) ? (c) : (a)))
-
-/* Subroutine for select_sort_split and sort_split. Sets group numbers for a
- group whose lowest position in I is pl and highest position is pm.*/
-
-#include <vector>
-#include <algorithm>
-
-template<typename T_Index, long T_Index_MAX=0>
-class LarssonSuffixSort {
-private:
- T_Index *I;
- T_Index *V;
- T_Index r;
- T_Index h;
- T_Index SWAPPtr(T_Index *p, T_Index *q) { T_Index tmp=*(p); *(p)=*(q); *(q)=tmp; return *(q);}
- std::vector<char> boundaries;
-
-public:
- T_Index INDEX_MAX;
- LarssonSuffixSort() {
- INDEX_MAX = T_Index_MAX;
- r = h = 0;
- I = V = NULL;
- }
- void operator()(T_Index *x, T_Index *p, T_Index n, T_Index k, T_Index l) {
- suffixsort(x,p,n,k,l);
- }
-
- void update_group(T_Index *pl, T_Index *pm)
- {
- int g;
-
- g=pm-I; /* group number.*/
- V[*pl]=g; /* update group number of first position.*/
- if (pl==pm) {
- /*MC*/
- assert(pl -I >= 0);
- boundaries[pl - I] = 1;
- // *pl=-1; /* one element, sorted group.*/
- }
- else
- do /* more than one element, unsorted group.*/
- V[*++pl]=g; /* update group numbers.*/
- while (pl<pm);
- }
-
- /* Quadratic sorting method to use for small subarrays. To be able to update
- group numbers consistently, a variant of selection sorting is used.*/
-
- void select_sort_split(T_Index *p, T_Index n) {
- T_Index *pa, *pb, *pi, *pn;
- T_Index f, v;
-
- pa=p; /* pa is start of group being picked out.*/
- pn=p+n-1; /* pn is last position of subarray.*/
- while (pa<pn) {
- for (pi=pb=pa+1, f=KEY(pa); pi<=pn; ++pi)
- if ((v=KEY(pi))<f) {
- f=v; /* f is smallest key found.*/
- SWAPPtr(pi, pa); /* place smallest element at beginning.*/
- pb=pa+1; /* pb is position for elements equal to f.*/
- } else if (v==f) { /* if equal to smallest key.*/
- SWAPPtr(pi, pb); /* place next to other smallest elements.*/
- ++pb;
- }
- update_group(pa, pb-1); /* update group values for new group.*/
- pa=pb; /* continue sorting rest of the subarray.*/
- }
- if (pa==pn) { /* check if last part is single element.*/
- assert(pa - I >= 0);
- // assert(boundaries[pa-I] == 0 );
- V[*pa]=pa-I;
- /*MC*/
- // *pa=-1; /* sorted group.*/
- boundaries[pa - I] = 1;
- }
- }
-
- /* Subroutine for sort_split, algorithm by Bentley & McIlroy.*/
-
- T_Index choose_pivot(T_Index *p, T_Index n) {
- T_Index *pl, *pm, *pn;
- T_Index s;
-
- pm=p+(n>>1); /* small arrays, middle element.*/
- if (n>7) {
- pl=p;
- pn=p+n-1;
- if (n>40) { /* big arrays, pseudomedian of 9.*/
- s=n>>3;
- pl=MED3(pl, pl+s, pl+s+s);
- pm=MED3(pm-s, pm, pm+s);
- pn=MED3(pn-s-s, pn-s, pn);
- }
- pm=MED3(pl, pm, pn); /* midsize arrays, median of 3.*/
- }
- return KEY(pm);
- }
-
- /* Sorting routine called for each unsorted group. Sorts the array of integers
- (suffix numbers) of length n starting at p. The algorithm is a ternary-split
- quicksort taken from Bentley & McIlroy, "Engineering a Sort Function",
- Software -- Practice and Experience 23(11), 1249-1265 (November 1993). This
- function is based on Program 7.*/
-
- void sort_split(T_Index *p, T_Index n)
- {
- T_Index *pa, *pb, *pc, *pd, *pl, *pm, *pn;
- T_Index f, v, s, t;
-
- if (n<7) { /* multi-selection sort smallest arrays.*/
- select_sort_split(p, n);
- return;
- }
-
- v=choose_pivot(p, n);
- pa=pb=p;
- pc=pd=p+n-1;
- while (1) { /* split-end partition.*/
- while (pb<=pc && (f=KEY(pb))<=v) {
- if (f==v) {
- SWAPPtr(pa, pb);
- ++pa;
- }
- ++pb;
- }
- while (pc>=pb && (f=KEY(pc))>=v) {
- if (f==v) {
- SWAPPtr(pc, pd);
- --pd;
- }
- --pc;
- }
- if (pb>pc)
- break;
- SWAPPtr(pb, pc);
- ++pb;
- --pc;
- }
- pn=p+n;
- if ((s=pa-p)>(t=pb-pa))
- s=t;
- for (pl=p, pm=pb-s; s; --s, ++pl, ++pm)
- SWAPPtr(pl, pm);
- if ((s=pd-pc)>(t=pn-pd-1))
- s=t;
- for (pl=pb, pm=pn-s; s; --s, ++pl, ++pm)
- SWAPPtr(pl, pm);
-
- s=pb-pa;
- t=pd-pc;
- if (s>0)
- sort_split(p, s);
- update_group(p+s, p+n-t-1);
- if (t>0)
- sort_split(p+n-t, t);
- }
-
- /* Bucketsort for first iteration.
-
-Input: x[0...n-1] holds integers in the range 1...k-1, all of which appear
-at least once. x[n] is 0. (This is the corresponding output of transform.) k
-must be at most n+1. p is array of size n+1 whose contents are disregarded.
-
-Output: x is V and p is I after the initial sorting stage of the refined
-suffix sorting algorithm.
-*/
-
- void bucketsort(T_Index *x, T_Index *p, T_Index n, T_Index k)
- {
- T_Index *pi, i, c, d, g;
-
- for (pi=p; pi<p+k; ++pi) {
- // *pi=-1; /* mark linked lists empty.*/
- assert(pi - p >= 0);
- assert(pi - p == pi - I);
- // boundaries[pi-p] = 0;
- }
- int *buckets = new int[k];
- T_Index *starts = new T_Index[k];
- /*MC+1*/
- for (i = 0; i < k; i++ ){
- buckets[i] = -1;
- }
- /*MC-1*/
- for (i=0; i<=n; ++i) {
- /*MC+2*/
- if (buckets[x[i]] == -1) {
- starts[x[i]] = i;
- }
- x[i]=buckets[c=x[i]]; /* insert in linked list.*/
- buckets[c]=i;
- //*x[i]=pi[c=x[i]]
- p[c] = i;
- /*MC-2*/
- }
- for (pi=p+k-1, i=n; pi>=p; --pi) {
- d=x[c=*pi]; /* c is position, d is next in list.*/
- x[c]=g=i; /* last position equals group number.*/
- // if (d>=0) { /* if more than one element in group.*/
- if (c != starts[pi - p]) {
- p[i--]=c; /* p is permutation for the sorted x.*/
- do {
- d=x[c=d]; /* next in linked list.*/
- x[c]=g; /* group number in x.*/
- p[i--]=c; /* permutation in p.*/
- }
- while (c != starts[pi - p]);
- //while (d>=0);
- } else {
- /*MC*/
- boundaries[i--]=true;
- // p[i--]=-1; /* one element, sorted group.*/
- }
- }
- delete[] starts;
- delete[] buckets;
- }
-
- /* Transforms the alphabet of x by attempting to aggregate several symbols into
- one, while preserving the suffix order of x. The alphabet may also be
- compacted, so that x on output comprises all integers of the new alphabet
- with no skipped numbers.
-
-Input: x is an array of size n+1 whose first n elements are positive
-integers in the range l...k-1. p is array of size n+1, used for temporary
-storage. q controls aggregation and compaction by defining the maximum value
-for any symbol during transformation: q must be at least k-l; if q<=n,
-compaction is guaranteed; if k-l>n, compaction is never done; if q is
-INT_MAX, the maximum number of symbols are aggregated into one.
-
-Output: Returns an integer j in the range 1...q representing the size of the
-new alphabet. If j<=n+1, the alphabet is compacted. The global variable r is
-set to the number of old symbols grouped into one. Only x[n] is 0.*/
-
- T_Index transform(T_Index *x, T_Index *p, T_Index n, T_Index k, T_Index l, T_Index q)
- {
- T_Index b, c, d, e, i, j, m, s;
- T_Index *pi, *pj;
-
- for (s=0, i=k-l; i; i>>=1)
- ++s; /* s is number of bits in old symbol.*/
- e=INDEX_MAX>>s; /* e is for overflow checking.*/
- for (b=d=r=0; r<n && d<=e && (c=d<<s|(k-l))<=q; ++r) {
- b=b<<s|(x[r]-l+1); /* b is start of x in chunk alphabet.*/
- d=c; /* d is max symbol in chunk alphabet.*/
- }
- m=(1<<(r-1)*s)-1; /* m masks off top old symbol from chunk.*/
- x[n]=l-1; /* emulate zero terminator.*/
- if (d<=n) { /* if bucketing possible, compact alphabet.*/
- for (pi=p; pi<=p+d; ++pi)
- *pi=0; /* zero transformation table.*/
- for (pi=x+r, c=b; pi<=x+n; ++pi) {
- p[c]=1; /* mark used chunk symbol.*/
- c=(c&m)<<s|(*pi-l+1); /* shift in next old symbol in chunk.*/
- }
- for (i=1; i<r; ++i) { /* handle last r-1 positions.*/
- p[c]=1; /* mark used chunk symbol.*/
- c=(c&m)<<s; /* shift in next old symbol in chunk.*/
- }
- for (pi=p, j=1; pi<=p+d; ++pi)
- if (*pi)
- *pi=j++; /* j is new alphabet size.*/
- for (pi=x, pj=x+r, c=b; pj<=x+n; ++pi, ++pj) {
- *pi=p[c]; /* transform to new alphabet.*/
- c=(c&m)<<s|(*pj-l+1); /* shift in next old symbol in chunk.*/
- }
- while (pi<x+n) { /* handle last r-1 positions.*/
- *pi++=p[c]; /* transform to new alphabet.*/
- c=(c&m)<<s; /* shift right-end zero in chunk.*/
- }
- } else { /* bucketing not possible, don't compact.*/
- for (pi=x, pj=x+r, c=b; pj<=x+n; ++pi, ++pj) {
- *pi=c; /* transform to new alphabet.*/
- c=(c&m)<<s|(*pj-l+1); /* shift in next old symbol in chunk.*/
- }
- while (pi<x+n) { /* handle last r-1 positions.*/
- *pi++=c; /* transform to new alphabet.*/
- c=(c&m)<<s; /* shift right-end zero in chunk.*/
- }
- j=d+1; /* new alphabet size.*/
- }
- x[n]=0; /* end-of-string symbol is zero.*/
- return j; /* return new alphabet size.*/
- }
-
- /* Makes suffix array p of x. x becomes inverse of p. p and x are both of size
- n+1. Contents of x[0...n-1] are integers in the range l...k-1. Original
- contents of x[n] is disregarded, the n-th symbol being regarded as
- end-of-string smaller than all other symbols.*/
-
- void suffixsort(T_Index *x, T_Index *p, T_Index n, T_Index k, T_Index l)
- {
- T_Index *pi, *pk;
- T_Index i, j, s, sl;
- boundaries.resize(n+1);
- fill(boundaries.begin(), boundaries.end(), 0);
-
- V=x; /* set global values.*/
- I=p;
-
- if (n>=k-l) { /* if bucketing possible,*/
- j=transform(V, I, n, k, l, n);
- bucketsort(V, I, n, j); /* bucketsort on first r positions.*/
- } else {
- transform(V, I, n, k, l, INDEX_MAX);
- for (i=0; i<=n; ++i)
- I[i]=i; /* initialize I with suffix numbers.*/
- h=0;
- sort_split(I, n+1); /* quicksort on first r positions.*/
- }
- h=r; /* number of symbols aggregated by transform.*/
-
- while (*I<=n) {
- pi=I; /* pi is first position of group.*/
- sl=0; /* sl is negated length of sorted groups.*/
- do {
- /*MC-3*/
- // if ((s=*pi)<0) {
- s = *pi;
- if (boundaries[pi - I] == 1) {
- // pi-=s; /* skip over sorted group.*/
- s = 1;
- pi+=s;
- sl+=s; /* add negated length to sl.*/
- } else {
- if (sl) {
- // *(pi+sl)=sl; /* combine sorted groups before pi.*/
- assert(boundaries[(pi-sl) - I] == 1);
- assert(pi - sl >= I);
- *(pi-sl)=sl; /* combine sorted groups before pi.*/
- sl=0;
- }
- pk=I+V[s]+1; /* pk-1 is last position of unsorted group.*/
- sort_split(pi, pk-pi);
- pi=pk; /* next group.*/
- }
- } while (pi<=I+n);
- if (sl) /* if the array ends with a sorted group.*/
- *(pi-sl)=sl; /* combine sorted groups at end of I.*/
- h=2*h; /* double sorted-depth.*/
- }
-
- for (i=0; i<=n; ++i) /* reconstruct suffix array from inverse.*/
- I[V[i]]=i;
- }
- };
-#endif // _BLASR_QSUFSORT_HPP_
diff --git a/libcpp/alignment/anchoring/AnchorParameters.hpp b/libcpp/alignment/anchoring/AnchorParameters.hpp
deleted file mode 100644
index ec7ac62..0000000
--- a/libcpp/alignment/anchoring/AnchorParameters.hpp
+++ /dev/null
@@ -1,35 +0,0 @@
-#ifndef _BLASR_ANCHOR_PARAMETERS_HPP_
-#define _BLASR_ANCHOR_PARAMETERS_HPP_
-
-#include <fstream>
-#include <iostream>
-#include "qvs/QualityValue.hpp"
-#include "DNASequence.hpp"
-
-class AnchorParameters {
-public:
- QualityValue branchQualityThreshold;
- DNALength minMatchLength;
- int maxMatchScore;
- int expand;
- int contextAlignLength;
- bool useLookupTable;
- int numBranches;
- int maxAnchorsPerPosition;
- int advanceExactMatches;
- DNALength maxLCPLength;
- bool stopMappingOnceUnique;
- int verbosity;
- bool removeEncompassedMatches;
- std::ostream *lcpBoundsOutPtr;
- int branchExpand;
-
- AnchorParameters();
-
- AnchorParameters &Assign(const AnchorParameters &rhs);
-
- AnchorParameters &operator=(const AnchorParameters &rhs);
-};
-
-
-#endif // _BLASR_ANCHOR_PARAMETERS_HPP_
diff --git a/libcpp/alignment/build.mk b/libcpp/alignment/build.mk
deleted file mode 120000
index 2247f36..0000000
--- a/libcpp/alignment/build.mk
+++ /dev/null
@@ -1 +0,0 @@
-makefile
\ No newline at end of file
diff --git a/libcpp/alignment/bwt/BWT.hpp b/libcpp/alignment/bwt/BWT.hpp
deleted file mode 100644
index ef91a3a..0000000
--- a/libcpp/alignment/bwt/BWT.hpp
+++ /dev/null
@@ -1,316 +0,0 @@
-#ifndef _BLASR_BWT_HPP_
-#define _BLASR_BWT_HPP_
-
-#include <iostream>
-#include <fstream>
-#include "Occ.hpp"
-#include "Pos.hpp"
-#include "suffixarray/SuffixArray.hpp"
-#include "PackedDNASequence.hpp"
-#include "FASTASequence.hpp"
-
-/*
- * Define an Occurrence table appropriate for Gb sized genomes.
- * Probably everything will end up using this.
- */
-typedef Occ <PackedDNASequence, unsigned int, unsigned short> GbOcc;
-
-/*
- * Define an Occurrence table appropriate for Mb sized genomes.
- */
-typedef Occ <PackedDNASequence, unsigned int, unsigned char> MbOcc;
-
-
-class SingleStoragePolicy {
- public:
- DNALength *spp, *epp;
- void Store(DNALength sp, DNALength ep) {
- *spp = sp;
- *epp = ep;
- }
-};
-
-class VectorStoragePolicy {
-public:
- std::vector<DNALength> *spvp, *epvp;
- void Store(DNALength sp, DNALength ep) {
- spvp->push_back(sp);
- epvp->push_back(ep);
- }
-};
-
-template<typename T_BWT_Sequence, typename T_DNASequence>
-class Bwt {
- public:
- T_BWT_Sequence bwtSequence;
- GbOcc occ;
- Pos<T_BWT_Sequence> pos;
- static const int CharCountSize = 7;
- int useDebugData;
- std::vector<DNALength> saCopy;
- DNALength charCount[CharCountSize];
- DNALength firstCharPos;
-
-
- void Write(std::string outName) {
- std::ofstream bwtOut;
- CrucialOpen(outName, bwtOut, std::ios::binary|std::ios::out);
- Write(bwtOut);
- }
-
- void PrintBWTString(std::ostream &out) {
- DNALength p;
- for (p = 0; p < bwtSequence.length; p++) {
- out << (char) ThreeBitToAscii[bwtSequence[p]];
- if (p % 50 == 49) out << std::endl;
- }
- if(p % 50 != 0) out << std::endl;
- }
-
- void Write(std::ostream &bwtOut) {
- bwtSequence.Write(bwtOut);
- bwtOut.write((char*)charCount, sizeof(DNALength)*CharCountSize);
- bwtOut.write((char*)&firstCharPos, sizeof(DNALength));
- bwtOut.write((char*)&useDebugData, sizeof(useDebugData));
- if (useDebugData) {
- bwtOut.write((char*)&saCopy[0], (bwtSequence.length-1) * sizeof(DNALength));
- }
- occ.Write(bwtOut);
- pos.Write(bwtOut);
- }
-
- int Read(std::string inName) {
- std::ifstream bwtIn;
- DNALength seqStorageSize;
- CrucialOpen(inName, bwtIn, std::ios::binary|std::ios::in);
- bwtSequence.Read(bwtIn);
- bwtIn.read((char*)charCount, sizeof(DNALength)*CharCountSize);
- bwtIn.read((char*)&firstCharPos, sizeof(DNALength));
- bwtIn.read((char*)&useDebugData, sizeof(useDebugData));
- if (useDebugData) {
- saCopy.resize(bwtSequence.length-1);
- bwtIn.read((char*)&saCopy[0], (bwtSequence.length-1) * sizeof(DNALength));
- }
- occ.Read(bwtIn, useDebugData);
- pos.Read(bwtIn);
- occ.InitializeBWT(bwtSequence);
- return 1;
- }
-
- void Print(std::ofstream &out) {
- bwtSequence.Print(out);
- }
-
- DNALength LFBacktrack(DNALength bwtPos) {
- Nucleotide curNuc = bwtSequence.Get(bwtPos);
- assert(curNuc < 5);
- DNALength bwtPrevPos = charCount[curNuc] + occ.Count(curNuc, bwtPos) - 1;
- return bwtPrevPos;
- }
-
- DNALength Locate(DNALength bwtPos) {
- DNALength seqPos;
- DNALength offset = 0;
- while (1) {
- if (pos.Lookup(bwtPos, seqPos)) {
- break;
- }
- else {
- DNALength bwtPrevPos;
- bwtPrevPos = LFBacktrack(bwtPos);
- if (useDebugData) {
- assert(saCopy[bwtPos-1] - 1 == saCopy[bwtPrevPos-1]);
- }
- bwtPos = bwtPrevPos;
- assert(bwtPos <= bwtSequence.length);
- /*
- * Boundary condition at the beginning of the bwt string.
- */
- if (bwtPos == firstCharPos) {
- seqPos = 1;
- break;
- }
- }
- ++offset;
- }
- return seqPos + offset;
- }
-
- DNALength Locate(DNALength sp, DNALength ep, std::vector<DNALength> &positions,
- int maxCount = 0) {
- DNALength bwtPos;
- DNALength seqPos;
- if (sp <= ep and (maxCount == 0 or ep - sp < maxCount)) {
- for (bwtPos = sp; bwtPos <= ep; bwtPos++) {
- if ((seqPos = Locate(bwtPos))) {
- positions.push_back(seqPos);
- }
- }
- }
- return ep - sp + 1;
- }
-
- DNALength Locate(T_DNASequence &seq, std::vector<DNALength> &positions,
- int maxCount =0) {
- DNALength ep, sp;
- Count(seq, sp, ep);
- return Locate(sp, ep, positions);
- }
-
- DNALength GetNumCharsLessThan(Nucleotide nuc) {
- return charCount[nuc];
- }
-
-
- void InitializeDNACharacterCount() {
- //
- // All counts start at 1 due to implicit encoding of $ character,
- // where $ is less than all other chars.
- //
- std::fill(charCount, &charCount[6], 0);
-
- DNALength p;
- Nucleotide nuc;
- for (p = 0; p < bwtSequence.length; p++) {
- nuc = bwtSequence[p];
- /*
- * Intentionally omit break commands so that charCount[4]
- * contains the counts of all characters 4 and below and so on.
- */
- switch(nuc) {
- case 5:
- //
- // 5 is out of order here because the '$' is stored after ACGTN
- // since it is a nonstandard character.
- //
- charCount[0]++;
- case 0: //A
- charCount[1]++;
- case 1: //C
- charCount[2]++;
- case 2: //G
- charCount[3]++;
- case 3: //T
- charCount[4]++;
- case 4: //N
- charCount[5]++;
- }
- }
- // sum
- charCount[6] = bwtSequence.length;
- }
-
- template<typename T_PStoragePolicy>
- int Count(T_DNASequence &seq, T_PStoragePolicy &StoragePolicy) {
-
- /*
- * Implement algorithm count directly from the FM-Index paper(s --
- * it's shown many times).
- */
- DNALength p = seq.length-1;
- DNALength sp, ep;
- Nucleotide c;
- int i;
-
- //
- // Original forumlation is using count offsets starting at 1.
- //
- Nucleotide tbn = ThreeBit[seq[p]];
- sp = charCount[tbn]; // = +1 (from paper) - 1 (0
- // offset not in paper).
- ep = charCount[tbn +1] - 1;
- StoragePolicy.Store(sp,ep);
- while (sp <= ep and p > 0) {
- c = ThreeBit[seq[p-1]];
- int cc = charCount[c];
- sp = cc + occ.Count(c,sp-1) + 1 - 1;
- ep = cc + occ.Count(c,ep) - 1;
- StoragePolicy.Store(sp,ep);
- p--;
- }
- return ep - sp + 1;
- }
-
- int Count(T_DNASequence &seq, DNALength &sp, DNALength &ep) {
- /*
- * Implement algorithm count directly from the FM-Index paper(s --
- * it's shown many times).
- */
- SingleStoragePolicy storagePolicy;
- storagePolicy.spp = &sp;
- storagePolicy.epp = &ep;
- return Count(seq, storagePolicy);
- }
-
- int Count(T_DNASequence &seq, std::vector<DNALength> &spv,
- std::vector<DNALength> &epv) {
- VectorStoragePolicy storagePolicy;
- storagePolicy.spvp = &spv;
- storagePolicy.epvp = &epv;
- return Count(seq, storagePolicy);
- }
-
- int Count(T_DNASequence &seq) {
- DNALength ep, sp;
- return Count(seq, sp, ep);
- }
-
- void InitializeBWTStringFromSuffixArray(T_DNASequence &origSeq, DNALength saIndex[]) {
- // extra +1 is for $.
- bwtSequence.Allocate(origSeq.length+1);
- if (useDebugData) {
- saCopy.resize(origSeq.length);
- }
-
- DNALength p;
-
- if (origSeq.length == 0) {
- //
- // No work to do, but even the null string has the sentinal
- // appended to it.
- //
- bwtSequence.Set(0,ThreeBit[(int)'$']);
- return;
- }
-
- //
- // By convention, bwt[0] = T[len(T)-1] because T[len(T)] == '$',
- // the lexicographic least character in the alphabet.
- //
- bwtSequence.Set(0, ThreeBit[origSeq[origSeq.length-1]]);
-
- for (p = 1; p < origSeq.length+1; p++) {
- if (useDebugData) {
- saCopy[p-1] = saIndex[p-1];
- }
- if (saIndex[p-1] > 0) {
- assert(ThreeBit[origSeq[saIndex[p-1]-1]] != 255);
- bwtSequence.Set(p, ThreeBit[origSeq[saIndex[p-1]-1]]);
- }
- else {
- //
- // The 0'th suffix corresponds to the one ending in the
- // sentinal '$'. Since this is explicitly encoded, we can
- // store a value in the bwt for '$'.
- //
- firstCharPos = p;
- bwtSequence.Set(p,ThreeBit[(int)'$']);
- }
- }
- }
-
- void InitializeFromSuffixArray(T_DNASequence &dnaSeq, DNALength saIndex[], int buildDebug=0) {
- useDebugData = buildDebug;
- InitializeBWTStringFromSuffixArray(dnaSeq, saIndex);
- InitializeDNACharacterCount();
-
- // sequence, major, minor bin sizes.
- occ.Initialize(bwtSequence, 4096, 64, buildDebug);
- pos.InitializeFromSuffixArray(saIndex, dnaSeq.length);
- }
-};
-
-typedef Bwt<PackedDNASequence, FASTASequence> BWT;
-
-
-#endif // _BLASR_BWT_HPP_
diff --git a/libcpp/alignment/bwt/Occ.hpp b/libcpp/alignment/bwt/Occ.hpp
deleted file mode 100644
index 0e2640b..0000000
--- a/libcpp/alignment/bwt/Occ.hpp
+++ /dev/null
@@ -1,217 +0,0 @@
-#ifndef _BLASR_OCC_HPP_
-#define _BLASR_OCC_HPP_
-
-#include <fstream>
-#include <vector>
-#include <algorithm>
-#include "DNASequence.hpp"
-#include "NucConversion.hpp"
-#include "utils.hpp"
-#include "matrix/Matrix.hpp"
-#include "matrix/FlatMatrix.hpp"
-
-template<typename T_BWTSequence, typename T_Major, typename T_Minor>
-class Occ {
-public:
- int majorBinSize;
- int minorBinSize;
- int hasDebugInformation;
- FlatMatrix2D<T_Major> major;
- FlatMatrix2D<T_Minor> minor;
- FlatMatrix2D<T_Major> full;
- static const unsigned int AlphabetSize = 5;
- T_BWTSequence *bwtSeqRef;
- DNALength numMajorBins, numMinorBins;
- void PrintBins(std::ostream &out) {
- out << "numMajor: " << numMajorBins << " numMinor: " << numMinorBins << std::endl;
- DNALength ma, mi, mii;
- mi = 0;
- int i;
- for (ma = 0; ma < numMajorBins; ma++) {
- out << "MAJOR: ";
- for (i = 0; i < 5; i++ ){ out << major[ma][i] << " "; } out << std::endl;
- for (mii = 0; mii < majorBinSize / minorBinSize && mi < numMinorBins; mii++, mi++) {
- out << " ";
- for (i = 0;i <5; i++ ){
- out << minor[mi][i] << " ";
- }
- out << std::endl;
- }
- }
- }
-
- void InitializeBWT(T_BWTSequence &bwtSeq) {
- bwtSeqRef = &bwtSeq;
- }
-
- void Initialize(T_BWTSequence &bwtSeq,
- int _majorBinSize=4096,
- int _minorBinSize=64,
- int _hasDebugInformation=0) {
- //
- // This reference is used when counting nucleotides. It assumes
- // the sequence does not change between initialization and
- // subsequent calls to count.
- //
- bwtSeqRef = &bwtSeq;
-
- majorBinSize = _majorBinSize;
- minorBinSize = _minorBinSize;
- hasDebugInformation = _hasDebugInformation;
- InitializeMajorBins(bwtSeq);
- InitializeMinorBins(bwtSeq);
- if (hasDebugInformation) {
- InitializeTestBins(bwtSeq);
- }
- }
-
- void InitializeMajorBins(T_BWTSequence &bwtSeq) {
- numMajorBins = CeilOfFraction(bwtSeq.length, (DNALength) majorBinSize);
- major.Allocate(numMajorBins, AlphabetSize);
- std::vector<DNALength> runningTotal;
- runningTotal.resize(AlphabetSize);
- fill(runningTotal.begin(), runningTotal.end(), 0);
- fill(&major.matrix[0], &major.matrix[numMajorBins*AlphabetSize], 0);
- DNALength p;
- DNALength binIndex = 0;
- for (p = 0; p < bwtSeq.length; p++) {
- Nucleotide nuc = ThreeBit[bwtSeq[p]];
- // only handle ACTGN, $==6, so skip counting that.
- if (nuc > AlphabetSize) continue;
- if (p % majorBinSize == 0) { //majorBinSize-1) {
- // cout << "storing at " << p<< " " << binIndex << std::endl;
- int n;
- for (n = 0; n < AlphabetSize; n++ ) {
- major[binIndex][n] = runningTotal[n];
- }
- binIndex++;
- }
- runningTotal[nuc]++;
- }
- }
-
- void InitializeTestBins(T_BWTSequence &bwtSeq) {
- full.Allocate(bwtSeq.length, AlphabetSize);
- fill(full.matrix, &full.matrix[bwtSeq.length * AlphabetSize],0);
- DNALength p;
- int n;
- for (p = 0; p < bwtSeq.length; p++) {
- Nucleotide nuc = ThreeBit[bwtSeq[p]];
- if (nuc > AlphabetSize) {
- for (n = 0; n < AlphabetSize; n++ ) {
- full[p][n] = full[p-1][n];
- }
- }
- else {
- full[p][nuc]++;
- if (p > 0) {
- for (n = 0; n < AlphabetSize; n++ ) {
- full[p][n] = full[p-1][n] + full[p][n];
- }
- }
- }
- }
- }
-
- void InitializeMinorBins(T_BWTSequence &bwtSeq) {
- numMinorBins = CeilOfFraction(bwtSeq.length, (DNALength) minorBinSize);
- minor.Allocate(numMinorBins, AlphabetSize);
-
- std::vector<DNALength> majorRunningTotal;
- majorRunningTotal.resize(AlphabetSize);
- std::fill(majorRunningTotal.begin(), majorRunningTotal.end(), 0);
- std::fill(&minor.matrix[0], &minor.matrix[numMinorBins*AlphabetSize], 0);
-
- DNALength p;
- DNALength minorBinIndex = 0;
- for (p = 0; p < bwtSeq.length; p++ ){
- Nucleotide nuc = ThreeBit[bwtSeq[p]];
- if (nuc > AlphabetSize) continue;
- //
- // The minor bins are running totals inside each major
- // bin. When the count hits a bin offset, reset the bin
- // counter.
- //
- if (p % majorBinSize == 0) {
- fill(majorRunningTotal.begin(), majorRunningTotal.end(), 0);
- }
- if (p % minorBinSize == 0) {
- int n;
- for (n = 0; n < AlphabetSize; n++ ) {
- minor[minorBinIndex][n] = majorRunningTotal[n];
- }
- minorBinIndex++;
- }
- majorRunningTotal[nuc]++;
- }
- }
-
- int Count(Nucleotide nuc, DNALength p ) {
- DNALength majorIndex = p / majorBinSize;
- DNALength minorIndex = p / minorBinSize;
- DNALength lastBinnedIndex = minorBinSize * (p / minorBinSize);
- //
- // This should be sort of O(1), since the last expression should
- // be made of bit operations that are fast.
- //
- Nucleotide smallNuc = ThreeBit[nuc];
- //assert(smallNuc < 5);
- DNALength nocc = major[majorIndex][smallNuc] + minor[minorIndex][smallNuc] + bwtSeqRef->CountNuc(lastBinnedIndex, p+1, nuc);
- // assert(full.matrix == NULL or full[p][smallNuc] == nocc);
- return nocc;
- }
-
- void Write(std::ostream &out) {
- out.write((char*) &majorBinSize, sizeof(majorBinSize));
- out.write((char*) &minorBinSize, sizeof(minorBinSize));
-
- out.write((char*) &numMajorBins, sizeof(numMajorBins));
- if (numMajorBins > 0) {
- out.write((char*) major[0], sizeof(T_Major) * numMajorBins*AlphabetSize);
- }
-
- out.write((char*) &numMinorBins, sizeof(numMinorBins));
- if (numMinorBins > 0) {
- out.write((char*) minor[0], sizeof(T_Minor) * numMinorBins*AlphabetSize);
- }
- if (hasDebugInformation) {
- DNALength bwtSeqLength = bwtSeqRef->length;
- out.write((char*)&bwtSeqLength, sizeof(bwtSeqLength));
- out.write((char*)&full.matrix[0], sizeof(DNALength)* bwtSeqLength * AlphabetSize);
- }
- }
-
- int Read(std::istream &in, int _hasDebugInformation) {
- hasDebugInformation = _hasDebugInformation;
- in.read((char*) &majorBinSize, sizeof(majorBinSize));
- in.read((char*) &minorBinSize, sizeof(minorBinSize));
- in.read((char*) &numMajorBins, sizeof(numMajorBins));
- if (numMajorBins > 0) {
- major.Resize(numMajorBins * AlphabetSize);
- in.read((char*) major[0], sizeof(T_Major) * numMajorBins * AlphabetSize);
- major.nRows = numMajorBins;
- major.nCols = AlphabetSize;
- }
- in.read((char*) &numMinorBins, sizeof(numMinorBins));
- if (numMinorBins > 0) {
- minor.Resize(numMinorBins * AlphabetSize);
- in.read((char*) minor[0], sizeof(T_Minor) * numMinorBins*AlphabetSize);
- minor.nRows = numMinorBins;
- minor.nCols = AlphabetSize;
- }
- if (hasDebugInformation) {
- DNALength bwtSeqLength;
- in.read((char*)&bwtSeqLength, sizeof(bwtSeqLength));
- if (full.matrix) {delete [] full.matrix;}
- full.matrix = new DNALength[bwtSeqLength *AlphabetSize];
- full.nRows = bwtSeqLength;
- full.nCols = AlphabetSize;
- in.read((char*)&full.matrix[0], sizeof(DNALength)* bwtSeqLength * AlphabetSize);
- }
- return 1;
- }
-
-};
-
-
-#endif // _BLASR_OCC_HPP_
diff --git a/libcpp/alignment/bwt/PackedHash.hpp b/libcpp/alignment/bwt/PackedHash.hpp
deleted file mode 100644
index f1fa540..0000000
--- a/libcpp/alignment/bwt/PackedHash.hpp
+++ /dev/null
@@ -1,350 +0,0 @@
-#ifndef _BLASR_PACKED_HASH_HPP_
-#define _BLASR_PACKED_HASH_HPP_
-
-#include <vector>
-#include <map>
-#include <iostream>
-#include <fstream>
-#include <cstring>
-#include "Types.h"
-#include "utils.hpp"
-#include "utils/BitUtils.hpp"
-#include "DNASequence.hpp"
-
-class PackedHash {
-public:
-
- DNALength tableLength;
- uint32_t *table;
- uint64_t *values;
- std::vector<int> hashLengths;
- static const uint32_t BinNumBits = 5;
- static const uint32_t BinSize = 1 <<(BinNumBits);
- PackedHash() {
- table = NULL;
- values = NULL;
- tableLength = 0;
- }
-
- ~PackedHash() {
- Free();
- }
-
- void Free() {
- // In general convertions between int and pointer is not desired,
- // Consequences depending on the implementation, as the resulting
- // pointers may incorrectly aligned. See C standard subclause 6.3.2.3.
- if (tableLength <= 0) {
- table = NULL;
- values = NULL;
- tableLength = 0;
- hashLengths.clear();
- return;
- }
-
- for(DNALength i = 0; i < tableLength; i++) {
- int nSetBits = CountBits(table[i]);
- if (nSetBits >= 3) {
- //values[i] is a pointer to a list of uint32 integers
- volatile uintptr_t iptr = values[i];
- uint32_t * ptr = (uint32_t *)iptr;
- if (ptr != NULL) {
- delete [] ptr;
- } //otherwise, values[i] is an uint_64.
- }
- }
- if (values) {delete [] values;}
- if (table) {delete [] table;}
- table = NULL;
- values = NULL;
- tableLength = 0;
- hashLengths.clear();
- }
-
- /*
- * Create a mask that retains the lower 5 bits (0 .. 31) of a
- * position so that pos % 32 may be computed by a shift.
- */
- static const uint32_t BinModMask = 0x1FU;
-
- void Allocate(uint32_t sequenceLength) {
- Free();
-
- tableLength = CeilOfFraction(sequenceLength, (DNALength) BinSize);
- table = new uint32_t[tableLength];
- values = new uint64_t[tableLength];
- std::fill(&table[0], &table[tableLength], 0);
- std::fill(&values[0], &values[tableLength], 0);
- hashLengths.resize(tableLength);
- std::fill(hashLengths.begin(), hashLengths.end(), 0);
- }
-
- void PrintBinSummary() {
- //
- // Report some stats on the hash.
- //
- DNALength p;
- std::map<int,int> countMap;
- int card;
- for (p = 0; p < tableLength; p++ ){
- card = CountBits(table[p]);
- countMap[card]++;
- }
- std::map<int,int>::iterator mapit;
- for (mapit = countMap.begin(); mapit != countMap.end(); ++mapit) {
- std::cout << mapit->first << " " << mapit->second << std::endl;
- }
- }
-
- uint32_t LookupBinAtPos(DNALength pos) {
- /*
- * Each bucket contains 32 positions. Membership is simply when
- * the bit at pos & BinModMask is set. There should never be
- * collisions of multiple positions (from different areas in the
- * genome) mapping to the same position in a bin.
- */
- return table[pos/BinSize] & (1 << (pos & BinModMask));
- }
-
- void ValueToList(uint64_t &storage, DNALength newValue, int newValuePos) {
-
- /*
- * This is called when one is attempting to add a spot to storage,
- * but there are already two values stored in it, so storage must
- * be converted to a pointer, and the values added to a list on
- * the heap. The size of the list is necessarily 3 at this point,
- * because there are two values in storage that must be moved to
- * the list, and the new value as well.
- * The values are copied to the list in sorted order, and sorting
- * is handled case-by-case since there are only 3 cases.
- */
-
- DNALength v0, v1;
- v0 = ((DNALength)storage);
- v1 = ((DNALength)(storage >> 32));
- DNALength *storagePtr = new DNALength[3];
- storage = (uint64_t) storagePtr;
-
- //
- // Only a couple of options, so handle them directly here
- //
- if (newValuePos == 0) {
- storagePtr[0] = newValue;
- storagePtr[1] = v0; storagePtr[2] = v1;
- }
- else if (newValuePos == 1) {
- storagePtr[0] = v0; storagePtr[1] = newValue; storagePtr[2] = v1;
- }
- else if (newValuePos == 2) {
- storagePtr[0] = v0; storagePtr[1] = v1; storagePtr[2] = newValue;
- }
- else {
- assert("ERROR! Somehow expected to only add 3 elements to an array of length 3, but the position of the new value is greater than the length of the array" && 0);
- }
- }
-
- void InsertValueInList(uint64_t &storage, int curStorageLength, DNALength newValue, int newValuePos) {
- /*
- * This simply creates a new list with size 1 larger than before,
- * and inserts the new value into its position that maintains
- * sorted order in the list.
- */
- DNALength *newListPtr = new DNALength[curStorageLength + 1];
- //
- // Copy the values from the old list making space for the new
- // value.
- //
- if (newValuePos > 0) {
- memcpy(newListPtr, ((DNALength*)storage), newValuePos * sizeof(DNALength));
- }
- if (newValuePos < curStorageLength) {
- memcpy(&newListPtr[newValuePos+1], &((DNALength*)storage)[newValuePos], (curStorageLength - newValuePos)*sizeof(uint32_t));
- }
- assert(curStorageLength < 32);
- newListPtr[newValuePos] = newValue;
- if (storage){delete[] ((DNALength*)storage);}
- storage = (uint64_t)newListPtr;
- }
-
- void DirectlyStoreValue(uint64_t &storage, int curStorageLength, DNALength value, int valuePos) {
- /*
- * In this instance, the value may be copied to either the first
- * half or the second half of 'storage', without having to turn
- * storage into a list. The values must be stored in sorted
- * order. If 'storage' is empty, the correct place is at the
- * beginning of storage. If there already is a value at the
- * beginning, it may be necessary to shift the existing value over
- * to keep everything in sorted order.
- */
-
- if (curStorageLength == 0) {
- //
- // Nothing here, just store the value.
- //
- storage = value;
- }
- else if (valuePos == 0) {
- //
- // Place the value at the beginning of the storage.
- //
- storage = storage << 32;
- storage = storage + value;
- }
- else {
- //
- // Place the value at the end of storage.
- //
- uint64_t longValue = value;
- longValue = longValue << 32;
- storage += longValue;
- }
- }
-
- int AddValue(DNALength pos, DNALength value) {
- //
- // The bucket is either a values[pos] that can store up to two
- // values, or it is a pointer to a list of values. The values are
- // always in order of their corresponding position in the BWT
- // string.
- // To add a value to this bucket, first check to see if
- // values[pos] has enough room to simply put it there, otherwise,
- // either a list already exists and the value must be inserted, or
- // the values[pos] must be converted to a list, and then the new
- // value inserted.
-
- //
- // First, operate on the assumption that no value gets added
- // twice.
- //
- UInt bin = pos / BinSize;
- UInt bit = pos & BinModMask;
- assert((table[bin] & ( 1 << bit)) == 0);
-
- //
- // Now, add the pos and determine where it is in the array.
- //
- table[bin] = table[bin] + ( 1 << bit);
-
- //
- // Mask off everything above this bit.
- //
- UInt mask = (UInt)-1;
- mask >>= (31 - bit);
- UInt lowerBits = table[bin] & mask;
- int rank = CountBits(lowerBits) - 1;
- int card = CountBits(table[bin]);
-
- if (card < 3) {
- DirectlyStoreValue(values[bin], card-1, value, rank);
- }
- else if (card == 3) {
- ValueToList(values[bin], value, rank);
- }
- else {
- InsertValueInList(values[bin], card-1, value, rank);
- }
- return card;
- }
-
- int LookupValue(DNALength pos, DNALength &value) {
-
- /*
- * Check to see if there is a value stored for 'pos'. If so,
- * store it in value, and return 1 for success.
- */
- UInt binIndex = pos/BinSize;
- UInt bin = table[binIndex];
- UInt setBit = bin & (1 << (pos & BinModMask));
- if (setBit == 0) {
- return 0;
- }
-
- //
- // GetSetBitPosition64 returns the position relative to the most
- // significant bit in a 64-bit word, starting at MSB = 1. This
- // should never be less than 32, since it's counting bits in a 32
- // bit word.
- //
-
- int bitPos = GetSetBitPosition32(setBit);
- UInt bitPosMask = ((UInt)-1) >> (32 - bitPos-1);;
-
- //
- // Determine how to interpret the value of this bucket. It is
- // either a pointer or two words. If there are more than two bits
- // set in this bucket, it is a pointer. Otherwise, pick the half
- // of the 64 bit word based on the index in the bucket.
- //
- int nSet = CountBits(bin);
- int bitRank = CountBits(bin & bitPosMask) - 1;
- assert(nSet > 0);
- if (nSet <= 2) {
- // return lower 32 bits
- if (bitRank == 0) {
- value = ((uint32_t)values[binIndex]);
- return 1;
- }
- else {
- value = ((uint32_t)(values[binIndex]>>32));
- return 1;
- }
- }
- else {
- /*
- * In this instance, values is a pointer rather than a pair of values.
- */
- value = (uint32_t) ((DNALength*)values[binIndex])[bitRank];
- return 1;
- }
- //
- // This is reached if nothing is stored in value. For now, this
- // shouldn't be reached, so make sure the program bails here.
- //
- assert(0);
- return 0;
- }
-
- /*
- * Define binary I/O routines for the packed hash. The sizes of the
- * tables are constant, but then the values table has some lists.
- * Those are written past the end of the tables treating the last
- * half of the file as a heap structure. They are simlarly read in.
- *
- */
-
- void Write(std::ostream &out) {
- out.write((char*) &tableLength,sizeof(tableLength));
- if (tableLength > 0) {
- out.write((char*) table, tableLength * sizeof(table[0]));
- out.write((char*) values, tableLength * sizeof(values[0]));
- }
- DNALength tablePos;
- for (tablePos = 0; tablePos < tableLength; tablePos++) {
- int nSetBits = CountBits(table[tablePos]);
- if( nSetBits > 2) {
- out.write((char*)values[tablePos], sizeof(uint32_t)*nSetBits);
- }
- }
- }
-
- void Read(std::istream &in) {
- Free();
- in.read((char*)&tableLength, sizeof(tableLength));
- if (tableLength > 0) {
- table = new uint32_t[tableLength];
- values = new uint64_t[tableLength];
- in.read((char*)table, sizeof(uint32_t)*tableLength);
- in.read((char*)values, sizeof(uint64_t)*tableLength);
- DNALength tablePos;
- for (tablePos = 0; tablePos < tableLength; tablePos++) {
- int nSetBits = CountBits(table[tablePos]);
- if (nSetBits > 2) {
- values[tablePos] = (uint64_t) new uint32_t[nSetBits];
- in.read((char*)values[tablePos], nSetBits * sizeof(uint32_t));
- }
- }
- }
- }
-};
-
-#endif // _BLASR_PACKED_HASH_HPP_
diff --git a/libcpp/alignment/bwt/Pos.hpp b/libcpp/alignment/bwt/Pos.hpp
deleted file mode 100644
index 06f6882..0000000
--- a/libcpp/alignment/bwt/Pos.hpp
+++ /dev/null
@@ -1,47 +0,0 @@
-#ifndef _BLASR_POS_HPP_
-#define _BLASR_POS_HPP_
-
-#include <fstream>
-#include <vector>
-
-#include "PackedHash.hpp"
-
-#include "DNASequence.hpp"
-#include "Types.h"
-#include "utils/BitUtils.hpp"
-
-template< typename T_BWT_Sequence>
-class Pos {
-public:
- static const unsigned int stride=8;
- PackedHash packedHash;
- std::vector<int> hashCount;
- std::vector<int> fullPos;
- int hasDebugInformation;
- void Write(std::ostream &out) {
- packedHash.Write(out);
- }
-
- void Read(std::istream &in) {
- packedHash.Read(in);
- }
-
- void InitializeFromSuffixArray(DNALength suffixArray[], DNALength suffixArrayLength) {
- DNALength p;
- packedHash.Allocate(suffixArrayLength);
- std::fill(hashCount.begin(), hashCount.end(), 0);
- for (p = 0; p < suffixArrayLength; p++ ){
- if (suffixArray[p] % stride==0){
- packedHash.AddValue(p,suffixArray[p]);
- }
- }
- }
-
- int Lookup(DNALength bwtPos, DNALength &seqPos) {
- return packedHash.LookupValue(bwtPos-1, seqPos);
- }
-
-};
-
-
-#endif // _BLASR_POS_HPP_
diff --git a/libcpp/alignment/datastructures/alignment/AlignedPair.h b/libcpp/alignment/datastructures/alignment/AlignedPair.h
deleted file mode 100644
index 588e832..0000000
--- a/libcpp/alignment/datastructures/alignment/AlignedPair.h
+++ /dev/null
@@ -1,19 +0,0 @@
-#ifndef ALIGNED_PAIR_H_
-#define ALIGNED_PAIR_H_
-
-#include <string>
-
-template<typename T_AlignChar=char>
-class AlignedPair {
- public:
- int length;
- T_AlignChar *tAlignmentSeq;
- T_AlignChar *qAlignmentSeq;
-};
-
-
-inline
-void ReadCompareSequencesAlignment {
-
-}
-#endif
diff --git a/libcpp/alignment/datastructures/alignment/Alignment.cpp b/libcpp/alignment/datastructures/alignment/Alignment.cpp
deleted file mode 100644
index d40aa39..0000000
--- a/libcpp/alignment/datastructures/alignment/Alignment.cpp
+++ /dev/null
@@ -1,512 +0,0 @@
-#include <cassert>
-#include <stdint.h>
-#include <vector>
-#include <string>
-#include <stdlib.h>
-#include <iostream>
-#include <ostream>
-#include <fstream>
-#include "Types.h"
-#include "DNASequence.hpp"
-#include "datastructures/alignment/Alignment.hpp"
-
-using namespace blasr;
-
-Alignment::Alignment() : AlignmentStats() {
- qName = ""; tName = "";
- qStrand = tStrand = 0;
- qPos = tPos = 0;
- qLength = tLength = 0;
-
- probability = 0;
- nCells = 0;
- nSampledPaths = 0;
- zScore = 0;
- score = probScore = sumQVScore = 0;
- qAlignLength = tAlignLength = 0;
-}
-
-void Alignment::CopyStats(Alignment &rhs) {
- AlignmentStats::CopyStats((AlignmentStats) rhs);
- probability = rhs.probability;
- probScore = rhs.probScore;
- sumQVScore = rhs.sumQVScore;
- nCells = rhs.nCells;
- nSampledPaths = rhs.nSampledPaths;
-}
-
-void Alignment::Clear() {
- qName = "";
- tName = "";
- blocks.clear();
- gaps.clear();
-}
-
-Alignment& Alignment::operator=(const Alignment &rhs) {
- qName = rhs.qName;
- tName = rhs.tName;
- qStrand = rhs.qStrand; tStrand = rhs.tStrand;
- qPos = rhs.qPos; tPos = rhs.tPos;
- qAlignLength = rhs.qAlignLength; tAlignLength = rhs.tAlignLength;
- qLength = rhs.qLength;
- tLength = rhs.tLength;
- zScore = rhs.zScore;
- blocks.clear();
- blocks = rhs.blocks;
- gaps.clear();
- gaps = rhs.gaps;
- nCells = rhs.nCells;
- nSampledPaths = rhs.nSampledPaths;
- AlignmentStats::Assign(rhs);
- return *this;
-}
-
-
-unsigned int Alignment::size() {
- return blocks.size();
-}
-
-void Alignment::Assign(Alignment &rhs) {
- ((AlignmentStats*)this)->Assign(rhs);
- qPos = rhs.qPos; tPos = rhs.tPos;
- qAlignLength = rhs.qAlignLength;
- tAlignLength = rhs.tAlignLength;
- qLength = rhs.qLength;
- zScore = rhs.zScore;
- qName = rhs.qName;
- tName = rhs.tName;
- qStrand = rhs.qStrand;
- tStrand = rhs.tStrand;
- nCells = rhs.nCells;
- std::vector<Block> empty;
- blocks.swap(empty);
- blocks.resize(rhs.size());
- int b;
- for (b = 0; b < rhs.blocks.size(); b++) {
- blocks[b].Assign(rhs.blocks[b]);
- }
-}
-int Alignment::ComputeNumAnchors(int minAnchorSize, int &nAnchors, int &nAnchorBases) {
- int i;
- nAnchors = 0;
- nAnchorBases = 0;
- for (i = 0; i < blocks.size(); i++) {
- if (blocks[i].length >= minAnchorSize) {
- nAnchors++;
- nAnchorBases += blocks[i].length;
- }
- }
- return nAnchors;
-}
-
-void Alignment::AllocateBlocks(int nBlocks) {
- blocks.resize(nBlocks);
-}
-
-void Alignment::AppendAlignmentGaps(Alignment &next, bool mergeFirst) {
- //
- // append all gaps belonging to ext to the gap list in this
- // alignment. The logic for determining just what the gap should
- // be between two separate alignments is somewhat complicated, and
- // should probably be handled outside this function. The default
- // to do this is to skip the first gap in the next alignment, and
- // assume that the code has handled computing the gap stored in
- // the last gap in this alignment correctly.
- //
- // At your own risk, you can simply merge the first gap in next
- // with the last gap in the current alignment.
-
- assert(gaps.size() > 0);
-
- // Ditto for the next alignment.
- assert(next.gaps.size() > 0);
-
- std::vector<GapList>::iterator secondGapIt = next.gaps.begin();
- if (mergeFirst) {
- // Merge the gap list in the first gap in next sequence to the
- // last gap in the current sequence.
- gaps[gaps.size()-1].insert(gaps[gaps.size()-1].end(), secondGapIt->begin(), secondGapIt->end());
- }
- // Append all other gaps to the current one.
- secondGapIt++;
- gaps.insert(gaps.end(), secondGapIt, next.gaps.end());
-}
-
-void Alignment::AppendAlignmentBlocks(Alignment &next, int qOffset, int tOffset) {
- VectorIndex n;
- Block tempBlock;
- for (n = 0; n < next.blocks.size(); n++ ) {
- tempBlock = next.blocks[n];
- tempBlock.qPos += qOffset;
- tempBlock.tPos += tOffset;
- blocks.push_back(tempBlock);
- }
-}
-
-void Alignment::AppendAlignment(Alignment &next) {
- int qOffset = next.qPos - qPos;
- int tOffset = next.tPos - tPos;
- AppendAlignmentBlocks(next, qOffset, tOffset);
-}
-
-/*
- Transform the series of operations in an optimal dynamic
- programming path to a block representation of the alignment.
-
- Since it is possible to have an adjacent insertion and deletion,
- the gap blocks are tracked in addition to the match blocks.
- */
-
-void Alignment::ArrowPathToAlignment(std::vector<Arrow> &optPath) {
- int q, t;
- VectorIndex a = 1;
- q = 0; t = 0;
- Block b;
- a = 0;
- bool beforeFirstBlock = true;
- while (a < optPath.size()) {
- //
- // Allow for there to be a block at the beginning
- // of the alignment, so process gap characters first.
- //
- if (!beforeFirstBlock) {
- if (optPath[a] == Diagonal) {
- // Start of a block;
- b.qPos = q;
- b.tPos = t;
- b.length = 0;
- while(a < optPath.size() and optPath[a] == Diagonal) {
- b.length++;
- a++;
- t++;
- q++;
- }
- blocks.push_back(b);
- }
- }
- gaps.push_back(GapList());
- int curGapList = gaps.size() - 1;
- //
- // Add gaps as condensed blocks of insertions or deletions. It
- // is possible there are multiple stretches of ins/del/ins/del
- // patterns, so have to loop over all of these.
- //
- while (a < optPath.size() and
- (optPath[a] == Left or
- optPath[a] == Up)) {
- if (a < optPath.size() and optPath[a] == Left) {
- int gapStart = a;
- while(a < optPath.size() and optPath[a] == Left) {
- t++;
- a++;
- }
- gaps[curGapList].push_back(Gap(Gap::Query, a - gapStart));
- continue;
- }
- else if (a < optPath.size() and optPath[a] == Up) {
- int gapStart = a;
- while(a < optPath.size() and optPath[a] == Up) {
- q++;
- a++;
- }
- gaps[curGapList].push_back(Gap(Gap::Target, a - gapStart));
- continue;
- }
- }
- if (a == optPath.size()) {
- if (gaps.size() > 0) {
- gaps[curGapList].clear();
- }
- }
- assert(a == optPath.size() or gaps[curGapList].size() != 0 or beforeFirstBlock == true);
- beforeFirstBlock = false;
- }
-}
-
-//
-// samtools / picard do not like the pattern
-// insertion/deletion/insertion (or the opposite). To get around
-// this, reorder the idi patterns to iid (or did to idd). This
-// produces the same scoring alignment, however it is reordered so
-// that Picard / samtools accepts the alignments.
-//
-void Alignment::OrderGapsByType() {
- int g;
- //
- // Gaps at the beginning and end of the sequence are hard to deal
- // with. Just get rid of them.
- //
- RemoveEndGaps();
- //
- // Start at 1 since the gaps at the beginning of the sequence are
- // removed.
- //
- for (g = 1; g < gaps.size(); g++ ) {
- if (gaps[g].size() <= 1) {
- continue;
- }
- Gap queryGap, targetGap;
- GapList condensedGapList;
- int gi;
- targetGap.seq = Gap::Target;
- queryGap.seq = Gap::Query;
- for (gi = 0; gi < gaps[g].size(); gi++) {
- if (gaps[g][gi].seq == Gap::Target) {
- targetGap.length += gaps[g][gi].length;
- }
- else {
- queryGap.length += gaps[g][gi].length;
- }
- }
- int nTypes = 0;
- gaps[g].clear();
- int matchExtend = 0;
- if (targetGap.length > queryGap.length) {
- targetGap.length -= queryGap.length;
- gaps[g].push_back(targetGap);
- matchExtend = queryGap.length;
- }
- else if (queryGap.length > targetGap.length) {
- queryGap.length -= targetGap.length;
- gaps[g].push_back(queryGap);
- matchExtend = targetGap.length;
- }
- else {
- matchExtend = targetGap.length;
- }
-
- if (matchExtend > 0) {
- assert(g>0);
- blocks[g-1].length += matchExtend;
- }
- //
- // When targetGap.length == queryGap.length, there is no gap, so
- // just leave the gap list cleared.
- //
- }
-}
-
-//
-// Transform an alignment that has up to one long gap in it to a
-// block based alignment.
-
-void
-Alignment::LongGapArrowPathToAlignment(
- std::vector<Arrow> &optPath, DNALength lengthOfLongGap) {
-
- DNALength i;
- int numLongGaps = 0;
-
- // Input checking.
- // Only one long gap is allowed per alignment. Make sure this is
- // the case on the input.
- //
- for (i = 0; i < optPath.size(); i++) {
- if (optPath[i] == AffineLongDelLeft or
- optPath[i] == AffineLongDelClose) {
- numLongGaps++;
- }
- }
-
- if (numLongGaps > 1) {
- std::cout << "ERROR. Only one long gap per alignment is allowed."
- << std::endl;
- exit(1);
- }
-
- //
- // First locate the position of the gap.
- // Also, change the gap to a normal arrow.
- //
- DNALength indexOfLongGap; // undefined until one is found
- bool aLongGapWasFound = false;
- Arrow longGapArrow; // will hold the type of the long gap
- int numBlocksBeforeGap = 0;
- int indexOfLastMatchBeforeGap = 0;
- // Now locate both the type of type of the arrow, and the
- // position
- for (i = 0; i < optPath.size(); i++) {
- //
- // Count the number of blocks. This will tell us where to insert
- // the gap.
- //
- if ( i > 0 and
- optPath[i-1] == Diagonal and
- optPath[i] != Diagonal ) {
- numBlocksBeforeGap++;
- indexOfLastMatchBeforeGap = i;
- }
- //
- // Look for the gap.
- //
- if (optPath[i] == AffineLongDelLeft or
- optPath[i] == AffineLongDelClose) {
- aLongGapWasFound = true;
- longGapArrow = optPath[i];
- indexOfLongGap = i;
- optPath[i] = Left;
- break;
- }
- }
-
- //
- // Next transform the path into an alignment that lacks the gap.
- //
- ArrowPathToAlignment(optPath);
-
- //
- // Finally, insert the gap into the block form of the alignment.
- //
-
- if (aLongGapWasFound and numBlocksBeforeGap < blocks.size()) {
- // Found a gap, add it.
-
- // First, find which gap corresponds to the long gap. This is
- // the hardest step. First, find how many arrow instructions
- // there are between the last block and the arrow.
-
- int numGapChars = indexOfLongGap - indexOfLastMatchBeforeGap + 1;
- int gi;
-
- // Define some variables for readability.
- int indexOfBlockBeforeGap;
- int gapIndex;
- gapIndex = numBlocksBeforeGap;
-
- assert(gapIndex < gaps.size());
-
- // There must be at least one gap here (the long deletion)
- assert(gaps[gapIndex].size() > 0);
-
- int cumulativeGapLength = 0;
- bool indexOfGapFound = false;
- for (gi = 0; gi < gaps[gapIndex].size(); gi++) {
- cumulativeGapLength += gaps[gapIndex][gi].length;
- if (cumulativeGapLength >= numGapChars) {
- // Found the gap where the long deletion happened.
- // Make sure this is on a deletion.
- assert(gaps[gapIndex][gi].seq == Gap::Query);
- indexOfGapFound = true;
- break;
- }
- }
-
- assert(indexOfGapFound == true);
- //
- // Found the gap corresponding to the long deletion.
- // Now, add in the length of the long gap, taking into account
- // the fact that there is already one base used in the previous
- // accounting of the gap.
- gaps[gapIndex][gi].length += lengthOfLongGap - 1;
-
- //
- // Now fix the offsets of the positions of the rest of the
- // blocks in the sequence.
- //
- UInt b;
- for (b = numBlocksBeforeGap; b < blocks.size(); b++) {
- blocks[b].tPos += lengthOfLongGap - 1;
- }
- }
-}
-
-//
-// The length of the aligned sequence in the query.
-//
-DNALength Alignment::QEnd() {
- if (blocks.size() > 0) {
- return blocks[blocks.size()-1].QEnd();
- }
- else { return 0; }
-}
-
-//
-// The lenght of the aligned sequence in the target.
-//
-DNALength Alignment::TEnd() {
- if (blocks.size() > 0) {
- return blocks[blocks.size()-1].TEnd();
- }
- else { return 0; }
-}
-
-DNALength Alignment::GenomicTBegin() {
- return tPos;
-}
-
-DNALength Alignment::GenomicTEnd() {
- return tPos + TEnd();
-}
-
-//
-// Some programs do not accept alignments that have gaps at their
-// ends. This is used to trim gaps at the ends of alignments (even
-// if the structure represents an acceptable alignment).
-//
-
-void Alignment::RemoveEndGaps() {
- if (gaps.size() > 0 and gaps[0].size() > 0) {
- int i;
- for (i = 0; i < gaps[0].size(); i++) {
- if (gaps[0][i].seq == Gap::Target) {
- qPos += gaps[0][i].length;
- }
- else {
- tPos += gaps[0][i].length;
- }
- }
- gaps[0].clear();
- }
-
- if (gaps.size() > 1 ) {
- int lastGap = gaps.size() - 1;
- gaps[lastGap].clear();
- }
-}
-
-
-MatchedAlignment& MatchedAlignment::Assign(MatchedAlignment &rhs) {
- ((Alignment*)(this))->Assign(rhs);
- refIndex = rhs.refIndex;
- readIndex = rhs.readIndex;
- tStart = rhs.tStart;
- tEnd = rhs.tEnd;
- qStart = rhs.qStart;
- qEnd = rhs.qEnd;
- tChromOffset = rhs.tChromOffset;
- return *this;
-}
-
-std::ostream& operator<<(std::ostream &out, const Block &b) {
- out << " q: " << b.qPos << " t: " << b.tPos << " len: " << b.length;
- return out;
-}
-
-Block& Block::Assign(Block &rhs) {
- qPos = rhs.qPos;
- tPos = rhs.tPos;
- length = rhs.length;
- return *this;
-}
-
-DNALength Block::QEnd() {
- return qPos + length;
-}
-
-DNALength Block::TEnd() {
- return tPos + length;
-}
-
-void Block::Clear() {
- qPos = tPos = length = 0;
-}
-
-Gap::Gap() {
- seq = Query;
- length = 0;
-}
-
-Gap::Gap(GapSeq seqP, int lengthP) {
- seq = seqP;
- length = lengthP;
-}
diff --git a/libcpp/alignment/datastructures/alignment/Alignment.hpp b/libcpp/alignment/datastructures/alignment/Alignment.hpp
deleted file mode 100644
index a10bbb6..0000000
--- a/libcpp/alignment/datastructures/alignment/Alignment.hpp
+++ /dev/null
@@ -1,184 +0,0 @@
-#ifndef _BLASR_ALIGNMENT_HPP_
-#define _BLASR_ALIGNMENT_HPP_
-
-#include "Path.h"
-#include <vector>
-#include <string>
-#include "DNASequence.hpp"
-#include "datastructures/alignment/AlignmentStats.hpp"
-
-namespace blasr {
-class Block {
-public:
- //
- // An alignment is a collection of blocks. The qPos and tPos in a block
- // is relative to the beginning of the alignment rather than the
- // target or query.
- //
- DNALength qPos, tPos, length;
- friend std::ostream &operator<<(std::ostream &out, const Block &b);
-
- Block& Assign(Block &rhs);
-
- DNALength QEnd();
-
- DNALength TEnd();
-
- void Clear();
-};
-
-class Gap {
-public:
- enum GapSeq {Query, Target};
- GapSeq seq;
- int length;
- Gap();
- Gap(GapSeq seqP, int lengthP);
-};
-
-typedef std::vector<Gap> GapList;
-
-class Alignment : public AlignmentStats {
-public:
- // the FASTA titles of each sequence
- std::string qName, tName;
-
- // Strands represented in the alignment, 0=forward, 1=reverse
- int qStrand, tStrand;
-
- // The starting pos in the text and query of the start of the
- // alignment, in the window that is matched.
- DNALength qPos, tPos;
- DNALength qAlignLength;
- DNALength tAlignLength;
- DNALength qLength;
- DNALength tLength;
-
- double probability;
- float zScore;
- float probScore;
- int sumQVScore;
- int nCells;
- int nSampledPaths;
- std::vector<Block> blocks;
- std::vector<GapList> gaps;
-
- Alignment();
-
- void CopyStats(Alignment &rhs);
-
- //
- // The position in the query is qPos + block[i].qPos
- // and the position in the text is tPos + block[i].tPos
- //
- void Clear();
-
- Alignment& operator=(const Alignment &rhs);
-
- unsigned int size();
-
- void Assign(Alignment &rhs);
-
- int ComputeNumAnchors(int minAnchorSize, int &nAnchors, int &nAnchorBases);
-
- void AllocateBlocks(int nBlocks);
-
- void AppendAlignmentGaps(Alignment &next, bool mergeFirst=false);
-
- void AppendAlignmentBlocks(Alignment &next, int qOffset = 0, int tOffset = 0);
-
- void AppendAlignment(Alignment &next);
-
- /*
- Transform the series of operations in an optimal dynamic
- programming path to a block representation of the alignment.
-
- Since it is possible to have an adjacent insertion and deletion,
- the gap blocks are tracked in addition to the match blocks.
- */
-
- void ArrowPathToAlignment(std::vector<Arrow> &optPath);
-
- //
- // samtools / picard do not like the pattern
- // insertion/deletion/insertion (or the opposite). To get around
- // this, reorder the idi patterns to iid (or did to idd). This
- // produces the same scoring alignment, however it is reordered so
- // that Picard / samtools accepts the alignments.
- //
- void OrderGapsByType();
-
- //
- // Transform an alignment that has up to one long gap in it to a
- // block based alignment.
-
- void LongGapArrowPathToAlignment(std::vector<Arrow> &optPath, DNALength lengthOfLongGap);
-
- //
- // The length of the aligned sequence in the query.
- //
- DNALength QEnd();
-
- //
- // The lenght of the aligned sequence in the target.
- //
- DNALength TEnd();
-
- DNALength GenomicTBegin();
-
- DNALength GenomicTEnd();
-
- //
- // Some programs do not accept alignments that have gaps at their
- // ends. This is used to trim gaps at the ends of alignments (even
- // if the structure represents an acceptable alignment).
- //
-
- void RemoveEndGaps();
-
-};
-
-//
-// This data structure holds two things: alignments, of course, and in addition
-// the coordinates of sequences that are successively refined in order to produce
-// the alignment. This is somewhat tricky when the target genome has been
-// transformed by some noise-reducing function phi(t).
-//
-// Before aligning a read, it is first mapped to the genome, or transformed
-// then mapped to the transformed genome. Because the mapping is inexact, the
-// region a read is mapped to is typically much larger than the read.
-// The coordinates of the mapped region are stored in tStart and tEnd
-// Alignments are performed in native nucleotide space (not transformed).
-
-// For now, the query is always qStart=0, qEnd = queryLength.
-
-
-//
-// When mapping a read to a set of concatenated chromosomes, each chromosome
-// has an offset into the file. Therefore though a sequence may be aligned
-// to a region starting at tStart, the relative offset into the chromosome
-// is tStart - tChromOffset. This is used when printing the coordinates of a match.
-//
-class MatchedAlignment : public Alignment {
-public:
- int refIndex;
- int readIndex;
- DNALength tStart, tEnd, qStart, qEnd;
- int tChromOffset;
-
- MatchedAlignment &Assign(MatchedAlignment &rhs);
-};
-
-
-/*
- * Create a structure for storing the information output by compare sequences.
- * Namely, the two string representations of the alignment.
- */
-class CompSeqAlignment : public Alignment {
- public:
- std::string tString, qString, alignString;
-};
-
-} // namespace blasr
-
-#endif // _BLASR_ALIGNMENT_HPP_
diff --git a/libcpp/alignment/datastructures/alignment/AlignmentCandidate.cpp b/libcpp/alignment/datastructures/alignment/AlignmentCandidate.cpp
deleted file mode 100644
index 111cfc9..0000000
--- a/libcpp/alignment/datastructures/alignment/AlignmentCandidate.cpp
+++ /dev/null
@@ -1,26 +0,0 @@
-#include "AlignmentCandidate.hpp"
-
-int SortAlignmentPointersByScore::operator() (T_AlignmentCandidate *lhs,
- T_AlignmentCandidate* rhs) {
- if (lhs->score == rhs->score) {
- return lhs->tPos + lhs->tAlignedSeqPos < rhs->tPos + rhs->tAlignedSeqPos;
- }
- else {
- return lhs->score < rhs->score;
- }
-}
-
-int SortAlignmentPointersByMapQV::operator() (T_AlignmentCandidate *lhs,
- T_AlignmentCandidate* rhs) {
- if (lhs->mapQV == rhs->mapQV) {
- if (lhs->score == rhs->score) {
- return lhs->tPos + lhs->tAlignedSeqPos < rhs->tPos + rhs->tAlignedSeqPos;
- }
- else {
- return lhs->score < rhs->score;
- }
- }
- else {
- return lhs->mapQV > rhs->mapQV;
- }
-}
diff --git a/libcpp/alignment/datastructures/alignment/AlignmentCandidate.hpp b/libcpp/alignment/datastructures/alignment/AlignmentCandidate.hpp
deleted file mode 100644
index 2e27142..0000000
--- a/libcpp/alignment/datastructures/alignment/AlignmentCandidate.hpp
+++ /dev/null
@@ -1,370 +0,0 @@
-#ifndef _ALIGNMENT_ALIGNMENT_CANDIDATE_HPP_
-#define _ALIGNMENT_ALIGNMENT_CANDIDATE_HPP_
-
-#include "Alignment.hpp"
-#include "DNASequence.hpp"
-#include "FASTQSequence.hpp"
-
-template<typename T_TSequence=FASTASequence, typename T_QSequence=FASTASequence>
-class AlignmentCandidate : public blasr::Alignment {
-
-private:
- void ReassignSequence(DNASequence &curSeq, bool curIsSubstring, DNASequence &newSeq) {
- //
- // If this sequence is in control of itself (it is not a substring
- // of anoter sequence), it should be freed here to avoid memory
- // leaks.
- //
- if (curIsSubstring == false) {
- curSeq.Free();
- }
- curSeq.seq = newSeq.seq;
- curSeq.length = newSeq.length;
- }
-
- void ReassignSequence(FASTQSequence &curSeq, bool curIsSubstring, FASTQSequence &newSeq) {
- //
- // Free the current sequence with the same rules as above.
- //
- if (curIsSubstring == false) {
- curSeq.Free();
- }
- curSeq.ReferenceSubstring(newSeq, 0, newSeq.length);
- }
-
- // TryReadingQVs is a helper function for ReadOptionalQVs. It checks if the
- // qvs that are supposed to be copied to a member of AlignmentCandidate are
- // in fact empty. If so, then don't substr or copy anything
- void TryReadingQVs(const std::string qvs, DNALength start, DNALength length,
- std::string *memberQVs) {
- if (qvs.size() == 0) {
- memberQVs->clear();
- } else {
- *memberQVs = qvs.substr(start, length);
- }
- }
-
-
-
-public:
- T_TSequence tAlignedSeq;
- T_QSequence qAlignedSeq;
- std::string insertionQV, deletionQV, mergeQV, substitutionQV, deletionTag, substitutionTag;
- std::vector<std::string> optionalQVNames;
- DNALength tAlignedSeqPos, qAlignedSeqPos;
- DNALength tAlignedSeqLength, qAlignedSeqLength;
- float pvalVariance, weightVariance, pvalNStdDev, weightNStdDev;
- int numSignificantClusters;
- int readIndex;
- //
- // [q/t]IsSubstring refers to whether or not the text or query
- // sequences are pointers into longer sequences. If they are,
- // then reassigning the target/query sequences just means
- // reassigning the seq and length values. If not, they occupy their
- // own space, and should have the same lifetime as the alignment
- // candidate object.
- //
-
- bool tIsSubstring, qIsSubstring;
- std::string tTitle, qTitle;
- float clusterScore, clusterWeight;
- //
- // For indexing into sequence index databases, tIndex stores which
- // target this match is from.
- //
- int tIndex;
-
- AlignmentCandidate&operator=(const AlignmentCandidate &rhs) {
- tAlignedSeq = rhs.tAlignedSeq;
- qAlignedSeq = rhs.qAlignedSeq;
- tAlignedSeqPos = rhs.tAlignedSeqPos;
- qAlignedSeqPos = rhs.qAlignedSeqPos;
- tAlignedSeqLength = rhs.tAlignedSeqLength;
- qAlignedSeqLength = rhs.qAlignedSeqLength;
- readIndex = rhs.readIndex;
- tIndex = rhs.tIndex;
- mapQV = rhs.mapQV;
- clusterScore = rhs.clusterScore;
- clusterWeight = rhs.clusterWeight;
- *((Alignment*)this) = ((Alignment&)rhs);
-
- pvalVariance = rhs.pvalVariance;
- pvalNStdDev = rhs.pvalNStdDev;
- weightVariance=rhs.weightVariance;
- weightNStdDev= rhs.weightNStdDev;
-
- insertionQV = rhs.insertionQV;
- deletionQV = rhs.deletionQV;
- substitutionQV = rhs.substitutionQV;
- mergeQV = rhs.mergeQV;
- substitutionTag = rhs.substitutionTag;
- deletionTag = rhs.deletionTag;
-
- return *this;
- }
-
- AlignmentCandidate() {
- /*
- * The default configuration of an alignment candidate is to have
- * the t and q sequences be substrings. This means that the
- * position of the substrings starts at 0 (no offset into a longer
- * string).
- */
- tIsSubstring = true;
- qIsSubstring = true;
- tTitle = "";
- qTitle = "";
- tAlignedSeqPos = 0;
- qAlignedSeqPos = 0;
- tAlignedSeqLength = 0;
- qAlignedSeqLength = 0;
- tIndex = 0;
- readIndex = 0;
- mapQV = 50;
- clusterScore = 0;
- clusterWeight = 0;
- numSignificantClusters = 0;
- pvalVariance = pvalNStdDev = 0;
- weightVariance = weightNStdDev = 0;
- }
-
- void Print(std::ostream & out = std::cout) {
- out << "An AlignmentCandidate object (mapQV "
- << mapQV << ", clusterscore " << clusterScore
- << ", tTitle: " << tTitle << ", qTitle: " << qTitle
- << ")." << std::endl;
- out << " query: " << qTitle << ", "
- << "qName: " << qName << ","
- << "qStrand: " << qStrand << ", "
- << "qPos: " << qPos << ", "
- << "qLen: " << qLength << ", "
- << "qAlignLength: " << qAlignLength << ", "
- << "qAlignedSeqPos:" << qAlignedSeqPos << ", "
- << "qAlignedSeqLen:" << qAlignedSeqLength << std::endl
- << " target: " << tTitle << ", "
- << "tName: " << tName << ","
- << "tStrand: " << tStrand << ", "
- << "tPos: " << tPos << ", "
- << "tLen: " << tLength << ", "
- << "tAlignLength: " << tAlignLength << ", "
- << "tAlignedSeqPos:" << tAlignedSeqPos << ", "
- << "tAlignedSeqLen:" << tAlignedSeqLength << std::endl;
- tAlignedSeq.Print(out);
- }
-
- AlignmentCandidate(const AlignmentCandidate &rhs) {
- *this = rhs;
- }
-
- DNALength GenomicTBegin() {
- return tAlignedSeqPos + tPos;
- }
-
- DNALength GenomicTEnd() {
- return tAlignedSeqPos + tPos + TEnd();
- }
-
- void GetQIntervalOnForwardStrand(int &qStart, int &qEnd) {
- GetQInterval(qStart, qEnd, true);
- }
-
- void GetQInterval(int &qStart, int &qEnd, bool useForwardStrand=false) {
- qStart = qEnd = 0;
- if (blocks.size() == 0) { return; }
- qStart = blocks[0].qPos + qAlignedSeqPos;
- qEnd = QEnd() + qAlignedSeqPos;
- if (useForwardStrand and qStrand == 1) {
- int forQEnd, forQStart;
- forQStart = qLength - qEnd;
- forQEnd = qLength - qStart;
- qStart = forQStart;
- qEnd = forQEnd;
- }
- }
-
- DNALength QAlignEnd() {
- return QEnd() + qPos + qAlignedSeqPos;
- }
-
- DNALength QAlignStart() {
- return qPos + qAlignedSeqPos;
- }
-
- DNALength TAlignStart() {
- return tPos + tAlignedSeqPos;
- }
-
- // Synonyms for T/QStart
- DNALength GetQBasesToStart() {
- return qPos + qAlignedSeqPos;
- }
- DNALength GetTBasesToStart() {
- return tPos + tAlignedSeqPos;
- }
-
- // ReadOptionalQVs populates the optional QV attributes of
- // AlignmentCandidate with values read from a vector.
- void ReadOptionalQVs(const std::vector<std::string>& optionalQVs,
- DNALength start, DNALength length) {
- TryReadingQVs(optionalQVs[0], start, length, &insertionQV);
- TryReadingQVs(optionalQVs[1], start, length, &deletionQV);
- TryReadingQVs(optionalQVs[2], start, length, &substitutionQV);
- TryReadingQVs(optionalQVs[3], start, length, &mergeQV);
- TryReadingQVs(optionalQVs[4], start, length, &substitutionTag);
- TryReadingQVs(optionalQVs[5], start, length, &deletionTag);
- }
-
- // CopyQVs fills a vector with optional QV attributes.
- void CopyQVs(std::vector<std::string> *optionalQVs) {
- optionalQVNames.clear();
- optionalQVs->clear();
- optionalQVs->push_back(insertionQV);
- optionalQVNames.push_back("InsertionQV");
- optionalQVs->push_back(deletionQV);
- optionalQVNames.push_back("DeletionQV");
- optionalQVs->push_back(substitutionQV);
- optionalQVNames.push_back("SubstitutionQV");
- optionalQVs->push_back(mergeQV);
- optionalQVNames.push_back("MergeQV");
- optionalQVs->push_back(substitutionTag);
- optionalQVNames.push_back("SubstitutionTag");
- optionalQVs->push_back(deletionTag);
- optionalQVNames.push_back("DeletionTag");
- }
-
- void AppendAlignment(AlignmentCandidate &next) {
-
- //
- // If the next alignment is empty, just return now.
- //
- if (next.blocks.size() == 0) {
- return;
- }
- //
- // It is necessary to determine how much after the first alignment
- // the second alignment starts, in order to
- assert(GetTBasesToStart() <= next.GetTBasesToStart());
- assert(GetQBasesToStart() <= next.GetQBasesToStart());
- assert(GetTBasesToStart() + TEnd() <= next.GetTBasesToStart());
- assert(GetQBasesToStart() + QEnd() <= next.GetQBasesToStart());
-
- //
- // qOffset is the offset of the frame of reference for the 'next'
- // alignment relative to this one. If the frame of reference is
- // the same (qOffset == 0 and tOffset == 0), then the alignment
- // blocks may simply be appended. If it is non zero, then the
- // location in the query or target where the alignment has started
- // is different, and the values of qPos or tPos need to be
- // adjusted accordingly.
-
- DNALength qOffset = next.qPos + next.qAlignedSeqPos - qPos - qAlignedSeqPos;
- DNALength tOffset = next.tPos + next.tAlignedSeqPos - tPos - tAlignedSeqPos;
- DNALength origQEnd = QEnd();
- DNALength origTEnd = TEnd();
-
- /* DNALength tGap = next.GetTBasesToStart() + next.blocks[0].tPos - (GetTBasesToStart() + TEnd());
- DNALength qGap = next.GetQBasesToStart() + next.blocks[0].qPos - (GetQBasesToStart() + QEnd());
- */
- DNALength tGap = next.GetTBasesToStart() - (GetTBasesToStart() + TEnd());
- DNALength qGap = next.GetQBasesToStart() - (GetQBasesToStart() + QEnd());
-
- //
-
- if ( gaps.size() > 0 and next.gaps.size() > 0 ) {
-
- //
- // Determine the gap between the two alignments in order to assign
- // the gap between them.
- DNALength commonGap = 0;
- DNALength gapDiff = 0;
-
- if (tGap >= qGap) {
- gapDiff = tGap - qGap;
- commonGap = tGap - gapDiff;
- tGap = gapDiff;
- qGap = 0;
- }
- else {
- gapDiff = qGap - tGap;
- commonGap = qGap - gapDiff;
- qGap = gapDiff;
- tGap = 0;
- }
-
- if (commonGap > 0) {
- // There is some portion of sequence between the two alignments
- // that is a common gap. Add a block representing this.
-
- blasr::Block block;
- block.qPos = origQEnd;
- block.tPos = origTEnd;
- block.length = commonGap;
- blocks.push_back(block);
- blasr::GapList emptyGap;
- gaps.push_back(emptyGap);
- }
-
- blasr::GapList endGapList;
- //
- // When gapDiff == 0, an empty list is appended.
- //
- if (next.gaps.size() > 0) {
- //
- // The first gap in the next alignment is already handled by
- // the gap created with the endGap. So get rid of the first
- // gaps.
- // next.gaps[0].resize(0);
- static const bool mergeFirstGap = true;
- AppendAlignmentGaps(next);
- }
- }
-
- //
- // Finally append all the blocks.
- //
- AppendAlignmentBlocks(next, qOffset, tOffset);
-
- }
-
- void FreeSubsequences() {
- if (tIsSubstring == false) {
- tAlignedSeq.Free();
- }
- if (qIsSubstring == false) {
- qAlignedSeq.Free();
- }
- }
-
- void ReassignTSequence(DNASequence &newSeq) {
- ReassignSequence(tAlignedSeq, tIsSubstring, newSeq);
- }
-
- template<typename T_Sequence>
- void ReassignQSequence(T_Sequence &newSeq) {
- ReassignSequence(qAlignedSeq, qIsSubstring, newSeq);
- }
-
- ~AlignmentCandidate() {
- qAlignedSeq.Free();
- tAlignedSeq.Free();
- }
-};
-//
-// Define a default alignment candidate for aligning quality-sequence
-// to a reference without quality.
-//
-typedef AlignmentCandidate<DNASequence,FASTQSequence> T_AlignmentCandidate;
-
-class SortAlignmentPointersByScore {
-public:
- /// Sort AlignmentCandidate pointer by score, then by target position.
- int operator()(T_AlignmentCandidate *lhs, T_AlignmentCandidate* rhs);
-};
-
-class SortAlignmentPointersByMapQV {
-public:
- /// Sort AlignmentCandidate pointer by mapQV, then by target position.
- int operator()(T_AlignmentCandidate *lhs, T_AlignmentCandidate* rhs);
-};
-
-#endif // _ALIGNMENT_ALIGNMENT_CANDIDATE_HPP_
diff --git a/libcpp/alignment/datastructures/alignment/AlignmentContext.cpp b/libcpp/alignment/datastructures/alignment/AlignmentContext.cpp
deleted file mode 100644
index 913a689..0000000
--- a/libcpp/alignment/datastructures/alignment/AlignmentContext.cpp
+++ /dev/null
@@ -1,35 +0,0 @@
-#include "AlignmentContext.hpp"
-
-AlignmentContext::AlignmentContext() {
- isPrimary = true;
- subreadIndex = 0;
- isFinal = true;
- nextSubreadPos = 0;
- hasNextSubreadPos = false;
- numProperlyAlignedSubreads = 0;
- allSubreadsProperlyAligned = false;
- nSubreads = 0;
- nextSubreadDir = 0;
- rNext = "";
- readGroupId = "";
- chipId = "";
- alignMode = NoAlignMode;
- editDist = 0;
-}
-
-bool AlignmentContext::IsFirst() {
- return subreadIndex == 0;
-}
-
-bool AlignmentContext::IsLast() {
- return subreadIndex == nSubreads-1;
-}
-
-bool AlignmentContext::AllSubreadsAligned() {
- if (numProperlyAlignedSubreads == nSubreads) {
- return true;
- }
- else {
- return false;
- }
-}
diff --git a/libcpp/alignment/datastructures/alignment/AlignmentContext.hpp b/libcpp/alignment/datastructures/alignment/AlignmentContext.hpp
deleted file mode 100644
index 69c57ce..0000000
--- a/libcpp/alignment/datastructures/alignment/AlignmentContext.hpp
+++ /dev/null
@@ -1,32 +0,0 @@
-#ifndef _BLASR_ALIGNMENT_CONTEXT_HPP_
-#define _BLASR_ALIGNMENT_CONTEXT_HPP_
-
-#include <string>
-#include "Enumerations.h"
-
-class AlignmentContext {
-public:
- bool isPrimary;
- int subreadIndex;
- int numProperlyAlignedSubreads;
- bool allSubreadsProperlyAligned;
- bool isFinal;
- int nextSubreadPos;
- int nextSubreadDir;
- bool hasNextSubreadPos;
- int nSubreads;
- std::string rNext;
- std::string readGroupId;
- std::string chipId;
- AlignMode alignMode;
- int editDist;
- AlignmentContext();
-
- bool IsFirst();
-
- bool IsLast();
-
- bool AllSubreadsAligned();
-};
-
-#endif // _BLASR_ALIGNMENT_CONTEXT_HPP_
diff --git a/libcpp/alignment/datastructures/alignment/AlignmentGapList.h b/libcpp/alignment/datastructures/alignment/AlignmentGapList.h
deleted file mode 100644
index 47fb01c..0000000
--- a/libcpp/alignment/datastructures/alignment/AlignmentGapList.h
+++ /dev/null
@@ -1,26 +0,0 @@
-#ifndef DATASTRUCTURES_ALIGNMENT_GAP_LIST_H_
-#define DATASTRUCTURES_ALIGNMENT_GAP_LIST_H_
-
-#include <vector>
-using namespace std;
-
-
-
-class Gap {
- public:
- enum GapSeq {Query, Target};
- GapSeq seq;
- int length;
- Gap() {
- seq = Query;
- length = 0;
- }
- Gap(GapSeq seqP, int lengthP) {
- seq = seqP;
- length = lengthP;
- }
-};
-
-typedef vector<Gap> GapList;
-
-#endif
diff --git a/libcpp/alignment/datastructures/alignment/AlignmentMap.cpp b/libcpp/alignment/datastructures/alignment/AlignmentMap.cpp
deleted file mode 100644
index 7e39d0b..0000000
--- a/libcpp/alignment/datastructures/alignment/AlignmentMap.cpp
+++ /dev/null
@@ -1,22 +0,0 @@
-#include <vector>
-#include <string>
-#include "AlignmentMap.hpp"
-
-using namespace std;
-
-void
-CreateSequenceToAlignmentMap(const string & alignedSequence,
- vector<int> & baseToAlignmentMap) {
- baseToAlignmentMap.resize(alignedSequence.size());
- int alignedPos, unalignedPos;
- for (alignedPos=0, unalignedPos=0;
- alignedPos < alignedSequence.size();
- alignedPos++) {
- if (not (alignedSequence[alignedPos] == ' ' or
- alignedSequence[alignedPos] == '-')) {
- baseToAlignmentMap[unalignedPos] = alignedPos;
- unalignedPos++;
- }
- }
- baseToAlignmentMap.resize(unalignedPos);
-}
diff --git a/libcpp/alignment/datastructures/alignment/AlignmentMap.hpp b/libcpp/alignment/datastructures/alignment/AlignmentMap.hpp
deleted file mode 100644
index 57752fc..0000000
--- a/libcpp/alignment/datastructures/alignment/AlignmentMap.hpp
+++ /dev/null
@@ -1,20 +0,0 @@
-#ifndef _BLASR_ALIGNMENT_MAP_HPP_
-#define _BLASR_ALIGNMENT_MAP_HPP_
-
-#include <vector>
-
-class AlignmentMap {
- public:
- int qPos, tPos;
- std::vector<int> alignPos;
-};
-
-
-// Build a map of positions from (unaligned) bases to an aligned sequence
-void
-CreateSequenceToAlignmentMap(const std::string & alignedSequence,
- std::vector<int> & baseToAlignmentMap);
-
-
-#endif // _BLASR_ALIGNMENT_MAP_HPP_
-
diff --git a/libcpp/alignment/datastructures/alignment/AlignmentStats.cpp b/libcpp/alignment/datastructures/alignment/AlignmentStats.cpp
deleted file mode 100644
index 3da5fe5..0000000
--- a/libcpp/alignment/datastructures/alignment/AlignmentStats.cpp
+++ /dev/null
@@ -1,29 +0,0 @@
-#include "AlignmentStats.hpp"
-
-using namespace blasr;
-
-AlignmentStats::AlignmentStats() {
- nMatch = nMismatch = nIns = nDel = 0;
- pctSimilarity = 0.0;
- mapQV = 0;
- score = 0;
-}
-
-AlignmentStats& AlignmentStats::Assign(const AlignmentStats &rhs) {
- nMatch = rhs.nMatch;
- nMismatch = rhs.nMismatch;
- nIns = rhs.nIns;
- nDel = rhs.nDel;
- pctSimilarity = rhs.pctSimilarity;
- score = rhs.score;
- return *this;
-}
-
-AlignmentStats& AlignmentStats::operator=(const AlignmentStats &rhs) {
- Assign(rhs);
- return *this;
-}
-
-void AlignmentStats::CopyStats(AlignmentStats rhs) {
- *this = rhs;
- }
diff --git a/libcpp/alignment/datastructures/alignment/AlignmentStats.hpp b/libcpp/alignment/datastructures/alignment/AlignmentStats.hpp
deleted file mode 100644
index 7f52e14..0000000
--- a/libcpp/alignment/datastructures/alignment/AlignmentStats.hpp
+++ /dev/null
@@ -1,25 +0,0 @@
-#ifndef _BLASR_ALIGNMENT_STATS_HPP_
-#define _BLASR_ALIGNMENT_STATS_HPP_
-
-namespace blasr {
-class AlignmentStats {
-public:
- int nMatch;
- int nMismatch;
- int nIns;
- int nDel;
- float pctSimilarity;
- int score;
- int mapQV;
- AlignmentStats();
-
- AlignmentStats &Assign(const AlignmentStats &rhs);
-
- AlignmentStats& operator=(const AlignmentStats &rhs);
-
- void CopyStats(AlignmentStats rhs);
-
-};
-}
-
-#endif // _BLASR_ALIGNMENT_STATS_HPP_
diff --git a/libcpp/alignment/datastructures/alignment/ByteAlignment.h b/libcpp/alignment/datastructures/alignment/ByteAlignment.h
deleted file mode 100644
index c5c34c9..0000000
--- a/libcpp/alignment/datastructures/alignment/ByteAlignment.h
+++ /dev/null
@@ -1,347 +0,0 @@
-#ifndef DATASTRUCTURES_ALIGNMENT_BYTE_ALIGNMENT_H_
-#define DATASTRUCTURES_ALIGNMENT_BYTE_ALIGNMENT_H_
-#include <vector>
-#include "algorithms/alignment/AlignmentUtils.hpp"
-#include "DNASequence.hpp"
-
-using namespace std;
-/*
- * These arrays are for going from the HDF byte alignment format to characters, or
- * from characters to the upper or lower nybble for translating from character
- * alignments to byte alignments.
- */
-
-typedef vector<unsigned char> ByteAlignment;
-static char QueryChar[256] = {
-' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', //0
-' ', ' ', ' ', ' ', ' ', ' ', 'A', 'A', 'A', 'A', //10
-'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', // 20
-'A', 'A', 'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', // 30
-'C', 'C', 'C', 'C', 'C', 'C', 'C', 'C', ' ', ' ', // 40
-' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', // 50
-' ', ' ', ' ', ' ', 'G', 'G', 'G', 'G', 'G', 'G', // 60
-'G', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'G', 'G', // 70
-' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', // 80
-' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', // 90
-' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', // 100
-' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', // 110
-' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', 'T', 'T', // 120
-'T', 'T', 'T', 'T', 'T', 'T', 'T', 'T', 'T', 'T', // 130
-'T', 'T', 'T', 'T', ' ', ' ', ' ', ' ', ' ', ' ', // 140
-' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', // 150
-' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', // 160
-' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', // 170
-' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', // 180
-' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', // 190
-' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', // 200
-' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', // 210
-' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', // 220
-' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', ' ', // 230
-'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', // 240
-'N', 'N', 'N', 'N', 'N', 'N' // 250
-};
-
-static char RefChar[256] = {
-' ', 'A', 'C', ' ', 'G', ' ', ' ', ' ', 'T', ' ',
-' ', ' ', ' ', ' ', ' ', 'N', ' ', 'A', 'C', ' ',
-'G', ' ', ' ', ' ', 'T', ' ', ' ', ' ', ' ', ' ',
-' ', 'N', ' ', 'A', 'C', ' ', 'G', ' ', ' ', ' ',
-'T', ' ', ' ', ' ', ' ', ' ', ' ', 'N', ' ', 'A',
-'C', ' ', 'G', ' ', ' ', ' ', 'T', ' ', ' ', ' ',
-' ', ' ', ' ', 'N', ' ', 'A', 'C', ' ', 'G', ' ',
-' ', ' ', 'T', ' ', ' ', ' ', ' ', ' ', ' ', 'N',
-' ', 'A', 'C', ' ', 'G', ' ', ' ', ' ', 'T', ' ',
-' ', ' ', ' ', ' ', ' ', 'N', ' ', 'A', 'C', ' ',
-'G', ' ', ' ', ' ', 'T', ' ', ' ', ' ', ' ', ' ',
-' ', 'N', ' ', 'A', 'C', ' ', 'G', ' ', ' ', ' ',
-'T', ' ', ' ', ' ', ' ', ' ', ' ', 'N', ' ', 'A',
-'C', ' ', 'G', ' ', ' ', ' ', 'T', ' ', ' ', ' ',
-' ', ' ', ' ', 'N', ' ', 'A', 'C', ' ', 'G', ' ',
-' ', ' ', 'T', ' ', ' ', ' ', ' ', ' ', ' ', 'N',
-' ', 'A', 'C', ' ', 'G', ' ', ' ', ' ', 'T', ' ',
-' ', ' ', ' ', ' ', ' ', 'N', ' ', 'A', 'C', ' ',
-'G', ' ', ' ', ' ', 'T', ' ', ' ', ' ', ' ', ' ',
-' ', 'N', ' ', 'A', 'C', ' ', 'G', ' ', ' ', ' ',
-'T', ' ', ' ', ' ', ' ', ' ', ' ', 'N', ' ', 'A',
-'C', ' ', 'G', ' ', ' ', ' ', 'T', ' ', ' ', ' ',
-' ', ' ', ' ', 'N', ' ', 'A', 'C', ' ', 'G', ' ',
-' ', ' ', 'T', ' ', ' ', ' ', ' ', ' ', ' ', 'N',
-' ', 'A', 'C', ' ', 'G', ' ', ' ', ' ', 'T', ' ',
-' ', ' ', ' ', ' ', ' ', ' '};
-
-
-
-static unsigned char RefAlignmentByte[256] = {0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
- 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
- 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
- 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
- 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
- 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
- 0, 0, 0, 0, 0, 1, 0, 2, 0, 0,
- 0, 4, 0, 0, 0, 0, 0, 0, 15, 0,
- 0, 0, 0, 0, 8, 0, 0, 0, 0, 0,
- 0, 0, 0, 0, 0, 0, 0, 1, 0, 2,
- 0, 0, 0, 4, 0, 0, 0, 0, 0, 0,
- 15, 0, 0, 0, 0, 0, 8, 0, 0, 0,
- 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
- 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
- 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
- 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
- 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
- 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
- 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
- 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
- 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
- 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
- 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
- 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
- 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
- 0, 0, 0, 0, 0, 0};
-
-
-static unsigned char QueryAlignmentByte[256] = { 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
- 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
- 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
- 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
- 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
- 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
- 0, 0, 0, 0, 0, 16, 0, 32, 0, 0,
- 0, 64, 0, 0, 0, 0, 0, 0, 240, 0,
- 0, 0, 0, 0, 128, 0, 0, 0, 0, 0,
- 0, 0, 0, 0, 0, 0, 0, 16, 0, 32,
- 0, 0, 0, 64, 0, 0, 0, 0, 0, 0,
- 240, 0, 0, 0, 0, 0, 128, 0, 0, 0,
- 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
- 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
- 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
- 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
- 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
- 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
- 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
- 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
- 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
- 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
- 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
- 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
- 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
- 0, 0, 0, 0, 0, 0};
-
-
-void MakeReverseComplementByteAlignment(const unsigned char *byteAlignment,
- UInt length,
- unsigned char *byteAlignmentRC) {
- unsigned char q,t;
- int i;
- for (i = 0; i < length; i++) {
- if (QueryChar[byteAlignment[i]] == ' ') { q = ' '; }
- else { q = ReverseComplementNuc[QueryChar[byteAlignment[i]]]; }
-
- if (RefChar[byteAlignment[i]] == ' ') { t = ' '; }
- else { t = ReverseComplementNuc[RefChar[byteAlignment[i]]]; }
-
- byteAlignmentRC[length - i - 1] = QueryAlignmentByte[q] + RefAlignmentByte[t];
- }
-}
-
-
-void ByteAlignmentToQueryString(const unsigned char* byteAlignment,
- UInt length,
- char* charAlignment) {
- int i;
- for (i = 0; i < length; i++) {
- charAlignment[i] = QueryChar[byteAlignment[i]];
- }
-}
-
-
-void ByteAlignmentToRefString(const unsigned char* byteAlignment,
- UInt length,
- char* charAlignment) {
- int i;
- for (i = 0; i < length; i++) {
- charAlignment[i] = RefChar[byteAlignment[i]];
- }
-}
-
-void RemoveGaps(string &gappedStr, string &ungappedStr) {
- ungappedStr = gappedStr;
- int i, i2;
- i = i2 = 0;
- for (i = 0; i < ungappedStr.size(); i++ ){
- if (ungappedStr[i] != ' ') {
- ungappedStr[i2] = ungappedStr[i];
- i2++;
- }
- }
- ungappedStr.resize(i2);
-}
-
-
-void GappedStringsToAlignment(string &gappedQuery, string &gappedRef, Alignment &alignment) {
-int qPos = 0, rPos = 0;
- int i = 0; // position in alignment string
- while (i < gappedQuery.size()) {
- while (i < gappedQuery.size() and (gappedQuery[i] == ' ' or gappedRef[i] == ' ')) {
- if (gappedQuery[i] != ' ') {
- qPos++;
- }
- if (gappedRef[i] != ' ') {
- rPos++;
- }
- i++;
- }
- int queryBlockStart, queryBlockEnd, refBlockStart, refBlockEndl;
- Block b;
- b.qPos = qPos;
- b.tPos = rPos;
- while (i < gappedQuery.size() and gappedQuery[i] != ' ' and gappedRef[i] != ' ') {
- i++;
- qPos++;
- rPos++;
- }
- b.length = qPos - b.qPos;
- alignment.blocks.push_back(b);
- }
-}
-
-
-void ByteAlignmentToAlignment(vector<unsigned char> &byteAlignment, Alignment &alignment) {
- string readSequence, refSequence;
- readSequence.resize(byteAlignment.size());
- refSequence.resize(byteAlignment.size());
-
- ByteAlignmentToQueryString(&byteAlignment[0], byteAlignment.size(), &readSequence[0]);
- ByteAlignmentToRefString(&byteAlignment[0], byteAlignment.size(), &refSequence[0]);
- GappedStringsToAlignment(readSequence, refSequence, alignment);
-}
-
-void AlignmentToByteAlignment(Alignment &alignment,
- DNASequence &querySeq, DNASequence &refSeq,
- vector<unsigned char> &byteAlignment) {
- string refStr, alignStr, queryStr;
- CreateAlignmentStrings(alignment, querySeq, refSeq,
- refStr, alignStr, queryStr);
- byteAlignment.resize(refStr.size());
- int i;
- for (i = 0; i < refStr.size(); i++) {
- byteAlignment[i] = RefAlignmentByte[refStr[i]] + QueryAlignmentByte[queryStr[i]];
- }
-}
-
-bool IsMatch(vector<unsigned char> &byteAlignment, int i) {
- if (QueryChar[byteAlignment[i]] != ' ' and
- RefChar[byteAlignment[i]] != ' ' and
- (QueryChar[byteAlignment[i]] == RefChar[byteAlignment[i]])) {
- return true;
- }
- else {
- return false;
- }
-}
-
-void CountStats(vector<unsigned char> &byteAlignment,
- int &nMatch, int &nMismatch, int &nIns, int &nDel,
- int start=0, int end=-1) {
- int i;
- if (end == -1) {
- end = byteAlignment.size();
- }
-
- nMatch = nMismatch = nIns = nDel = 0;
-
- for (i = start; i < end; i++) {
- if (QueryChar[byteAlignment[i]] == ' ') {
- nDel++;
- }
- else if (RefChar[byteAlignment[i]] == ' ') {
- nIns++;
- }
- else if (RefChar[byteAlignment[i]] != QueryChar[byteAlignment[i]]) {
- nMismatch++;
- }
- else {
- nMatch++;
- }
- }
-}
-
-int CountBasesInReference(vector<unsigned char> &byteAlignment) {
- int i;
- int nBases = 0;
- for (i = 0; i < byteAlignment.size(); i++) {
- if (RefChar[byteAlignment[i]] != ' ') {
- nBases++;
- }
- }
- return nBases;
-}
-
-int CountBasesInQuery(vector<unsigned char> &byteAlignment) {
- int i;
- int nBases = 0;
- for (i = 0; i < byteAlignment.size(); i++) {
- if (QueryChar[byteAlignment[i]] != ' ') {
- nBases++;
- }
- }
- return nBases;
-}
-
-int CountNMatches(vector<unsigned char> &byteAlignment) {
- int nMatches = 0;
- int i;
- for (i = 0; i < byteAlignment.size(); i++) {
- if (IsMatch(byteAlignment, i)) {
- nMatches++;
- }
- }
- return nMatches;
-}
-
-float ComputePacBioAccuracy(vector<unsigned char> &byteAlignment) {
- int m, mm, i, d;
- CountStats(byteAlignment, m, mm, d, i);
- int readLength = CountBasesInQuery(byteAlignment);
- return 1 - (1.0*mm + d + i)/readLength;
-}
-
-
-float ComputePercentIdentity(vector<unsigned char> &byteAlignment) {
- int i;
- int nMatch = CountNMatches(byteAlignment);
- return (1.0*nMatch) / byteAlignment.size();
-}
-
-void CreateSequenceToAlignmentMap(vector<unsigned char> &byteAlignment,
- vector<int> &baseToAlignmentMap) {
- int alignPos, ungappedAlignPos;
- int alignmentLength = byteAlignment.size();
- baseToAlignmentMap.resize(alignmentLength);
- for (ungappedAlignPos = 0, alignPos = 0;
- alignPos < alignmentLength;
- alignPos++) {
-
- if (QueryChar[byteAlignment[alignPos]] != ' ') {
- baseToAlignmentMap[ungappedAlignPos] = alignPos;
- ++ungappedAlignPos;
- }
- }
- baseToAlignmentMap.resize(ungappedAlignPos);
-}
-
-void CreateAlignmentToSequenceMap(vector<unsigned char> &byteAlignment,
- vector<int> &alignmentToBaseMap) {
- int alignPos, ungappedAlignPos;
- int alignmentLength = byteAlignment.size();
- alignmentToBaseMap.resize(alignmentLength);
- for (ungappedAlignPos = 0, alignPos = 0;
- alignPos < alignmentLength;
- alignPos++) {
- if (QueryChar[byteAlignment[alignPos]] != ' ') {
- alignmentToBaseMap[alignPos] = ungappedAlignPos;
- ++ungappedAlignPos;
- }
- }
-}
-
-#endif
diff --git a/libcpp/alignment/datastructures/alignment/CmpFile.cpp b/libcpp/alignment/datastructures/alignment/CmpFile.cpp
deleted file mode 100644
index 9270fc9..0000000
--- a/libcpp/alignment/datastructures/alignment/CmpFile.cpp
+++ /dev/null
@@ -1,6 +0,0 @@
-#include "CmpFile.hpp"
-
-void CmpFile::StoreReadType(std::string &readTypeStringP) {
- readTypeString = readTypeStringP;
- readType = ReadType::ParseReadType(readTypeString);
-}
diff --git a/libcpp/alignment/datastructures/alignment/CmpFile.hpp b/libcpp/alignment/datastructures/alignment/CmpFile.hpp
deleted file mode 100644
index 76682e4..0000000
--- a/libcpp/alignment/datastructures/alignment/CmpFile.hpp
+++ /dev/null
@@ -1,33 +0,0 @@
-#ifndef _BLASR_CMP_FILE_HPP_
-#define _BLASR_CMP_FILE_HPP_
-
-#include "reads/ReadType.hpp"
-#include "datastructures/alignment/CmpIndexedStringTable.h"
-#include "saf/AlnGroup.hpp"
-#include "saf/AlnInfo.hpp"
-#include "saf/RefGroup.hpp"
-#include "saf/RefInfo.hpp"
-#include "saf/MovieInfo.hpp"
-#include "Enumerations.h"
-
-#include <vector>
-
-class CmpFile {
- public:
- int lastRow;
- std::string readTypeString, index, version, commandLine;
- ReadType::ReadTypeEnum readType;
-
- void StoreReadType(std::string &readTypeStringP);
-
- CmpIndexedStringTable readGroupTable, movieNameTable, refSeqTable;
- vector<string> colNames;
- PlatformId platformId;
- AlnGroup alnGroup;
- AlnInfo alnInfo;
- RefGroup refGroup;
- RefInfo refInfo;
- MovieInfo movieInfo;
-};
-
-#endif
diff --git a/libcpp/alignment/datastructures/alignment/CmpIndexedStringTable.h b/libcpp/alignment/datastructures/alignment/CmpIndexedStringTable.h
deleted file mode 100644
index 2530a40..0000000
--- a/libcpp/alignment/datastructures/alignment/CmpIndexedStringTable.h
+++ /dev/null
@@ -1,67 +0,0 @@
-#ifndef DATASTRUCTURES_ALIGNMENT_CMP_INDEXED_STRING_TABLE_H_
-#define DATASTRUCTURES_ALIGNMENT_CMP_INDEXED_STRING_TABLE_H_
-
-#include <vector>
-#include <string>
-#include <map>
-using namespace std;
-
-class CmpIndexedStringTable {
- public:
-
- void resize(int size) {
- names.resize(size);
- ids.resize(size);
- }
-
- void StoreArrayIndexMap() {
- int i;
- for (i = 0; i < ids.size(); i++) {
- idToArrayIndex[ids[i]] = i;
- }
- }
-
- //
- // The terminology of Index here is confusing.
- // Actually 'Index' is equivalent to 'id'.
- // Each id represents index of an indexed string.
- // That's why an id is called an 'Index' in this function.
- // GetNameAtIndex returns name of an indexed string,
- // whose index is the given value
- //
- bool GetNameAtIndex(int index, string &name) {
- map<int,int>::iterator mapIt;
- mapIt = idToArrayIndex.find(index);
- if (mapIt != idToArrayIndex.end()) {
- name = names[mapIt->second];
- return true;
- }
- else {
- return false;
- }
- }
-
- //
- // Here 'Id' means indexes of indexed strings,
- // 'Index' means index of an 'Id' in ids
- //
- bool GetIndexOfId(int id, int &index) {
- map<int,int>::iterator mapIt;
- mapIt = idToArrayIndex.find(id);
- if (mapIt != idToArrayIndex.end()) {
- index = mapIt->second;
- return true;
- }
- else {
- return false;
- }
- }
- vector<int> ids;
- vector<string> names;
- map<int,int> idToArrayIndex;
-};
-
-
-
-
-#endif
diff --git a/libcpp/alignment/datastructures/alignment/CmpReadGroupTable.h b/libcpp/alignment/datastructures/alignment/CmpReadGroupTable.h
deleted file mode 100644
index 92a070c..0000000
--- a/libcpp/alignment/datastructures/alignment/CmpReadGroupTable.h
+++ /dev/null
@@ -1,22 +0,0 @@
-#ifndef DATASTRUCTURES_ALIGNMENT_CMP_READ_GROUP_TABLE_H_
-#define DATASTRUCTURES_ALIGNMENT_CMP_READ_GROUP_TABLE_H_
-
-#include <vector>
-#include <string>
-using namespace std;
-
-class CmpReadGroupTable {
- public:
- void resize(int size) {
- readGroupNameIds.resize(size);
- readGroupNames.resize(size);
- }
- vector<int> readGroupNameIds;
- vector<string> readGroupNames;
- int lastRow;
-};
-
-
-
-
-#endif
diff --git a/libcpp/alignment/datastructures/alignment/CmpRefSeqTable.h b/libcpp/alignment/datastructures/alignment/CmpRefSeqTable.h
deleted file mode 100644
index 91caf1b..0000000
--- a/libcpp/alignment/datastructures/alignment/CmpRefSeqTable.h
+++ /dev/null
@@ -1,22 +0,0 @@
-#ifndef DATASTRUCTURES_ALIGNMENT_CMP_REF_SEQ_TABLE_H_
-#define DATASTRUCTURES_ALIGNMENT_CMP_REF_SEQ_TABLE_H_
-
-#include <vector>
-#include <string>
-using namespace std;
-
-class CmpRefSeqTable {
- public:
- void resize(int size) {
- refSeqNameIds.resize(size);
- refSeqNames.resize(size);
- }
- vector<int> refSeqNameIds;
- vector<string> refSeqNames;
- int lastRow;
-};
-
-
-
-
-#endif
diff --git a/libcpp/alignment/datastructures/alignment/FilterCriteria.cpp b/libcpp/alignment/datastructures/alignment/FilterCriteria.cpp
deleted file mode 100644
index 16f4bff..0000000
--- a/libcpp/alignment/datastructures/alignment/FilterCriteria.cpp
+++ /dev/null
@@ -1,371 +0,0 @@
-/*
- * =====================================================================================
- *
- * Filename: FilterCriteria.h
- *
- * Description: Criteria for filtering alignment hits.
- *
- * Version: 1.0
- * Created: 04/14/2015 11:33:00 AM
- * Revision: none
- * Compiler: gcc
- *
- * Author: Yuan Li (yli), yli at pacificbiosciences.com
- * Company: Pacific Biosciences
- *
- * =====================================================================================
- */
-
-#include "FilterCriteria.hpp"
-
-Score::Score(const float & value, const ScoreSign & sign)
- : _value(value)
- , _sign(sign)
-{ }
-
-Score::Score(const Score & another)
- : _value(another._value)
- , _sign(another._sign)
-{ }
-
-Score::~Score() { }
-
-float Score::Value() const { return _value; }
-
-ScoreSign Score::Sign() const { return _sign; }
-
-bool Score::operator == (const Score & another) const {
- return (another.Value() - this->_value < errorunit and
- another.Value() - this->_value > -errorunit);
-}
-
-bool Score::BetterThan(const Score & another) const {
- if (this->_value == another.Value()) return false;
- if (this->_sign == ScoreSign::POSITIVE) return (this->_value > another.Value());
- else return (this->_value < another.Value());
-}
-
-bool Score::BetterThanOrEqual(const Score & another) const {
- return BetterThan(another) or ((*this) == another);
-}
-
-bool Score::WorseThan(const Score & another) const {
- return (not BetterThanOrEqual(another));
-}
-
-/// -----------------------------------------
-/// HitPolicy
-/// -----------------------------------------
-HitPolicy::HitPolicy(const std::string & hitPolicyStr, const ScoreSign & sign) {
- // Create a multiple hit policy.
- std::string str(hitPolicyStr);
- std::transform(str.begin(), str.end(), str.begin(), ::toupper);
-
- if (str == "RANDOM") { _hit = HitPolicyEnum::RANDOM; }
- else if (str == "ALL") { _hit = HitPolicyEnum::ALL; }
- else if (str == "ALLBEST") { _hit = HitPolicyEnum::ALLBEST; }
- else if (str == "RANDOMBEST") { _hit = HitPolicyEnum::RANDOMBEST; }
- else if (str == "LEFTMOST") { _hit = HitPolicyEnum::LEFTMOST; }
- else {
- std::cout <<"ERROR, the specified multiple hit policy "
- << hitPolicyStr <<" is not supported." << std::endl;
- exit(1);
- }
-
- _sign = sign;
-}
-
-HitPolicy::~HitPolicy(void) { }
-
-ScoreSign HitPolicy::Sign() const {
- return _sign;
-}
-
-bool HitPolicy::IsRandom() const { return _hit == HitPolicyEnum::RANDOM; }
-
-bool HitPolicy::IsRandombest() const { return _hit == HitPolicyEnum::RANDOMBEST; }
-
-bool HitPolicy::IsAll() const {return _hit == HitPolicyEnum::ALL; }
-
-bool HitPolicy::IsAllbest() const {return _hit == HitPolicyEnum::ALLBEST; }
-
-bool HitPolicy::IsLeftmost() const {return _hit == HitPolicyEnum::LEFTMOST; }
-
-const std::string HitPolicy::ToString() const {
- switch (_hit) {
- case (HitPolicyEnum::RANDOM) : return "random";
- case (HitPolicyEnum::RANDOMBEST): return "randombest";
- case (HitPolicyEnum::ALL) : return "all";
- case (HitPolicyEnum::ALLBEST) : return "allbest";
- case (HitPolicyEnum::LEFTMOST) : return "leftmost";
- default: {
- assert(false);
- }
- }
-}
-
-std::ostream & HitPolicy::operator << (std::ostream & os) {
- return os << this->ToString();
-}
-
-const std::string HitPolicy::Help(const std::string & pad) const{
- std::stringstream ss;
- ss << "(" << this->ToString()
- << ") Specify a policy to treat multiple hits from "
- << "[all, allbest, random, randombest, leftmost]\n" << pad
- << " all : report all alignments.\n" << pad
- << " allbest : report all equally top scoring alignments.\n" << pad
- << " random : report a random alignment.\n" << pad
- << " randombest: report a random alignment from multiple "
- << "equally top scoring alignments.\n" << pad
- << " leftmost : report an alignment which has the best alignment"
- << "score and has the smallest mapping coordinate in any reference.";
- return ss.str();
-}
-
-std::vector<T_AlignmentCandidate*>
-HitPolicy::Apply(const std::vector<T_AlignmentCandidate*> alnPtrs,
- const bool & createRand,
- const int & passedRand) const {
- // Shallow copy pointers.
- if (alnPtrs.empty() or IsAll()) return alnPtrs;
-
- int rint = createRand?rand():passedRand;
- if (IsRandom()) {
- return std::vector<T_AlignmentCandidate*>({alnPtrs[rint%alnPtrs.size()]});
- }
-
- std::vector<T_AlignmentCandidate*> ret = alnPtrs;
- // Sort AlignmentCandidate pointers according to score and target start position.
- ScoreSign sign = this->Sign();
- std::sort(ret.begin(), ret.end(), SortAlignmentPointersByScore());
-
- // Get the best alignments whose alignment scores are the best.
- // Assume that input alignments share the same query name and
- // are sorted by score and tPos asscendingly: worst, ...., best
- int bestScore = ret[0]->score;
- ret.erase(std::remove_if(ret.begin(), ret.end(),
- [&bestScore](const T_AlignmentCandidate* x)->bool{return x->score != bestScore;}),
- ret.end());
-
- if (IsAllbest()) {
- return ret;
- } else if (IsRandombest()) {
- return std::vector<T_AlignmentCandidate*>({ret[rint%ret.size()]});
- } else if (IsLeftmost()) {
- return std::vector<T_AlignmentCandidate*>({ret[0]});
- } else {
- assert("Unsupported hit policy" == 0);
- }
-}
-
-/*
-std::vector<AlignmentCandidate<>> HitPolicy::Apply(std::vector<AlignmentCandidate<>> & records) const {
- if (records.empty() or IsALL()) return;
- sort(records.begin(), records.end(), compareByQNameScoreTStart);
- assert(records.size() > 0);
-
- if (IsRandom) {
- //records = vector<AlignmentCandidate>({records[
- }
-}
-*/
-
-#ifdef USE_PBBAM
-bool HitPolicy::compareByQNameScoreTStart(const PacBio::BAM::BamRecord & a, const PacBio::BAM::BamRecord & b) const {
- assert(a.Impl().HasTag(AS) and b.Impl().HasTag(AS));
- const int aScore = a.Impl().TagValue(AS).ToInt32();
- const int bScore = b.Impl().TagValue(AS).ToInt32();
- if (a.FullName() == b.FullName()) {
- if (aScore == bScore)
- return a.ReferenceStart() < b.ReferenceEnd();
- return Score(aScore, _sign).WorseThan(Score(bScore, _sign));
- }
- return (a.FullName() < b.FullName());
-}
-
-bool HitPolicy::compareByScoreTStart(const PacBio::BAM::BamRecord & a, const PacBio::BAM::BamRecord & b) const {
- assert(a.Impl().HasTag(AS) and b.Impl().HasTag(AS));
- assert(a.FullName() == b.FullName());
- const int aScore = a.Impl().TagValue(AS).ToInt32();
- const int bScore = b.Impl().TagValue(AS).ToInt32();
- if (aScore == bScore)
- return a.ReferenceStart() < b.ReferenceEnd();
- return Score(aScore, _sign).WorseThan(Score(bScore, _sign));
-}
-
-std::vector<PacBio::BAM::BamRecord>
-HitPolicy::Apply(const std::vector<PacBio::BAM::BamRecord> & records,
- const bool & createRand,
- const int & passedRand) const {
- if (records.empty() or IsAll()) return records;
-
- int rint = createRand?rand():passedRand;
- //cout << "FilterCriteria " << ", " << records[0].FullName() << ", " << rint << endl;
- if (IsRandom()) {
- return std::vector<PacBio::BAM::BamRecord>({records[rint%records.size()]});
- }
-
- std::vector<PacBio::BAM::BamRecord> ret = records;
- // Sort bam records according to score and target start position.
- ScoreSign sign = this->Sign();
- std::sort(ret.begin(), ret.end(),
- [&sign](const PacBio::BAM::BamRecord & a,
- const PacBio::BAM::BamRecord & b)->bool {
- assert(a.Impl().HasTag(AS) and b.Impl().HasTag(AS));
- assert(a.FullName() == b.FullName());
- const int aScore = a.Impl().TagValue(AS).ToInt32();
- const int bScore = b.Impl().TagValue(AS).ToInt32();
- if (aScore == bScore) return a.ReferenceStart() < b.ReferenceEnd();
- else return Score(aScore, sign).WorseThan(Score(bScore, sign));
- });
-
- // Get the best alignments whose alignment scores are the best.
- // Assume that input alignments share the same query name and
- // are sorted by score and tPos asscendingly: worst, ...., best
- int bestScore = ret[0].Impl().TagValue(AS).ToInt32();
- ret.erase(std::remove_if(ret.begin(), ret.end(),
- [&bestScore](const PacBio::BAM::BamRecord & x)->bool{return x.Impl().TagValue(AS).ToInt32() != bestScore;}),
- ret.end());
-
- if (IsAllbest()) {
- return ret;
- } else if (IsRandombest()) {
- return std::vector<PacBio::BAM::BamRecord>({ret[rint%ret.size()]});
- } else if (IsLeftmost()) {
- return std::vector<PacBio::BAM::BamRecord>({ret[0]});
- } else {
- assert("Unsupported hit policy" == 0);
- }
-}
-#endif
-
-/// -----------------------------------------
-/// FilterCriteria
-/// -----------------------------------------
-FilterCriteria::FilterCriteria(const DNALength & minAlnLength,
- const float & minPctSimilarity,
- const float & minPctAccuracy,
- const bool & useScore,
- const Score & score)
- : _minAlnLength(minAlnLength)
- , _minPctSimilarity(minPctSimilarity)
- , _minPctAccuracy(minPctAccuracy)
- , _useScore(useScore)
- , _scoreCutoff(score)
- , _verbose(false)
-{ }
-
-FilterCriteria::~FilterCriteria(void) { }
-
-/*
-const std::string FilterCriteria::Help(const std::string & pad) {
- return std::string (pad + minAlnLengthHelp() +
- pad + minPctSimilarityHelp() +
- pad + minPctAccuracyHelp() +
- pad + scoreSignHelp() +
- pad + scoreCutoffHelp());
-}*/
-
-const std::string FilterCriteria::MinAlnLengthHelp() {
- return std::string("(") + std::to_string(_minAlnLength) + ") " +
- "Report alignments only if their lengths are greater than minAlnLength.";
-}
-
-const std::string FilterCriteria::MinPctSimilarityHelp() {
- return std::string("(") + std::to_string(static_cast<int>(_minPctSimilarity)) + ") " +
- "Report alignments only if their percentage similairty is greater than minPctSimilarity.";
-}
-
-const std::string FilterCriteria::MinPctAccuracyHelp() {
- return std::string("(") + std::to_string(static_cast<int>(_minPctAccuracy)) + ") " +
- "Report alignments only if their percentage accuray is greater than minAccuracy.";
-}
-
-const std::string FilterCriteria::ScoreSignHelp() {
- return "(-1) Whether higher or lower scores are better. -1: lower is better; 1: higher is better.";
-}
-
-const std::string FilterCriteria::ScoreCutoffHelp() {
- return "(INF) Report alignments only if their scores are no worse than score cut off.";
-}
-
-bool FilterCriteria::MakeSane(std::string & errMsg) const{
- if (_minPctSimilarity > 100 or _minPctSimilarity < 0) {
- errMsg = "ERROR, minimum similarity not in [0, 100].";
- return false;
- }
- if (_minPctAccuracy > 100 or _minPctAccuracy < 0) {
- errMsg = "ERROR, minimum accuracy not in [0, 100].";
- return false;
- }
- return true;
-}
-
-void FilterCriteria::Verbose(bool verbose) { _verbose = verbose; }
-
-/*
-template<typename T_TSequence, typename T_QSequence>
-bool FilterCriteria::Satisfy(AlignmentCandidate<T_TSequence, T_QSequence> & a) const;
-//bool FilterCriteria::Satisfy(AlignmentCandidate<> & a) const {
- float pctAccuracy = 100 * a.nMatch / static_cast<float>(a.nMismatch
- + a.nMatch + a.nIns + a.nDel);
- Score s(a.score, _scoreCutoff.Sign());
- return Satisfy(a.qAlignedSeqLength, a.pctSimilarity, pctAccuracy, s);
-}
-*/
-
-bool FilterCriteria::Satisfy(const DNALength & alnLength,
- const float & pctSimilarity,
- const float & pctAccuracy,
- const Score & score) const {
- if (alnLength < _minAlnLength) {
- if (_verbose > 0)
- std::cout << "Alignment length " << alnLength << " is too short." << std::endl;
- return false;
- }
- if (pctSimilarity < _minPctSimilarity) {
- if (_verbose > 0)
- std::cout << "Percentage similarity " << pctSimilarity << " is too low." << std::endl;
- return false;
- }
- if (pctAccuracy < _minPctAccuracy) {
- if (_verbose > 0)
- std::cout << "Percentage accuracy " << pctAccuracy << " is too low." << std::endl;
- return false;
- }
- if (_useScore and not score.BetterThanOrEqual(_scoreCutoff)) {
- if (_verbose)
- std::cout << "Alignment score " << score.Value() << " worse than cut off." << std::endl;
- return false;
- }
-
- return true;
-}
-
-#ifdef USE_PBBAM
-bool FilterCriteria::Satisfy(const PacBio::BAM::BamRecord & record) const {
- assert(record.IsMapped() and record.Impl().HasTag(AS));
- DNALength alnLength = static_cast<DNALength>(record.Sequence(PacBio::BAM::Orientation::NATIVE, true, true).size());
- PacBio::BAM::Cigar cigar = record.CigarData();
-
- uint32_t nMatch = 0, nMismatch = 0, nIns = 0, nDel = 0;
- for(auto op: cigar) {
- uint32_t n = op.Length();
- switch (op.Type()) {
- case PacBio::BAM::CigarOperationType::SEQUENCE_MATCH: nMatch += n; break;
- case PacBio::BAM::CigarOperationType::SEQUENCE_MISMATCH: nMismatch += n; break;
- case PacBio::BAM::CigarOperationType::ALIGNMENT_MATCH: nMismatch += n; break;
- case PacBio::BAM::CigarOperationType::INSERTION: nIns += n; break;
- case PacBio::BAM::CigarOperationType::DELETION: nDel += n; break;
- default: break;
- }
- }
- //TODO: Use = X instead of M in blasr.
-
- float pctSimilarity = 100 * nMatch / static_cast<float>(alnLength);
- float pctAccuracy = 100 * nMatch / static_cast<float>(nMismatch + nMatch + nIns + nDel);
- Score s(static_cast<float>(record.Impl().TagValue("AS").ToInt32()), ScoreSign::NEGATIVE);
- return Satisfy(alnLength, pctSimilarity, pctAccuracy, s);
-}
-#endif
diff --git a/libcpp/alignment/datastructures/alignment/FilterCriteria.hpp b/libcpp/alignment/datastructures/alignment/FilterCriteria.hpp
deleted file mode 100644
index 778e659..0000000
--- a/libcpp/alignment/datastructures/alignment/FilterCriteria.hpp
+++ /dev/null
@@ -1,165 +0,0 @@
-#ifndef _BLASR_FILTER_CRITERIA_HPP_
-#define _BLASR_FILTER_CRITERIA_HPP_
-#include <string>
-#include <iostream>
-#include <vector>
-#include <algorithm> // transform
-#include <ctype.h> // toupper
-#include "AlignmentCandidate.hpp"
-
-
-/// POSITIVE - larger score value is better.
-/// NEGATIVE - smaller score value is better.
-enum class ScoreSign {NEGATIVE=-1, POSITIVE=1};
-static const std::string AS = "AS";
-
-class Score {
-public:
- Score(const float & value, const ScoreSign & sign);
- Score(const Score & another);
- ~Score();
-
- /// \returns float score value in [0, 100]
- float Value() const;
-
- /// \returns score sign, NEGATIVE or POSITIVE
- ScoreSign Sign() const;
-
- bool operator == (const Score & another) const;
-
- /// \returns true if this score value is better than another's.
- bool BetterThan(const Score & another) const;
-
- /// \returns true if this score value is better than or equal to another's.
- bool BetterThanOrEqual(const Score & another) const;
-
- /// \returns true if this score value is worse than another's.
- bool WorseThan(const Score & another) const;
-
-private:
- float _value;
- ScoreSign _sign;
- static constexpr float errorunit = 1e-6;
-};
-
-class HitPolicy {
- /// \name Hit Policy
- /// \{
-public:
-
- /// \note Constructor
- HitPolicy(const std::string & hitPolicyStr, const ScoreSign & sign);
- ~HitPolicy(void);
-
- const std::string ToString() const;
- std::ostream & operator << (std::ostream & os);
-
- /// \returns score sign, NEGATIVE or POSITIVE
- ScoreSign Sign() const;
-
- /// \returns a help string describing hit policies.
- const std::string Help(const std::string & pad = "") const;
-
- /// \returns true if HitPolicy is RANDOM.
- bool IsRandom() const;
-
- /// \returns true if HitPolicy is RANDOMBEST.
- bool IsRandombest() const;
-
- /// \returns true if HitPolicy is ALL.
- bool IsAll() const;
-
- /// \returns true if HitPolicy is ALLBEST.
- bool IsAllbest() const;
-
- /// \returns true if HitPolicy is LEFTMOST.
- bool IsLeftmost() const;
-
- /// Apply hit policy on a list of AlignmentCandidate pointers.
- /// \returns apply hit policy and return alignment candidate pointers.
- /// \params createRand, call rand() to generate a random number
- /// or use the random number passed from caller.
- /// \params passedRand, random int passed from caller
- std::vector<T_AlignmentCandidate*>
- Apply(const std::vector<T_AlignmentCandidate*> alnPtrs,
- const bool & createRand = true,
- const int & passedRand = 0) const;
-
- //std::vector<AlignmentCandidate<>> &
- //Apply(std::vector<AlignmentCandidate<>> & records) const;
-
-#ifdef USE_PBBAM
- /// Compare aligned bamRecords by query names, scores and target positions.
- bool compareByQNameScoreTStart(const PacBio::BAM::BamRecord & a,
- const PacBio::BAM::BamRecord & b) const;
-
- /// Compare aligned bamRecords by scores and target positions.
- /// \note BamRecords must share the same query name.
- bool compareByScoreTStart(const PacBio::BAM::BamRecord & a,
- const PacBio::BAM::BamRecord & b) const;
-
- std::vector<PacBio::BAM::BamRecord>
- Apply(const std::vector<PacBio::BAM::BamRecord> & records,
- const bool & createRand = true,
- const int & passedRand = 0) const;
-#endif
-
-private:
- enum class HitPolicyEnum{RANDOM, ALL, ALLBEST, RANDOMBEST, LEFTMOST};
- HitPolicyEnum _hit;
- ScoreSign _sign;
- /// \}
-};
-
-class FilterCriteria {
- /// \name FilterCriteria
- /// \{
-public:
- FilterCriteria(const DNALength & minAlnLength,
- const float & minPctSimilarity,
- const float & minPctAccuracy,
- const bool & useScore,
- const Score & score);
- ~FilterCriteria(void);
- bool MakeSane(std::string & errMsg) const;
- void Verbose(bool verbose);
-
- template<typename T_TSequence, typename T_QSequence>
- bool Satisfy(AlignmentCandidate<T_TSequence, T_QSequence> * a) const;
-
-#ifdef USE_PBBAM
- bool Satisfy(const PacBio::BAM::BamRecord & record) const;
-#endif
-
-public:
- /// \retuns a string describing criteria for filtering alignments.
- // const std::string Help(const std::string & pad = "");
- const std::string MinAlnLengthHelp();
- const std::string MinPctSimilarityHelp();
- const std::string MinPctAccuracyHelp();
- const std::string ScoreSignHelp();
- const std::string ScoreCutoffHelp();
-
-private:
- DNALength _minAlnLength;
- float _minPctSimilarity;
- float _minPctAccuracy;
- bool _useScore;
- Score _scoreCutoff;
- bool _verbose;
-
- bool Satisfy(const DNALength & alnLength,
- const float & pctSimilarity,
- const float & pctAccuracy,
- const Score & score) const;
- /// \}
-};
-
-template<typename T_TSequence, typename T_QSequence>
-bool FilterCriteria::Satisfy(AlignmentCandidate<T_TSequence, T_QSequence> * a) const {
- float pctAccuracy = 100 * a->nMatch / static_cast<float>(a->nMismatch
- + a->nMatch + a->nIns + a->nDel);
- Score s(a->score, _scoreCutoff.Sign());
- return Satisfy(a->qAlignedSeqLength, a->pctSimilarity, pctAccuracy, s);
-}
-#endif //_BLASR_FILTER_CRITERIA_HPP_
diff --git a/libcpp/alignment/datastructures/alignment/Path.h b/libcpp/alignment/datastructures/alignment/Path.h
deleted file mode 100644
index a71b605..0000000
--- a/libcpp/alignment/datastructures/alignment/Path.h
+++ /dev/null
@@ -1,23 +0,0 @@
-#ifndef _BLASR_PATH_H_
-#define _BLASR_PATH_H_
-
-enum Arrow { Diagonal, Up, Left,
- AffineInsUp, AffineInsOpen, AffineInsClose,
- AffineDelLeft, AffineDelOpen, AffineDelClose,
- AffineHPInsUp, AffineHPInsOpen, AffineHPInsClose,
- NoArrow,
- DiagonalXYZ,
- InsertX,InsertY,InsertZ, // imply diagonal yz/xz/xy
- DiagonalXY, DiagonalYZ, DiagonalXZ, // imply insertion of Z/X/Y,
- //
- // These are used to denote an affine gap has been closed
- // from a different matrix. This is used in OneGap alignment.
- //
- AffineLongDelLeft, AffineLongDelClose,
- AffineLongIns, AffineLongInsClose,
- Star
-};
-
-enum MatrixLabel {Match, AffineHPIns, AffineIns, AffineDel, AffineHPDel};
-
-#endif
diff --git a/libcpp/alignment/datastructures/alignment/SAMToAlignmentCandidateAdapter.cpp b/libcpp/alignment/datastructures/alignment/SAMToAlignmentCandidateAdapter.cpp
deleted file mode 100644
index 32de362..0000000
--- a/libcpp/alignment/datastructures/alignment/SAMToAlignmentCandidateAdapter.cpp
+++ /dev/null
@@ -1,461 +0,0 @@
-#include <algorithm>
-#include "utils/SMRTTitle.hpp"
-#include "SAMToAlignmentCandidateAdapter.hpp"
-
-void InitializeCandidateFromSAM(SAMAlignment &sam,
- AlignmentCandidate<> &candidate) {
- candidate.qName = sam.qName;
- candidate.tName = sam.rName;
- candidate.tPos = sam.pos;
- candidate.mapQV = sam.mapQV;
-}
-
-int ProcessGap(std::vector<int> &lengths, std::vector<char> &ops,
- int &opIndex, int opEnd, blasr::GapList &gaps,
- int &qAdvance, int &tAdvance) {
- //
- // Default is no gap.
- //
- qAdvance = tAdvance = 0;
- gaps.clear();
- if (opIndex >= lengths.size()) {
- return opIndex;
- }
-
- //
- // Look to see if the suffix of operations stars with a gap.
- //
- if (ops[opIndex] != 'I' and
- ops[opIndex] != 'D') {
- return opIndex;
- }
-
- while (opIndex < opEnd and (ops[opIndex] == 'I' or ops[opIndex] == 'D')) {
- if (ops[opIndex] == 'I') {
- gaps.push_back(blasr::Gap(blasr::Gap::Target, lengths[opIndex]));
- qAdvance += lengths[opIndex];
- }
- else {
- assert(ops[opIndex] == 'D');
- gaps.push_back(blasr::Gap(blasr::Gap::Query, lengths[opIndex]));
- tAdvance += lengths[opIndex];
- }
- opIndex++;
- }
- return opIndex;
-}
-
-int AdvancePastClipping(std::vector<int> &lengths,
- std::vector<char> &ops,
- int &opIndex,
- int &numSoftClipped) {
- int numClipped = 0;
- numSoftClipped = 0;
- while (opIndex < lengths.size() and IsClipping(ops[opIndex])) {
- numClipped += lengths[opIndex];
- if (ops[opIndex] == 'S') {
- numSoftClipped+= lengths[opIndex];
- }
-
- ++opIndex;
- }
- return numClipped;
-}
-
-int AdvancePastSkipped(std::vector<int> &lengths,
- std::vector<char> &ops,
- int &opIndex) {
- int numSkipped = 0;
- while (opIndex < lengths.size() and IsSkipped(ops[opIndex])) {
- numSkipped += lengths[opIndex];
- opIndex++;
- }
- return numSkipped;
-}
-
-int ProcessMatch(std::vector<int> &lengths, std::vector<char> &ops,
- int &opIndex, int opEnd) {
-
- //
- // Make sure this starts on some sort of blockn
- //
-
- int blockLength = 0;
- while (opIndex < opEnd and (IsAssignChar(ops[opIndex]))) {
- blockLength += lengths[opIndex];
- opIndex++;
- }
- return blockLength;
-}
-
-void CIGAROpsToBlocks(std::vector<int> &lengths, std::vector<char> &ops,
- int cigarStart,
- int cigarEnd,
- AlignmentCandidate<> &aln) {
- cigarStart = 0;
- cigarEnd = lengths.size();
- CIGAROpsToBlocks(lengths, ops, cigarStart, cigarEnd, aln);
-}
-
-int AdvancePosToAlignmentEnd(std::vector<char> &ops, int &pos) {
- int start = pos;
- while (pos < ops.size() and ops[pos] != 'N' and !IsClipping(ops[pos])) {
- pos++;
- }
- return pos - start;
-}
-
-int GetAlignedQueryLengthByCIGARSum(std::vector<char> &ops, std::vector<int> &lengths) {
- int i;
- for (i = 0; i < ops.size(); i++) {
- if (ops[i] != 'S' && ops[i] != 'H') {
- break;
- }
- }
- int queryLength = 0;
- for (; i < ops.size() && ops[i] != 'S' && ops[i] != 'H'; i++) {
- if (IsAssignChar(ops[i]) or ops[i] == 'I' or ops[i] == 'N') {
- queryLength += lengths[i];
- }
- }
- return queryLength;
-}
-
-int GetAlignedReferenceLengthByCIGARSum(std::vector<char> &ops, std::vector<int> &lengths) {
- int i;
- for (i = 0; i < ops.size(); i++) {
- if (ops[i] != 'S' && ops[i] != 'H') {
- break;
- }
- }
- int refLength = 0;
- for (; i < ops.size() && ops[i] != 'S' && ops[i] != 'H'; i++) {
- if (IsAssignChar(ops[i]) or ops[i] == 'D' or ops[i] == 'N') {
- refLength += lengths[i];
- }
- }
- return refLength;
-}
-
-void CIGAROpsToBlocks(std::vector<int> &lengths, std::vector<char> &ops,
- int &cigarPos,
- int &cigarEnd,
- int &qPos, int &tPos,
- AlignmentCandidate<> &aln) {
-
- int gapIndex = 0;
- DNALength qStart = qPos, tStart = tPos;
- assert(cigarPos >= cigarEnd or !IsClipping(ops[cigarPos]));
-
- //
- // Advance past any skipped portion.
- //
- int numSkipped = AdvancePastSkipped(lengths, ops, cigarPos);
- tPos += numSkipped;
-
- //
- // Process the gaps before the first match.
- //
-
- //
- // If there is nothing left, just bail.
- blasr::GapList gap;
-
- cigarEnd = cigarPos;
- AdvancePosToAlignmentEnd(ops, cigarEnd);
- if (cigarPos >= cigarEnd) {
- return;
- }
-
- //
- // Process any gap that the aligner produces before the first match
- // begins.
- //
- int qAdvance, tAdvance;
- ProcessGap(lengths, ops, cigarPos, cigarEnd, gap, qAdvance, tAdvance);
- aln.gaps.push_back(gap);
- qPos += qAdvance;
- tPos += tAdvance;
- //
- // Now add gaps.
- //
- while(cigarPos < cigarEnd) {
- //
- // The next operation must be a match.
- //
- int matchLength = ProcessMatch(lengths, ops, cigarPos, cigarEnd);
- blasr::Block b;
- b.qPos = qPos - qStart;
- b.tPos = tPos - tStart;
- b.length = matchLength;
- aln.blocks.push_back(b);
- qPos += b.length;
- tPos += b.length;
-
- ProcessGap(lengths, ops, cigarPos, cigarEnd, gap, qAdvance, tAdvance);
- aln.gaps.push_back(gap);
- tPos += tAdvance;
- qPos += qAdvance;
- }
-
-}
-
-void SAMAlignmentsToCandidates(SAMAlignment &sam,
- std::vector<FASTASequence> &referenceSequences,
- std::map<std::string,int> & refNameToRefListIndex,
- std::vector<AlignmentCandidate<> > &candidates,
- bool parseSmrtTitle,
- bool keepRefAsForward,
- bool copyQVs) {
- //
- // First determine how many alignments there are from CIGAR string.
- //
- std::vector<int> lengths;
- std::vector<char> ops;
- sam.cigar.Vectorize(lengths, ops);
-
- DNASequence querySeq;
- // For now just reference the query sequence.
- querySeq.deleteOnExit = false;
- querySeq.seq = (Nucleotide*) sam.seq.c_str();
- querySeq.length = sam.seq.size();
-
- DNALength samTEnd = 0;
- DNALength samTStart = sam.pos - 1;
-
- std::vector<std::string> optionalQVs;
- if (copyQVs) {
- sam.CopyQVs(&optionalQVs);
- }
- if (keepRefAsForward == false and IsReverseComplement(sam.flag)) {
- ReverseAlignmentOperations(lengths, ops);
- DNASequence rcQuerySeq;
- querySeq.CopyAsRC(rcQuerySeq);
- //
- // Zero out the query seq so that the string memory is not
- // deleted.
- //
- querySeq.seq = NULL;
- querySeq.length = 0;
- querySeq = rcQuerySeq;
- rcQuerySeq.Free();
- samTEnd = GetAlignedReferenceLengthByCIGARSum(ops, lengths);
-
- // We also need to reverse any optional QVs
- if (copyQVs) {
- for(int i=0; i<optionalQVs.size(); i++) {
- std::reverse(optionalQVs[i].begin(), optionalQVs[i].end());
- }
- }
- }
-
-
- int i;
- int offset = 0;
- if (ops.size() == 0) {
- return;
- }
- bool alignmentStarted = false;
- bool onFirstMatch = true;
- int curAlignment;
-
- //
- // Advance past any clipping. This advances in both query and
- // reference position.
- //
- int cigarPos = 0;
- int qPos = 0;
- int tPos = 0;
-
- DNALength queryPosOffset = 0;
- if (parseSmrtTitle) {
- //
- // The aligned sequence is really a subread of a full
- // sequence. The position of the aligments start at 0, the
- // beginning of the query sequence, but in the sam file, they
- // may appear as subreads, and are offset from the start of the
- // subread. By convention, the subread coordinates are embedded
- // in the title of the query, if it is a smrtTitle.
- // Two types of smrtTitle are supported:
- // movie/zmw/start_end
- // movie/zmw/start_end/start2_end2
- SMRTTitle stitle = SMRTTitle(sam.qName);
-
- if (not stitle.isSMRTTitle) {
- std::cout << "ERROR. Could not parse title " << sam.qName << std::endl;
- exit(1);
- }
- queryPosOffset = stitle.start;
- }
- else if (sam.xs) {
- queryPosOffset += sam.xs - 1;
- }
-
-
- while (cigarPos < lengths.size()) {
- int numClipped;
- //
- // Sequence clipping becomes offsets into the q/t alignedSeqPos
- //
-
-
- int numSoftClipped;
- numClipped = AdvancePastClipping(lengths, ops, cigarPos, numSoftClipped);
-
- //
- // End loop now.
- //
- if (cigarPos >= lengths.size()) {
- break;
- }
- qPos += numSoftClipped;
-
- //
- // Skipped sequences are just advances in the tPos.
- //
- int numSkipped = AdvancePastSkipped(lengths, ops, cigarPos);
- tPos += numSkipped;
-
- if (cigarPos >= lengths.size()) {
- break;
- }
-
-
- AlignmentCandidate<> alignment;
- //
- // The aligned sequence must start at a match therefore the tpos
- // and qpos are 0.
- //
- alignment.qPos = 0;
- alignment.tPos = 0;
-
- // qAlignStart is the start of the alignment relative to the sequence in the SAM file.
- DNALength qAlignStart = qPos;
- // tAlignStart is the start of the alignment in the genome.
- DNALength tAlignStart = tPos;
-
- int cigarEnd = cigarPos;
- AdvancePosToAlignmentEnd(ops, cigarEnd);
-
- CIGAROpsToBlocks(lengths, ops,
- cigarPos, cigarEnd,
- qPos, tPos,
- alignment);
-
-
- DNALength queryLengthSum = GetAlignedQueryLengthByCIGARSum(ops, lengths);
- DNALength refLengthSum = GetAlignedReferenceLengthByCIGARSum(ops, lengths);
- alignment.qAlignedSeqLength = qPos - qAlignStart;
- alignment.tAlignedSeqLength = tPos - tAlignStart;
-
- //
- // Assign candidate sequences.
- //
- // First, the query sequence is straight from the SAM line.
- ((DNASequence*)&alignment.qAlignedSeq)->Copy(querySeq, qAlignStart, alignment.qAlignedSeqLength);
- if (copyQVs) {
- alignment.ReadOptionalQVs(optionalQVs, qAlignStart, alignment.qAlignedSeqLength);
- }
-
- // The SAM Alignments a
- alignment.qStrand = IsReverseComplement(sam.flag);
- alignment.tStrand = 0;
- alignment.mapQV = sam.mapQV;
-
- //
- // Assign the offsets into the original sequence where the
- // subsequence starts.
- //
-
- alignment.qAlignedSeqPos = queryPosOffset + qAlignStart;
- alignment.tAlignedSeqPos = samTStart + tAlignStart;
-
- if (sam.rName == "*") {
- //
- // No reference, do not add the alignment to the list of
- // candidates.
- //
- continue;
- }
- else {
- int refIndex;
- int s = refNameToRefListIndex.size();
- if (refNameToRefListIndex.find(sam.rName) == refNameToRefListIndex.end()) {
- std::cout <<" ERROR. SAM Reference " << sam.rName << " is not found in the list of reference contigs." << std::endl;
- exit(1);
- }
-
- refIndex = refNameToRefListIndex[sam.rName];
-
- alignment.tLength = referenceSequences[refIndex].length;
- alignment.qLength = sam.seq.size();
- alignment.qName = sam.qName;
- alignment.tName = sam.rName;
-
-
- if (keepRefAsForward == false and alignment.qStrand == 1) {
-
- //
- // Now that the reference sequence has been copied, if it is
- // on the reverse strand, make the reverse complement for
- // proper printing.
- //
- alignment.tAlignedSeqPos = samTStart + (samTEnd - tAlignStart - alignment.tAlignedSeqLength);
- if (alignment.tAlignedSeqLength > referenceSequences[refIndex].length ||
- alignment.tAlignedSeqPos > referenceSequences[refIndex].length ||
- alignment.tAlignedSeqLength + alignment.tAlignedSeqPos > referenceSequences[refIndex].length + 2) {
- //alignment.tAlignedSeqPos is 1 based and unsigned.
- std::cout << "WARNING. The mapping of read " << alignment.qName
- << " to reference " << alignment.tName
- << " is out of bounds." << std::endl
- << " StartPos (" << alignment.tAlignedSeqPos
- << ") + AlnLength (" << alignment.tAlignedSeqLength
- << ") > RefLength (" << referenceSequences[refIndex].length
- << ") + 2 " << std::endl;
- continue;
- }
- ((DNASequence*)&alignment.tAlignedSeq)->Copy(referenceSequences[refIndex], alignment.tAlignedSeqPos, alignment.tAlignedSeqLength);
- alignment.tAlignedSeq.ReverseComplementSelf();
- // either ref or read is defined as being in the forward
- // orientation. Here, since refAsForward is false, the read
- // is forward. Since the read is forward, the aligned
- // sequences are stored as the reverse complement of the read
- // and the references.
- //
- alignment.tStrand = 1;
- alignment.qStrand = 0;
- }
- else {
- if (alignment.tAlignedSeqLength > referenceSequences[refIndex].length ||
- alignment.tAlignedSeqPos > referenceSequences[refIndex].length ||
- alignment.tAlignedSeqLength + alignment.tAlignedSeqPos > referenceSequences[refIndex].length + 2) {
- //alignment.tAlignedSeqPos is 1 based and unsigned.
- std::cout << "WARNING. The mapping of read " << alignment.qName
- << " to reference " << alignment.tName
- << " is out of bounds." << std::endl
- << " StartPos (" << alignment.tAlignedSeqPos
- << ") + AlnLength (" << alignment.tAlignedSeqLength
- << ") > RefLength (" << referenceSequences[refIndex].length
- << ") + 2 " << std::endl;
- continue;
- }
- ((DNASequence*)&alignment.tAlignedSeq)->Copy(referenceSequences[refIndex],
- alignment.tAlignedSeqPos,
- alignment.tAlignedSeqLength);
- }
- }
-
- if (alignment.blocks.size() > 0) {
- candidates.push_back(alignment);
- }
- }
- if (candidates.size() > 0 and keepRefAsForward == false and candidates[0].tStrand == 1) {
- std::reverse(candidates.begin(), candidates.end());
- }
- querySeq.Free();
-}
-
-void ReverseAlignmentOperations(std::vector<int> &lengths, std::vector<char> &ops) {
- reverse(lengths.begin(), lengths.end());
- reverse(ops.begin(), ops.end());
-}
diff --git a/libcpp/alignment/datastructures/alignment/SAMToAlignmentCandidateAdapter.hpp b/libcpp/alignment/datastructures/alignment/SAMToAlignmentCandidateAdapter.hpp
deleted file mode 100644
index 344aa60..0000000
--- a/libcpp/alignment/datastructures/alignment/SAMToAlignmentCandidateAdapter.hpp
+++ /dev/null
@@ -1,79 +0,0 @@
-#ifndef _BLASR_SAM_TO_ALIGNMENT_CANDIDATE_ADAPTER_HPP_
-#define _BLASR_SAM_TO_ALIGNMENT_CANDIDATE_ADAPTER_HPP_
-
-#include <map>
-
-#include "sam/SAMAlignment.hpp"
-#include "sam/SAMFlag.h"
-#include "datastructures/alignment/AlignmentCandidate.hpp"
-
-void InitializeCandidateFromSAM(SAMAlignment &sam,
- AlignmentCandidate<> &candidate);
-
-//
-// Change a list of gap operations into a gap structure between
-// blocks.
-//
-int ProcessGap(std::vector<int> &lengths, std::vector<char> &ops,
- int &opIndex, int opEnd, blasr::GapList &gaps,
- int &qAdvance, int &tAdvance);
-
-inline bool IsClipping(char c) {
- return (c == 'S' or c == 'H');
-}
-
-inline int IsSkipped(char c) {
- return c == 'N';
-}
-//
-//
-// Returns true if the corresponding characters are assigned to each
-// other in the alignment. This is either a match or a mismatch.
-//
-
-inline bool IsAssignChar(char c) {
- return (c == 'M' or c == 'X' or c == '=');
-}
-
-int AdvancePastClipping(std::vector<int> &lengths,
- std::vector<char> &ops,
- int &opIndex,
- int &numSoftClipped);
-
-int AdvancePastSkipped(std::vector<int> &lengths,
- std::vector<char> &ops,
- int &opIndex);
-
-
-
-int ProcessMatch(std::vector<int> &lengths, std::vector<char> &ops,
- int &opIndex, int opEnd);
-
-
-void CIGAROpsToBlocks(std::vector<int> &lengths, std::vector<char> &ops,
- int cigarStart,
- int cigarEnd,
- AlignmentCandidate<> &aln);
-
-int AdvancePosToAlignmentEnd(std::vector<char> &ops, int &pos);
-
-int GetAlignedQueryLengthByCIGARSum(std::vector<char> &ops, std::vector<int> &lengths);
-
-int GetAlignedReferenceLengthByCIGARSum(std::vector<char> &ops, std::vector<int> &lengths);
-
-void CIGAROpsToBlocks(std::vector<int> &lengths, std::vector<char> &ops,
- int &cigarPos,
- int &cigarEnd,
- int &qPos, int &tPos,
- AlignmentCandidate<> &aln);
-
-void ReverseAlignmentOperations(std::vector<int> &lengths, std::vector<char> &ops);
-
-void SAMAlignmentsToCandidates(SAMAlignment &sam,
- std::vector<FASTASequence> &referenceSequences,
- std::map<std::string,int> & refNameToRefListIndex,
- std::vector<AlignmentCandidate<> > &candidates,
- bool parseSmrtTitle = false,
- bool keepRefAsForward = true,
- bool copyQVs = false);
-#endif
diff --git a/libcpp/alignment/datastructures/alignmentset/AlignmentSetToCmpH5Adapter.hpp b/libcpp/alignment/datastructures/alignmentset/AlignmentSetToCmpH5Adapter.hpp
deleted file mode 100644
index 9884edc..0000000
--- a/libcpp/alignment/datastructures/alignmentset/AlignmentSetToCmpH5Adapter.hpp
+++ /dev/null
@@ -1,84 +0,0 @@
-#ifndef _BLASR_ALIGNMENT_SET_TO_CMPH5_ADAPTER_HPP_
-#define _BLASR_ALIGNMENT_SET_TO_CMPH5_ADAPTER_HPP_
-
-#include "utils/SMRTReadUtils.hpp"
-#include "HDFCmpFile.hpp"
-#include "sam/AlignmentSet.hpp"
-#include "datastructures/alignment/AlignmentCandidate.hpp"
-#include "datastructures/alignment/ByteAlignment.h"
-#include "algorithms/alignment/DistanceMatrixScoreFunction.hpp"
-
-class RefGroupNameId {
- public:
- std::string name;
- unsigned int id;
- RefGroupNameId() {
- id = 0;
- name = "";
- }
-
- RefGroupNameId(std::string n, unsigned int i) {
- name = n; id = i;
- }
-
- RefGroupNameId(const RefGroupNameId &rhs) {
- name = rhs.name;
- id = rhs.id;
- }
-};
-
-// number of zmws per SMRTCell for springfield: 163482
-const unsigned int numZMWsPerMovieSpringField = 163482;
-
-template<typename T_CmpFile>
-class AlignmentSetToCmpH5Adapter {
-public:
- // Map reference name to reference group (/RefGroup) name and ID.
- std::map<std::string, RefGroupNameId> refNameToRefGroupNameandId;
- std::map<std::string, unsigned int> knownMovies;
- std::map<std::string, unsigned int> knownPaths;
- unsigned int numAlignments;
- std::map<std::string, int> refNameToRefInfoIndex;
-
- void Initialize() {
- numAlignments = 0;
- }
-
- template<typename T_Reference>
- void StoreReferenceInfo(std::vector<T_Reference> &references,
- T_CmpFile &cmpFile);
-
- unsigned int StoreMovieInfo(std::string movieName, T_CmpFile &cmpFile);
-
-
- // Given a reference name, find whether there exists a refGroup
- // (e.g. /ref000001) associated with it.
- // If not, create a refGroup and update refNameToRefGroupNameandId.
- // Finally, return its associated refGroup ID.
- unsigned int StoreRefGroup(std::string refName, T_CmpFile & cmpFile);
-
- unsigned int StorePath(std::string & path, T_CmpFile &cmpFile);
-
- void RemoveGapsAtEndOfAlignment(AlignmentCandidate<> &alignment);
-
- void StoreAlignmentCandidate(AlignmentCandidate<> &alignment,
- int alnSegment,
- T_CmpFile &cmpFile,
- int moleculeNumber = -1,
- bool copyQVs=false);
-
- void StoreAlignmentCandidateList(std::vector<AlignmentCandidate<> > &alignments,
- T_CmpFile &cmpFile,
- int moleculeNumber=-1,
- bool copyQVs=false);
-
- void StoreAlignmentCandidate(AlignmentCandidate<> alignment,
- T_CmpFile &cmpFile) {
- StoreAlignmentCandidate(alignment, 0, cmpFile);
- }
-
-};
-
-#include "AlignmentSetToCmpH5AdapterImpl.hpp"
-
-#endif
diff --git a/libcpp/alignment/datastructures/alignmentset/AlignmentSetToCmpH5AdapterImpl.hpp b/libcpp/alignment/datastructures/alignmentset/AlignmentSetToCmpH5AdapterImpl.hpp
deleted file mode 100644
index 6604930..0000000
--- a/libcpp/alignment/datastructures/alignmentset/AlignmentSetToCmpH5AdapterImpl.hpp
+++ /dev/null
@@ -1,256 +0,0 @@
-#ifndef _BLASR_ALIGNMENT_SET_TO_CMPH5_ADAPTER_IMPL_HPP_
-#define _BLASR_ALIGNMENT_SET_TO_CMPH5_ADAPTER_IMPL_HPP_
-
-#include "AlignmentSetToCmpH5AdapterImpl.hpp"
-
-template<typename T_CmpFile>
-unsigned int AlignmentSetToCmpH5Adapter<T_CmpFile>::StoreMovieInfo(
- std::string movieName, T_CmpFile &cmpFile) {
-
- std::map<std::string, unsigned int>::iterator mapIt;
- mapIt = knownMovies.find(movieName);
- if (mapIt != knownMovies.end()) {
- return mapIt->second;
- }
- else {
- unsigned int id = cmpFile.movieInfoGroup.AddMovie(movieName);
- knownMovies[movieName] = id;
- return id;
- }
-}
-
-template<typename T_CmpFile>
-template<typename T_Reference>
-void AlignmentSetToCmpH5Adapter<T_CmpFile>::StoreReferenceInfo(
- std::vector<T_Reference> &references, T_CmpFile &cmpFile) {
- for (int r = 0; r < references.size(); r++) {
- std::string sequenceName, md5;
- sequenceName = references[r].GetSequenceName();
- md5 = references[r].GetMD5();
- unsigned int length = references[r].GetLength();
-
- // Add this reference to /RefInfo.
- // Don't create /ref0000x and register it in /RefGroup at this point,
- // because this reference may not map to any alignments at all.
- cmpFile.AddRefInfo(sequenceName, length, md5);
-
- // Update refNameToRefInfoIndex
- if (refNameToRefInfoIndex.find(sequenceName) != refNameToRefInfoIndex.end()) {
- cout << "ERROR. Reference name " << sequenceName
- << " is not unique." << endl;
- exit(1);
- }
- refNameToRefInfoIndex[sequenceName] = r;
- }
-}
-
-template<typename T_CmpFile>
-unsigned int AlignmentSetToCmpH5Adapter<T_CmpFile>::StoreRefGroup(
- std::string refName, T_CmpFile & cmpFile) {
- // Find out whether there is a refGroup associated with refName.
- std::map<std::string, RefGroupNameId>::iterator mapIt;
- mapIt = refNameToRefGroupNameandId.find(refName);
- if (mapIt != refNameToRefGroupNameandId.end()) {
- // An existing refGroup is associated with this refName.
- return mapIt->second.id;
- } else {
- // No refGroup is associated with refName, create one.
- int refInfoIndex = refNameToRefInfoIndex[refName];
- unsigned int refInfoId = refInfoIndex + 1;
-
- std::string refGroupName;
- unsigned int refGroupId = cmpFile.AddRefGroup(refName, refInfoId, refGroupName);
-
- // Update refNameToRefGroupNameandId.
- refNameToRefGroupNameandId[refName] = RefGroupNameId(refGroupName, refGroupId);
- return refGroupId;
- }
-}
-
-template<typename T_CmpFile>
-unsigned int AlignmentSetToCmpH5Adapter<T_CmpFile>::StorePath(
- std::string & path, T_CmpFile &cmpFile) {
- if (knownPaths.find(path) != knownPaths.end()) {
- return knownPaths[path];
- }
- else {
- unsigned int id = cmpFile.alnGroupGroup.AddPath(path);
- knownPaths[path] = id;
- return id;
- }
-}
-
-template<typename T_CmpFile>
-void AlignmentSetToCmpH5Adapter<T_CmpFile>::RemoveGapsAtEndOfAlignment(AlignmentCandidate<> &alignment) {
- int numEndDel = 0, numEndIns = 0;
- if (alignment.gaps.size() > 0) {
- int lastGap = alignment.gaps.size() - 1;
- int g;
- for (g = 0; g < alignment.gaps[lastGap].size(); g++) {
- if (alignment.gaps[lastGap][g].seq == Gap::Target) {
- numEndIns += alignment.gaps[lastGap][g].length;
- }
- else if (alignment.gaps[lastGap][g].seq == Gap::Query) {
- numEndDel += alignment.gaps[lastGap][g].length;
- }
- }
- }
- alignment.qAlignedSeqLength -= numEndIns;
- alignment.tAlignedSeqLength -= numEndDel;
-}
-
-template<typename T_CmpFile>
-void AlignmentSetToCmpH5Adapter<T_CmpFile>::StoreAlignmentCandidate(
- AlignmentCandidate<> &alignment,
- int alnSegment,
- T_CmpFile &cmpFile,
- int moleculeNumber,
- bool copyQVs) {
- //
- // Find out where the movie is going to get stored.
- //
- std::string movieName;
- int holeNumber = 0;
- bool nameParsedProperly;
-
- nameParsedProperly = ParsePBIReadName(alignment.qName, movieName, holeNumber);
- if (!nameParsedProperly) {
- std::cout <<"ERROR. Attempting to store a read with name "
- << alignment.qName << " that does not " << std::endl
- << "appear to be a PacBio read." << std::endl;
- exit(1);
- }
-
- unsigned int movieId = StoreMovieInfo(movieName, cmpFile);
-
- // Check whether the reference is in /RefInfo.
- std::map<std::string, int>::iterator mapIt;
- mapIt = refNameToRefInfoIndex.find(alignment.tName);
- if (mapIt == refNameToRefInfoIndex.end()) {
- std::cout << "ERROR. The reference name " << alignment.tName
- << " was not found in the list of references." << std::endl;
- std::cout << "Perhaps a different reference file was aligned to than " << std::endl
- << "what was provided for SAM conversion. " << std::endl;
- exit(1);
- }
-
- // Store refGroup
- unsigned int refGroupId = StoreRefGroup(alignment.tName, cmpFile);
- std::string refGroupName = refNameToRefGroupNameandId[alignment.tName].name;
- assert(refGroupId == refNameToRefGroupNameandId[alignment.tName].id);
-
- if (cmpFile.refGroupIdToArrayIndex.find(refGroupId) == cmpFile.refGroupIdToArrayIndex.end()) {
- std::cout << "ERROR. The reference ID is not indexed. "
- << "This is an internal inconsistency." << std::endl;
- exit(1);
- }
-
- int refGroupIndex= cmpFile.refGroupIdToArrayIndex[refGroupId];
- assert(refGroupIndex + 1 == refGroupId);
-
- std::string path = "/" + refGroupName + "/" + movieName;
- unsigned int pathId = StorePath(path, cmpFile);
- int pathIndex = pathId - 1;
-
- vector<unsigned int> alnIndex;
- alnIndex.resize(22);
-
- RemoveGapsAtEndOfAlignment(alignment);
-
- /*
- * Store the alignment string
- */
- vector<unsigned char> byteAlignment;
- AlignmentToByteAlignment(alignment,
- alignment.qAlignedSeq, alignment.tAlignedSeq,
- byteAlignment);
-
- unsigned int offsetBegin, offsetEnd;
- cmpFile.StoreAlnArray(byteAlignment, alignment.tName, movieName, offsetBegin, offsetEnd);
- // Copy QVs into cmp.h5
- if (copyQVs) {
- std::vector<std::string> optionalQVs;
- alignment.CopyQVs(&optionalQVs);
- for (int qv_i=0; qv_i<optionalQVs.size(); qv_i++) {
- std::string *qvName = &alignment.optionalQVNames[qv_i];
- std::string *qvString = &optionalQVs[qv_i];
-
- // If the qvString is empty, then the alignment is missing the quality
- // value
- if (qvString->size() == 0) {
- continue;
- }
-
- unsigned int qvOffsetBegin, qvOffsetEnd;
- if (qvName->compare(qvName->size() - 3, 3, "Tag") == 0) {
- std::vector<char> qvVector;
- QVsToCmpH5QVs(*qvString, byteAlignment, true, &qvVector);
- cmpFile.StoreTags(qvVector, alignment.tName, *qvName,
- movieName, &qvOffsetBegin, &qvOffsetEnd);
- } else {
- std::vector<UChar> qvVector;
- QVsToCmpH5QVs(*qvString, byteAlignment, false, &qvVector);
- cmpFile.StoreQVs(qvVector, alignment.tName, *qvName,
- movieName, &qvOffsetBegin, &qvOffsetEnd);
- }
- assert(qvOffsetBegin == offsetBegin);
- assert(qvOffsetEnd == offsetEnd);
- }
- }
-
- numAlignments++;
-
- DistanceMatrixScoreFunction<DNASequence, DNASequence> distScoreFn;
- //distScoreFn does not matter since the score is not stored.
- ComputeAlignmentStats(alignment, alignment.qAlignedSeq.seq, alignment.tAlignedSeq.seq, distScoreFn);
-
- /*
- The current AlnIndex column names:
- (0): "AlnID", "AlnGroupID", "MovieID", "RefGroupID", "tStart",
- (5): "tEnd", "RCRefStrand", "HoleNumber", "SetNumber",
- (9): "StrobeNumber", "MoleculeID", "rStart", "rEnd", "MapQV", "nM",
- (15): "nMM", "nIns", "nDel", "Offset_begin", "Offset_end",
- (20): "nBackRead", "nReadOverlap"
- */
- if (moleculeNumber == -1) {
- moleculeNumber = numZMWsPerMovieSpringField * (movieId - 1) + holeNumber;
- }
- alnIndex[0] = numAlignments; // AlnId
- alnIndex[1] = pathId; // AlnGroupID
- alnIndex[2] = movieId; // MovieID
- alnIndex[3] = refGroupId; // RefGroupID
- alnIndex[4] = alignment.tAlignedSeqPos; // tStart
- alnIndex[5] = alignment.tAlignedSeqPos + alignment.tAlignedSeqLength; // tEnd
- alnIndex[6] = alignment.tStrand; // RCRefStrand
- alnIndex[7] = holeNumber;
- alnIndex[8] = 0; // SET NUMBER -- parse later!!!!
- alnIndex[9] = alnSegment; // strobenumber
- alnIndex[10] = moleculeNumber;
- alnIndex[11] = alignment.qAlignedSeqPos;
- alnIndex[12] = alignment.qAlignedSeqPos + alignment.qAlignedSeqLength;
- alnIndex[13] = alignment.mapQV;
- alnIndex[14] = alignment.nMatch;
- alnIndex[15] = alignment.nMismatch;
- alnIndex[16] = alignment.nIns;
- alnIndex[17] = alignment.nDel;
- alnIndex[18] = offsetBegin;
- alnIndex[19] = offsetEnd;
- alnIndex[20] = 0;
- alnIndex[21] = 0;
- cmpFile.alnInfoGroup.WriteAlnIndex(alnIndex);
-}
-
-template<typename T_CmpFile>
-void AlignmentSetToCmpH5Adapter<T_CmpFile>::StoreAlignmentCandidateList(
- std::vector<AlignmentCandidate<> > &alignments,
- T_CmpFile &cmpFile,
- int moleculeNumber,
- bool copyQVs) {
-
- int a;
- for (a = 0; a < alignments.size(); a++) {
- StoreAlignmentCandidate(alignments[a], a, cmpFile, moleculeNumber, copyQVs);
- }
-}
-
-#endif
diff --git a/libcpp/alignment/datastructures/alignmentset/SAMQVConversion.cpp b/libcpp/alignment/datastructures/alignmentset/SAMQVConversion.cpp
deleted file mode 100644
index 05e867d..0000000
--- a/libcpp/alignment/datastructures/alignmentset/SAMQVConversion.cpp
+++ /dev/null
@@ -1,27 +0,0 @@
-#include <cstddef>
-#include <assert.h>
-#include "FASTQSequence.hpp"
-#include "SAMQVConversion.hpp"
-
-void QualityVectorToPrintable(unsigned char *data, int length) {
- if (data == NULL) {
- return;
- }
- for (int i = 0; i < length; i++) {
- data[i] = (((unsigned char)data[i]) == MAX_STORED_QUALITY) ? MAX_PRINTED_QUALITY : (unsigned char)data[i];
- data[i] = (((unsigned char)data[i]) == SENTINAL) ? MAP_SENTINAL : (unsigned char)data[i];
- assert(data[i] != 255);
- }
-}
-
-void QualityStringToStored(unsigned char *data, int length) {
- if (data == NULL) {
- return;
- }
- for (int i = 0; i < length; i++) {
- data[i] = data[i] - FASTQSequence::charToQuality;
- data[i] = ((unsigned char)data[i]) == MAX_PRINTED_QUALITY ? MAX_STORED_QUALITY : (unsigned char)data[i];
- data[i] = ((unsigned char)data[i]) == MAP_SENTINAL ? SENTINAL : (unsigned char)data[i];
- }
-}
-
diff --git a/libcpp/alignment/datastructures/alignmentset/SAMQVConversion.hpp b/libcpp/alignment/datastructures/alignmentset/SAMQVConversion.hpp
deleted file mode 100644
index 1a8312f..0000000
--- a/libcpp/alignment/datastructures/alignmentset/SAMQVConversion.hpp
+++ /dev/null
@@ -1,15 +0,0 @@
-#ifndef _BLASR_SAMQVConversion_HPP_
-#define _BLASR_SAMQVConversion_HPP_
-
-
-#define MAX_PRINTED_QUALITY 93
-#define MAX_STORED_QUALITY 100
-#define SENTINAL 255
-#define MAP_SENTINAL 93
-
-
-void QualityVectorToPrintable(unsigned char *data, int length);
-
-void QualityStringToStored(unsigned char *data, int length) ;
-
-#endif
diff --git a/libcpp/alignment/datastructures/alignmentset/SAMSupplementalQVList.cpp b/libcpp/alignment/datastructures/alignmentset/SAMSupplementalQVList.cpp
deleted file mode 100644
index 2f0558e..0000000
--- a/libcpp/alignment/datastructures/alignmentset/SAMSupplementalQVList.cpp
+++ /dev/null
@@ -1,71 +0,0 @@
-#include "SAMSupplementalQVList.hpp"
-
-const char* SupplementalQVList::qvNames[] = {"InsertionQV", "DeletionQV", "SubstitutionQV", "MergeQV", "SubstitutionTag", "DeletionTag"};
-const char* SupplementalQVList::qvTags[] = {"iq", "dq", "sq", "mq", "st", "dt"};
-
-// Only the first 4 tags are quality values.
-int SupplementalQVList::nqvTags = 4;
-int SupplementalQVList::nTags = 6;
-
-int SupplementalQVList::UseQV(std::vector<std::string> &qvList) {
- int i;
- useqv = 0;
- for (i = 0; i < qvList.size(); i++) {
- int j;
- for (j = 0; j < nTags; j++) {
- if (qvList[i] == qvNames[j]) {
- useqv |= 1 << j;
- break;
- }
- }
- if (j == nTags) {
- return 1;
- }
- }
- return 0;
-}
-
-void SupplementalQVList::FormatQVOptionalFields(SMRTSequence &alignedSubsequence) {
- int i;
- for (i = 0; i < nqvTags; i++) {
- if (alignedSubsequence.GetQVPointerByIndex(i+1)->data == NULL) {
- // mask off this quality value since it does not exist
- useqv = useqv & ~(1 << i);
- }
- }
- for (i = 0; i < nqvTags; i++) {
- if (useqv & (1 << i)) {
- QualityVectorToPrintable(alignedSubsequence.GetQVPointerByIndex(i+1)->data, alignedSubsequence.length);
- }
- }
-}
-
-void SupplementalQVList::PrintQVOptionalFields(SMRTSequence &alignedSubsequence, std::ostream &out) {
- int i = 0;
- for (i = 0; i < nqvTags; i++) {
- if (alignedSubsequence.GetQVPointerByIndex(i+1)->data == NULL) {
- // mask off this quality value since it does not exist
- useqv = useqv & ~(1 << i);
- }
- }
- for (i = 0; i < nTags; i++) {
- if (alignedSubsequence.GetQVPointerByIndex(i+1) != NULL and (useqv & (1 << i)) ) {
- out << "\t" << qvTags[i] << ":Z:";
- alignedSubsequence.PrintAsciiRichQuality(out, i + 1, 0);
- }
- }
- if (alignedSubsequence.substitutionTag != NULL and (useqv & SubstitutionTag)) {
- out << "\t" << qvTags[I_SubstitutionTag-1] << ":Z:";
- alignedSubsequence.PrintAsciiRichQuality(out, I_SubstitutionTag, 0);
- }
- if (alignedSubsequence.deletionTag != NULL and (useqv & DeletionTag)) {
- out << "\t" << qvTags[I_DeletionTag-1] << ":Z:";
- alignedSubsequence.PrintAsciiRichQuality(out, I_DeletionTag, 0);
- }
-}
-
-void SupplementalQVList::clear() {
- for (int j = 0; j < nTags; j++) {
- useqv &= 0 << j;
- }
-}
diff --git a/libcpp/alignment/datastructures/alignmentset/SAMSupplementalQVList.hpp b/libcpp/alignment/datastructures/alignmentset/SAMSupplementalQVList.hpp
deleted file mode 100644
index 1ea8baa..0000000
--- a/libcpp/alignment/datastructures/alignmentset/SAMSupplementalQVList.hpp
+++ /dev/null
@@ -1,27 +0,0 @@
-#ifndef _BLASR_SAMSUPPLEMENTALQVLIST_HPP_
-#define _BLASR_SAMSUPPLEMENTALQVLIST_HPP_
-#include "SMRTSequence.hpp"
-#include "SAMQVConversion.hpp"
-
-class SupplementalQVList {
-public:
- //enum QVList {InsertionQV=0x1, DeletionQV=0x2, SubstitutionQV=0x4, MergeQV=0x8, SubstitutionTag=0x10, DeletionTag=0x20};
- //enum QVIndex {I_InsertionQV=1,I_DeletionQV=2,I_SubstitutionQV=3,I_MergeQV=4,I_SubstitutionTag=5,I_DeletionTag=6};
- //defined in FASTQSequence.
- unsigned int useqv;
- void SetDefaultQV() {
- useqv = InsertionQV | DeletionQV | SubstitutionQV | MergeQV | DeletionTag;
- }
- static const char* qvTags[];
- static const char* qvNames[];
- static int nqvTags;
- static int nTags;
-
- int UseQV(std::vector<std::string> &qvList);
- void FormatQVOptionalFields(SMRTSequence &alignedSubsequence);
-
- void PrintQVOptionalFields(SMRTSequence &alignedSubsequence, std::ostream &out);
- void clear();
-};
-
-#endif
diff --git a/libcpp/alignment/datastructures/anchoring/AnchorParameters.cpp b/libcpp/alignment/datastructures/anchoring/AnchorParameters.cpp
deleted file mode 100644
index 8b435b9..0000000
--- a/libcpp/alignment/datastructures/anchoring/AnchorParameters.cpp
+++ /dev/null
@@ -1,44 +0,0 @@
-#include "AnchorParameters.hpp"
-
-AnchorParameters::AnchorParameters() {
- branchQualityThreshold = 0;
- minMatchLength = 0;
- maxMatchScore = 0;
- expand = 0;
- contextAlignLength = 0;
- useLookupTable = true;
- numBranches = 0;
- maxAnchorsPerPosition = 1000;
- advanceExactMatches = 0;
- maxLCPLength = 0; // 0 Defaults to full lcp length
- stopMappingOnceUnique = false;
- removeEncompassedMatches=false;
- verbosity = 0;
- lcpBoundsOutPtr = NULL;
- branchExpand = 0;
-}
-
-AnchorParameters &AnchorParameters::Assign(const AnchorParameters &rhs) {
- //
- // Manually handle assignment in case there is some deep copy
- // that is necessary eventually.
- //
- branchQualityThreshold = rhs.branchQualityThreshold;
- minMatchLength = rhs.minMatchLength;
- maxMatchScore = rhs.maxMatchScore;
- expand = rhs.expand;
- contextAlignLength = rhs.contextAlignLength;
- numBranches = rhs.numBranches;
- maxAnchorsPerPosition = rhs.maxAnchorsPerPosition;
- advanceExactMatches = rhs.advanceExactMatches;
- maxLCPLength = rhs.maxLCPLength;
- stopMappingOnceUnique = rhs.stopMappingOnceUnique;
- verbosity = rhs.verbosity;
- removeEncompassedMatches= rhs.removeEncompassedMatches;
- branchExpand = rhs.branchExpand;
- return *this;
-}
-
-AnchorParameters &AnchorParameters::operator=(const AnchorParameters &rhs) {
- return this->Assign(rhs);
-}
diff --git a/libcpp/alignment/datastructures/anchoring/AnchorParameters.hpp b/libcpp/alignment/datastructures/anchoring/AnchorParameters.hpp
deleted file mode 100644
index 8ca5474..0000000
--- a/libcpp/alignment/datastructures/anchoring/AnchorParameters.hpp
+++ /dev/null
@@ -1,35 +0,0 @@
-#ifndef _BLASR_ANCHOR_PARAMETERS_HPP_
-#define _BLASR_ANCHOR_PARAMETERS_HPP_
-
-#include <fstream>
-#include <iostream>
-#include "qvs/QualityValue.hpp"
-#include "DNASequence.hpp"
-
-class AnchorParameters {
-public:
- QualityValue branchQualityThreshold;
- int minMatchLength;
- int maxMatchScore;
- int expand;
- int contextAlignLength;
- bool useLookupTable;
- int numBranches;
- int maxAnchorsPerPosition;
- int advanceExactMatches;
- int maxLCPLength;
- bool stopMappingOnceUnique;
- int verbosity;
- bool removeEncompassedMatches;
- std::ostream *lcpBoundsOutPtr;
- int branchExpand;
-
- AnchorParameters();
-
- AnchorParameters &Assign(const AnchorParameters &rhs);
-
- AnchorParameters &operator=(const AnchorParameters &rhs);
-};
-
-
-#endif // _BLASR_ANCHOR_PARAMETERS_HPP_
diff --git a/libcpp/alignment/datastructures/anchoring/ClusterList.cpp b/libcpp/alignment/datastructures/anchoring/ClusterList.cpp
deleted file mode 100644
index f562ed6..0000000
--- a/libcpp/alignment/datastructures/anchoring/ClusterList.cpp
+++ /dev/null
@@ -1,75 +0,0 @@
-#include "datastructures/anchoring/ClusterList.hpp"
-
-ClusterList::ClusterList() {
- lowerSizeLimit = 20;
- lowerSizeLimitNumAnchors = 1;
- curp = cure = 0;
- onContigStart = true;
- curIndex = 0;
-}
-
-void ClusterList::Clear() {
- onContigStart = true;
- numBases.clear();
- startPos.clear();
- numAnchors.clear();
-}
-
-bool ClusterList::Store(int n, DNALength p, DNALength e, int b) {
- bool intervalIsEclipsed = true;
- bool intervalEclipses = false;
- if (onContigStart == true) {
- curp = p;
- cure = e;
- intervalIsEclipsed = false;
- }
- else {
- if (curp <= p and cure >= e) {
- intervalIsEclipsed = true;
- }
- else {
- if (p <= curp and e >= cure) {
- intervalEclipses = true;
- }
- intervalIsEclipsed = false;
- }
- }
- if (intervalIsEclipsed == false) {
- //
- // The current interval is unique: it does not eclipse any
- // other intervals and is not eclipsed by any.
- //
- if (n >= lowerSizeLimit) {
- if (intervalEclipses == false or onContigStart) {
- numBases.push_back(n);
- startPos.push_back(p);
- numAnchors.push_back(b);
- onContigStart = false;
- //
- // Record where the last interval is. Since ther intervals
- // are sorted by position, only need to compare against the
- // current interval to make sure they are not overlapping
- // other intervals.
- //
- curp = p; cure = e;
- }
- else {
- //
- // The new interval eclipses the last one added.
- //
- if (n > numBases[numBases.size()-1]) {
- numBases[numBases.size()-1] = n;
- startPos[startPos.size()-1] = p;
- numAnchors[numAnchors.size()-1] = b;
- curp = p; cure = e;
- }
- }
- }
- }
- return !intervalIsEclipsed;
-}
-
-void ClusterList::ResetCoordinates() {
- onContigStart = true;
-}
-
diff --git a/libcpp/alignment/datastructures/anchoring/ClusterList.hpp b/libcpp/alignment/datastructures/anchoring/ClusterList.hpp
deleted file mode 100644
index 055446f..0000000
--- a/libcpp/alignment/datastructures/anchoring/ClusterList.hpp
+++ /dev/null
@@ -1,25 +0,0 @@
-#ifndef _BLASR_CLUSTER_LIST_HPP_
-#define _BLASR_CLUSTER_LIST_HPP_
-
-#include <vector>
-#include "DNASequence.hpp"
-
-class ClusterList {
-public:
- std::vector<int> numBases;
- std::vector<int> numAnchors;
- std::vector<unsigned int> startPos;
- std::vector<int> indices;
- int lowerSizeLimit;
- int lowerSizeLimitNumAnchors;
- DNALength curp, cure; // cur - p, and cur - e.
- int curIndex;
- bool onContigStart;
-
- ClusterList();
- void Clear();
- bool Store(int n, DNALength p, DNALength e, int b);
- void ResetCoordinates();
-};
-
-#endif
diff --git a/libcpp/alignment/datastructures/anchoring/MatchPos.cpp b/libcpp/alignment/datastructures/anchoring/MatchPos.cpp
deleted file mode 100644
index e6d7ec3..0000000
--- a/libcpp/alignment/datastructures/anchoring/MatchPos.cpp
+++ /dev/null
@@ -1,59 +0,0 @@
-#include "MatchPos.hpp"
-
-
-MatchPos::MatchPos(const MatchPos &rhs) {
- (*this) = rhs;
-}
-
-int MatchPos::GetMultiplicity() const {
- return m;
-}
-
-MatchWeight MatchPos::GetWeight() const {
- if (m > 0) {
- return (1.0*l)/m;
- } else {
- return 0;
- }
-}
-
-UInt MatchPos::GetT() {
- return t;
-}
-
-UInt MatchPos::GetQ() {
- return (UInt) q;
-}
-
-UInt MatchPos::GetW() {
- return w;
-}
-
-std::ostream& operator<<(std::ostream & out, MatchPos &p) {
- out << p.q << "\t" << p.t <<"\t"<< p.l << "\t"<< p.m;
- return out;
-}
-
-
-ChainedMatchPos::ChainedMatchPos(DNALength pt, DNALength pq, DNALength pl, int pm) : MatchPos(pt, pq, pl, pm) {
- score = 0;
- chainPrev = NULL;
-}
-
-ChainedMatchPos::ChainedMatchPos() : MatchPos() {
- score = 0;
- chainPrev = NULL;
-}
-
-int ChainedMatchPos::SetScore(int _score) {
- return (score = _score);
-}
-
-ChainedMatchPos* ChainedMatchPos::SetChainPrev(ChainedMatchPos *_chainPrev) {
- return (chainPrev = _chainPrev);
-}
-
-std::ostream& operator<<(std::ostream & out, ChainedMatchPos &p) {
- out << p.q << "\t" << p.t <<"\t"<< p.l << "\t"<< p.m;
- return out;
-}
diff --git a/libcpp/alignment/datastructures/anchoring/MatchPos.hpp b/libcpp/alignment/datastructures/anchoring/MatchPos.hpp
deleted file mode 100644
index 513b3d2..0000000
--- a/libcpp/alignment/datastructures/anchoring/MatchPos.hpp
+++ /dev/null
@@ -1,192 +0,0 @@
-#ifndef _BLASR_MATCH_POS_HPP_
-#define _BLASR_MATCH_POS_HPP_
-
-#include <vector>
-#include <algorithm>
-#include <ostream>
-#include "Types.h"
-#include "DNASequence.hpp"
-
-class MatchPos {
-public:
- DNALength t, q;
- MatchWeight w;
- DNALength l;
- int m; // multiplicity
-
- inline MatchPos(DNALength pt, DNALength pq, DNALength pl, int pm = 0);
-
- MatchPos (const MatchPos &rhs);
-
- inline MatchWeight Size();
-
- inline MatchPos();
-
- inline MatchPos& operator=(const MatchPos &rhs);
-
- inline DNALength GetLength() const;
-
- int GetMultiplicity() const;
-
- MatchWeight GetWeight() const;
-
- inline DNALength GetX() const;
-
- inline DNALength GetY() const;
-
- UInt GetT();
-
- UInt GetQ();
-
- UInt GetW();
-
- friend std::ostream& operator<<(std::ostream & out, MatchPos &p);
-};
-
-inline MatchPos::MatchPos(DNALength pt, DNALength pq, DNALength pl, int pm) :
- t(pt), q(pq), l(pl), m(pm), w(0){ }
-
-inline MatchPos::MatchPos() {
- t = q = -1;
- l = 0;
- w = 0;
- m = 0;
-}
-
-inline MatchWeight MatchPos::Size() {
- return l;
-}
-
-inline MatchPos& MatchPos::operator=(const MatchPos &rhs) {
- t = rhs.t; q = rhs.q; w = rhs.w;
- l = rhs.l;
- m = rhs.m;
- return *this;
-}
-
-inline DNALength MatchPos::GetLength() const {
- return l;
-}
-
-inline DNALength MatchPos::GetX() const {
- return q;
-}
-
-inline DNALength MatchPos::GetY() const {
- return t;
-}
-
-
-class ChainedMatchPos : public MatchPos {
-private:
- int score;
- ChainedMatchPos *chainPrev;
-
-public:
- ChainedMatchPos(DNALength pt, DNALength pq, DNALength pl, int pm);
-
- ChainedMatchPos();
-
- inline ChainedMatchPos(const ChainedMatchPos &rhs);
-
- inline int GetScore();
-
- int SetScore(int _score);
-
- ChainedMatchPos* SetChainPrev(ChainedMatchPos *_chainPrev);
-
- inline ChainedMatchPos* GetChainPrev();
-
- inline ChainedMatchPos &operator=(const ChainedMatchPos &rhs);
-
- friend std::ostream& operator<<(std::ostream & out, ChainedMatchPos &p);
-
-};
-
-inline ChainedMatchPos::ChainedMatchPos(const ChainedMatchPos &rhs) {
- (*this) = rhs;
-}
-
-inline ChainedMatchPos* ChainedMatchPos::GetChainPrev() {
- return chainPrev;
-}
-
-inline int ChainedMatchPos::GetScore() {
- return score;
-}
-
-inline ChainedMatchPos &ChainedMatchPos::operator=(const ChainedMatchPos &rhs) {
- ((MatchPos&)(*this)) = ((MatchPos&)rhs);
- return *this;
-}
-
-
-template<typename T_MatchPos>
-class CompareMatchPos {
- public:
- int operator()(const T_MatchPos &lhs, const T_MatchPos &rhs) const {
- if (lhs.t < rhs.t)
- return 1;
- else if (lhs.t > rhs.t)
- return 0;
- else {
- return lhs.q < rhs.q;
- }
- }
-};
-
-typedef std::vector<MatchPos> MatchPosList;
-
-template<typename T_MatchPos>
-class CompareMatchPosByWeight {
- public:
- int operator()(const T_MatchPos &a, const T_MatchPos &b) const {
- return a.l < b.l;
- }
-};
-
-template<typename T_MatchPos>
-class CompareMatchPosIndexByWeight {
- public:
- std::vector<T_MatchPos> *list;
- int operator()(const int i, const int j) const {
- return ((*list)[i].w > (*list)[j].w);
- }
-};
-
-
-template<typename T_MatchPos>
-class CompareMatchPosIndexByTextPos {
- public:
- std::vector<T_MatchPos> *list;
- int operator()(const int i, const int j) const {
- return (*list)[i].t < (*list)[j].t;
- }
-};
-
-
-template<typename T_MatchPos>
-void SortMatchPosList(std::vector<T_MatchPos> &mpl) {
- std::sort(mpl.begin(), mpl.end(), CompareMatchPos<T_MatchPos>());
-}
-
-template<typename T_MatchPos>
-void SortMatchPosListByWeight(std::vector<T_MatchPos> &mpl) {
- std::sort(mpl.begin(), mpl.end(), CompareMatchPosByWeight<T_MatchPos>());
-}
-
-template<typename T_MatchPos>
-void SortMatchPosIndexListByWeight(std::vector<T_MatchPos> &mpl, std::vector<int> &indices) {
- CompareMatchPosIndexByWeight<T_MatchPos> cmp;
- cmp.list = &mpl;
- std::sort(indices.begin(), indices.end(), cmp);
-}
-
-template<typename T_MatchPos>
-void SortMatchPosIndexListByTextPos(std::vector<T_MatchPos> &mpl, std::vector<int> &indices) {
- CompareMatchPosIndexByTextPos<T_MatchPos> cmp;
- cmp.list = &mpl;
- std::sort(indices.begin(), indices.end(), cmp);
-}
-
-#endif // _BLASR_MATCH_POS_HPP_
diff --git a/libcpp/alignment/datastructures/anchoring/WeightedInterval.cpp b/libcpp/alignment/datastructures/anchoring/WeightedInterval.cpp
deleted file mode 100644
index 173eb89..0000000
--- a/libcpp/alignment/datastructures/anchoring/WeightedInterval.cpp
+++ /dev/null
@@ -1,181 +0,0 @@
-#include "datastructures/anchoring/WeightedInterval.hpp"
-
-WeightedInterval::WeightedInterval(){}
-
-void WeightedInterval::Init(int _size, int _start, int _end,
- int _readIndex, float _pValue) {
- size = _size;
- start = _start;
- end = _end;
- readIndex = _readIndex;
- pValue = _pValue;
- qStart = 0;
- qEnd = 0;
- nAnchors = 0;
- totalAnchorSize = 0;
- pValueVariance = 0;
- pValueNStdDev = 0;
- sizeVariance = 0;
- sizeNStdDev = 0;
-}
-
-WeightedInterval::WeightedInterval(int _size, int _start, int _end,
- int _readIndex, float _pValue) {
- Init(_size, _start, _end, _readIndex, _pValue);
-}
-
-WeightedInterval::WeightedInterval(int _size, int _start, int _end,
- int _readIndex, float _pValue, int _qStart, int _qEnd){
- Init(_size, _start, _end, _readIndex, _pValue);
- qStart = _qStart;
- qEnd = _qEnd;
-}
-
-WeightedInterval::WeightedInterval(int _size, unsigned int _nAnchors,
- unsigned int _totalAnchorSize, int _start, int _end, int _readIndex,
- float _pValue, int _qStart, int _qEnd,
- std::vector<ChainedMatchPos> &_matches) {
-
- Init(_size, _start, _end, _readIndex, _pValue);
- qStart = _qStart;
- qEnd = _qEnd;
- matches = _matches;
- nAnchors = _nAnchors;
- totalAnchorSize = _totalAnchorSize;
-}
-
-float WeightedInterval::PValue() const {
- return pValue;
-}
-
-int WeightedInterval::Size() const {
- return size;
-}
-
-int WeightedInterval::GetStrandIndex() const {
- return readIndex;
-}
-
-void WeightedInterval::SetPValueVariance(float v) {
- pValueVariance = v;
-}
-
-void WeightedInterval::SetPValueNStdDev(float v) {
- pValueNStdDev = v;
-}
-
-void WeightedInterval::SetSizeVariance(float v) {
- sizeVariance = v;
-}
-
-void WeightedInterval::SetSizeNStdDev(float v) {
- sizeNStdDev = v;
-}
-
-int WeightedInterval::operator<(const WeightedInterval &intv) const {
- if (size == intv.size) {
- return start > intv.start;
- }
- else {
- return size < intv.size;
- }
-}
-
-int WeightedInterval::operator==(const WeightedInterval &intv) const {
- return size == intv.size;
-}
-
-// Functions of class CompareWeightedIntervalByPValue
-int CompareWeightedIntervalByPValue::operator()(const WeightedInterval &a,
- const WeightedInterval &b) const {
- if (a.PValue() != b.PValue()) {
- return a.PValue() < b.PValue();
- }
- else {
- return a.start < b.start;
- }
-}
-
-// Functions of class WeightedIntervalSet
-WeightedIntervalSet::WeightedIntervalSet() {
- maxSize = 0;
-}
-
-WeightedIntervalSet::WeightedIntervalSet(int maxSizeP): maxSize(maxSizeP) {
-}
-
-bool WeightedIntervalSet::insert(WeightedInterval &intv) {
- intv.isOverlapping = false;
-
- //
- // Make sure this interval is not contained inside any other
- // weighted intervals.
- //
- WeightedIntervalSet::iterator it = (*this).begin();
- WeightedIntervalSet::iterator endit = (*this).end();
- bool isContained = false;
- while (it != endit and isContained == false) {
- if (intv.qStart >= (*it).qStart and intv.qEnd <= (*it).qEnd and
- intv.start >= (*it).start and intv.end <= (*it).end and
- intv.readIndex == (*it).readIndex and
- intv.pValue >= (*it).pValue) {
- //
- // This already overlaps an existing interval, don't bother
- // trying to add it.
- //
- isContained = true;
- intv.isOverlapping = true;
- } else if((*it).start >= intv.start and
- (*it).end <= intv.end and
- (*it).qStart >= intv.qStart and
- (*it).qEnd <= intv.qEnd and
- (*it).readIndex == intv.readIndex and
- (*it).pValue >= intv.pValue) {
- WeightedIntervalSet::iterator next = it;
- ++next;
- this->erase(it);
- it = next;
- } else {
- ++it;
- }
- }
-
- //
- // Take a peek to see if this interval is too low of a score to
- // bother attempting to add at all.
- //
- if (size() >= maxSize and maxSize > 0) {
- WeightedIntervalSet::iterator last = (*this).end();
- last--;
-
- if (last->pValue < intv.pValue) {
- return false;
- }
- }
-
- if (isContained == false) {
- bool addInsert = false;
- if (size() == 0) {
- addInsert = true;
- }
- else {
- it = end();
- --it;
- if (size() < maxSize or (*it).pValue > intv.pValue) {
- addInsert = true;
- //
- // Keep the size of the stack the same if it is at the limit.
- //
- if (maxSize != 0 and size() >= maxSize and size() > 0) {
- erase(it);
- }
- }
- }
- if (addInsert) {
- ((T_WeightedIntervalMultiSet*)this)->insert(intv);
- }
- return true;
- }
- return false;
-}
-
diff --git a/libcpp/alignment/datastructures/anchoring/WeightedInterval.hpp b/libcpp/alignment/datastructures/anchoring/WeightedInterval.hpp
deleted file mode 100644
index 052da90..0000000
--- a/libcpp/alignment/datastructures/anchoring/WeightedInterval.hpp
+++ /dev/null
@@ -1,85 +0,0 @@
-#ifndef _BLASR_WEIGHTED_INTERVAL_HPP_
-#define _BLASR_WEIGHTED_INTERVAL_HPP_
-
-#include <vector>
-#include <set>
-#include "DNASequence.hpp"
-#include "datastructures/anchoring/MatchPos.hpp"
-
-class WeightedInterval {
-public:
- DNALength size; // not necessarily end - start + 1
- DNALength start;
- DNALength end;
- DNALength qStart, qEnd;
- int readIndex;
- float pValue;
- std::vector<int> positions;
- std::vector<ChainedMatchPos> matches;
- float pValueVariance, pValueNStdDev;
- float sizeVariance, sizeNStdDev;
- int nAnchors;
- int totalAnchorSize;
- bool isOverlapping;
-
- WeightedInterval();
-
- WeightedInterval(int _size, int _start, int _end,
- int _readIndex, float _pValue =0.0);
-
- WeightedInterval(int _size, int _start, int _end,
- int _readIndex, float _pValue, int _qStart, int _qEnd);
-
- WeightedInterval(int _size, unsigned int _nAnchors,
- unsigned int _totalAnchorSize, int _start, int _end,
- int _readIndex, float _pValue, int _qStart, int _qEnd,
- std::vector<ChainedMatchPos> &_matches);
-
- void Init(int _size, int _start, int _end,
- int _readIndex, float _pValue);
-
- int GetStrandIndex() const;
- void SetPValueVariance(float v);
- void SetPValueNStdDev(float v);
- void SetSizeVariance(float v);
- void SetSizeNStdDev(float v);
- int operator<(const WeightedInterval &intv) const;
- int operator==(const WeightedInterval &intv) const;
-
- friend std::ostream & operator << (std::ostream & out, WeightedInterval & wi) {
- out << wi.size << " " << wi.start << " " << wi.end
- << " " << wi.qStart << " " << wi.qEnd << " " << wi.readIndex
- << " " << wi.pValue ;
- return out;
- }
-
- float PValue() const;
- int Size() const;
-};
-
-class CompareWeightedIntervalByPValue {
-public:
- int operator()(const WeightedInterval& a, const WeightedInterval& b) const;
-};
-
-typedef std::vector<WeightedInterval> WeightedIntervalVector;
-
-typedef std::multiset<WeightedInterval, CompareWeightedIntervalByPValue>
-T_WeightedIntervalMultiSet;
-
-class WeightedIntervalSet: public T_WeightedIntervalMultiSet {
-public:
- int maxSize;
- WeightedIntervalSet();
- WeightedIntervalSet(int maxSizeP);
- bool insert(WeightedInterval &intv);
- friend std::ostream & operator << (std::ostream & out, WeightedIntervalSet & wis) {
- WeightedIntervalSet::iterator it;
- for (it = wis.begin(); it != wis.end(); it++) {
- out << *((WeightedInterval*)&(*it)) << std::endl;
- }
- return out;
- }
-};
-
-#endif
diff --git a/libcpp/alignment/files/BaseSequenceIO.cpp b/libcpp/alignment/files/BaseSequenceIO.cpp
deleted file mode 100644
index ec39903..0000000
--- a/libcpp/alignment/files/BaseSequenceIO.cpp
+++ /dev/null
@@ -1,77 +0,0 @@
-#include <cstdlib>
-#include "BaseSequenceIO.hpp"
-
-using namespace std;
-
-void BaseSequenceIO::SetFiles(FileType &pFileType, std::string &pFileName) {
- fileType = pFileType;
- fileName = pFileName;
-}
-
-FileType BaseSequenceIO::GetFileType() {
- return fileType;
-}
-
-int BaseSequenceIO::DetermineFileTypeByExtension(string &fileName,
- FileType &type, bool exitOnFailure) {
-
- string::size_type dotPos = fileName.rfind(".");
- if (dotPos != string::npos) {
- string extension;
- extension.assign(fileName, dotPos+1, fileName.size() - (dotPos+1));
- if (extension == "fasta" or
- extension == "fa" or
- extension == "fas" or
- extension == "fsta" or
- extension == "screen"
- ) {
- type = Fasta;
- return 1;
- }
- else if (extension == "h5") {
- dotPos = fileName.rfind(".", dotPos-1);
- extension.assign(fileName, dotPos+1, fileName.size() - (dotPos + 1));
- if (extension == "pls.h5" or extension == "plx.h5" ) {
- type = HDFPulse;
- return 1;
- }
- else if (extension == "bas.h5" or extension == "bax.h5") {
- type = HDFBase;
- return 1;
- }
- else if (extension == "ccs.h5") {
- type = HDFCCSONLY;
- return 1;
- }
- else {
- type = None;
- return 0;
- }
- }
- else if (extension == "fastq" or
- extension == "fq") {
- type = Fastq;
- return 1;
- }
- else if (extension == "4bit" or
- extension == "fourbit") {
- type = Fourbit;
- assert("Four bit reading is not yet implemented for the reader agglomerate!" == 0);
- return 1;
- }
- else if (extension == "bam") {
- type = PBBAM;
- return 1;
- }
- else {
- type = None;
- if (exitOnFailure) {
- cout << "ERROR, file type '." << extension << "' is not understood to be one of pls.h5, fasta, fastq, nor bam. " << endl;
- exit(1);
- }
- return 0;
- }
- return 0;
- }
- return 0;
-}
diff --git a/libcpp/alignment/files/BaseSequenceIO.hpp b/libcpp/alignment/files/BaseSequenceIO.hpp
deleted file mode 100644
index 1b187d2..0000000
--- a/libcpp/alignment/files/BaseSequenceIO.hpp
+++ /dev/null
@@ -1,26 +0,0 @@
-#ifndef _BLASR_DATA_FILE_TYPE_HPP_
-#define _BLASR_DATA_FILE_TYPE_HPP_
-
-#include <string>
-#include <iostream>
-#include <cassert>
-#include "Enumerations.h"
-
-class BaseSequenceIO {
-
-protected:
-
- FileType fileType;
- std::string fileName;
-
-public:
-
- void SetFiles(FileType &pFileType, std::string &pFileName);
-
- FileType GetFileType();
-
- static int DetermineFileTypeByExtension(std::string &fileName, FileType &type,
- bool exitOnFailure=true);
-};
-
-#endif // _BLASR_DATA_FILE_TYPE_HPP_
diff --git a/libcpp/alignment/files/CCSIterator.cpp b/libcpp/alignment/files/CCSIterator.cpp
deleted file mode 100644
index 7edf650..0000000
--- a/libcpp/alignment/files/CCSIterator.cpp
+++ /dev/null
@@ -1,28 +0,0 @@
-#include "files/CCSIterator.hpp"
-
-void CCSIterator::Initialize(CCSSequence *_seqPtr) {
- seqPtr = _seqPtr;
- curPass = 0;
- numPasses = seqPtr->passDirection.size();
-}
-
-int CCSIterator::GetNext(int &direction, int &startBase, int &numBases) {
- if (curPass >= numPasses) {
- return 0;
- }
- else {
- direction = seqPtr->passDirection[curPass];
- startBase = seqPtr->passStartBase[curPass];
- numBases = seqPtr->passNumBases[curPass];
- ++curPass;
- return 1;
- }
-}
-
-void CCSIterator::Reset() {
- curPass = 0;
-}
-
-int CCSIterator::GetNumPasses() {
- return numPasses;
-}
diff --git a/libcpp/alignment/files/CCSIterator.hpp b/libcpp/alignment/files/CCSIterator.hpp
deleted file mode 100644
index 6f97641..0000000
--- a/libcpp/alignment/files/CCSIterator.hpp
+++ /dev/null
@@ -1,21 +0,0 @@
-#ifndef _BLASR_BASE_CCS_ITERATOR_HPP_
-#define _BLASR_BASE_CCS_ITERATOR_HPP_
-
-#include "CCSSequence.hpp"
-
-class CCSIterator {
-public:
- CCSSequence *seqPtr;
- int curPass;
- int numPasses;
-
- virtual void Initialize(CCSSequence *_seqPtr);
-
- virtual int GetNext(int &direction, int &startBase, int &numBases);
-
- void Reset();
-
- int GetNumPasses();
-};
-
-#endif
diff --git a/libcpp/alignment/files/FragmentCCSIterator.cpp b/libcpp/alignment/files/FragmentCCSIterator.cpp
deleted file mode 100644
index d02876c..0000000
--- a/libcpp/alignment/files/FragmentCCSIterator.cpp
+++ /dev/null
@@ -1,109 +0,0 @@
-#include "files/FragmentCCSIterator.hpp"
-
-
-void FragmentCCSIterator::
-Initialize(CCSSequence *_seqPtr, RegionTable *_regionTablePtr) {
- seqPtr = _seqPtr;
- regionTablePtr = _regionTablePtr;
- curPass = 0;
- numPasses = 0;
- subreadIntervals.clear();
- readIntervalDirection.clear();
-
- int hqRegionStart, hqRegionEnd, hqRegionScore;
- hqRegionStart = hqRegionEnd = hqRegionScore = 0;
-
- bool hasHQRegion = LookupHQRegion(seqPtr->zmwData.holeNumber,
- *regionTablePtr, hqRegionStart, hqRegionEnd, hqRegionScore);
-
- if (not hasHQRegion) {
- return; // Don't bother if there is no HQ region.
- }
-
- //
- // Since this iterator covers all passes, and not just those
- // included in the ccs, the the regions need to be loaded.
- //
- CollectSubreadIntervals(*seqPtr, regionTablePtr, subreadIntervals);
- if (subreadIntervals.size() == 0) { return;}
-
- readIntervalDirection.resize(subreadIntervals.size());
- fill(readIntervalDirection.begin(), readIntervalDirection.end(), 2);
-
- //
- // Assign the read interval directions based on the pass direction
- // for the pass that has a similar start position. This allows
- // some wiggle although in practice they coordinates of the pass
- // start base and the template should always match up.
- //
- int i, j;
- for (i = 0; i < subreadIntervals.size(); i++) {
- for (j = 0; j < seqPtr->passStartBase.size(); j++) {
- if (abs( ((int)subreadIntervals[i].start) -
- ((int)seqPtr->passStartBase[j]) ) < 10) {
- readIntervalDirection[i] = seqPtr->passDirection[j];
- break;
- }
- }
- }
-
- int firstAssignedSubread = 0;
- while (firstAssignedSubread < subreadIntervals.size() and
- readIntervalDirection[firstAssignedSubread] == 2) {
- firstAssignedSubread++;
- }
-
- if (firstAssignedSubread == subreadIntervals.size()) {
- // None of the subread has been assigned a direction, guess.
- firstAssignedSubread = 0;
- readIntervalDirection[0] = 0;
- }
-
- // Assign directions to intervals to the left of the first assigned.
- if (firstAssignedSubread < subreadIntervals.size() and
- subreadIntervals.size() > 0) {
- int curSubreadDir = readIntervalDirection[firstAssignedSubread];
- assert(curSubreadDir == 0 or curSubreadDir == 1);
- for (i = firstAssignedSubread - 1; i >= 0; i--) {
- curSubreadDir = (curSubreadDir==0)?1:0;
- readIntervalDirection[i] = curSubreadDir;
- }
- }
-
- // Assign directions to intervals which are to the right of the first
- // assigned and whose direction is unknown.
- for (i = firstAssignedSubread + 1; i < subreadIntervals.size(); i++) {
- int & di = readIntervalDirection[i];
- int dp = readIntervalDirection[i-1];
- if (di != 0 and di != 1) {
- di = (dp==0)?1:0;
- }
- }
-
- //
- // So far, subreadIntervals have been sorted and each assigned
- // a passDirection. But since all or part of a subreadInterval
- // may not be in the HQ region, we need to trim low quality regions
- // from subreads, remove subreads which do not have any high quality
- // regions from subreadIntervals and their corresponding pass directions
- // from readIntervalDirection.
- //
- GetHighQualitySubreadsIntervals(subreadIntervals,
- readIntervalDirection,
- hqRegionStart, hqRegionEnd);
- // Update number of passes.
- numPasses = subreadIntervals.size();
-}
-
-int FragmentCCSIterator::
-GetNext(int &direction, int &startBase, int &numBases) {
- if (curPass >= subreadIntervals.size()) {
- return 0;
- }
- direction = int(readIntervalDirection[curPass]);
- startBase = int(subreadIntervals[curPass].start);
- numBases = int(subreadIntervals[curPass].end - subreadIntervals[curPass].start);
- ++curPass;
- return 1;
-}
-
diff --git a/libcpp/alignment/files/FragmentCCSIterator.hpp b/libcpp/alignment/files/FragmentCCSIterator.hpp
deleted file mode 100644
index 620491f..0000000
--- a/libcpp/alignment/files/FragmentCCSIterator.hpp
+++ /dev/null
@@ -1,23 +0,0 @@
-#ifndef _BLASR_FRAGMENT_CCS_ITERATOR_HPP_
-#define _BLASR_FRAGMENT_CCS_ITERATOR_HPP_
-
-#include <vector>
-#include "reads/RegionTable.hpp"
-#include "utils/RegionUtils.hpp"
-#include "files/CCSIterator.hpp"
-
-
-class FragmentCCSIterator : public CCSIterator {
-public:
- RegionTable *regionTablePtr;
- std::vector<ReadInterval> subreadIntervals;
- std::vector<int> readIntervalDirection;
-
- virtual
- void Initialize(CCSSequence *_seqPtr, RegionTable *_regionTablePtr);
-
- virtual
- int GetNext(int & direction, int & startBase, int & numBases);
-};
-
-#endif
diff --git a/libcpp/alignment/files/ReaderAgglomerate.cpp b/libcpp/alignment/files/ReaderAgglomerate.cpp
deleted file mode 100644
index ff04a08..0000000
--- a/libcpp/alignment/files/ReaderAgglomerate.cpp
+++ /dev/null
@@ -1,505 +0,0 @@
-#include "files/ReaderAgglomerate.hpp"
-
-void ReaderAgglomerate::SetToUpper() {
- fastaReader.SetToUpper();
-}
-
-void ReaderAgglomerate::InitializeParameters() {
- start = 0;
- stride = 1;
- subsample = 1.1;
- readQuality = 1;
- useRegionTable = true;
- ignoreCCS = true;
- readType = ReadType::SUBREAD;
-#ifdef USE_PBBAM
- bamFilePtr = NULL;
- entireFileQueryPtr = NULL;
-#endif
-}
-
-ReaderAgglomerate::ReaderAgglomerate() {
- InitializeParameters();
-}
-
-ReaderAgglomerate::ReaderAgglomerate(float _subsample) {
- this->InitializeParameters();
- subsample = _subsample;
-}
-
-ReaderAgglomerate::ReaderAgglomerate(int _stride) {
- this->InitializeParameters();
- stride = _stride;
-}
-
-ReaderAgglomerate::ReaderAgglomerate(int _start, int _stride) {
- this->InitializeParameters();
- start = _start;
- stride = _stride;
-}
-
-void ReaderAgglomerate::GetMovieName(string &movieName) {
- if (fileType == Fasta || fileType == Fastq) {
- movieName = fileName;
- }
- else if (fileType == HDFPulse || fileType == HDFBase) {
- movieName = hdfBasReader.GetMovieName();
- }
- else if (fileType == HDFCCS || fileType == HDFCCSONLY) {
- movieName = hdfCcsReader.GetMovieName();
- }
- else if (fileType == PBBAM) {
-#ifdef USE_PBBAM
- assert("Reading movie name from BAM using ReaderAgglomerate is not supported." == 0);
-#endif
- }
-}
-
-void ReaderAgglomerate::GetChemistryTriple(string & bindingKit,
- string & sequencingKit, string & baseCallerVersion) {
- if (fileType == HDFPulse || fileType == HDFBase) {
- hdfBasReader.GetChemistryTriple(bindingKit, sequencingKit, baseCallerVersion);
- }
- else if (fileType == HDFCCS || fileType == HDFCCSONLY) {
- hdfCcsReader.GetChemistryTriple(bindingKit, sequencingKit, baseCallerVersion);
- }
- else if (fileType == PBBAM) {
-#ifdef USE_PBBAM
- assert("Reading chemistry triple from BAM using ReaderAgglomerate is not supported." == 0);
-#endif
- } else {
- sequencingKit = bindingKit = baseCallerVersion = "";
- }
-}
-
-void ReaderAgglomerate::SetReadType(const ReadType::ReadTypeEnum & readType_) {
- readType = readType_;
-}
-
-ReadType::ReadTypeEnum ReaderAgglomerate::GetReadType() {
- return readType;
-}
-
-bool ReaderAgglomerate::FileHasZMWInformation() {
- return (fileType == HDFPulse || fileType == HDFBase ||
- fileType == HDFCCS || fileType == HDFCCSONLY);
-}
-
-void ReaderAgglomerate::SkipReadQuality() {
- readQuality = 0;
-}
-
-void ReaderAgglomerate::IgnoreCCS() {
- ignoreCCS = true;
-}
-
-void ReaderAgglomerate::UseCCS() {
- ignoreCCS = false;
- hdfBasReader.SetReadBasesFromCCS();
-}
-
-int ReaderAgglomerate::Initialize(string &pFileName) {
- if (DetermineFileTypeByExtension(pFileName, fileType)) {
- fileName = pFileName;
- return Initialize();
- }
- return false;
-}
-
-bool ReaderAgglomerate::SetReadFileName(string &pFileName) {
- if (DetermineFileTypeByExtension(pFileName, fileType)) {
- fileName = pFileName;
- return true;
- }
- else {
- return false;
- }
-}
-
-int ReaderAgglomerate::Initialize(FileType &pFileType, string &pFileName) {
- SetFiles(pFileType, pFileName);
- return Initialize();
-}
-
-#define UNREACHABLE() \
- cout << "ERROR! Hit unreachable code in " << __FILE__ << ':' << __LINE__ << endl; \
- assert(0)
-
-bool ReaderAgglomerate::HasRegionTable() {
- switch(fileType) {
- case PBBAM:
- case Fasta:
- case Fastq:
- return false;
- break;
- case HDFPulse:
- case HDFBase:
- return hdfBasReader.HasRegionTable();
- break;
- case HDFCCSONLY:
- case HDFCCS:
- return hdfCcsReader.HasRegionTable();
- break;
- case Fourbit:
- case None:
- UNREACHABLE();
- break;
- }
- return false;
-}
-
-#ifdef USE_PBBAM
-
-#define GET_NEXT_FROM_BAM() \
- numRecords = (bamIterator == entireFileQueryPtr->end())?0:1;\
- if (numRecords != 0) {seq.Copy(*bamIterator); bamIterator++;}
-
-#define RESET_PBBAM_PTRS() \
- if (bamFilePtr != NULL) {delete bamFilePtr; bamFilePtr = NULL;} \
- if (entireFileQueryPtr != NULL) {delete entireFileQueryPtr; entireFileQueryPtr = NULL;}
-
-#endif
-
-int ReaderAgglomerate::Initialize() {
- int init = 1;
- switch(fileType) {
- case Fasta:
- init = fastaReader.Init(fileName);
- break;
- case Fastq:
- init = fastqReader.Init(fileName);
- break;
- case HDFCCSONLY:
- ignoreCCS = false;
- hdfCcsReader.SetReadBasesFromCCS();
- hdfCcsReader.InitializeDefaultIncludedFields();
- init = hdfCcsReader.Initialize(fileName);
- if (init == 0) return 0;
- break;
- case HDFPulse:
- case HDFBase:
- //
- // Here one needs to test and see if the hdf file contains ccs.
- // If this is the case, then the file type is HDFCCS.
- if (hdfCcsReader.BasFileHasCCS(fileName) and !ignoreCCS) {
- fileType = HDFCCS;
- hdfCcsReader.InitializeDefaultIncludedFields();
- init = hdfCcsReader.Initialize(fileName);
- if (init == 0) return 0;
- }
- else {
- hdfBasReader.InitializeDefaultIncludedFields();
- init = hdfBasReader.Initialize(fileName);
- //
- // This code is added so that meaningful names are printed
- // when running on simulated data that contains the coordinate
- // information.
- if (init == 0) return 0;
- }
- break;
- case PBBAM:
-#ifdef USE_PBBAM
- RESET_PBBAM_PTRS();
- try {
- bamFilePtr = new PacBio::BAM::BamFile(fileName);
- } catch (std::exception e) {
- cout << "ERROR! Failed to open " << fileName
- << ": " << e.what() << endl;
- return 0;
- }
- entireFileQueryPtr = new PacBio::BAM::EntireFileQuery(*bamFilePtr);
- bamIterator = entireFileQueryPtr->begin();
- break;
-#endif
- case HDFCCS:
- case Fourbit:
- case None:
- UNREACHABLE();
- break;
- }
- readGroupId = "";
- if (init == 0 || (start > 0 && Advance(start) == 0) ){
- return 0;
- };
- if (fileType != PBBAM) {
- // All reads from a non-PBBAM file must have the same read group id.
- // Reads from a PABBAM file may come from different read groups.
- // We have sync reader.readGroupId and SMRTSequence.readGroupId everytime
- // GetNext() is called.
- string movieName; GetMovieName(movieName);
- readGroupId = MakeReadGroupId(movieName, readType);
- }
- return 1;
-}
-
-ReaderAgglomerate & ReaderAgglomerate::operator=(ReaderAgglomerate &rhs) {
- fileType = rhs.fileType;
- fileName = rhs.fileName;
- return *this;
-}
-
-bool ReaderAgglomerate::Subsample(float rate) {
- bool retVal = true;
- while( (rand() % 100 + 1) > (rate * 100) and (retVal = Advance(1)));
- return retVal;
-}
-
-int ReaderAgglomerate::GetNext(FASTASequence &seq) {
- int numRecords = 0;
- if (Subsample(subsample) == 0) {
- return 0;
- }
- switch(fileType) {
- case Fasta:
- numRecords = fastaReader.GetNext(seq);
- break;
- case Fastq:
- numRecords = fastqReader.GetNext(seq);
- break;
- case HDFPulse:
- case HDFBase:
- numRecords = hdfBasReader.GetNext(seq);
- break;
- case HDFCCSONLY:
- case HDFCCS:
- cout << "ERROR! Reading CCS into a structure that cannot handle it." << endl;
- assert(0);
- break;
- case PBBAM:
-#ifdef USE_PBBAM
- GET_NEXT_FROM_BAM();
- break;
-#endif
- case Fourbit:
- case None:
- UNREACHABLE();
- break;
- }
- seq.CleanupOnFree();
- return numRecords;
-}
-
-int ReaderAgglomerate::GetNext(FASTQSequence &seq) {
- int numRecords = 0;
- if (Subsample(subsample) == 0) {
- return 0;
- }
- switch(fileType) {
- case Fasta:
- numRecords = fastaReader.GetNext(seq);
- break;
- case Fastq:
- numRecords = fastqReader.GetNext(seq);
- break;
- case HDFPulse:
- case HDFBase:
- numRecords = hdfBasReader.GetNext(seq);
- break;
- case PBBAM:
-#ifdef USE_PBBAM
- GET_NEXT_FROM_BAM();
- break;
-#endif
- case HDFCCSONLY:
- case HDFCCS:
- cout << "ERROR! Reading CCS into a structure that cannot handle it." << endl;
- assert(0);
- break;
- case Fourbit:
- case None:
- UNREACHABLE();
- break;
- }
- if (stride > 1)
- Advance(stride-1);
- return numRecords;
-}
-
-int ReaderAgglomerate::GetNext(SMRTSequence &seq) {
- int numRecords = 0;
-
- if (Subsample(subsample) == 0) {
- return 0;
- }
- switch(fileType) {
- case Fasta:
- numRecords = fastaReader.GetNext(seq);
- break;
- case Fastq:
- numRecords = fastqReader.GetNext(seq);
- break;
- case HDFPulse:
- case HDFBase:
- numRecords = hdfBasReader.GetNext(seq);
- break;
- case HDFCCSONLY:
- cout << "ERROR! Reading CCS into a structure that cannot handle it." << endl;
- assert(0);
- break;
- case HDFCCS:
- assert(ignoreCCS == false);
- assert(hdfBasReader.readBasesFromCCS == true);
- numRecords = hdfBasReader.GetNext(seq);
- break;
- case PBBAM:
-#ifdef USE_PBBAM
- GET_NEXT_FROM_BAM();
- break;
-#endif
- case Fourbit:
- case None:
- UNREACHABLE();
- break;
- }
- // A sequence read from a Non-BAM files does not have read group id
- // and should be empty, use this->readGroupId instead. Otherwise,
- // read group id should be loaded from BamRecord to SMRTSequence,
- // update this->readGroupId accordingly.
- if (fileType != PBBAM) seq.SetReadGroupId(readGroupId);
- else readGroupId = seq.GetReadGroupId();
-
- if (stride > 1)
- Advance(stride-1);
- return numRecords;
-}
-
-int ReaderAgglomerate::GetNextBases(SMRTSequence &seq, bool readQVs) {
- int numRecords = 0;
-
- if (Subsample(subsample) == 0) {
- return 0;
- }
- switch(fileType) {
- case Fasta:
- cout << "ERROR! Can not GetNextBases from a Fasta File." << endl;
- assert(0);
- break;
- case Fastq:
- cout << "ERROR! Can not GetNextBases from a Fastq File." << endl;
- assert(0);
- break;
- case HDFPulse:
- case HDFBase:
- numRecords = hdfBasReader.GetNextBases(seq, readQVs);
- break;
- case HDFCCSONLY:
- cout << "ERROR! Reading CCS into a structure that cannot handle it." << endl;
- assert(0);
- break;
- case HDFCCS:
- cout << "ERROR! Can not GetNextBases from a CCS File." << endl;
- assert(0);
- break;
- case PBBAM:
-#ifdef USE_PBBAM
- cout << "ERROR! Can not GetNextBases from a BAM File." << endl;
-#endif
- case Fourbit:
- case None:
- UNREACHABLE();
- break;
- }
-
- if (fileType != PBBAM) seq.SetReadGroupId(readGroupId);
- else readGroupId = seq.GetReadGroupId();
-
- if (stride > 1)
- Advance(stride-1);
- return numRecords;
-}
-
-int ReaderAgglomerate::GetNext(CCSSequence &seq) {
- int numRecords = 0;
- if (Subsample(subsample) == 0) {
- return 0;
- }
-
- switch(fileType) {
- case Fasta:
- // This just reads in the fasta sequence as if it were a ccs sequence
- numRecords = fastaReader.GetNext(seq);
- seq.subreadStart = 0;
- seq.subreadEnd = 0;
- break;
- case Fastq:
- numRecords = fastqReader.GetNext(seq);
- seq.subreadStart = 0;
- seq.subreadEnd = 0;
- break;
- case HDFPulse:
- case HDFBase:
- numRecords = hdfBasReader.GetNext(seq);
- break;
- case HDFCCSONLY:
- case HDFCCS:
- numRecords = hdfCcsReader.GetNext(seq);
- break;
- case PBBAM:
-#ifdef USE_PBBAM
- cout << "ERROR! Could not read BamRecord as CCSSequence" << endl;
-#endif
- case Fourbit:
- case None:
- UNREACHABLE();
- break;
- }
-
- if (fileType != PBBAM) seq.SetReadGroupId(readGroupId);
- else readGroupId = seq.GetReadGroupId();
-
- if (stride > 1)
- Advance(stride-1);
- return numRecords;
-}
-
-
-int ReaderAgglomerate::Advance(int nSteps) {
- int i;
- switch(fileType) {
- case Fasta:
- return fastaReader.Advance(nSteps);
- case HDFPulse:
- case HDFBase:
- return hdfBasReader.Advance(nSteps);
- case HDFCCSONLY:
- case HDFCCS:
- return hdfCcsReader.Advance(nSteps);
- case Fastq:
- return fastqReader.Advance(nSteps);
- case PBBAM:
- case Fourbit:
- case None:
- UNREACHABLE();
- break;
- }
- return false;
-}
-
-void ReaderAgglomerate::Close() {
- switch(fileType) {
- case Fasta:
- fastaReader.Close();
- break;
- case Fastq:
- fastqReader.Close();
- break;
- case HDFPulse:
- case HDFBase:
- hdfBasReader.Close();
- break;
- case HDFCCSONLY:
- case HDFCCS:
- hdfCcsReader.Close();
- break;
- case PBBAM:
-#ifdef USE_PBBAM
- RESET_PBBAM_PTRS();
- break;
-#endif
- case Fourbit:
- case None:
- UNREACHABLE();
- break;
- }
-}
-
diff --git a/libcpp/alignment/files/ReaderAgglomerate.hpp b/libcpp/alignment/files/ReaderAgglomerate.hpp
deleted file mode 100644
index 0955498..0000000
--- a/libcpp/alignment/files/ReaderAgglomerate.hpp
+++ /dev/null
@@ -1,136 +0,0 @@
-#ifndef _BLASR_READER_AGGLOMERATE_HPP_
-#define _BLASR_READER_AGGLOMERATE_HPP_
-
-#include <cstdlib>
-
-#include "Enumerations.h"
-#include "reads/ReadType.hpp"
-#include "files/BaseSequenceIO.hpp"
-
-#include "FASTAReader.hpp"
-#include "FASTQReader.hpp"
-#include "CCSSequence.hpp"
-#include "SMRTSequence.hpp"
-#include "StringUtils.hpp"
-
-#include "HDFBasReader.hpp"
-#include "HDFCCSReader.hpp"
-
-#ifdef USE_PBBAM
-#include "pbbam/BamFile.h"
-#include "pbbam/EntireFileQuery.h"
-#include "pbbam/BamRecord.h"
-#endif
-
-class ReaderAgglomerate : public BaseSequenceIO {
- FASTAReader fastaReader;
- FASTQReader fastqReader;
- int readQuality;
- int stride;
- int start;
- float subsample;
- bool useRegionTable;
- bool ignoreCCS;
- ReadType::ReadTypeEnum readType;
-
-public:
- //
- // Create interfaces for reading hdf
- //
- T_HDFBasReader<SMRTSequence> hdfBasReader;
- HDFCCSReader<CCSSequence> hdfCcsReader;
- vector<SMRTSequence> readBuffer;
- vector<CCSSequence> ccsBuffer;
- string readGroupId;
-
-public:
- void SetToUpper();
-
- void InitializeParameters();
- ReaderAgglomerate();
-
- ReaderAgglomerate(float _subsample);
-
- ReaderAgglomerate(int _stride);
-
- ReaderAgglomerate(int _start, int _stride);
-
- void GetMovieName(string &movieName);
-
- /// Get BindingKit, SequencingKit and Base Caller Version from h5.
- ///
- /// /param [out] sequencingKit - sequencingKit from
- /// /ScanData/RunInfo/SequencingKit.
- ///
- /// /param [out] bindingKit - BindingKit from
- /// /ScanData/RunInfo/BindingKit.
- ///
- /// /param [out] baseCallerVersion - Base Caller Version
- /// from /PulseData/BaseCalls/ChangeListID.
- ///
- void GetChemistryTriple(string & bindingKit,
- string & sequencingKit,
- string & baseCallerVersion);
-
- bool FileHasZMWInformation();
-
- void SkipReadQuality();
-
- void IgnoreCCS();
-
- void UseCCS();
-
- int Initialize(string &pFileName);
-
- bool SetReadFileName(string &pFileName);
-
- int Initialize(FileType &pFileType, string &pFileName);
-
- bool HasRegionTable();
-
- int Initialize();
-
- ReaderAgglomerate &operator=(ReaderAgglomerate &rhs);
-
- bool Subsample(float rate);
-
- // Set read type to SUBREAD, CCS, or UNKNOWN.
- void SetReadType(const ReadType::ReadTypeEnum & readType_);
-
- // returns read type, SUBREAD, CCS, or UNKNOWN
- ReadType::ReadTypeEnum GetReadType();
-
-public:
- int GetNext(FASTASequence &seq);
- int GetNext(FASTQSequence &seq);
- int GetNext(SMRTSequence &seq);
- int GetNext(CCSSequence &seq);
-
- template<typename T_Sequence>
- int GetNext(T_Sequence & seq, int & randNum);
-
- int GetNextBases(SMRTSequence & seq, bool readQVs);
-
- int Advance(int nSteps);
-
- void Close();
-
-#ifdef USE_PBBAM
-public:
- // Define reader to fetch sequences from bam.
- PacBio::BAM::BamFile * bamFilePtr;
- PacBio::BAM::EntireFileQuery * entireFileQueryPtr;
- PacBio::BAM::EntireFileQuery::iterator bamIterator;
-#endif
-};
-
-
-template<typename T_Sequence>
-int ReadChunkByNReads(ReaderAgglomerate &reader, vector<T_Sequence> &reads, int maxNReads);
-
-template<typename T_Sequence>
-int ReadChunkBySize (ReaderAgglomerate &reader, vector<T_Sequence> &reads, int maxMemorySize);
-
-#include "files/ReaderAgglomerateImpl.hpp"
-
-#endif
diff --git a/libcpp/alignment/files/ReaderAgglomerateImpl.hpp b/libcpp/alignment/files/ReaderAgglomerateImpl.hpp
deleted file mode 100644
index c50fafa..0000000
--- a/libcpp/alignment/files/ReaderAgglomerateImpl.hpp
+++ /dev/null
@@ -1,44 +0,0 @@
-#ifndef _BLASR_READER_AGGLOMERATE_IMPL_HPP_
-#define _BLASR_READER_AGGLOMERATE_IMPL_HPP_
-
-template<typename T_Sequence>
-int ReaderAgglomerate::GetNext(T_Sequence & seq, int & randNum) {
- randNum = rand();
- return GetNext(seq);
-}
-
-template<typename T_Sequence>
-int ReadChunkByNReads(ReaderAgglomerate &reader, vector<T_Sequence> &reads, int maxNReads) {
- T_Sequence seq;
- int nReads = 0;
- while(nReads < maxNReads) {
- if (reader.GetNext(seq)) {
- reads.push_back(seq);
- ++nReads;
- }
- else {
- break;
- }
- }
- return nReads;
-}
-
-template<typename T_Sequence>
-int ReadChunkBySize (ReaderAgglomerate &reader, vector<T_Sequence> &reads, int maxMemorySize) {
- T_Sequence seq;
- int nReads = 0;
- int totalStorage = 0;
- while (totalStorage < maxMemorySize) {
- if (reader.GetNext(seq)) {
- reads.push_back(seq);
- totalStorage += seq.GetStorageSize();
- nReads++;
- }
- else {
- break;
- }
- }
- return nReads;
-}
-
-#endif
diff --git a/libcpp/alignment/format/BAMPrinter.hpp b/libcpp/alignment/format/BAMPrinter.hpp
deleted file mode 100644
index db70308..0000000
--- a/libcpp/alignment/format/BAMPrinter.hpp
+++ /dev/null
@@ -1,29 +0,0 @@
-#ifndef _BLASR_FORMAT_BAMPRINTER_HPP_
-#define _BLASR_FORMAT_BAMPRINTER_HPP_
-
-#ifdef USE_PBBAM
-#include <sstream>
-#include <stdint.h>
-#include "format/SAMPrinter.hpp"
-#include "pbbam/BamHeader.h"
-#include "pbbam/BamWriter.h"
-
-template<typename T_Sequence>
-void AlignmentToBamRecord(T_AlignmentCandidate & alignment,
- T_Sequence & read, PacBio::BAM::BamRecord & bamRecord,
- AlignmentContext & context, SupplementalQVList & qvList,
- Clipping clipping, bool cigarUseSeqMatch);
-
-namespace BAMOutput {
-
-template<typename T_Sequence>
-void PrintAlignment(T_AlignmentCandidate &alignment, T_Sequence &read,
- PacBio::BAM::BamWriter &bamWriter, AlignmentContext &context,
- SupplementalQVList & qvList, Clipping clipping,
- bool cigarUseSeqMatch=false);
-}
-
-#include "BAMPrinterImpl.hpp"
-
-#endif
-#endif
diff --git a/libcpp/alignment/format/BAMPrinterImpl.hpp b/libcpp/alignment/format/BAMPrinterImpl.hpp
deleted file mode 100644
index 9dd66c6..0000000
--- a/libcpp/alignment/format/BAMPrinterImpl.hpp
+++ /dev/null
@@ -1,168 +0,0 @@
-#ifndef _BLASR_BAM_PRINTER_IMPL_HPP_
-#define _BLASR_BAM_PRINTER_IMPL_HPP_
-
-#ifdef USE_PBBAM
-
-#include <algorithm>
-#include "utils/SMRTTitle.hpp"
-using namespace BAMOutput;
-using namespace std;
-#include "pbbam/BamRecord.h"
-#include "pbbam/BamFile.h"
-
-template<typename T_Sequence>
-void AlignmentToBamRecord(T_AlignmentCandidate & alignment,
- T_Sequence & read, PacBio::BAM::BamRecord & bamRecord,
- AlignmentContext & context, SupplementalQVList & qvList,
- Clipping clipping, bool cigarUseSeqMatch) {
- assert(clipping == SAMOutput::soft or clipping == SAMOutput::subread);
-
- // Build from scratch if input reads are not from pbbam files.
- // Otherwise, use API provided by pbbam to make alignments from bamRecords.
-
- bool buildFromScratch = false;
- if (dynamic_cast<SMRTSequence*>(&read) == NULL) {
- //not SMRTSequence
- buildFromScratch = true;
- } else { //is SMRTSequence, but not copied from bam.
- if (not read.copiedFromBam) {
- buildFromScratch = true;
- }
- }
-
- // build cigar string.
- string cigarString;
- T_Sequence alignedSequence;
- DNALength prefixSoftClip = 0, suffixSoftClip = 0;
- DNALength prefixHardClip = 0, suffixHardClip = 0;
- CreateCIGARString(alignment, read, cigarString, clipping,
- prefixSoftClip, suffixSoftClip,
- prefixHardClip, suffixHardClip,
- cigarUseSeqMatch);
- SetAlignedSequence(alignment, read, alignedSequence, clipping);
- PacBio::BAM::Cigar cigar = PacBio::BAM::Cigar::FromStdString(cigarString);
-
- // build flag
- uint16_t flag;
- BuildFlag(alignment, context, flag);
-
- // Get sequence string.
- string seqString;
- seqString.assign((char*)alignedSequence.seq, alignedSequence.length);
-
- // Get alignment starting position on reference sequence forward strand.
- PacBio::BAM::Position pos = 0;
- PacBio::BAM::Strand strand;
- if (alignment.tStrand == 0) {
- pos = static_cast<PacBio::BAM::Position>(alignment.TAlignStart());
- strand = PacBio::BAM::Strand::FORWARD;
- } else {
- pos = static_cast<PacBio::BAM::Position>(alignment.tLength - (alignment.TAlignStart() + alignment.TEnd()));
- strand = PacBio::BAM::Strand::REVERSE;
- }
-
- if (buildFromScratch) {
- SMRTTitle smrtTitle(alignment.qName);
- if (smrtTitle.isSMRTTitle) {
- bamRecord.Impl().Name(smrtTitle.ToString());
- } else {
- cout << "ERROR, can not convert non-pacbio reads to pbbam record." << endl;
- exit(-1);
- }
- bamRecord.Impl().SetSequenceAndQualities(seqString, alignedSequence.qual.ToString());
- bamRecord.Impl().CigarData(cigar);
- bamRecord.Impl().Bin(0);
- bamRecord.Impl().InsertSize(0);
- bamRecord.Impl().MapQuality(static_cast<uint8_t>(alignment.mapQV));
- bamRecord.Impl().MatePosition(static_cast<PacBio::BAM::Position>(-1));
- bamRecord.Impl().MateReferenceId(static_cast<int32_t>(-1));
- bamRecord.Impl().Position(pos);
- bamRecord.Impl().ReferenceId(static_cast<int32_t>(alignment.tIndex));
-
- if (strand == PacBio::BAM::Strand::REVERSE) {
- bamRecord.Impl().SetReverseStrand(true);
- }
-
- // Add tags required for bax->bam.
- PacBio::BAM::TagCollection tags;
- tags["RG"] = context.readGroupId;
- if (dynamic_cast<CCSSequence*>(&read) == NULL) { // subread
- tags["qs"] = read.subreadStart;
- tags["qe"] = read.subreadEnd;
- /// Number of passes for a subread should always be 1.
- tags["np"] = 1;
- } else { // ccs read
- /// Number of passes for ccs reads.
- tags["np"] = (static_cast<CCSSequence*>(&read))->numPasses;
- }
- tags["zm"] = read.zmwData.holeNumber;
-
- // Build QV tags.
- // Skip tags not define in BAM specification 3.0.
- // including XL, XT, XQ, XS, XE, YS, YE.
- //
- // Write out optional quality values. If qvlist does not
- // have any qv's signaled to print, this is a no-op.
- //
- // First transform characters that are too large to printable ones.
- qvList.FormatQVOptionalFields(alignedSequence);
-
- // Add QVs to BamRecordImpl.
- string insertionQVs, deletionQVs, substitutionQVs, mergeQVs, substitutionTags, deletionTags;
- bool alnReverse = (alignment.tStrand == 1); // reverse-complement alignment
- // If this is a reverse-complement alignment, bases and QVs of
- // alignedSequence are reverse(-complement) of the sequence read
- // from bax.h5 file. With PB BAM specification 3.0, QVs will be stored
- // in BAM Record, therefore, reverse orders of QVs before add QV tags.
- if (alignedSequence.GetQVs("InsertionQV", insertionQVs, alnReverse)) {
- tags["iq"] = insertionQVs;
- }
- if (alignedSequence.GetQVs("DeletionQV", deletionQVs, alnReverse)) {
- tags["dq"] = deletionQVs;
- }
- if (alignedSequence.GetQVs("SubstitutionQV", substitutionQVs, alnReverse)) {
- tags["sq"] = substitutionQVs;
- }
- if (alignedSequence.GetQVs("MergeQV", mergeQVs, alnReverse)) {
- tags["mq"] = mergeQVs;
- }
- // substitutionTag is not included by default
- if (alignedSequence.GetQVs("DeletionTag", deletionTags, alnReverse)) {
- tags["dt"] = deletionTags;
- }
- bamRecord.Impl().Tags(tags);
- } else {
- // The following code can be used to hard-clip reads, if needed.
- // PacBio::BAM::Position clipStart = read.bamRecord.QueryStart() + alignment.QAlignStart();
- // PacBio::BAM::Position clipEnd = read.bamRecord.QueryStart() + alignment.QAlignEnd();
- // bamRecord = PacBio::BAM::BamRecord::Clipped(read.bamRecord,
- // PacBio::BAM::ClipType::CLIP_TO_QUERY,
- // clipStart, clipEnd).
- bamRecord = PacBio::BAM::BamRecord::Mapped(read.bamRecord,
- static_cast<int32_t>(alignment.tIndex),
- static_cast<PacBio::BAM::Position>(pos),
- strand, cigar,
- static_cast<uint8_t>(alignment.mapQV));
- }
-
- // Add tags common for bax->bam and bam->bam.
- bamRecord.Impl().AddTag("AS", alignment.score);
- bamRecord.Impl().AddTag("NM", context.editDist);
-
- // Set Flag
- bamRecord.Impl().Flag(static_cast<uint32_t>(flag));
-
-}
-
-template<typename T_Sequence>
-void BAMOutput::PrintAlignment(T_AlignmentCandidate &alignment, T_Sequence &read,
- PacBio::BAM::BamWriter &bamWriter, AlignmentContext &context,
- SupplementalQVList & qvList, Clipping clipping, bool cigarUseSeqMatch) {
-
- PacBio::BAM::BamRecord bamRecord;
- AlignmentToBamRecord(alignment, read, bamRecord, context, qvList, clipping, cigarUseSeqMatch);
- bamWriter.Write(bamRecord);
-}
-#endif
-
-#endif
diff --git a/libcpp/alignment/format/CompareSequencesPrinter.cpp b/libcpp/alignment/format/CompareSequencesPrinter.cpp
deleted file mode 100644
index 581664a..0000000
--- a/libcpp/alignment/format/CompareSequencesPrinter.cpp
+++ /dev/null
@@ -1,10 +0,0 @@
-#include "CompareSequencesPrinter.hpp"
-
-void CompareSequencesOutput::PrintHeader(std::ostream &out) {
- out << "qName qLength qStart qEnd qStrand "
- << "tName tLength tStart tEnd tStrand "
- << "score numMatch numMismatch numIns numDel "
- << "mapQV qAlignedSeq matchPattern tAlignedSeq"
- << std::endl;
-}
-
diff --git a/libcpp/alignment/format/CompareSequencesPrinter.hpp b/libcpp/alignment/format/CompareSequencesPrinter.hpp
deleted file mode 100644
index bd5fe34..0000000
--- a/libcpp/alignment/format/CompareSequencesPrinter.hpp
+++ /dev/null
@@ -1,21 +0,0 @@
-#ifndef _BLASR_COMPARE_SEQUENCES_PRINTER_HPP_
-#define _BLASR_COMPARE_SEQUENCES_PRINTER_HPP_
-
-#include <fstream>
-#include <iostream>
-#include "algorithms/alignment/AlignmentUtils.hpp"
-
-namespace CompareSequencesOutput{
-
-void PrintHeader(std::ostream &out);
-
-template<typename T_Alignment, typename T_QuerySequence, typename T_TargetSequence>
-void Print(T_Alignment &alignment,
- T_QuerySequence &qseq, T_TargetSequence &tseq,
- std::ostream &out, bool refForward=true);
-
-}
-
-#include "CompareSequencesPrinterImpl.hpp"
-
-#endif
diff --git a/libcpp/alignment/format/CompareSequencesPrinterImpl.hpp b/libcpp/alignment/format/CompareSequencesPrinterImpl.hpp
deleted file mode 100644
index e285780..0000000
--- a/libcpp/alignment/format/CompareSequencesPrinterImpl.hpp
+++ /dev/null
@@ -1,77 +0,0 @@
-#ifndef _BLASR_COMPARE_SEQUENCES_PRINTER_IMPL_HPP_
-#define _BLASR_COMPARE_SEQUENCES_PRINTER_IMPL_HPP_
-
-template<typename T_Alignment, typename T_QuerySequence, typename T_TargetSequence>
-void CompareSequencesOutput::Print(T_Alignment &alignment,
- T_QuerySequence &qseq, T_TargetSequence &tseq,
- std::ostream &out, bool refForward) {
-
- std::string queryStr, alignStr, textStr;
- CreateAlignmentStrings(alignment, qseq, tseq, textStr, alignStr, queryStr);
-
- if (refForward == false) {
- if (alignment.qStrand == 1 and alignment.tStrand == 0) {
- DNALength alignedSeqToEnd = 0;
- // DNALength alignedTSeqToEnd = 0;
- if (alignment.blocks.size() > 0) {
- // First compute the offset of the reverse of the substring that was aligned.
-
- alignedSeqToEnd = alignment.qLength - (alignment.qAlignedSeqPos + alignment.qAlignedSeq.length);
- DNALength alignEndToSubstrEnd = alignment.qAlignedSeq.length - (alignment.qPos + alignment.blocks[alignment.blocks.size()-1].qPos + alignment.blocks[alignment.blocks.size()-1].length);
- alignment.qPos = alignEndToSubstrEnd;
- }
- alignment.qAlignedSeqPos = alignedSeqToEnd;
- alignment.qStrand = 0;
- alignment.tStrand = 1;
-
- }
- }
-
- PrintCompareSequencesAlignmentStats(alignment, out);
- // change the spaces in the align string to *s for easy parsing of alignment
- VectorIndex i;
- for (i = 0; i < alignStr.size(); i++ ) {
- if (alignStr[i] == ' ') alignStr[i] = '*';
- }
-
- if (refForward == false and alignment.tStrand == 1) {
- //
- // Build reverse complement strings.
- //
- std::string queryStrRC, alignStrRC, textStrRC;
- queryStrRC.resize(queryStr.size());
- alignStrRC.resize(alignStr.size());
- textStrRC.resize(alignStr.size());
-
- DNALength pos;
- DNALength alignStringLength = alignStr.size();
- for (pos = 0; pos < alignStringLength; pos++ ) {
- if (queryStr[pos] != '-') {
- queryStrRC[alignStringLength-pos-1] = ReverseComplementNuc[queryStr[pos]];
- }
- else {
- queryStrRC[alignStringLength-pos-1] = '-';
- }
- alignStrRC[alignStringLength-pos-1] = alignStr[pos];
-
- if (textStr[pos] != '-') {
- textStrRC[alignStringLength-pos-1] = ReverseComplementNuc[textStr[pos]];
- }
- else {
- textStrRC[alignStringLength-pos-1] = '-';
- }
- }
- queryStr = queryStrRC;
- alignStr = alignStrRC;
- textStr = textStrRC;
- }
-
- // Headers of m5 format are:
- // qName qSeqLength qStart qEnd qStrand
- // tName tSeqLength tStart tEnd tStrand
- // score numMatch numMismatch numIns numDel
- // mapQV qAlignedSeq matchPattern tAlignedSeq
- out << queryStr << " " << alignStr << " " << textStr << std::endl;
-}
-
-#endif
diff --git a/libcpp/alignment/format/IntervalPrinter.cpp b/libcpp/alignment/format/IntervalPrinter.cpp
deleted file mode 100644
index e9cd328..0000000
--- a/libcpp/alignment/format/IntervalPrinter.cpp
+++ /dev/null
@@ -1,70 +0,0 @@
-#include "IntervalPrinter.hpp"
-
-void IntervalOutput::Print(T_AlignmentCandidate &alignment,
- std::ostream &outFile) {
-
- int mapQV = alignment.mapQV;
- int lastBlock = alignment.blocks.size()-1;
- if (lastBlock < 0) return;
-
- outFile << alignment.qName << " " << alignment.tName << " "
- << alignment.score << " "
- << alignment.pctSimilarity << " "
- << alignment.qStrand << " "
- << alignment.QAlignStart() << " "
- << alignment.QAlignEnd() << " "
- << alignment.qLength << " "
- << alignment.tStrand << " "
- << alignment.TAlignStart() << " "
- << (alignment.tAlignedSeqPos + alignment.tPos
- + alignment.blocks[lastBlock].tPos
- + alignment.blocks[lastBlock].length) << " "
- << alignment.tLength << " "
- << mapQV << std::endl;
- //Remove the last four fields from m4 format.
- //<< " " << alignment.nCells << " " << alignment.clusterScore
- //<< " " << alignment.probScore << " "
- //<< alignment.numSignificantClusters
-}
-
-// Print an alignment from a sam file in Interval (m 4) format.
-void IntervalOutput::PrintFromSAM(AlignmentCandidate<> &alignment,
- std::ostream &outFile) {
-
- int mapQV = alignment.mapQV;
- int lastBlock = alignment.blocks.size()-1;
- if (lastBlock < 0) return;
-
- outFile << alignment.qName << " "
- << alignment.tName << " "
- << alignment.score << " "
- << alignment.pctSimilarity << " "
- << alignment.qStrand << " "
- << alignment.QAlignStart() << " "
- << alignment.QAlignEnd() << " "
- << alignment.qLength << " "
- << alignment.tStrand << " ";
-
- DNALength tS = alignment.TAlignStart();
- DNALength tE = alignment.tAlignedSeqPos + alignment.tPos
- + alignment.blocks[lastBlock].tPos
- + alignment.blocks[lastBlock].length;
-
- if (alignment.tStrand == 1) {
- // Since the alignment is from a SAM file and the reference
- // is reverse, compute tS and tE in the coordinate of the reverse
- // complementary sequence
- DNALength tmp = tS;
- tS = alignment.tLength - tE;
- tE = alignment.tLength - tmp;
- }
- outFile << tS << " " << tE << " " << alignment.tLength << " "
- << mapQV << std::endl;
-}
-
-void IntervalOutput::PrintHeader(std::ostream &out) {
- out << "qName tName score percentSimilarity qStrand "
- << "qStart qEnd qLength tStrand tStart tEnd tLength mapQV"
- << std::endl;
- //ncells clusterScore probscore numSigClusters" << endl;
-}
diff --git a/libcpp/alignment/format/IntervalPrinter.hpp b/libcpp/alignment/format/IntervalPrinter.hpp
deleted file mode 100644
index a1efdfc..0000000
--- a/libcpp/alignment/format/IntervalPrinter.hpp
+++ /dev/null
@@ -1,21 +0,0 @@
-#ifndef _BLASR_INTERVAL_ALIGNMENT_PRINTER_HPP_
-#define _BLASR_INTERVAL_ALIGNMENT_PRINTER_HPP_
-
-#include "datastructures/alignment/AlignmentCandidate.hpp"
-#include "FASTQSequence.hpp"
-
-namespace IntervalOutput{
-
-void Print(T_AlignmentCandidate &alignment,
- std::ostream &outFile);
-
-// Print an alignment from a sam file in Interval (m 4) format.
-void PrintFromSAM(AlignmentCandidate<> &alignment,
- std::ostream &outFile);
-
-void PrintHeader(std::ostream &out);
-
-}
-
-
-#endif
diff --git a/libcpp/alignment/format/SAMHeaderPrinter.cpp b/libcpp/alignment/format/SAMHeaderPrinter.cpp
deleted file mode 100644
index c5c8eca..0000000
--- a/libcpp/alignment/format/SAMHeaderPrinter.cpp
+++ /dev/null
@@ -1,432 +0,0 @@
-#include "format/SAMHeaderPrinter.hpp"
-
-const std::string SAMVERSION("1.5");
-const std::string PBBAMVERSION("3.0b7");
-const std::string PACBIOPL("PACBIO");
-
-std::vector<SAMHeaderItem> MakeSAMHeaderItems(const std::string & fromString){
- std::vector<SAMHeaderItem> items;
-
- std::vector<std::string> vs;
- Splice(fromString, ";", vs);
- std::vector<std::string>::iterator it;
- for (it = vs.begin(); it != vs.end(); it++) {
- items.push_back(SAMHeaderItem(*it));
- }
- return items;
-}
-
-// SAMHeaderItem
-SAMHeaderItem::SAMHeaderItem(const std::string & fromString) {
- std::size_t pos = fromString.find("=");
- if (pos != std::string::npos) {
- _key = fromString.substr(0, pos);
- _val = fromString.substr(pos + 1);
- }
-}
-
-std::string SAMHeaderItem::ToString() {
- std::stringstream ss;
- if (_key != "") ss << _key << "=" << _val;
- return ss.str();
-}
-
-// SAMHeaderTag
-SAMHeaderTag::SAMHeaderTag(const std::string & fromString) {
- size_t pos = fromString.find(":");
- if (pos != string::npos) {
- _tagName = fromString.substr(0, pos);
- string tagValue = fromString.substr(pos + 1);
- if (tagValue.find("=") != std::string::npos) {
- AddItems(tagValue);
- } else {
- _tagValue = tagValue;
- }
- } else {
- cout << "Unable to parse SAM/BAM header" << fromString << endl;
- exit(1);
- }
-}
-
-std::string SAMHeaderTag::ToString() {
- std::stringstream ss;
- if (_tagName != "") {
- ss << _tagName << ":";
- if (_tagValue != "") {
- ss << _tagValue;
- } else {
- std::vector<SAMHeaderItem>::iterator it;
- for(it = _tagItems.begin(); it != _tagItems.end(); it++) {
- if (it != _tagItems.begin() and (*it).ToString() != "") {
- ss << ";";
- }
- ss << (*it).ToString();
- }
- }
- }
- return ss.str();
-}
-
-std::string SAMHeaderTag::TagName() const {
- return _tagName;
-}
-
-void SAMHeaderTag::AddItem(SAMHeaderItem & item) {
- _tagItems.push_back(item);
-}
-
-void SAMHeaderTag::AddItem(const std::string & fromString) {
- _tagItems.push_back(SAMHeaderItem(fromString));
-}
-
-void SAMHeaderTag::AddItems(const std::string & fromString) {
- // SAM Header Items: key=value;key=value
- std::vector<SAMHeaderItem> items = MakeSAMHeaderItems(fromString);
- _tagItems.insert(_tagItems.begin(), items.begin(), items.end());
-}
-
-// SAMHeaderGroup
-SAMHeaderGroup::SAMHeaderGroup(const std::string & fromString) {
- if (fromString == "" || fromString[0] != '@') return;
- std::vector<std::string> vs;
- Splice(fromString.substr(1), "\t", vs);
- if (vs.size() >= 1) {
- std::vector<std::string>::iterator it = vs.begin();
- _groupName = (*it);
- it++;
- for(; it != vs.end(); it++) {
- _tags.push_back(SAMHeaderTag(*it));
- }
- }
-}
-
-std::string SAMHeaderGroup::ToString() {
- std::stringstream ss;
- ss << "@" << _groupName;
- SAMHeaderTags::iterator it;
- for (it = _tags.begin(); it != _tags.end(); it++) {
- ss << "\t" << (*it).ToString();
- }
- return ss.str();
-}
-
-std::ostream & operator << (std::ostream& os, SAMHeaderGroup & g) {
- return os << g.ToString();
-}
-
-/// returns true if this SAMHeaderGroup contains a tag tagName.
-bool SAMHeaderGroup::HasTag(std::string tagName) {
- for(SAMHeaderTags::iterator it = _tags.begin(); it != _tags.end(); it++) {
- if ((*it).TagName() == tagName) {
- return true;
- }
- }
- return false;
-}
-
-/// returns value of a tag if it exists, otherwise, return an empty string.
-std::string SAMHeaderGroup::Tag(const std::string & tagName) {
- for(SAMHeaderTags::iterator it = _tags.begin(); it != _tags.end(); it++) {
- if ((*it).TagName() == tagName) {
- return (*it).ToString();
- }
- }
- return "";
-}
-
-// SAMHeaderGroupWithID
-std::string SAMHeaderGroupWithID::ID() const {return _id;}
-
-SAMHeaderGroupWithID::SAMHeaderGroupWithID(const std::string & fromString)
-: SAMHeaderGroup(fromString) {
- assert (HasTag("ID"));
- if (not HasTag("ID")) {
- assert("ERROR! SAM Header read/program group must has ID tag." == 0);
- }
- _id = Tag("ID");
-}
-
-// SAMHeaderRG
-SAMHeaderRG::SAMHeaderRG(const std::string & id, const std::string & pl,
- const std::string & pu, const std::vector<SAMHeaderItem> & dsItems) {
- _groupName = "RG";
- _id = id;
- _tags.push_back(SAMHeaderTag("ID", id));
- _tags.push_back(SAMHeaderTag("PU", pu));
- _tags.push_back(SAMHeaderTag("PL", pl));
- _tags.push_back(SAMHeaderTag("DS", dsItems));
-}
-
-SAMHeaderRG::SAMHeaderRG(const std::string & fromString)
-:SAMHeaderGroupWithID(fromString) {
- if (_groupName != "RG") {
- assert("ERROR! SAM Header read group should start with @RG" == 0);
- }
-}
-
-// SAMHeaderPG
-SAMHeaderPG::SAMHeaderPG(const std::string & id, const std::string & progName,
- const std::string & progVersion, const std::string & commandLine) {
- _groupName = "PG";
- _id = id;
- _tags.push_back(SAMHeaderTag("ID", id));
- _tags.push_back(SAMHeaderTag("PN", progName));
- _tags.push_back(SAMHeaderTag("VN", progVersion));
- _tags.push_back(SAMHeaderTag("CL", commandLine));
-}
-
-SAMHeaderPG::SAMHeaderPG(const std::string & fromString)
-: SAMHeaderGroupWithID(fromString) {
- if (_groupName != "PG") {
- assert("ERROR! SAM Header program group must start with @PG" == 0);
- }
-}
-
-// SAMHeaderSQ
-SAMHeaderSQ::SAMHeaderSQ(const std::string & sn, const DNALength & ln, const std::string & md5)
-: SAMHeaderSQ(sn, std::to_string(ln), md5) {}
-
-SAMHeaderSQ::SAMHeaderSQ(const std::string & sn, const string & ln, const std::string & md5)
-: SAMHeaderGroup() {
- _groupName = "SQ";
- _tags.push_back(SAMHeaderTag("SN", sn));
- _tags.push_back(SAMHeaderTag("LN", ln));
- _tags.push_back(SAMHeaderTag("M5", md5));
-}
-
-SAMHeaderSQ::SAMHeaderSQ(const std::string & fromString)
-: SAMHeaderGroup(fromString) {
- if (_groupName != "SQ") {
- assert("ERROR! SAM Header soring order must start with @SO" == 0);
- }
-}
-
-// SAMHeaderPrinter
-std::string SAMHeaderPrinter::ToString() {
- std::stringstream ss;
- ss << _hd.ToString()
- << _sqs.ToString()
- << _rgs.ToString()
- << _pgs.ToString()
- << _cos.ToString();
- return ss.str();
-}
-/*
-/// Add a SAM Header @RG entry, including the following tags:
-/// ID (identifier), PL (platform), PU (platform unit),
-/// DS (description, which may have many items)
-SAMHeaderPrinter & SAMHeaderPrinter::AddRG(std::string & id, std::string & pl, std::string & pu, std::string & ds) {
- _rgs.Add(SAMHeaderRG(id, pl, pu, ds));
- return *this;
-}*/
-
-/// Add a SAM Header @RG entry from string, which may contain arbitary tags.
-SAMHeaderPrinter & SAMHeaderPrinter::AddRG(const std::string & fromString) {
- _rgs.Add(SAMHeaderRG(fromString));
- return *this;
-}
-
-/// Add a SAM Header @PG entry, including the following tags:
-/// ID, progName, progVersion, commandLine. @PG must have unique ID.
-SAMHeaderPrinter & SAMHeaderPrinter::AddPG(std::string & id, std::string & progName, std::string & progVersion, std::string & commandLine) {
- _pgs.Add(SAMHeaderPG(id, progName, progVersion, commandLine));
- return *this;
-}
-
-/// Add a SAM Header @PG entry from string, which may contain arbitary tags.
-SAMHeaderPrinter & SAMHeaderPrinter::AddPG(const std::string & fromString) {
- _pgs.Add(SAMHeaderPG(fromString));
- return *this;
-}
-
-/// Add a SAM Header @CO entry from string.
-SAMHeaderPrinter & SAMHeaderPrinter::AddCO(const std::string & fromString) {
- _cos.Add(fromString);
- return *this;
-}
-
-/// \returns SAMHeaderGroup @HD
-SAMHeaderGroup SAMHeaderPrinter::MakeHD(const std::string & sortingOrder) {
- std::stringstream ss;
- ss << "@HD" << "\t"
- << "VN:" << SAMVERSION << "\t"
- << "SO:" << sortingOrder << "\t"
- << "pb:" << PBBAMVERSION << std::endl;
- return SAMHeaderGroup(ss.str());
-}
-
-/// \returns SAMHeaderSQs, SAM Header @SQ groups
-SAMHeaderSQs SAMHeaderPrinter::MakeSQs(SequenceIndexDatabase<FASTASequence> & seqdb) {
- SAMHeaderSQs sqs;
- for (int i = 0; i < seqdb.nSeqPos-1; i++) {
- std::string md5 = "";
- if (seqdb.md5.size() == seqdb.nSeqPos - 1) {
- md5 = seqdb.md5[i];
- }
- string seqName;
- seqdb.GetName(i, seqName);
- sqs.Add(SAMHeaderSQ(seqName, seqdb.GetLengthOfSeq(i), md5));
- }
- return sqs;
-}
-
-SAMHeaderPrinter::SAMHeaderPrinter(const std::string & sortingOrder,
- SequenceIndexDatabase<FASTASequence> & seqdb,
- const std::vector<std::string> & readsFiles,
- const ReadType::ReadTypeEnum & readType,
- const SupplementalQVList & samQVs,
- const std::string & progName,
- const std::string & progVersion,
- const std::string & commandLine)
- :_sortingOrder(sortingOrder), _readsFiles(readsFiles), _seqdb(seqdb) {
- if (readsFiles.size() == 0) {
- assert("Must specify input reads files" == 0);
- }
- // all read types supported, no check needed.
-
- // Determine fileType based on extension of the first read file.
- std::string rf = readsFiles[0];
- BaseSequenceIO::DetermineFileTypeByExtension(rf, fileType);
-
- // Make @HD, @SQ, @RG
- _hd = MakeHD(sortingOrder);
- _sqs = MakeSQs(seqdb);
- _rgs = MakeRGs(readsFiles, readType, samQVs);
-
- // Make PGs and COs
- _pgs = MakePGs(readsFiles, progName, progVersion, commandLine);
- _cos = MakeCOs(readsFiles);
-}
-
-/// \param[in] readsFiles - incoming reads files in BAM or other formats
-/// \param[in] readType - read type, must be either SUBREAD or CCS or UNKNOWN
-/// \param[in] samQVs - SupplementalQVList, an object that handles which
-/// QVs to print in SAM/BAM file.
-SAMHeaderRGs SAMHeaderPrinter::MakeRGs(const std::vector<std::string> & readsFiles,
- const ReadType::ReadTypeEnum & readType,
- const SupplementalQVList & samQVs) {
- SAMHeaderRGs rgs;
-
- if (fileType != PBBAM) {
- ReaderAgglomerate * reader = new ReaderAgglomerate();
- std::vector<std::string>::const_iterator rfit;
- for(rfit = readsFiles.begin(); rfit != readsFiles.end(); rfit++) {
- std::string rf(*rfit);
- reader->SetReadFileName(rf);
- reader->SetReadType(readType);
- reader->Initialize();
-
- // Get movie name from ReaderAgglomerate
- std::string movieName;
- reader->GetMovieName(movieName);
-
- string bindingKit, sequencingKit, baseCallerVersion;
- reader->GetChemistryTriple(bindingKit, sequencingKit, baseCallerVersion);
- reader->Close();
-
- std::vector<SAMHeaderItem> dsItems;
- dsItems.push_back(SAMHeaderItem("READTYPE", ReadType::ToString(readType)));
- dsItems.push_back(SAMHeaderItem("BINDINGKIT", bindingKit));
- dsItems.push_back(SAMHeaderItem("SEQUENCINGKIT", sequencingKit));
- dsItems.push_back(SAMHeaderItem("BASECALLERVERSION", baseCallerVersion));
-
- // Add QVs, e.g., InsertionQV=iq;DeletionQV=dq;...
- if (samQVs.useqv) {
- for (int i = 0; i < samQVs.nTags; i++) {
- if (samQVs.useqv & (1 << i)) {
- dsItems.push_back(SAMHeaderItem(samQVs.qvNames[i], samQVs.qvTags[i]));
- }
- }
- }
- rgs.Add(SAMHeaderRG(reader->readGroupId, PACBIOPL, movieName, dsItems));
- }
- delete reader;
- } else {
-#ifdef USE_PBBAM
- // TODO: use Derek's API to merge bamHeaders from different files when
- // it is in place. Use the following code for now.
- std::vector<std::string>::const_iterator rfit;
- for(rfit = readsFiles.begin(); rfit != readsFiles.end(); rfit++) {
- try {
- PacBio::BAM::BamFile bamFile(*rfit);
- PacBio::BAM::BamHeader header = bamFile.Header();
- // Get read groups from bam header.
- std::vector<PacBio::BAM::ReadGroupInfo> vrgs = header.ReadGroups();
- std::vector<PacBio::BAM::ReadGroupInfo>::iterator rgit;
- for (rgit = vrgs.begin(); rgit != vrgs.end(); rgit++) {
- rgs.Add(SAMHeaderRG((*rgit).ToSam()));
- }
- } catch (std::exception e) {
- cout << "ERROR, unable to open bam file " << (*rfit) << endl;
- exit(1);
- }
- }
-#else
- REQUEST_PBBAM_ERROR();
-#endif
- }
- return rgs;
-}
-
-
-SAMHeaderPGs SAMHeaderPrinter::MakePGs(const std::vector<std::string> & readsFiles,
- const std::string & progName, const std::string & progVersion,
- const std::string & commandLine) {
- SAMHeaderPGs pgs;
-
- // program id, unique identifier for @PG lines;
- int prog_id = 1;
-
- if (fileType != PBBAM) {
- // Reads files are not in BAM format, no other @PG lines.
- } else {
-#ifdef USE_PBBAM
- // Reads files are in BAM format, keep all @PG lines from Bam files.
- // TODO: use Derek's API to merge bamHeaders from different files when
- // it is in place. Use the following code for now.
- std::vector<std::string>::const_iterator rfit;
- for(rfit = readsFiles.begin(); rfit != readsFiles.end(); rfit++) {
- PacBio::BAM::BamFile bamFile(*rfit);
- PacBio::BAM::BamHeader bamHeader = bamFile.Header();
- std::vector<PacBio::BAM::ProgramInfo> progs = bamHeader.Programs();
- std::vector<PacBio::BAM::ProgramInfo>::iterator it;
- for (it = progs.begin(); it != progs.end(); it++) {
- pgs.Add(SAMHeaderPG((*it).ToSam()));
- prog_id++; // Increase prog_id;
- }
- }
-#else
- REQUEST_PBBAM_ERROR();
-#endif
- }
-
- pgs.Add(SAMHeaderPG(std::to_string(prog_id), progName, progVersion, commandLine));
- return pgs;
-}
-
-SAMHeaderCOs SAMHeaderPrinter::MakeCOs(const std::vector<std::string> & readsFiles) {
- SAMHeaderCOs cos;
-
- if (fileType == PBBAM) {
-#ifdef USE_PBBAM
- // Reads files are in BAM format, keep all @CO lines from Bam files.
- std::vector<std::string>::const_iterator rfit;
- for(rfit = readsFiles.begin(); rfit != readsFiles.end(); rfit++) {
- PacBio::BAM::BamFile bamFile(*rfit);
- PacBio::BAM::BamHeader bamHeader = bamFile.Header();
- cos.Append(bamHeader.Comments());
- }
-#else
- REQUEST_PBBAM_ERROR();
-#endif
- } // reads files are not in BAM format, no comments.
- return cos;
-}
-
-#ifdef USE_PBBAM
-PacBio::BAM::BamHeader SAMHeaderPrinter::ToBamHeader() {
- std::string headerStr = ToString();
- return PacBio::BAM::BamHeader(headerStr);
-}
-#endif
-
diff --git a/libcpp/alignment/format/SAMHeaderPrinter.hpp b/libcpp/alignment/format/SAMHeaderPrinter.hpp
deleted file mode 100644
index 0b95da1..0000000
--- a/libcpp/alignment/format/SAMHeaderPrinter.hpp
+++ /dev/null
@@ -1,311 +0,0 @@
-#ifndef _BLASR_FILE_SAM_HEADER_PRINTER_
-#define _BLASR_FILE_SAM_HEADER_PRINTER_
-
-#include <string>
-#include <vector>
-#include <set>
-#include <iostream>
-#include <sstream>
-#include "Types.h"
-#include "Enumerations.h"
-#include "StringUtils.hpp"
-#include "files/BaseSequenceIO.hpp"
-#include "files/ReaderAgglomerate.hpp"
-#include "datastructures/alignmentset/SAMSupplementalQVList.hpp"
-
-/// This is a simple implementation for generating SAM Headers.
-/// It is provided such that libblasr can compile with and without
-/// linking to lib PBBAM.
-/// * When compiled without linking to lib PBBAM, blasr should be
-/// able to produce SAM output.
-/// * When compiled with lib PBBAM, blasr should be able to produce
-/// SAM and BAM output. If input is one or more than one BAM files,
-/// @PG and @CO info will be kept.
-
-#define REQUEST_PBBAM_ERROR() \
- assert("libblasr must be compiled with lib PBBAM to consume bam files." == 0)
-
-class SAMHeaderItem {
-/// SAM Header Item: key=value
-public:
- SAMHeaderItem(const std::string & key, const std::string & val)
- :_key(key), _val(val) {}
-
- SAMHeaderItem(const std::string & fromString);
-
- std::string ToString();
-
-private:
- std::string _key;
- std::string _val;
-};
-
-std::vector<SAMHeaderItem> MakeSAMHeaderItems(const std::string & fromString);
-
-class SAMHeaderTag {
-public:
- SAMHeaderTag() {}
-
- /// ID:12345
- SAMHeaderTag(const std::string & tagName, const std::string & tagValue)
- :_tagName(tagName), _tagValue(tagValue) {}
-
- /// DS:READTYPE=SUBREAD;BINDKINGKIT=123456
- SAMHeaderTag(const std::string & tagName, const std::vector<SAMHeaderItem> & tagItems)
- :_tagName(tagName), _tagItems(tagItems) {}
-
- SAMHeaderTag(const std::string & fromString);
-
-public:
- std::string ToString();
-
- std::string TagName() const;
-
- void AddItem(SAMHeaderItem & item);
-
- void AddItem(const std::string & fromString);
-
- void AddItems(const std::string & fromString);
-
-private:
- std::string _tagName;
- std::string _tagValue;
- std::vector<SAMHeaderItem> _tagItems;
-};
-
-typedef std::vector<SAMHeaderTag> SAMHeaderTags;
-
-class SAMHeaderGroup {
-public:
- SAMHeaderGroup() {}
-
- SAMHeaderGroup(const std::string & groupName, const SAMHeaderTags & tags)
- :_groupName(groupName), _tags(tags) {}
-
- SAMHeaderGroup(const std::string & fromString);
-
- std::string ToString();
-
- /// returns true if this SAMHeaderGroup contains a tag tagName.
- bool HasTag(std::string tagName);
-
- /// returns value of a tag if it exists, otherwise, return an empty string.
- std::string Tag(const std::string & tagName);
-
-protected:
- std::string _groupName;
-
- SAMHeaderTags _tags;
-};
-
-class SAMHeaderGroupWithID : public SAMHeaderGroup {
-public:
- SAMHeaderGroupWithID() {}
-
- SAMHeaderGroupWithID(const std::string & fromString);
-
- std::string ID() const;
-
-protected:
- std::string _id;
-};
-
-std::ostream & operator << (std::ostream& os, SAMHeaderGroup & g);
-
-class SAMHeaderRG : public SAMHeaderGroupWithID {
- /// SAM Header @RG entry, containing ID, PL, PU, DS tags.
- /// ID: Read group Id Tag, which must be unique for read groups.
- /// PL: PacBio platform Tag, e.g., PacBio.
- /// PU: PacBio platform unit Tag, e.g., m1473.....p0
- /// DS: Description Items for this @RG entry, including READTYPE, BINDKINGKIT,
- /// SEQUENCEKIT, BASECALLERVERSION.
- /// The following is an example:
- /// @RG ID:abcdefgh PL:PacBio PU:m1473...p0 DS:READTYPE=SUBREAD;BINDINGKIT=123456;SEQUENCINGKIT=123456;BASECALLERVERSION=2.3
-public:
- SAMHeaderRG(const std::string & id, const std::string & pl, const std::string & pu, const std::vector<SAMHeaderItem> & dsItems);
-
- SAMHeaderRG(const std::string & fromString);
-};
-
-class SAMHeaderPG: public SAMHeaderGroupWithID {
-public:
- SAMHeaderPG(const std::string & id, const std::string & progName, const std::string & progVersion, const std::string & commandLine);
-
- SAMHeaderPG(const std::string & fromString);
-};
-
-class SAMHeaderSQ: public SAMHeaderGroup {
-public:
- SAMHeaderSQ(const std::string & sn, const DNALength & ln, const std::string & md5);
-
- SAMHeaderSQ(const std::string & sn, const string & ln, const std::string & md5);
-
- SAMHeaderSQ(const std::string & fromString);
-};
-
-template <class T>
-class SAMHeaderGroups {
-public:
- SAMHeaderGroups() {}
-
- // Add a SAM Header group regardless
- void Add(const T & group);
-
- void Append(const std::vector<T> & groups);
-
- std::string ToString();
-
-protected:
- std::vector<T> _groups;
-};
-
-template <class T>
-class SAMHeaderGroupsWithID : public SAMHeaderGroups<T> {
-public:
- SAMHeaderGroupsWithID(): SAMHeaderGroups<T>() {}
-
- /// Add a SAM Header group with unique ID if it does not exist.
- void Add(const T & g) ;
-
- /// Check whether a group already exists or not.
- /// \returns true if g.ID() already exists in _groups, otherwise false.
- bool Contain(const T & g);
-};
-
-typedef SAMHeaderGroupsWithID<SAMHeaderRG> SAMHeaderRGs;
-// FIXME: @PG groups should have unique IDs according to SAM spec v1.5,
-// However, PacBio tools such as blasr and bax2bam use prog name as prog id.
-typedef SAMHeaderGroups<SAMHeaderPG> SAMHeaderPGs;
-typedef SAMHeaderGroups<SAMHeaderSQ> SAMHeaderSQs;
-typedef SAMHeaderGroups<std::string> SAMHeaderCOs;
-
-class SAMHeaderPrinter {
-public:
- /// SAMHeaderPrinter constructor
- /// \param[in] sortingOrder - sorting order of alignments.
- /// \param[in] seqdb - database of target sequences.
- /// \param[in] readsFiles - input reads files, file format
- /// can be FASTA, FASTQ, BAS.H5, BAX.H5, BAM.
- /// \param[in] samQVs - samQVs that will be printed.
- /// \param[in] readType - read type, must be either SUBREAD or CCS or UNKNOWN
- /// \param[in] progName - program which calls SMAHeaderPrinter
- /// \param[in] progVersion - program version.
- /// \param[in] commandLine - command line to call program.
- SAMHeaderPrinter(const std::string & sortingOrder,
- SequenceIndexDatabase<FASTASequence> & seqdb,
- const std::vector<std::string> & readsFiles,
- const ReadType::ReadTypeEnum & readType,
- const SupplementalQVList & samQVs,
- const std::string & progName,
- const std::string & progVersion,
- const std::string & commandLine);
-
- /// \returns SAM header in string.
- std::string ToString();
-
-public:
-#ifdef USE_PBBAM
- /// Converts this SAMHeader to PacBio::BAM::BamHeader, must be compiled with pbbam
- /// \returns a PacBio::BAM::BamHeader.
- PacBio::BAM::BamHeader ToBamHeader();
-#endif
-
- /// Add a SAM Header @RG entry, including the following tags:
- /// ID (identifier), PL (platform), PU (platform unit),
- /// DS (description, which may have many items)
- SAMHeaderPrinter & AddRG(std::string & id, std::string & pl, std::string & pu, std::string & ds);
-
- /// Add a SAM Header @RG entry from string, which may contain arbitary tags.
- SAMHeaderPrinter & AddRG(const std::string & fromString);
-
- /// Add a SAM Header @PG entry, including the following tags:
- /// ID, progName, progVersion, commandLine. @PG must have unique ID.
- SAMHeaderPrinter & AddPG(std::string & id, std::string & progName, std::string & progVersion, std::string & commandLine);
-
- /// Add a SAM Header @PG entry from string, which may contain arbitary tags.
- SAMHeaderPrinter & AddPG(const std::string & fromString);
-
- /// Add a SAM Header @CO entry from string.
- SAMHeaderPrinter & AddCO(const std::string & fromString);
-
-private:
- const std::string & _sortingOrder;
- const std::vector<std::string> & _readsFiles;
- SequenceIndexDatabase<FASTASequence> & _seqdb;
- FileType fileType;
-
- SAMHeaderGroup _hd; //@HD VN:? SO:? pb:?
- SAMHeaderSQs _sqs; //@SQ SN:? LN:? M5:?
- SAMHeaderRGs _rgs; //@RG ID:? PU:? PL:? DS:key=val;key=val;key=val
- SAMHeaderPGs _pgs; //@PG VN:? CL:?
- SAMHeaderCOs _cos; //@CO
-
-private:
- /// \returns SAMHeaderGroup @HD
- static SAMHeaderGroup MakeHD(const std::string & sortingOrder);
-
- /// \returns SAMHeaderSQs, SAM Header @SQ groups
- SAMHeaderSQs MakeSQs(SequenceIndexDatabase<FASTASequence> & seqdb);
-
- /// \returns SAMHeaderRGs @RG groups
- /// \param[in] readsFiles - incoming reads files in BAM or other formats
- /// \param[in] readType - read type, must be either SUBREAD or CCS or UNKNOWN
- /// \param[in] samQVs - SupplementalQVList, an object that handles which
- /// QVs to print in SAM/BAM file.
- SAMHeaderRGs MakeRGs(const std::vector<std::string> & readsFiles,
- const ReadType::ReadTypeEnum & readType,
- const SupplementalQVList & samQVs);
-
- /// \returns SAMHeaderPGs @PG groups
- /// \param[in] readsFiles - incoming reads files in BAM or other formats
- /// \param[in] progName - program which calls SMAHeaderPrinter
- /// \param[in] progVersion - program version.
- /// \param[in] commandLine - command line to call program.
- SAMHeaderPGs MakePGs(const std::vector<std::string> & readsFiles,
- const std::string & progName, const std::string & progVersion,
- const std::string & commandLine);
-
- /// \returns SAMHeaderPGs @CO groups
- /// \param[in] readsFiles - incoming reads files in BAM or other formats
- SAMHeaderCOs MakeCOs(const std::vector<std::string> & readsFiles);
-};
-
-// template<class T> SAMHeaderGroups
-template<class T>
-void SAMHeaderGroups<T>::Add(const T & group) {
- this->_groups.push_back(group);
-}
-
-template<class T>
-void SAMHeaderGroups<T>::Append(const std::vector<T> & groups) {
- for(int i = 0; i < groups.size(); i++) {
- this->Add(groups[i]);
- }
-}
-
-template<class T>
-std::string SAMHeaderGroups<T>::ToString() {
- std::stringstream ss;
- for (int i = 0; i < this->_groups.size(); i++) {
- ss << this->_groups[i] << std::endl;
- }
- return ss.str();
-}
-
-// template<class T> SAMHeaderGroupsWithID
-template <class T>
-void SAMHeaderGroupsWithID<T>::Add(const T & g) {
- if (not this->Contain(g)) {this->_groups.push_back(g);}
-}
-
-template <class T>
-bool SAMHeaderGroupsWithID<T>::Contain(const T & g) {
- typename std::vector<T>::iterator it;
- for(it = this->_groups.begin(); it < this->_groups.end(); it++) {
- if ((*it).ID() == g.ID()) {
- return true;
- }
- }
- return false;
-}
-#endif
diff --git a/libcpp/alignment/format/SAMPrinter.cpp b/libcpp/alignment/format/SAMPrinter.cpp
deleted file mode 100644
index c44c40a..0000000
--- a/libcpp/alignment/format/SAMPrinter.cpp
+++ /dev/null
@@ -1,188 +0,0 @@
-#include "SAMPrinter.hpp"
-#include <algorithm> //reverse
-
-using namespace SAMOutput;
-
-void SAMOutput::BuildFlag(T_AlignmentCandidate &alignment, AlignmentContext &context, uint16_t &flag) {
-
- /*
- * Much of the flags are commented out for now since they do not
- * generate PICARD compliant SAM. This needs to be worked out.
- */
-
-
- //
- // Without supporting strobe, assume 1 segment per template.
- flag = 0;
- /*
- if (context.nSubreads > 1) {
- flag |= MULTI_SEGMENTS;
- }*/
-
- // if (context.AllSubreadsAligned() and context.nSubreads > 1) {
- // flag |= ALL_SEGMENTS_ALIGNED;
- // }
-
- if (alignment.tStrand == 1) {
- flag |= SEQ_REVERSED;
- }
- /*
- if (context.hasNextSubreadPos == false and context.nSubreads > 1) {
- flag |= NEXT_SEGMENT_UNMAPPED;
- }
- if (context.nextSubreadDir == 1) {
- flag |= SEQ_NEXT_REVERSED;
- }
- if (context.IsFirst() and context.nSubreads > 1) {
- flag |= FIRST_SEGMENT;
- }
- */
- else if (context.nSubreads > 1) {
- /*
- * Remember, if you're not first, you're last.
- */
- // flag |= LAST_SEGMENT;
- }
- if (context.isPrimary == false) {
- flag |= SECONDARY_ALIGNMENT;
- }
-}
-
-void SAMOutput::CreateDNAString(DNASequence &seq,
- DNASequence &clippedSeq,
- //
- // Trimming is used for both hard non-clipping
- // so it is called trim instead of clip.
- //
- int trimFront,
- int trimEnd) {
- assert(seq.length - trimEnd >= trimFront);
-
- clippedSeq.seq = &seq.seq[trimFront];
- clippedSeq.length = seq.length - trimEnd - trimFront;
-}
-
-void SAMOutput::AddGaps(T_AlignmentCandidate &alignment, int gapIndex,
- std::vector<int> &opSize, std::vector<char> &opChar) {
- int g;
- for (g = 0; g < alignment.gaps[gapIndex].size(); g++) {
- if (alignment.gaps[gapIndex][g].seq == blasr::Gap::Query) {
- opSize.push_back(alignment.gaps[gapIndex][g].length);
- opChar.push_back('D');
- }
- else if (alignment.gaps[gapIndex][g].seq == blasr::Gap::Target) {
- opSize.push_back(alignment.gaps[gapIndex][g].length);
- opChar.push_back('I');
- }
- }
-}
-
-void SAMOutput::AddMatchBlockCigarOps(DNASequence & qSeq, DNASequence & tSeq,
- blasr::Block & b, DNALength & qSeqPos, DNALength & tSeqPos,
- std::vector<int> & opSize, std::vector<char> & opChar) {
- DNALength qPos = qSeqPos + b.qPos, tPos = tSeqPos + b.tPos, n = 0;
- bool started = false, prevSeqMatch = false;
- for(DNALength i = 0; i < b.length; i++) {
- bool curSeqMatch = (qSeq[qPos + i] == tSeq[tPos + i]);
- if (started) {
- if (curSeqMatch == prevSeqMatch) opSize[opSize.size()-1]++;
- else {
- opSize.push_back(1);
- opChar.push_back(curSeqMatch?'=':'X');
- }
- } else {
- started = true;
- opSize.push_back(1);
- opChar.push_back(curSeqMatch?'=':'X');
- }
- prevSeqMatch = curSeqMatch;
- }
-}
-
-void SAMOutput::CreateNoClippingCigarOps(T_AlignmentCandidate &alignment,
- std::vector<int> &opSize, std::vector<char> &opChar, bool cigarUseSeqMatch) {
- //
- // Create the cigar string for the aligned region of a read,
- // excluding the clipping.
- //
- int b;
- // Each block creates a match NM (N=block.length)
- int nBlocks = alignment.blocks.size();
- int nGaps = alignment.gaps.size();
- opSize.clear();
- opChar.clear();
- //
- // Add gaps at the beginning of the alignment.
- //
- if (nGaps > 0) {
- AddGaps(alignment, 0, opSize, opChar);
- }
- for (b = 0; b < nBlocks; b++) {
- //
- // Determine the gap before printing the match, since it is
- // possible that the qurey and target are gapped at the same
- // time, which merges into a mismatch.
- //
- int qGap=0, tGap=0, commonGap=0;
- int matchLength = alignment.blocks[b].length;
- if (nGaps == 0) {
- if (b + 1 < nBlocks) {
- qGap = alignment.blocks[b+1].qPos - alignment.blocks[b].qPos - alignment.blocks[b].length;
- tGap = alignment.blocks[b+1].tPos - alignment.blocks[b].tPos - alignment.blocks[b].length;
- int commonGap;
- commonGap = abs(qGap - tGap);
- qGap -= commonGap;
- tGap -= commonGap;
- matchLength += commonGap;
- if (cigarUseSeqMatch) {
- AddMatchBlockCigarOps(alignment.qAlignedSeq,
- alignment.tAlignedSeq,
- alignment.blocks[b],
- alignment.qPos, alignment.tPos,
- opSize, opChar);
- } else {
- opSize.push_back(matchLength);
- opChar.push_back('M');
- }
- assert((qGap > 0 and tGap == 0) or (qGap == 0 and tGap > 0));
- if (qGap > 0) {
- opSize.push_back(qGap);
- opChar.push_back('I');
- }
- if (tGap > 0) {
- opSize.push_back(tGap);
- opChar.push_back('D');
- }
- }
- }
- else {
- if (cigarUseSeqMatch) {
- AddMatchBlockCigarOps(alignment.qAlignedSeq,
- alignment.tAlignedSeq,
- alignment.blocks[b],
- alignment.qPos, alignment.tPos,
- opSize, opChar);
- } else {
- opSize.push_back(matchLength);
- opChar.push_back('M');
- }
- int gapIndex = b+1;
- AddGaps(alignment, gapIndex, opSize, opChar);
- }
- }
- if (alignment.tStrand == 1) {
- std::reverse(opSize.begin(), opSize.end());
- std::reverse(opChar.begin(), opChar.end());
- }
-}
-
-void SAMOutput::CigarOpsToString(std::vector<int> &opSize, std::vector<char> &opChar,
- std::string &cigarString) {
- std::stringstream sstrm;
- int i, nElem;
- for (i = 0, nElem = opSize.size(); i < nElem; i++) {
- sstrm << opSize[i] << opChar[i];
- }
- cigarString = sstrm.str();
-}
-
diff --git a/libcpp/alignment/format/SAMPrinter.hpp b/libcpp/alignment/format/SAMPrinter.hpp
deleted file mode 100644
index c47f8ec..0000000
--- a/libcpp/alignment/format/SAMPrinter.hpp
+++ /dev/null
@@ -1,93 +0,0 @@
-#ifndef _BLASR_FORMAT_SAMPRINTER_HPP_
-#define _BLASR_FORMAT_SAMPRINTER_HPP_
-
-#include <sstream>
-#include <stdint.h>
-#include "SMRTSequence.hpp"
-#include "datastructures/alignment/AlignmentCandidate.hpp"
-#include "datastructures/alignment/AlignmentContext.hpp"
-#include "datastructures/alignment/Alignment.hpp"
-#include "datastructures/alignment/Alignment.hpp"
-#include "datastructures/alignmentset/SAMSupplementalQVList.hpp"
-
-
-#define MULTI_SEGMENTS 0x1
-#define ALL_SEGMENTS_ALIGNED 0x2
-#define SEGMENT_UNMAPPED 0x4
-#define NEXT_SEGMENT_UNMAPPED 0x8
-#define SEQ_REVERSED 0x10
-#define SEQ_NEXT_REVERSED 0x20
-#define FIRST_SEGMENT 0x40
-#define LAST_SEGMENT 0x80
-#define SECONDARY_ALIGNMENT 0x100
-#define NO_PASS_QUALITY 0x200
-#define PCR_OR_OPTICAL_DUPLICATE 0x400
-
-namespace SAMOutput {
-
-enum Clipping {hard, soft, subread, none};
-
-void BuildFlag(T_AlignmentCandidate &alignment, AlignmentContext &context, uint16_t &flag);
-
-//
-// Trimming is used for both hard non-clipping
-// so it is called trim instead of clip.
-//
-void CreateDNAString(DNASequence &seq, DNASequence &clippedSeq,
- int trimFront=0, int trimEnd=0);
-
-void AddGaps(T_AlignmentCandidate &alignment, int gapIndex,
- std::vector<int> &opSize, std::vector<char> &opChar);
-
-// Add sequence match/mismatch CIGAR string Ops for block b.
-void AddMatchBlockCigarOps(DNASequence & qSeq, DNASequence & tSeq, blasr::Block & b,
- DNALength & qSeqPos, DNALength & tSeqPos,
- std::vector<int> & opSize, std::vector<char> & opChar);
-
-// If cigarUseSeqMatch is true, cigar string uses '=' and 'X'
-// instead of 'M' to represent sequence match and mismatch;
-void CreateNoClippingCigarOps(T_AlignmentCandidate &alignment,
- std::vector<int> &opSize, std::vector<char> &opChar,
- bool cigarUseSeqMatch = false);
-//
-//
-// The aligned sequence is either the sequence from the first
-// aligned base to the last (hard and no clipping), or first high
-// quality base to the last high quality base (soft clipping).
-//
-template<typename T_Sequence>
-void SetAlignedSequence(T_AlignmentCandidate &alignment, T_Sequence &read,
- T_Sequence &alignedSeq, Clipping clipping = none);
-
-template<typename T_Sequence>
-void SetSoftClip(T_AlignmentCandidate &alignment, T_Sequence &read,
- DNALength hardClipPrefix, DNALength hardClipSuffix,
- DNALength &softClipPrefix, DNALength &softClipSuffix);
-
-template<typename T_Sequence>
-void SetHardClip(T_AlignmentCandidate &alignment, T_Sequence &read,
- DNALength &prefixClip, DNALength &suffixClip);
-
-void CigarOpsToString(std::vector<int> &opSize, std::vector<char> &opChar,
- std::string &cigarString);
-
-//
-// Straight forward: create the cigar string allowing some clipping
-// The read is provided to give length and hq information.
-//
-template<typename T_Sequence>
-void CreateCIGARString(T_AlignmentCandidate &alignment, T_Sequence &read,
- std::string &cigarString, Clipping clipping,
- DNALength &prefixSoftClip, DNALength &suffixSoftClip,
- DNALength &prefixHardClip, DNALength &suffixHardClip,
- bool cigarUseSeqMatch = false);
-
-template<typename T_Sequence>
-void PrintAlignment(T_AlignmentCandidate &alignment, T_Sequence &read,
- std::ostream &samFile, AlignmentContext &context,
- SupplementalQVList & qvList, Clipping clipping = none,
- bool cigarUseSeqMatch = false);
-}
-
-#include "SAMPrinterImpl.hpp"
-#endif // _BLASR_FORMAT_SAMPRINTER_HPP_
diff --git a/libcpp/alignment/format/SAMPrinterImpl.hpp b/libcpp/alignment/format/SAMPrinterImpl.hpp
deleted file mode 100644
index f83d1a9..0000000
--- a/libcpp/alignment/format/SAMPrinterImpl.hpp
+++ /dev/null
@@ -1,304 +0,0 @@
-#include <algorithm> //max
-#include <utility> //swap
-#include <assert.h> //assert
-
-using namespace SAMOutput;
-
-
-template<typename T_Sequence>
-void SAMOutput::SetAlignedSequence(T_AlignmentCandidate &alignment, T_Sequence &read,
- T_Sequence &alignedSeq,
- Clipping clipping) {
- //
- // In both no, and hard clipping, the dna sequence that is output
- // solely corresponds to the aligned sequence.
- //
- DNALength clippedReadLength = 0;
- DNALength clippedStartPos = 0;
-
- if (clipping == none or clipping == hard) {
- DNALength qStart = alignment.QAlignStart();
- DNALength qEnd = alignment.QAlignEnd();
- clippedReadLength = qEnd - qStart;
- clippedStartPos = qStart;
- }
- else if (clipping == soft) {
- clippedReadLength = read.length - read.lowQualityPrefix - read.lowQualitySuffix;
- clippedStartPos = read.lowQualityPrefix;
- }
- else if (clipping == subread) {
- clippedReadLength = read.subreadEnd - read.subreadStart;
- clippedStartPos = read.subreadStart;
- }
- else {
- std::cout <<" ERROR! The clipping must be none, hard, subread, or soft when setting the aligned sequence." << std::endl;
- assert(0);
- }
-
- //
- // Set the aligned sequence according to the clipping boundaries.
- //
- if (alignment.tStrand == 0) {
- alignedSeq.ReferenceSubstring(read, clippedStartPos, clippedReadLength);
- }
- else {
- T_Sequence subSeq;
- subSeq.ReferenceSubstring(read, clippedStartPos, clippedReadLength);
- subSeq.MakeRC(alignedSeq);
- assert(alignedSeq.deleteOnExit);
- }
-}
-
-template<typename T_Sequence>
-void SAMOutput::SetSoftClip(T_AlignmentCandidate &alignment,
- T_Sequence &read,
- DNALength hardClipPrefix,
- DNALength hardClipSuffix,
- DNALength &softClipPrefix,
- DNALength &softClipSuffix) {
- DNALength qStart, qEnd;
- qStart = alignment.QAlignStart();
- qEnd = alignment.QAlignEnd();
-
- assert(qStart >= hardClipPrefix);
- softClipPrefix = alignment.QAlignStart() - hardClipPrefix;
- assert(alignment.QAlignEnd() + hardClipSuffix <= read.length);
- softClipSuffix = read.length - hardClipSuffix - alignment.QAlignEnd();
-}
-
-template<typename T_Sequence>
-void SAMOutput::SetHardClip(T_AlignmentCandidate &alignment,
- T_Sequence &read,
- DNALength &prefixClip,
- DNALength &suffixClip) {
- //
- // Set the hard clipping assuming the read is in the forward
- // direction.
- //
- prefixClip = alignment.QAlignStart();
- suffixClip = read.length - alignment.QAlignEnd();
- if (alignment.tStrand == 1) {
- //
- // If the read is instead reverse, swap the clipping lengths.
- //
- std::swap(prefixClip, suffixClip);
- }
-}
-
-
-//
-// Straight forward: create the cigar string allowing some clipping
-// The read is provided to give length and hq information.
-//
-template<typename T_Sequence>
-void SAMOutput::CreateCIGARString(T_AlignmentCandidate &alignment,
- T_Sequence &read,
- std::string &cigarString,
- Clipping clipping,
- DNALength & prefixSoftClip, DNALength & suffixSoftClip,
- DNALength & prefixHardClip, DNALength & suffixHardClip,
- bool cigarUseSeqMatch) {
-
- cigarString = "";
- // All cigarString use the no clipping core
- std::vector<int> opSize;
- std::vector<char> opChar;
- CreateNoClippingCigarOps(alignment, opSize, opChar, cigarUseSeqMatch);
-
- // Clipping needs to be added
-
- if (clipping == hard) {
- SetHardClip(alignment, read, prefixHardClip, suffixHardClip);
- if (prefixHardClip > 0) {
- opSize.insert(opSize.begin(), prefixHardClip);
- opChar.insert(opChar.begin(), 'H');
- }
- if (suffixHardClip > 0) {
- opSize.push_back(suffixHardClip);
- opChar.push_back('H');
- }
- prefixSoftClip = 0;
- suffixSoftClip = 0;
- }
- if (clipping == soft or clipping == subread) {
- //
- // Even if clipping is soft, the hard clipping removes the
- // low quality regions
- //
- if (clipping == soft) {
- prefixHardClip = read.lowQualityPrefix;
- suffixHardClip = read.lowQualitySuffix;
- }
- else if (clipping == subread) {
- prefixHardClip = std::max((DNALength) read.subreadStart, read.lowQualityPrefix);
- suffixHardClip = std::max((DNALength)(read.length - read.subreadEnd), read.lowQualitySuffix);
- }
-
- SetSoftClip(alignment, read, prefixHardClip, suffixHardClip, prefixSoftClip, suffixSoftClip);
-
- if (alignment.tStrand == 1) {
- std::swap(prefixHardClip, suffixHardClip);
- std::swap(prefixSoftClip, suffixSoftClip);
- }
-
- //
- // Insert the hard and soft clipping so that they are in the
- // order H then S if both exist.
- //
- if (prefixSoftClip > 0) {
- opSize.insert(opSize.begin(), prefixSoftClip);
- opChar.insert(opChar.begin(), 'S');
- }
- if (prefixHardClip > 0) {
- opSize.insert(opSize.begin(), prefixHardClip);
- opChar.insert(opChar.begin(), 'H');
- }
-
- //
- // Append the hard and soft clipping so they are in the order S
- // then H.
- //
- if (suffixSoftClip > 0) {
- opSize.push_back(suffixSoftClip);
- opChar.push_back('S');
- }
- if (suffixHardClip > 0) {
- opSize.push_back(suffixHardClip);
- opChar.push_back('H');
- }
- }
-
- CigarOpsToString(opSize, opChar, cigarString);
-}
-
-template<typename T_Sequence>
-void SAMOutput::PrintAlignment(T_AlignmentCandidate &alignment,
- T_Sequence &read,
- std::ostream &samFile,
- AlignmentContext &context,
- SupplementalQVList & qvList,
- Clipping clipping,
- bool cigarUseSeqMatch) {
-
- std::string cigarString;
- uint16_t flag;
- T_Sequence alignedSequence;
- DNALength prefixSoftClip = 0, suffixSoftClip = 0;
- DNALength prefixHardClip = 0, suffixHardClip = 0;
-
- CreateCIGARString(alignment, read, cigarString, clipping, prefixSoftClip, suffixSoftClip, prefixHardClip, suffixHardClip, cigarUseSeqMatch);
- SetAlignedSequence(alignment, read, alignedSequence, clipping);
- BuildFlag(alignment, context, flag);
- samFile << alignment.qName << "\t"
- << flag << "\t"
- << alignment.tName << "\t"; // RNAME
- if (alignment.tStrand == 0) {
- samFile << alignment.TAlignStart() + 1 << "\t";
- // POS, add 1 to get 1 based coordinate system
- }
- else {
- samFile << alignment.tLength - (alignment.TAlignStart() + alignment.TEnd()) + 1 << "\t"; // includes - 1 for rev-comp, +1 for one-based
- }
- samFile << (int) alignment.mapQV << "\t"// MAPQ
- << cigarString << "\t"; // CIGAR
-
- //
- // Determine RNEXT
-
- std::string rNext;
- rNext = "*";
- /*
- if (context.hasNextSubreadPos == false) {
- rNext = "*";
- }
- else {
- if (context.rNext == alignment.tName) {
- rNext = "=";
- }
- else {
- rNext = context.rNext;
- }
- }
- */
- samFile << rNext << "\t"; // RNEXT
-
- DNALength nextSubreadPos = 0;
- /*
- if (context.hasNextSubreadPos) {
- nextSubreadPos = context.nextSubreadPos + 1;
- }*/
- samFile << nextSubreadPos << "\t"; // RNEXT, add 1 for 1 based
- // indexing
-
- //DNALength tLen = alignment.GenomicTEnd() - alignment.GenomicTBegin();
- //SAM v1.5, tLen is set as 0 for single-segment template
- samFile << 0 << "\t"; // TLEN
- // Print the sequence on one line, and suppress printing the
- // newline (by setting the line length to alignedSequence.length
- (static_cast<DNASequence*>(&alignedSequence))->PrintSeq(samFile, 0); // SEQ
- samFile << "\t";
- if (alignedSequence.qual.data != NULL && qvList.useqv == 0) {
- alignedSequence.PrintAsciiQual(samFile, 0); // QUAL
- }
- else {
- samFile <<"*";
- }
- samFile << "\t";
- //
- // Add optional fields
- //
- samFile << "RG:Z:" << context.readGroupId << "\t";
- samFile << "AS:i:" << alignment.score << "\t";
-
- //
- // "RG" read group Id
- // "AS" alignment score
- // "XS" read alignment start position without counting previous soft clips (1 based)
- // "XE" read alignment end position without counting previous soft clips (1 based)
- // "XL" aligned read length
- // "XQ" query sequence length
- // "XT" # of continues reads, always 1 for blasr
- // "NM" edit distance
- // "FI" read alignment start position (1 based)
- //
-
- DNALength qAlignStart = alignment.QAlignStart();
- DNALength qAlignEnd = alignment.QAlignEnd();
-
- if (clipping == none) {
- samFile << "XS:i:" << qAlignStart + 1 << "\t";
- samFile << "XE:i:" << qAlignEnd + 1 << "\t";
- }
- else if (clipping == hard or clipping == soft or clipping == subread) {
- DNALength xs = prefixHardClip;
- DNALength xe = read.length - suffixHardClip;
- if (alignment.tStrand == 1) {
- xs = suffixHardClip;
- xe = read.length - prefixHardClip;
- }
- samFile << "XS:i:" << xs + 1 << "\t"; // add 1 for 1-based indexing in sam
- assert(read.length - suffixHardClip == prefixHardClip + alignedSequence.length);
- samFile << "XE:i:" << xe + 1 << "\t";
- }
- samFile << "YS:i:" << read.subreadStart << "\t";
- samFile << "YE:i:" << read.subreadEnd << "\t";
- samFile << "ZM:i:" << read.zmwData.holeNumber << "\t";
- samFile << "XL:i:" << alignment.qAlignedSeq.length << "\t";
- samFile << "XT:i:1\t"; // reads are allways continuous reads, not
- // referenced based circular consensus when
- // output by blasr.
- samFile << "NM:i:" << context.editDist << "\t";
- samFile << "FI:i:" << alignment.qAlignedSeqPos + 1;
- // Add query sequence length
- samFile << "\t" << "XQ:i:" << alignment.qLength;
-
- //
- // Write out optional quality values. If qvlist does not
- // have any qv's signaled to print, this is a no-op.
- //
- // First transform characters that are too large to printable ones.
- qvList.FormatQVOptionalFields(alignedSequence);
- qvList.PrintQVOptionalFields(alignedSequence, samFile);
-
- samFile << std::endl;
-}
diff --git a/libcpp/alignment/format/StickAlignmentPrinter.hpp b/libcpp/alignment/format/StickAlignmentPrinter.hpp
deleted file mode 100644
index 11f6b39..0000000
--- a/libcpp/alignment/format/StickAlignmentPrinter.hpp
+++ /dev/null
@@ -1,123 +0,0 @@
-#ifndef _BLASR_STICK_ALIGNMENT_PRINTER_HPP_
-#define _BLASR_STICK_ALIGNMENT_PRINTER_HPP_
-
-#include <string>
-#include <iostream>
-#include <fstream>
-#include "datastructures/alignment/Alignment.hpp"
-#include "algorithms/alignment/AlignmentUtils.hpp"
-
-template<typename T_Alignment, typename T_QuerySequence, typename T_TargetSequence>
-void StickPrintAlignment(T_Alignment &alignment,
- T_QuerySequence &query, T_TargetSequence &text, std::ostream &out,
- unsigned int qPrintStart = 0,
- unsigned int tPrintStart = 0,
- int maxPrintLength = 50) {
- //
- // Eventually hack to add options for alignment format.
- //
- std::string queryStr, alignStr, textStr;
- char gapChar = '-';
- //
- // [q/t]PrintStart are the beginning/ending of the subsequence that
- // is being printed however the actual alignment begins at
- // [q/t]PrintStart + alignment->[q/t]Pos, since there may be a small
- // gap between the beginning of the alignment and the beginning of
- // the substring that is aligned.
- //
- out << " Query: " << alignment.qName << endl;
- out << " Target: " << alignment.tName << endl;
- out << " Model: a hybrid of global/local non-affine alignment" <<endl;
- out << " Raw score: " << alignment.score << endl;
- out << " Map QV: " << alignment.mapQV << endl;
- out << " Query strand: " << alignment.qStrand << endl;
- out << " Target strand: " << alignment.tStrand << endl;
- if (alignment.blocks.size() > 0) {
- out << " QueryRange: " << qPrintStart + alignment.qPos //alignment.blocks[0].qPos
- << " -> "
- << (qPrintStart + alignment.qPos +
- + alignment.blocks[alignment.blocks.size() - 1 ].qPos
- + alignment.blocks[alignment.blocks.size() - 1 ].length) << " of " << alignment.qLength << endl;
- out << " TargetRange: " << tPrintStart + alignment.tPos //alignment.blocks[0].tPos
- << " -> "
- // << (tPrintStart + alignment.blocks[alignment.blocks.size() - 1].tPos +
- << (tPrintStart + alignment.tPos +
- alignment.blocks[alignment.blocks.size() - 1 ].tPos +
- alignment.blocks[alignment.blocks.size() - 1].length) << " of " << alignment.tLength << endl;
- }
- else {
- out << " QueryRange: NONE " << endl;
- out << " TargetRange: NONE " << endl;
- }
-
- if (alignment.blocks.size() == 0)
- return;
- CreateAlignmentStrings(alignment, query.seq, text.seq, textStr, alignStr, queryStr, query.length, text.length);
-
- //
- // Process any gaps at the beginning of
- // the alignment.
- //
-
- DNALength qPos, tPos;
-
- int coordsPrintWidth = MAX(GetNumberWidth(alignment.qPos + qPrintStart + query.length),
- GetNumberWidth(alignment.tPos + tPrintStart + query.length));
-
- //
- // Now print the alignment
- VectorIndex lineLength = maxPrintLength;
- if (lineLength > textStr.size())
- lineLength = textStr.size();
-
- std::string textLine, queryLine, alignLine;
- DNALength pos = 0;
- tPos = alignment.tPos;
- qPos = alignment.qPos;
- int spacePad = 2;
- std::string coordPadding(spacePad, ' ');
- std::string alignStrPadding(coordsPrintWidth + spacePad, ' ');
-
- while (lineLength > 0) {
- textLine.assign(textStr, pos, lineLength);
- alignLine.assign(alignStr, pos, lineLength);
- queryLine.assign(queryStr, pos, lineLength);
- out.width(coordsPrintWidth);
- out << qPrintStart + qPos;
- out.width(0);
- out << coordPadding << queryLine << endl;
- out << alignStrPadding << alignLine << endl;
- out.width(coordsPrintWidth);
- out << tPrintStart + tPos ;
- out.width(0);
- out << coordPadding << textLine << endl;
- out << endl;
-
- pos += lineLength;
- tPos += lineLength;
- qPos += lineLength;
- //
- // Adjust tPos and qPos for indels.
- //
- VectorIndex p;
- for (p = 0; p < textLine.size(); p++) {
- if (textLine[p] == gapChar)
- tPos--;
- }
- for (p = 0; p < queryLine.size(); p++) {
- if (queryLine[p] == gapChar)
- qPos--;
- }
-
- lineLength = maxPrintLength;
- if (textStr.size() < (pos +lineLength)) {
- // sets lineLength to 0 on the last iteration
- lineLength = textStr.size() - pos;
- }
- else {
- lineLength = maxPrintLength;
- }
- }
-}
-
-#endif // _BLASR_STICK_ALIGNMENT_PRINTER_HPP_
diff --git a/libcpp/alignment/format/SummaryPrinter.cpp b/libcpp/alignment/format/SummaryPrinter.cpp
deleted file mode 100644
index 6704bce..0000000
--- a/libcpp/alignment/format/SummaryPrinter.cpp
+++ /dev/null
@@ -1,26 +0,0 @@
-#include "SummaryPrinter.hpp"
-
-void SummaryOutput::Print(
- AlignmentCandidate<DNASequence,FASTQSequence> &alignment,
- std::ostream &outFile) {
-
- int lastBlock = alignment.blocks.size()-1;
- outFile << alignment.qName << " "
- << alignment.tName << " "
- << alignment.qStrand << " "
- << alignment.tStrand << " "
- << alignment.score << " "
- << alignment.pctSimilarity << " "
- << alignment.tAlignedSeqPos + alignment.blocks[0].tPos << " "
- << alignment.tAlignedSeqPos + alignment.blocks[lastBlock].tPos + alignment.blocks[lastBlock].length << " "
- << alignment.tLength << " "
- << alignment.qAlignedSeqPos + alignment.blocks[0].qPos << " "
- << alignment.qAlignedSeqPos + alignment.blocks[lastBlock].qPos + alignment.blocks[lastBlock].length << " "
- << alignment.qLength << " " << alignment.nCells << std::endl;
-}
-
-void SummaryOutput::PrintHeader(std::ostream &out) {
- out << "qName tName qStrand tStrand score percentSimilarity tStart tEnd tLength qStart qEnd qLength nCells"
- << std::endl;
-}
-
diff --git a/libcpp/alignment/format/SummaryPrinter.hpp b/libcpp/alignment/format/SummaryPrinter.hpp
deleted file mode 100644
index 5cc9c29..0000000
--- a/libcpp/alignment/format/SummaryPrinter.hpp
+++ /dev/null
@@ -1,14 +0,0 @@
-#ifndef SUMMARY_ALIGNMENT_PRINTER_H_
-#define SUMMARY_ALIGNMENT_PRINTER_H_
-
-#include "datastructures/alignment/AlignmentCandidate.hpp"
-#include "FASTQSequence.hpp"
-
-namespace SummaryOutput{
-
- void Print(AlignmentCandidate<DNASequence,FASTQSequence> &alignment, std::ostream &outFile);
-
- void PrintHeader(std::ostream &out);
-}
-
-#endif
diff --git a/libcpp/alignment/format/VulgarPrinter.hpp b/libcpp/alignment/format/VulgarPrinter.hpp
deleted file mode 100644
index a4505cf..0000000
--- a/libcpp/alignment/format/VulgarPrinter.hpp
+++ /dev/null
@@ -1,53 +0,0 @@
-#ifndef _BLASR_VULGAR_ALIGNMENT_PRINTER_HPP_
-#define _BLASR_VULGAR_ALIGNMENT_PRINTER_HPP_
-
-#include <string>
-#include <sstream>
-
-namespace VulgarOutput{
-template <typename T_Alignment>
-int CreateVulgarString(T_Alignment &alignment, std::string &vstring) {
- std::stringstream vstream;
- VectorIndex b;
- int tGap, qGap, cGap;
- if (alignment.blocks.size() == 0) {
- vstring = "";
- return 1;
- }
- for (b = 0; b < alignment.blocks.size() - 1; b++) {
- tGap = (alignment.blocks[b+1].tPos
- - (alignment.blocks[b].length +
- alignment.blocks[b].tPos));
- qGap = (alignment.blocks[b+1].qPos
- - (alignment.blocks[b].length +
- alignment.blocks[b].qPos));
- if (tGap > 0 and qGap > 0)
- cGap = abs(tGap - qGap);
- else
- cGap = 0;
- tGap -= cGap;
- qGap -= cGap;
- vstream << " M " << alignment.blocks[b].length + cGap;
- if (tGap > 0) {
- vstream << " D " << tGap;
- }
- else {
- vstream << " I " << qGap;
- }
- }
- if (alignment.blocks.size() > 0) {
- vstream << " M " << alignment.blocks[alignment.blocks.size() - 1].length;
- }
- vstring = vstream.str();
- return 1;
-}
-
-template <typename T_Alignment>
-void Print(T_Alignment &alignment, std::ostream &out) {
- std::string vstring;
- CreateVulgarString(alignment, vstring);
- out << vstring;
-}
-}
-
-#endif
diff --git a/libcpp/alignment/format/XMLPrinter.hpp b/libcpp/alignment/format/XMLPrinter.hpp
deleted file mode 100644
index 076518e..0000000
--- a/libcpp/alignment/format/XMLPrinter.hpp
+++ /dev/null
@@ -1,84 +0,0 @@
-#ifndef _BLASR_XML_PRINTER_HPP_
-#define _BLASR_XML_PRINTER_HPP_
-
-#include "utils/SimpleXMLUtils.hpp"
-
-namespace XMLOutput{
-
-template<typename T_Alignment, typename T_Sequence>
-void Print(T_Alignment &alignment,
- T_Sequence &query, T_Sequence &text, std::ostream &out,
- int qPrintStart = 0,
- int tPrintStart = 0,
- int maxPrintLength = 50) {
- /*
- * Sample alignment:
- *
- <hit name="x15_y33_1220208-0008_m081205_152444_Uni_p2_b15" unalignedLength="1301" start="1051" end="1016" strand="-" targetStart="1" targetEnd="44" targetStrand="+">
- <zScore value="-6.091"/>
- <nInsert value="1" percent="2.86" />
- <nDelete value="9" percent="25.71" />
- <nMismatch value="1" percent="2.86" />
- <nCorrect value="24" percent="68.57" />
- <alignment><query>
- AG--CGTTCC-TATGG-TG-GGGTCGTTA-ACT---GTCGCCAG
- </query><target>
- AGCCCG-TCCTTATGGTTGAGGGTTGTTACACTTCGGTCGCCAG
- </target></alignment>
- </hit>
- */
- char strand[2] = {'+', '-'};
- std::string tAlignStr, alignStr, qAlignStr;
- CreateAlignmentStrings(alignment, query.seq, text.seq, tAlignStr, alignStr, qAlignStr);
- int alignLength = tAlignStr.size();
- if (alignLength == 0) {
- alignLength = 1; // Make sure there are no divide by zero.
- alignment.nIns = 0;
- alignment.nDel = 0;
- alignment.nMismatch = 0;
- alignment.nMatch = 0;
- }
- out << BeginDataEntry(std::string("hit"),
- CreateKeywordValuePair(std::string("name"), alignment.qName) +
- CreateKeywordValuePair(std::string("unalignedLength"), alignment.qLength) +
- CreateKeywordValuePair(std::string("start"), alignment.qPos) +
- CreateKeywordValuePair(std::string("end"), alignment.qPos + alignment.qAlignLength) +
- CreateKeywordValuePair(std::string("strand"), strand[alignment.qStrand]) +
- CreateKeywordValuePair(std::string("targetStart"), alignment.tPos) +
- CreateKeywordValuePair(std::string("targetEnd"), alignment.tPos + alignment.tAlignLength) +
- CreateKeywordValuePair(std::string("targetStrand"), strand[alignment.tStrand]))
- << std::endl;
- out << CreateDataEntry(std::string("zScore"),
- CreateKeywordValuePair(std::string("value"), alignment.zScore))
- << std::endl;
- out << CreateDataEntry(std::string("nInsert"),
- CreateKeywordValuePair(std::string("value"), alignment.nIns) + " " +
- CreateKeywordValuePair(std::string("percent"), alignment.nIns*0.5/alignLength))
- << std::endl;
- out << CreateDataEntry(std::string("nDelete"),
- CreateKeywordValuePair(std::string("value"), alignment.nDel) + " " +
- CreateKeywordValuePair(std::string("percent"), alignment.nDel*0.5/alignLength))
- << std::endl;
- out << CreateDataEntry(std::string("nMismatch"),
- CreateKeywordValuePair(std::string("value"), alignment.nMismatch) + " " +
- CreateKeywordValuePair(std::string("percent"), alignment.nMismatch*0.5/alignLength))
- << std::endl;
- out << CreateDataEntry(std::string("nCorrect"),
- CreateKeywordValuePair(std::string("value"), alignment.nMatch) + " " +
- CreateKeywordValuePair(std::string("percent"), alignment.nMatch*0.5/alignLength))
- << std::endl;
-
- out << CreateStartEntry(std::string("alignment"), std::string(""))
- << CreateStartEntry(std::string("query"), std::string(""))
- << std::endl;
- out << qAlignStr << std::endl;
- out << CreateEndEntry(std::string("query")) << std::endl;
- out << CreateStartEntry(std::string("target"), std::string(""))
- << std::endl;
- out << tAlignStr << std::endl;
- out << CreateEndEntry(std::string("target")) << std::endl;
- out << CreateEndEntry(std::string("alignment")) << std::endl;
- out << CreateEndEntry(std::string("hit")) << std::endl;
-}
-}
-#endif
diff --git a/libcpp/alignment/ipc/SharedMemoryAllocator.hpp b/libcpp/alignment/ipc/SharedMemoryAllocator.hpp
deleted file mode 100644
index 5599b63..0000000
--- a/libcpp/alignment/ipc/SharedMemoryAllocator.hpp
+++ /dev/null
@@ -1,33 +0,0 @@
-#ifndef _BLASR_SHARED_MEMORY_ALLOCATOR_HPP_
-#define _BLASR_SHARED_MEMORY_ALLOCATOR_HPP_
-
-#include <iostream>
-#include <string>
-#include <errno.h>
-#include <fcntl.h>
-#include <unistd.h>
-#include <sys/mman.h>
-
-template<typename T_Data>
-int AllocateMappedShare(std::string &handle, int dataLength, T_Data *&dataPtr, int &shmId) {
- std::cout << "opening shm" << std::endl;
- shmId = shm_open(handle.c_str(), O_CREAT| O_RDWR, S_IRUSR | S_IWUSR);
- if (ftruncate(shmId, sizeof(T_Data[dataLength])) == -1) {
- std::cout <<" ftruncate error: " << errno << std::endl;
- }
- std::cout << "done truncating." << std::endl;
- dataPtr = (T_Data*) mmap(NULL, sizeof(T_Data[dataLength]),
- PROT_READ | PROT_WRITE, MAP_SHARED, shmId, 0);
- if (dataPtr == MAP_FAILED) {
- //
- // Handle this better later on.
- //
- std::cout << "ERROR, MEMORY MAP FAILED." << std::endl;
- exit(1);
- }
- std::cout << "done mapping." << std::endl;
- return dataLength;
-}
-
-
-#endif // _BLASR_SHARED_MEMORY_ALLOCATOR_HPP_
diff --git a/libcpp/alignment/makefile b/libcpp/alignment/makefile
deleted file mode 100644
index 0cfd1d6..0000000
--- a/libcpp/alignment/makefile
+++ /dev/null
@@ -1,52 +0,0 @@
-all:
-
-include ../rules.mk
-include ../defines.mk
-
-CXXOPTS := -std=c++11 -pedantic -MMD -MP -Wno-long-long
-INCLUDES += . ${LIBPBDATA_INCLUDE} ${LIBPBIHDF_INCLUDE} ${HDF5_INCLUDE} ${PBBAM_INCLUDE} ${HTSLIB_INCLUDE} ${BOOST_INCLUDE}
-DEP_LIBS += ${LIBPBDATA_LIB} ${HDF5_LIB} ${PBBAM_LIB} ${HTSLIB_LIB} ${ZLIB_LIB}
-LDFLAGS += $(patsubst %,$(dirname %),${DEP_LIBS})
-
-all: libblasr.a libblasr.so
-
-sources := $(wildcard algorithms/alignment/*.cpp) \
- $(wildcard algorithms/alignment/sdp/*.cpp) \
- $(wildcard algorithms/anchoring/*.cpp) \
- $(wildcard algorithms/compare/*.cpp) \
- $(wildcard algorithms/sorting/*.cpp) \
- $(wildcard datastructures/alignment/*.cpp) \
- $(wildcard datastructures/alignmentset/*.cpp) \
- $(wildcard datastructures/anchoring/*.cpp) \
- $(wildcard datastructures/tuplelists/*.cpp) \
- $(wildcard suffixarray/*.cpp) \
- $(wildcard qvs/*.cpp) \
- $(wildcard statistics/*.cpp) \
- $(wildcard tuples/*.cpp) \
- $(wildcard utils/*.cpp) \
- $(wildcard files/*.cpp) \
- $(wildcard format/*.cpp) \
- $(wildcard simulator/*.cpp) \
- $(wildcard *.cpp)
-
-ifdef nohdf
-sources := $(filter-out files/% utils/FileOfFileNames.cpp format/SAMHeaderPrinter.cpp, $(sources))
-endif
-
-objects := $(sources:.cpp=.o)
-shared_objects := $(sources:.cpp=.shared.o)
-dependencies := $(objects:.o=.d) $(shared_objects:.o=.d)
-
-libblasr.a: $(objects)
- $(AR) $(ARFLAGS) $@ $^
-
-libblasr.so: $(shared_objects) $(DEP_LIBS)
- $(CXX) $(LD_SHAREDFLAGS) -o $@ -Wl,-soname,$@ $^
-
-clean:
- @rm -f libblasr.a libblasr.so
- @rm -f $(objects) $(shared_objects) $(dependencies)
- @find . -type f -name \*.o -delete
- @find . -type f -name \*.d -delete
-
--include $(dependencies)
diff --git a/libcpp/alignment/old.Makefile b/libcpp/alignment/old.Makefile
deleted file mode 100644
index 099a7d0..0000000
--- a/libcpp/alignment/old.Makefile
+++ /dev/null
@@ -1,113 +0,0 @@
-
-include ../common.mk
-
-# To enable building a shared library, invoke as "make SHARED_LIB=true ..."
-ifneq ($(SHARED_LIB),)
- # Generating shared library
- CXX_SHAREDFLAGS := -fPIC
- LD_SHAREDFLAGS := -shared -fPIC
- TARGET_LIB := libblasr.so
- # Developers should set these to appropriate defaults (other systems
- # will override these on the command line):
- HDF5_LIB := ../../../../prebuilt.out/prebuilt.out/hdf5/hdf5-1.8.12/centos-5/lib/libhdf5.so
- ZLIB_LIB := ../../../../prebuilt.tmpsrc/zlib/zlib_1.2.8/_output/install/lib/libz.so
- HTSLIB_LIB := ../../../staging/PostPrimary/pbbam/_output/install-build/lib/libpbbam.so
- PBBAM_LIB := ../../../staging/PostPrimary/pbbam/third-party/htslib/_output/install-build/lib/libhts.so
- LIBPBDATA_LIB := ../../../staging/PostPrimary/pbbam/third-party/htslib/_output/install-build/lib/libhts.so
-else
- # Generating shared library
- CXX_SHAREDFLAGS :=
- LD_SHAREDFLAGS :=
- TARGET_LIB := libblasr.a
- HDF5_LIB :=
- ZLIB_LIB :=
- HTSLIB_LIB :=
- PBBAM_LIB :=
- LIBPBDATA_LIB :=
-endif
-
-DEP_LIBS := $(HDF5_LIB) $(ZLIB_LIB) $(HTSLIB_LIB) $(PBBAM_LIB) $(PBDATA_LIB)
-
-LIBPBDATA_INCLUDE := ../pbdata
-LIBPBIHDF_INCLUDE := ../hdf
-PBBAM_INCLUDE := $(PBBAM)/include
-HTSLIB_INCLUDE ?= $(HTSLIB)
-
-INCLUDES = -I$(LIBPBDATA_INCLUDE) \
- -I$(LIBPBIHDF_INCLUDE) \
- -I.
-ifneq ($(HDF5_INC),)
-INCLUDES += -I$(HDF5_INC)
-else
-HDF_HEADERS := hdf5-1.8.12-headers
-INCLUDES += -I../hdf/$(HDF_HEADERS)/src -I../hdf/$(HDF_HEADERS)/c++/src
-endif
-
-ifneq ($(ZLIB_ROOT), notfound)
- INCLUDES += -I$(ZLIB_ROOT)/include
-endif
-
-ifeq ($(origin nopbbam), undefined)
- INCLUDES += -I$(PBBAM_INCLUDE) -I$(HTSLIB_INCLUDE) -I$(BOOST_INCLUDE)
-endif
-
-CXXOPTS := -std=c++11 -pedantic -Wno-long-long -MMD -MP
-
-sources := $(wildcard algorithms/alignment/*.cpp) \
- $(wildcard algorithms/alignment/sdp/*.cpp) \
- $(wildcard algorithms/anchoring/*.cpp) \
- $(wildcard algorithms/compare/*.cpp) \
- $(wildcard algorithms/sorting/*.cpp) \
- $(wildcard datastructures/alignment/*.cpp) \
- $(wildcard datastructures/alignmentset/*.cpp) \
- $(wildcard datastructures/anchoring/*.cpp) \
- $(wildcard datastructures/tuplelists/*.cpp) \
- $(wildcard suffixarray/*.cpp) \
- $(wildcard qvs/*.cpp) \
- $(wildcard statistics/*.cpp) \
- $(wildcard tuples/*.cpp) \
- $(wildcard utils/*.cpp) \
- $(wildcard files/*.cpp) \
- $(wildcard format/*.cpp) \
- $(wildcard simulator/*.cpp) \
- $(wildcard *.cpp)
-
-ifdef nohdf
-sources := $(filter-out files/% utils/FileOfFileNames.cpp, $(sources))
-endif
-
-objects := $(sources:.cpp=.o)
-shared_objects := $(sources:.cpp=.shared.o)
-dependencies := $(objects:.o=.d) $(shared_objects:.o=.d)
-
-all : CXXFLAGS ?= -O3
-
-debug : CXXFLAGS ?= -g -ggdb -fno-inline
-
-profile : CXXFLAGS ?= -Os -pg
-
-g: CXXFLAGS = -g -ggdb -fno-inline -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer
-
-all debug profile g: $(TARGET_LIB)
-
-libblasr.a: $(objects)
- $(AR_pp) $(ARFLAGS) $@ $^
-
-libblasr.so: $(shared_objects) $(DEP_LIBS)
- $(CXX_pp) $(LD_SHAREDFLAGS) -o $@ $^
-
-%.o: %.cpp
- $(CXX) $(CXXOPTS) $(CXXFLAGS) $(LEGACY) $(INCLUDES) -MF"$(@:%.o=%.d)" -MT"$(@:%.o=%.o) $(@:%.o=%.d)" -c $< -o $@
-
-%.shared.o: %.cpp
- $(CXX_pp) $(CXX_SHAREDFLAGS) $(CXXOPTS) $(CXXFLAGS) $(LEGACY) $(INCLUDES) -MF"$(@:%.o=%.d)" -MT"$(@:%.o=%.o) $(@:%.o=%.d)" -c $< -o $@
-
-# .INTERMEDIATE: $(objects)
-
-clean:
- @rm -f libblasr.a libblasr.so
- @rm -f $(objects) $(shared_objects) $(dependencies)
- @find . -type f -name \*.o -delete
- @find . -type f -name \*.d -delete
-
--include $(dependencies)
diff --git a/libcpp/alignment/qvs/QualityValueProfile.cpp b/libcpp/alignment/qvs/QualityValueProfile.cpp
deleted file mode 100644
index f1c3c2f..0000000
--- a/libcpp/alignment/qvs/QualityValueProfile.cpp
+++ /dev/null
@@ -1,41 +0,0 @@
-#include "QualityValueProfile.hpp"
-
-QualityValueProfile::QualityValueProfile(int _wordSize,
- int _numQualityValues) {
- wordSize = _wordSize;
- numQualityValues = _numQualityValues;
- // Initialize the tuple metrics to map from seq->index
- tm.Initialize(wordSize);
- nWords = 1 << (2*wordSize);
- // Initialize the matrix of quality values.
- profile.Grow(nWords, numQualityValues);
- profile.Initialize(0);
-}
-
-void QualityValueProfile::Update(Nucleotide *seq, QualityValue qv) {
- DNATuple tuple;
- if (tuple.FromStringLR(seq, tm)) {
- profile.Set(tuple.tuple, qv, profile(tuple.tuple, qv) + 1);
- }
-}
-
-void QualityValueProfile::Print(std::ofstream &out) {
- out << wordSize << " " << numQualityValues
- << " " << CDF_GRANULARITY << std::endl;
- profile.Print(out);
-}
-
-void QualityValueProfile::ProfileToCDF() {
- int qv;
- int wordIndex;
- for (wordIndex = 0 ; wordIndex < nWords; wordIndex++) {
- int totalSamples = 0;
- for (qv = 0; qv < numQualityValues; qv++) {
- totalSamples += profile(wordIndex, qv);
- profile.Set(wordIndex, qv, totalSamples);
- }
- for (qv = 0; qv < numQualityValues; qv++ ){
- profile.Set(wordIndex, qv, ((profile(wordIndex,qv) * 1.0) / totalSamples) * CDF_GRANULARITY);
- }
- }
-}
diff --git a/libcpp/alignment/qvs/QualityValueProfile.hpp b/libcpp/alignment/qvs/QualityValueProfile.hpp
deleted file mode 100644
index a410fe9..0000000
--- a/libcpp/alignment/qvs/QualityValueProfile.hpp
+++ /dev/null
@@ -1,23 +0,0 @@
-#ifndef _BLASR_QUALITY_VALUE_PROFILE_HPP_
-#define _BLASR_QUALITY_VALUE_PROFILE_HPP_
-
-#include <fstream>
-#include "tuples/DNATuple.hpp"
-#include "tuples/TupleMetrics.hpp"
-#include "matrix/FlatMatrix.hpp"
-#include "qvs/QualityValue.hpp"
-
-class QualityValueProfile {
- int wordSize;
- int numQualityValues;
- FlatMatrix2D<int> profile;
- int nWords;
- TupleMetrics tm;
-public:
- static const int CDF_GRANULARITY = 10000;
- QualityValueProfile(int _wordSize, int _numQualityValues);
- void Update(Nucleotide *seq, QualityValue qv);
- void Print(std::ofstream &out);
- void ProfileToCDF();
-};
-#endif
diff --git a/libcpp/alignment/simulator/CDFMap.hpp b/libcpp/alignment/simulator/CDFMap.hpp
deleted file mode 100644
index 9a66a51..0000000
--- a/libcpp/alignment/simulator/CDFMap.hpp
+++ /dev/null
@@ -1,44 +0,0 @@
-#ifndef _SIMULATOR_CDF_MAP_HPP_
-#define _SIMULATOR_CDF_MAP_HPP_
-#include <algorithm>
-#include <vector>
-#include <assert.h>
-#include "statistics/StatUtils.hpp"
-
-template<typename T_Data>
-class CDFMap {
-public:
- std::vector<int> cdf;
- std::vector<T_Data> data;
- /* Tests:
- * indices 0 1 2 3 4 5 6
- * lengths: 1 3 5 9 10 10 11
- * lengthHistogram.data: 1 3 5 9 10 11
- * lengthHistogram.cdf : 1 2 3 4 6 7
- *
- * lengths: 1 3 5 9 10 11
- * lengthHistogram.data: 1 3 5 9 10 11
- * lengthHistogram.cdf : 1 2 3 4 5 6
- *
- * lengths: 10
- * lengthHistogram.data: 10
- * lengthHistogram.cdf : 1
- */
- int SelectRandomValue(T_Data &value);
-
-};
-
-template<typename T_Data>
-int CDFMap<T_Data>::SelectRandomValue(T_Data &value)
-{
- std::vector<int>::iterator search_it;
- assert(cdf.size() >= 0);
- int randomIndex = RandomInt(cdf[cdf.size()-1]);
- search_it = lower_bound(cdf.begin(), cdf.end(), randomIndex);
- assert(search_it != cdf.end());
- int valueIndex = search_it - cdf.begin();
- value = data[valueIndex];
- return valueIndex;
-}
-
-#endif
diff --git a/libcpp/alignment/simulator/ContextOutputList.hpp b/libcpp/alignment/simulator/ContextOutputList.hpp
deleted file mode 100644
index 5023463..0000000
--- a/libcpp/alignment/simulator/ContextOutputList.hpp
+++ /dev/null
@@ -1,100 +0,0 @@
-#ifndef _SIMULATOR_CONTEXT_OUTPUT_LIST_HPP_
-#define _SIMULATOR_CONTEXT_OUTPUT_LIST_HPP_
-
-#include <stdlib.h>
-#include <map>
-#include <iostream>
-#include <fstream>
-#include <string>
-#include "utils.hpp"
-#include "simulator/OutputList.hpp"
-
-
-class ContextOutputList {
-public:
- std::map<std::string, OutputList*> outputMap;
- int contextLength;
- int ParsePair(std::string &output, std::string &outStr, int &outCount){
- std::string contextStr, outCountStr;
- int i;
- for (i = 0; i < output.size(); i++) {
- if (output[i] == '=') {
- int start = 0;
- while(start < i and (output[start] == ' ' or output[start] == '\t')) { start++;}
- outStr.assign(&output[start], i-start);
- outCountStr.assign(&output[i+1], output.size()-i-1);
- outCount = atoi(outCountStr.c_str());
- return 1;
- }
- }
- return 0;
- }
-
- int SampleRandomContext(std::string refContext, std::string &readContext) {
- //
- // Chec to see if there is a distribution for this ref context, if
- // not, just return the ref context so that things may proceed,
- // but return a fail code.
- //
- if (outputMap.find(refContext) == outputMap.end()) {
- readContext = refContext;
- return 0;
- }
- else {
- outputMap[refContext]->SelectRandomContect(readContext);
- return 1;
- }
- }
-
-
- void Read(std::string &inName) {
- ifstream in;
- CrucialOpen(inName, in, std::ios::in);
- Read(in);
- }
-
- void Read(ifstream &in) {
- int nLines = 0;
- contextLength = 0;
- while(in) {
- std::string context;
- if (!(in >> context)) break;
-
- contextLength = context.size();
- std::string outputsLine;
- getline(in,outputsLine);
- // parse ctx=num; pairs
- int i;
- int e;
- i = 0;
- if (outputMap.find(context) == outputMap.end()) {
- outputMap[context] = new OutputList;
- }
-
- while(i < outputsLine.size()) {
- e = i+1;
- while(e < outputsLine.size() and outputsLine[e] != ';') e++;
- std::string pairStr;
- pairStr.assign(&outputsLine[i], e-i);
- if (e > i + 1) {
- std::string outStr;
- int outCount;
- ParsePair(pairStr, outStr, outCount);
- outputMap[context]->AddOutput(outStr, outCount);
- }
- i = e + 1;
- }
- outputMap[context]->StoreCumulativeCounts();
- }
- }
-
- void Free() {
- std::map<std::string,OutputList*>::iterator mapIt;
- for (mapIt = outputMap.begin(); mapIt != outputMap.end(); ++mapIt) {
- if (mapIt->second) {delete mapIt->second;}
- }
- }
-};
-
-
-#endif
diff --git a/libcpp/alignment/simulator/ContextSample.cpp b/libcpp/alignment/simulator/ContextSample.cpp
deleted file mode 100644
index 798df30..0000000
--- a/libcpp/alignment/simulator/ContextSample.cpp
+++ /dev/null
@@ -1,53 +0,0 @@
-#include "ContextSample.hpp"
-
-ContextSample::ContextSample() {
- minSamples = 0;
- maxSamples = 0;
- reachedMinSamples = 0;
-}
-
-int ContextSample::GetNSamples() {
- return samples.size();
-}
-
-int ContextSample::AppendSample(SMRTSequence &seq, DNALength pos) {
- //
- // Check to see if the space has been sampled enough.
- //
- if (maxSamples != 0 and samples.size() >= maxSamples)
- return 0;
-
- samples.resize(samples.size()+1);
- samples[samples.size()-1].CreateFromRead(seq,pos);
- if (samples.size() > minSamples and reachedMinSamples == 0) {
- reachedMinSamples = 1;
- return 1;
- }
- else {
- return 0;
- }
-}
-
-QualitySample* ContextSample::GetRandomQualitySample() {
- int sampleIndex = RandomInt(samples.size());
- return &samples[sampleIndex];
-}
-
-void ContextSample::Write(std::ofstream &out) {
- int s;
- int sampleSize = samples.size();
- out.write((char*) &sampleSize, sizeof(sampleSize));
- for (s = 0; s < samples.size(); s++ ){
- samples[s].Write(out);
- }
-}
-
-void ContextSample::Read(std::ifstream &in) {
- int s;
- int sampleSize;
- in.read((char*)&sampleSize, sizeof(sampleSize));
- samples.resize(sampleSize);
- for (s = 0; s < sampleSize; s++ ){
- samples[s].Read(in);
- }
-}
diff --git a/libcpp/alignment/simulator/ContextSample.hpp b/libcpp/alignment/simulator/ContextSample.hpp
deleted file mode 100644
index c7aa5c2..0000000
--- a/libcpp/alignment/simulator/ContextSample.hpp
+++ /dev/null
@@ -1,30 +0,0 @@
-#ifndef _SIMULATOR_CONTEXT_SAMPLE_HPP_
-#define _SIMULATOR_CONTEXT_SAMPLE_HPP_
-
-#include<string>
-#include<vector>
-#include<iostream>
-#include "simulator/QualitySample.hpp"
-#include "statistics/StatUtils.hpp"
-
-class ContextSample {
-public:
- std::vector<QualitySample> samples;
- int minSamples;
- int maxSamples;
- int reachedMinSamples;
-
- ContextSample();
-
- int GetNSamples();
-
- int AppendSample(SMRTSequence &seq, DNALength pos);
-
- QualitySample* GetRandomQualitySample();
-
- void Write(std::ofstream &out);
-
- void Read(std::ifstream &in);
-};
-
-#endif
diff --git a/libcpp/alignment/simulator/ContextSet.cpp b/libcpp/alignment/simulator/ContextSet.cpp
deleted file mode 100644
index 1d84d72..0000000
--- a/libcpp/alignment/simulator/ContextSet.cpp
+++ /dev/null
@@ -1,35 +0,0 @@
-#include "ContextSet.hpp"
-
-ContextSampleMap::ContextSampleMap() {
- contextLength = 0;
-}
-
-void ContextSampleMap::Write(std::ofstream &out) {
- T_ContextSampleMap::iterator mapIt, mapEnd;
- int mapSize = this->size();
- out.write((char*)&contextLength, sizeof(contextLength));
- out.write((char*)&mapSize, sizeof(mapSize));
- mapEnd = this->end();
- for(mapIt = this->begin(); mapIt != mapEnd; ++mapIt) {
- out.write(mapIt->first.c_str(), contextLength);
- mapIt->second->Write(out);
- }
-}
-
-void ContextSampleMap::Read(std::ifstream &in) {
- in.read((char*)&contextLength, sizeof(contextLength));
- int numContext;
- in.read((char*)&numContext, sizeof(numContext));
- int i;
- char *context = new char[contextLength+1];
- context[contextLength] = '\0';
- for (i = 0; i < numContext; i++) {
- in.read(context, contextLength);
- std::string contextString = context;
- // Allocate the context
- (*this)[contextString] = new ContextSample;
- (*this)[contextString]->Read(in);
- }
- delete[] context;
-}
-
diff --git a/libcpp/alignment/simulator/ContextSet.hpp b/libcpp/alignment/simulator/ContextSet.hpp
deleted file mode 100644
index 7441f08..0000000
--- a/libcpp/alignment/simulator/ContextSet.hpp
+++ /dev/null
@@ -1,19 +0,0 @@
-#ifndef _SIMULATOR_CONTEXT_SET_HPP_
-#define _SIMULATOR_CONTEXT_SET_HPP_
-
-#include <map>
-#include <iostream>
-#include "ContextSample.hpp"
-
-typedef std::map<std::string, ContextSample*> T_ContextSampleMap;
-
-class ContextSampleMap : public T_ContextSampleMap {
-public:
- int contextLength;
-
- ContextSampleMap();
- void Write(std::ofstream &out);
- void Read(std::ifstream &in);
-};
-
-#endif
diff --git a/libcpp/alignment/simulator/LengthHistogram.cpp b/libcpp/alignment/simulator/LengthHistogram.cpp
deleted file mode 100644
index e135db2..0000000
--- a/libcpp/alignment/simulator/LengthHistogram.cpp
+++ /dev/null
@@ -1,58 +0,0 @@
-#include "simulator/LengthHistogram.hpp"
-
-int LengthHistogram::Read(std::string &inName) {
- std::ifstream in;
- CrucialOpen(inName, in, std::ios::in);
- return Read(in);
-}
-
-int LengthHistogram::Read(std::ifstream &in) {
- while(in) {
- int length, count;
- in >> length;
- in >> count;
- lengthHistogram.data.push_back(length);
- if (lengthHistogram.cdf.size() == 0) {
- lengthHistogram.cdf.push_back(count);
- }
- else {
- lengthHistogram.cdf.push_back(lengthHistogram.cdf[lengthHistogram.cdf.size()-1] + count);
- }
- }
- return 1;
-}
-
-void LengthHistogram::GetRandomLength(int &length) {
- lengthHistogram.SelectRandomValue(length);
-}
-
-void LengthHistogram::BuildFromAlignmentLengths(std::vector<int> &lengths) {
- int i;
- sort(lengths.begin(), lengths.end());
- int f;
- for (f = 0, i = 1; i < lengths.size(); i++) {
- if (lengths[i] != lengths[f]) {
- lengthHistogram.data.push_back(lengths[f]);
- lengthHistogram.cdf.push_back(i);
- f = i;
- }
- }
- if (lengths.size() != 0) {
- lengthHistogram.data.push_back(lengths[lengths.size()-1]);
- lengthHistogram.cdf.push_back(lengths.size());
- }
- /* Tests:
- * indices 0 1 2 3 4 5 6
- * lengths: 1 3 5 9 10 10 11
- * lengthHistogram.data: 1 3 5 9 10 11
- * lengthHistogram.cdf : 1 2 3 4 6 7
- *
- * lengths: 1 3 5 9 10 11
- * lengthHistogram.data: 1 3 5 9 10 11
- * lengthHistogram.cdf : 1 2 3 4 5 6
- *
- * lengths: 10
- * lengthHistogram.data: 10
- * lengthHistogram.cdf : 1
- */
-}
diff --git a/libcpp/alignment/simulator/LengthHistogram.hpp b/libcpp/alignment/simulator/LengthHistogram.hpp
deleted file mode 100644
index 28c5e51..0000000
--- a/libcpp/alignment/simulator/LengthHistogram.hpp
+++ /dev/null
@@ -1,24 +0,0 @@
-#ifndef _SIMULATOR_LENGTH_HISTOGRAM_HPP_
-#define _SIMULATOR_LENGTH_HISTOGRAM_HPP_
-
-#include <iostream>
-#include <string>
-#include <vector>
-#include "simulator/CDFMap.hpp"
-#include "alignment/CmpAlignment.hpp"
-#include "utils.hpp"
-
-class LengthHistogram {
-public:
- CDFMap<int> lengthHistogram;
-
- int Read(std::string &inName);
-
- int Read(std::ifstream &in);
-
- void GetRandomLength(int &length);
-
- void BuildFromAlignmentLengths(std::vector<int> &lengths);
-};
-
-#endif
diff --git a/libcpp/alignment/simulator/OutputList.hpp b/libcpp/alignment/simulator/OutputList.hpp
deleted file mode 100644
index 352c047..0000000
--- a/libcpp/alignment/simulator/OutputList.hpp
+++ /dev/null
@@ -1,57 +0,0 @@
-#ifndef _SIMULATOR_OUTPUT_LIST_HPP_
-#define _SIMULATOR_OUTPUT_LIST_HPP_
-
-#include <string>
-#include <vector>
-
-#include "CDFMap.hpp"
-
-class Output {
-public:
- std::string output;
- int count;
-};
-
-class OutputList {
-public:
- int totalCount;
- std::vector<Output> outputs;
- CDFMap<std::vector<Output>::iterator> cdf;
-
- OutputList() {
- totalCount = 0;
- }
-
- int AddOutput(std::string str, int count) {
- outputs.resize(outputs.size()+1);
- outputs[outputs.size()-1].output = str;
- outputs[outputs.size()-1].count = count;
- totalCount += count;
- }
-
- void StoreCumulativeCounts() {
- int outputIndex;
- int total = 0;
- for (outputIndex = 0; outputIndex < outputs.size(); outputIndex++) {
- total += outputs[outputIndex].count;
- cdf.cdf.push_back(total);
- cdf.data.push_back(outputs.begin() + outputIndex);
- }
- assert(total == totalCount);
- }
-
- int ReturnUniformRandomContextIt(std::vector<Output>::iterator &outputIt) {
- return cdf.SelectRandomValue(outputIt);
- }
-
- int SelectRandomContect(std::string &outputContext) {
- std::vector<Output>::iterator outIt;
- ReturnUniformRandomContextIt(outIt);
- outputContext = outIt->output;
- return outIt - outputs.begin();
- }
-
-};
-
-
-#endif
diff --git a/libcpp/alignment/simulator/OutputSample.hpp b/libcpp/alignment/simulator/OutputSample.hpp
deleted file mode 100644
index 528ecd3..0000000
--- a/libcpp/alignment/simulator/OutputSample.hpp
+++ /dev/null
@@ -1,59 +0,0 @@
-#ifndef _SIMULATOR_OUTPUT_SAMPLE_HPP_
-#define _SIMULATOR_OUTPUT_SAMPLE_HPP_
-
-#include "QualitySample.hpp"
-#include "SMRTSequence.hpp"
-
-class OutputSample {
-public:
- enum Type {Match, Insertion, Deletion, Substitution};
-
- std::vector<QualitySample> qualities;
- std::vector<Nucleotide> nucleotides;
- Type type;
-
- void Resize(int size) {
- qualities.resize(size);
- nucleotides.resize(size);
- }
-
- int CopyFromSeq(SMRTSequence &seq, int pos, int length=1) {
- Resize(length);
- int i;
- for (i = 0; i < length; i++) {
- qualities[i].CopyFromSequence(seq, pos+i);
- nucleotides[i] = seq.seq[pos+i];
- }
- }
-
- void Write(std::ofstream &out) {
-
- out.write((char*) &type, sizeof(type));
- int nNuc = nucleotides.size();
-
- out.write((char*)&nNuc, sizeof(int));
- int i;
- for (i = 0; i < qualities.size(); i++) {
- qualities[i].Write(out);
- }
- assert(nNuc == qualities.size());
- out.write((char*) &nucleotides[0], sizeof(Nucleotide)*nucleotides.size());
-
- }
-
- void Read(std::ifstream &in) {
- in.read((char*) &type, sizeof(Type));
- int nNuc;
- in.read((char*) &nNuc, sizeof(int));
- qualities.resize(nNuc);
- int i;
- for (i = 0; i < nNuc; i++) {
- qualities[i].Read(in);
- }
- nucleotides.resize(nNuc);
- in.read((char*) &nucleotides[0], sizeof(Nucleotide)* nNuc);
-
- }
-};
-
-#endif
diff --git a/libcpp/alignment/simulator/OutputSampleList.hpp b/libcpp/alignment/simulator/OutputSampleList.hpp
deleted file mode 100644
index f2da93f..0000000
--- a/libcpp/alignment/simulator/OutputSampleList.hpp
+++ /dev/null
@@ -1,33 +0,0 @@
-#ifndef _SIMULATOR_OUTPUT_SAMPLE_LIST_HPP_
-#define _SIMULATOR_OUTPUT_SAMPLE_LIST_HPP_
-
-#include <vector>
-#include "OutputSample.hpp"
-
-class OutputSampleList: public std::vector<OutputSample> {
-public:
- void Write(ofstream &out) {
- int nElem = this->size();
- out.write((char*)&nElem, sizeof(int));
- if (nElem > 0) {
- int i;
- for (i = 0; i < nElem; i++) {
- (*this)[i].Write(out);
- }
- }
- }
-
- void Read(std::ifstream &in) {
- int nElem;
- in.read((char*) &nElem, sizeof(int));
- if (nElem > 0) {
- this->resize(nElem);
- int i;
- for (i = 0; i < nElem; i++) {
- (*this)[i].Read(in);
- }
- }
- }
-};
-
-#endif
diff --git a/libcpp/alignment/simulator/OutputSampleListSet.hpp b/libcpp/alignment/simulator/OutputSampleListSet.hpp
deleted file mode 100644
index dbfe8d0..0000000
--- a/libcpp/alignment/simulator/OutputSampleListSet.hpp
+++ /dev/null
@@ -1,123 +0,0 @@
-#ifndef SIMULATOR_OUTPUT_SAMPLE_LIST_SET_H_
-#define SIMULATOR_OUTPUT_SAMPLE_LIST_SET_H_
-
-#include <map>
-#include <string>
-#include <iostream>
-#include "OutputSampleList.hpp"
-
-
-using namespace std;
-
-typedef map<string, OutputSampleList> OutputSampleListMap;
-class OutputSampleListSet {
- public:
- OutputSampleListMap listMap;
- vector<string> keys;
- int keyLength;
- int nSufficient;
- int sampleSpaceSize;
- int keySize;
- int minSamples;
- int maxSamples;
- vector<int> lengths;
- OutputSampleListSet(int keySizeP) {
- minSamples = 500;
- maxSamples = 2000;
- nSufficient = 0;
- keySize = keySizeP;
- sampleSpaceSize = 1 << (2*keySize);
- }
-
- void Write(ofstream &out) {
- // Say how many elements to write.
- OutputSampleListMap::iterator mapIt;
- int setSize = listMap.size();
- out.write((char*) &setSize, sizeof(int));
- int keySize = 0;
- // Say how large each element is.
- if (listMap.size() > 0) {
- keySize = listMap.begin()->first.size();
- }
- out.write((char*)&keySize, sizeof(int));
-
- for (mapIt = listMap.begin(); mapIt != listMap.end(); ++mapIt) {
- string mapItKey = mapIt->first;
- out.write((char*) mapItKey.c_str(), sizeof(char) * mapItKey.size());
- mapIt->second.Write(out);
- }
- int numLengths = lengths.size();
- out.write((char*) &numLengths, sizeof(int));
- int i;
- for ( i = 0; i < lengths.size(); i++) {
- out.write((char*) &lengths[i], sizeof(int));
- }
- }
-
- void Read(string &inName) {
- ifstream in;
- CrucialOpen(inName, in, std::ios::in|std::ios::binary);
- Read(in);
- in.close();
- }
-
- void Read(ifstream &in) {
- int setSize;
- in.read((char*) &setSize, sizeof(int));
- in.read((char*) &keyLength, sizeof(int));
-
- if (keyLength == 0 or setSize == 0) { return; }
- char *key = new char[keyLength+1];
- key[keyLength] = '\0';
- int i;
- for (i = 0; i < setSize; i++) {
- in.read(key, sizeof(char)*keyLength);
- listMap[key].Read(in);
- }
- int numLengths;
- in.read((char*) &numLengths, sizeof(int));
- if (numLengths > 0) {
- lengths.resize(numLengths);
- }
- for (i = 0; i < numLengths; i++) {
- in.read((char*) &lengths[i], sizeof(int));
- }
- if (key) {delete [] key; key = NULL;}
- }
-
- void AppendOutputSample(string key, OutputSample &sample) {
- if (listMap[key].size() < minSamples) {
- if (listMap[key].size() < maxSamples) {
- listMap[key].push_back(sample);
- }
- if (listMap[key].size() == minSamples) {
- nSufficient++;
- cout << nSufficient << " / " << sampleSpaceSize << endl;
- }
- }
- }
-
- bool Sufficient() {
- return nSufficient == sampleSpaceSize;
- }
-
- void SampleRandomSample(string key, OutputSample &sample) {
- if (listMap.find(key) == listMap.end()) {
- cout << listMap.size() << endl;
- cout <<"ERROR, " << key << " is not a sampled context." << endl;
- int i;
- for (i = 0; i < key.size(); i++) {
- char c = toupper(key[i]);
- if (c != 'A' and c != 'C' and c != 'G' and c != 'T') {
- cout << "The nucleotide " << c << " is not supported." << endl;
- }
- }
- exit(1);
- }
- sample = listMap[key][RandomInt(listMap[key].size())];
- }
-
-
-};
-
-#endif
diff --git a/libcpp/alignment/simulator/QualitySample.cpp b/libcpp/alignment/simulator/QualitySample.cpp
deleted file mode 100644
index 1f15b95..0000000
--- a/libcpp/alignment/simulator/QualitySample.cpp
+++ /dev/null
@@ -1,77 +0,0 @@
-#include "QualitySample.hpp"
-
-void QualitySample::CopyFromSequence(SMRTSequence &seq, int pos) {
- qv[0] = seq.qual[pos];
- qv[1] = seq.deletionQV[pos];
- qv[2] = seq.insertionQV[pos];
- qv[3] = seq.substitutionQV[pos];
- tags[0] = seq.deletionTag[pos];
- tags[1] = seq.substitutionTag[pos];
- frameValues[0] = seq.pulseIndex[pos];
- frameValues[1] = seq.preBaseFrames[pos];
- frameValues[2] = seq.widthInFrames[pos];
-}
-
-void QualitySample::Write(std::ofstream &out) {
- out.write((char*)qv, sizeof(qv[0])*NQV);
- out.write((char*)frameValues, sizeof(frameValues[0])*NFV);
- out.write((char*)tags, sizeof(tags[0])*NT);
-}
-
-void QualitySample::Read(std::ifstream &in) {
- in.read((char*)qv, sizeof(QualityValue)*NQV);
- in.read((char*)frameValues, sizeof(frameValues[0])*NFV);
- in.read((char*)tags, sizeof(tags[0])*NT);
-}
-
-void QualitySample::CreateFromRead(SMRTSequence &seq, DNALength pos) {
- /*
- * For now create with a static set of values:
- * qvs:
- * 0 QualityValue
- * 1 DeletionQV
- * 2 InsertionQV
- * 3 SubstitutionQV
- * tags:
- * 0 DeletionTag
- * 1 SubstitutionTag
- * PulseData
- * 0 PulseIndex
- * 1 PreBaseFrames
- * 2 WidthInFrames
- */
- // qv.resize(4);
- std::fill(&qv[0], &qv[NQV], 0);
- if (seq.qual.Empty() == false){
- qv[0] = seq.qual[pos];
- }
- if (seq.deletionQV.Empty() == false) {
- qv[1] = seq.deletionQV[pos];
- }
- if (seq.insertionQV.Empty() == false ){
- qv[2] = seq.insertionQV[pos];
- }
- if (seq.substitutionQV.Empty() == false){
- qv[3] = seq.substitutionQV[pos];
- }
- std::fill(&tags[0], &tags[NT], 0);
- if (seq.deletionTag){
- tags[0] = seq.deletionTag[pos];
- }
- if (seq.substitutionTag) {
- tags[1] = seq.substitutionTag[pos];
- }
-
- std::fill(&frameValues[0], &frameValues[NFV], 0);
- if (seq.pulseIndex) {
- frameValues[0] = seq.pulseIndex[pos];
- }
-
- if (seq.preBaseFrames) {
- frameValues[1] = seq.preBaseFrames[pos];
- }
-
- if (seq.widthInFrames) {
- frameValues[2] = seq.widthInFrames[pos];
- }
-}
diff --git a/libcpp/alignment/simulator/QualitySample.hpp b/libcpp/alignment/simulator/QualitySample.hpp
deleted file mode 100644
index 3f0a181..0000000
--- a/libcpp/alignment/simulator/QualitySample.hpp
+++ /dev/null
@@ -1,28 +0,0 @@
-#ifndef _SIMULATOR_QUALITY_SAMPLE_HPP_
-#define _SIMULATOR_QUALITY_SAMPLE_HPP_
-
-#include <iostream>
-#include "Types.h"
-#include "SMRTSequence.hpp"
-#include "qvs/QualityValue.hpp"
-
-#define NQV 4
-#define NFV 3
-#define NT 2
-
-class QualitySample {
-public:
- QualityValue qv[NQV];
- HalfWord frameValues[NFV];
- Nucleotide tags[NT];
-
- void CopyFromSequence(SMRTSequence &seq, int pos);
-
- void Write(std::ofstream &out);
-
- void Read(std::ifstream &in);
-
- void CreateFromRead(SMRTSequence &seq, DNALength pos);
-};
-
-#endif
diff --git a/libcpp/alignment/statistics/AnchorDistributionTable.hpp b/libcpp/alignment/statistics/AnchorDistributionTable.hpp
deleted file mode 100644
index c789b4d..0000000
--- a/libcpp/alignment/statistics/AnchorDistributionTable.hpp
+++ /dev/null
@@ -1,43518 +0,0 @@
-#ifndef STATISTICS_ANCHOR_DISTRIBUTION_TABLE_H_
-#define STATISTICS_ANCHOR_DISTRIBUTION_TABLE_H_
-
-static int anchorMinKValues[] = {10,25,1};
-static int anchorReadLengths[] = {100,3000,10};
-static int anchorReadAccuracies[] = {70,95,1};
-static float meanNumAnchors[] = {
-0.83,0.91,1.07,1.08,1.18,1.21,1.39,1.46,1.54,1.64,
-1.69,1.83,1.87,1.96,2.08,2.11,2.22,2.35,2.38,2.46,
-2.57,2.60,2.66,2.65,2.82,3.03,3.08,3.06,3.26,3.31,
-3.32,3.38,3.58,3.67,3.69,3.85,3.81,3.88,4.05,4.16,
-4.32,4.43,4.44,4.38,4.44,4.52,4.65,4.90,4.73,4.90,
-4.98,5.11,5.21,5.31,5.37,5.49,5.54,5.70,5.59,5.75,
-5.89,6.02,6.10,6.18,6.33,6.37,6.59,6.36,6.56,6.65,
-6.72,6.74,6.85,7.01,7.08,7.18,7.24,7.27,7.36,7.57,
-7.43,7.63,7.80,7.81,8.12,7.86,8.11,8.20,8.29,8.33,
-8.43,8.39,8.71,8.81,8.70,8.75,8.92,8.94,9.24,9.21,
-9.11,9.36,9.32,9.41,9.62,9.60,9.73,9.91,9.80,9.82,
-10.09,10.17,10.20,10.27,10.33,10.39,10.57,10.46,10.72,10.91,
-10.80,11.10,11.25,11.11,11.45,11.21,11.25,11.45,11.65,11.56,
-11.91,12.01,11.90,11.97,12.09,12.25,12.12,12.21,12.54,12.53,
-12.61,12.37,12.88,12.88,13.03,12.94,13.12,13.23,13.37,13.26,
-13.40,13.47,13.70,13.60,13.72,13.79,14.00,13.99,14.04,13.95,
-14.27,14.16,14.57,14.47,14.65,14.68,14.93,14.98,14.89,15.01,
-15.08,15.24,15.21,15.25,15.21,15.59,15.64,15.81,15.64,15.86,
-15.98,16.17,16.13,16.11,16.15,16.15,16.25,16.42,16.61,16.56,
-16.78,16.62,17.07,16.83,17.13,17.18,17.13,17.51,17.57,17.73,
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-13.14,13.28,13.52,13.59,13.82,14.07,14.22,14.35,14.65,14.83,
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-16.87,16.94,17.16,17.34,17.63,17.69,17.91,18.10,18.29,18.48,
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-22.34,22.55,22.57,22.88,23.16,23.28,23.40,23.61,23.78,23.99,
-24.22,24.22,24.59,24.61,24.99,25.07,25.29,25.34,25.61,26.03,
-25.89,26.12,26.34,26.48,26.81,27.01,27.18,27.27,27.51,27.77,
-27.69,27.95,28.19,28.42,28.54,28.86,28.93,28.93,29.24,29.47,
-29.66,29.82,29.92,30.21,30.37,30.63,30.79,30.83,31.41,31.10,
-31.56,31.66,31.92,32.14,32.15,32.54,32.71,32.69,33.09,33.36,
-33.48,33.43,33.93,33.92,34.12,34.32,34.54,34.64,34.79,34.94,
-35.21,35.24,35.65,35.66,35.85,36.10,36.33,36.39,36.79,36.89,
-36.97,37.15,37.25,37.58,37.78,38.02,38.09,38.59,38.66,38.61,
-38.71,39.16,39.35,39.39,39.55,39.83,39.98,40.32,40.28,40.54,
-40.62,40.71,41.15,41.23,41.19,41.60,41.85,41.98,42.09,42.35,
-42.52,42.43,42.87,43.19,43.30,43.35,43.64,43.74,43.65,44.30,
-44.29,44.58,44.77,44.73,45.17,45.28,45.63,45.68,45.83,46.11,
-46.44,46.37,46.48,46.81,46.90,47.32,47.40,47.36,47.62,47.93,
-47.90,48.15,48.41,48.58,48.77,48.93,49.11,49.32,49.56,49.59,
-49.94,50.17,50.11,50.29,50.63,50.61,51.05,51.01,51.30,51.67,
-51.77,51.91,52.05,52.18,52.35,52.60,52.93,52.83,53.22,53.48,
-53.68,53.72,53.82,54.10,54.18,54.38,54.84,54.76,54.99,55.38,
-1.94,2.12,2.37,2.53,2.72,2.84,3.01,3.14,3.38,3.52,
-3.69,3.87,4.04,4.19,4.47,4.58,4.79,4.92,5.10,5.24,
-5.46,5.70,5.73,5.98,6.12,6.21,6.51,6.71,6.83,7.08,
-7.17,7.26,7.55,7.67,7.79,8.04,8.19,8.38,8.54,8.78,
-8.90,9.09,9.32,9.42,9.61,9.78,9.97,10.10,10.32,10.43,
-10.74,10.75,10.95,11.16,11.32,11.54,11.64,11.90,11.91,12.22,
-12.46,12.40,12.70,12.79,13.09,13.19,13.39,13.59,13.69,13.89,
-14.14,14.23,14.30,14.69,14.76,14.94,15.06,15.38,15.46,15.59,
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-17.64,17.74,17.98,18.06,18.26,18.37,18.57,18.71,18.81,19.13,
-19.46,19.47,19.49,19.78,20.02,20.06,20.18,20.45,20.59,20.83,
-21.12,21.18,21.40,21.50,21.65,21.76,22.05,22.31,22.38,22.62,
-22.72,22.92,23.01,23.08,23.45,23.56,23.70,23.84,24.17,24.35,
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-26.33,26.33,26.51,26.69,27.02,27.08,27.06,27.35,27.55,27.58,
-27.93,28.14,28.11,28.48,28.47,28.76,28.93,29.25,29.33,29.39,
-29.55,29.89,29.95,30.04,30.27,30.38,30.81,30.86,30.86,31.16,
-31.44,31.53,31.69,31.81,32.19,32.15,32.38,32.47,32.70,32.84,
-33.20,33.32,33.42,33.55,33.77,34.03,34.05,34.36,34.61,34.56,
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-36.58,36.66,37.02,37.13,37.19,37.56,37.70,37.59,37.86,38.25,
-38.25,38.34,38.42,38.79,39.08,39.13,39.24,39.39,39.46,39.67,
-39.97,40.17,40.16,40.50,40.67,40.93,41.03,41.13,41.35,41.66,
-41.72,41.72,42.05,42.13,42.35,42.39,42.56,43.04,43.26,43.30,
-43.27,43.74,43.73,43.80,44.11,44.41,44.44,44.56,44.71,45.21,
-45.26,45.44,45.61,45.56,45.61,46.01,46.18,46.19,46.41,46.70,
-46.81,47.16,47.28,47.58,47.59,47.66,47.87,48.25,48.40,48.39,
-48.61,48.70,49.06,49.26,49.37,49.63,49.66,49.74,50.10,50.20,
-50.49,50.69,50.50,50.79,50.92,51.10,51.37,51.55,51.76,51.77,
-1.87,2.06,2.22,2.39,2.57,2.68,2.87,3.01,3.20,3.29,
-3.50,3.65,3.79,4.00,4.18,4.30,4.48,4.69,4.77,4.91,
-5.08,5.33,5.45,5.53,5.76,6.04,6.09,6.27,6.38,6.63,
-6.72,6.96,7.08,7.32,7.35,7.67,7.72,7.92,8.09,8.17,
-8.35,8.53,8.75,8.95,9.07,9.20,9.32,9.43,9.78,9.82,
-10.02,10.09,10.35,10.49,10.60,10.79,10.94,11.15,11.28,11.46,
-11.65,11.82,11.95,12.10,12.20,12.37,12.58,12.77,12.93,13.06,
-13.20,13.44,13.53,13.71,13.97,14.09,14.17,14.46,14.73,14.76,
-14.86,15.05,15.18,15.24,15.54,15.68,15.82,15.96,16.17,16.27,
-16.51,16.75,16.85,16.78,17.15,17.39,17.41,17.66,17.76,17.97,
-18.11,18.41,18.60,18.62,18.82,18.97,19.00,19.27,19.39,19.61,
-19.72,19.72,20.00,20.21,20.54,20.50,20.53,20.87,21.02,21.05,
-21.22,21.51,21.63,21.93,22.10,22.22,22.40,22.48,22.71,22.83,
-22.96,23.21,23.38,23.48,23.59,23.80,24.02,24.11,24.39,24.34,
-24.72,24.69,24.94,25.20,25.29,25.38,25.62,25.72,25.91,25.95,
-26.12,26.46,26.52,26.74,26.90,26.89,27.19,27.40,27.65,27.62,
-27.77,28.03,28.14,28.19,28.71,28.62,28.77,28.90,29.15,29.53,
-29.66,29.56,29.71,30.04,30.07,30.20,30.45,30.68,31.02,31.12,
-31.14,31.24,31.41,31.55,31.86,31.86,32.05,32.28,32.47,32.49,
-32.70,32.83,32.87,33.06,33.48,33.41,33.71,33.89,34.02,34.22,
-34.30,34.27,34.58,34.67,34.90,35.20,35.24,35.39,35.65,35.88,
-36.08,36.10,36.30,36.29,36.62,36.69,36.99,36.95,37.17,37.56,
-37.53,37.59,37.88,37.98,38.20,38.31,38.54,38.56,38.98,38.91,
-39.19,39.31,39.57,39.63,39.88,40.23,40.12,40.43,40.39,40.73,
-40.60,40.99,41.07,41.46,41.60,41.66,41.87,41.93,42.16,42.25,
-42.43,42.63,42.97,43.04,43.10,43.19,43.56,43.63,43.60,43.93,
-43.90,44.23,44.30,44.58,44.62,44.76,45.06,45.09,45.45,45.60,
-45.63,45.98,46.05,46.23,46.47,46.55,46.88,46.69,47.13,46.92,
-47.48,47.48,47.63,47.47,47.86,47.95,48.11,48.45,48.30,48.82,
-1.77,1.91,2.11,2.22,2.35,2.56,2.63,2.85,3.00,3.16,
-3.32,3.43,3.60,3.74,3.95,4.00,4.18,4.40,4.54,4.72,
-4.78,4.98,5.10,5.30,5.42,5.59,5.74,5.86,6.07,6.15,
-6.30,6.47,6.67,6.80,6.90,7.13,7.16,7.40,7.55,7.78,
-7.91,7.95,8.11,8.44,8.53,8.64,8.76,8.97,9.05,9.23,
-9.43,9.51,9.71,9.86,10.05,10.19,10.29,10.53,10.57,10.72,
-10.99,11.03,11.15,11.43,11.59,11.58,11.79,11.92,12.16,12.46,
-12.48,12.51,12.73,12.90,13.06,13.16,13.47,13.50,13.76,13.85,
-13.90,14.16,14.21,14.44,14.69,14.76,14.85,15.13,15.15,15.21,
-15.56,15.64,15.90,15.96,16.09,16.28,16.53,16.62,16.71,16.87,
-17.02,17.20,17.38,17.47,17.56,17.76,17.83,18.16,18.15,18.33,
-18.47,18.83,18.79,19.00,19.26,19.26,19.50,19.64,19.86,19.95,
-20.03,20.15,20.44,20.53,20.63,20.86,20.94,21.19,21.26,21.38,
-21.70,21.66,21.93,22.12,22.20,22.28,22.50,22.77,22.70,22.80,
-23.25,23.21,23.24,23.54,23.71,23.87,24.05,24.31,24.25,24.63,
-24.47,24.84,25.01,25.01,25.48,25.49,25.43,25.77,25.92,25.97,
-26.20,26.33,26.41,26.49,26.84,26.83,26.95,27.30,27.40,27.56,
-27.80,27.93,28.13,28.05,28.18,28.69,28.45,28.69,28.96,29.02,
-29.08,29.34,29.40,29.73,29.62,29.88,30.19,30.03,30.26,30.43,
-30.88,30.97,31.06,31.25,31.44,31.58,31.63,31.84,32.08,32.15,
-32.35,32.41,32.63,32.75,32.94,33.10,33.15,33.35,33.38,33.44,
-33.92,34.08,34.14,34.19,34.32,34.47,34.72,34.87,35.15,35.15,
-35.42,35.36,35.68,35.65,35.98,36.12,36.28,36.37,36.59,36.69,
-36.87,37.00,37.14,37.30,37.72,37.71,37.79,37.80,38.07,38.25,
-38.34,38.39,38.78,38.84,38.98,39.06,38.96,39.36,39.56,39.74,
-40.01,40.04,40.40,40.47,40.50,40.71,40.71,40.93,41.09,41.18,
-41.44,41.57,41.83,41.98,41.92,42.25,42.30,42.44,42.58,42.89,
-42.83,43.01,43.21,43.41,43.50,43.54,43.76,44.12,44.36,44.09,
-44.40,44.67,44.73,44.83,45.12,45.20,45.59,45.59,45.85,45.94,
-1.66,1.78,1.93,2.13,2.22,2.36,2.47,2.67,2.79,3.02,
-3.02,3.23,3.40,3.53,3.65,3.88,3.94,4.13,4.21,4.33,
-4.49,4.70,4.79,4.95,5.12,5.22,5.42,5.56,5.62,5.85,
-6.03,6.16,6.30,6.39,6.55,6.66,6.89,6.94,7.15,7.25,
-7.41,7.51,7.69,7.81,7.93,8.11,8.20,8.44,8.52,8.66,
-8.84,8.89,9.13,9.18,9.36,9.54,9.71,9.88,10.00,10.02,
-10.25,10.32,10.58,10.69,10.88,10.94,11.17,11.25,11.40,11.59,
-11.65,11.86,11.92,12.17,12.40,12.36,12.59,12.68,12.85,13.02,
-13.16,13.27,13.38,13.66,13.72,13.81,13.99,14.15,14.16,14.33,
-14.53,14.58,14.90,14.97,15.09,15.47,15.44,15.63,15.66,15.73,
-16.06,16.13,16.32,16.42,16.46,16.78,16.82,16.86,17.12,17.23,
-17.45,17.52,17.75,17.96,17.88,18.24,18.17,18.43,18.64,18.60,
-18.88,19.02,19.27,19.30,19.57,19.53,19.81,19.67,19.93,20.18,
-20.21,20.31,20.57,20.78,20.72,21.10,21.08,21.33,21.40,21.61,
-21.77,21.98,22.12,22.07,22.19,22.38,22.51,22.84,22.90,22.93,
-23.27,23.19,23.39,23.68,23.79,23.77,24.09,24.00,24.31,24.51,
-24.59,24.67,24.87,25.07,25.14,25.33,25.47,25.66,25.75,26.07,
-25.89,26.24,26.21,26.53,26.55,26.75,27.02,27.03,27.25,27.55,
-27.52,27.70,27.79,27.83,28.02,27.95,28.40,28.61,28.62,28.74,
-28.92,29.15,29.15,29.45,29.48,29.56,29.79,29.66,30.23,30.34,
-30.30,30.56,30.66,30.54,30.90,30.98,31.18,31.46,31.54,31.72,
-31.64,31.98,31.99,32.04,32.36,32.64,32.70,32.78,33.07,32.94,
-33.31,33.34,33.38,33.54,33.86,33.73,33.93,34.23,34.47,34.59,
-34.68,34.64,34.85,35.06,35.16,35.39,35.59,35.60,35.78,35.83,
-36.18,36.36,36.36,36.28,36.48,36.83,37.00,37.02,37.22,37.24,
-37.70,37.60,37.81,37.83,37.99,38.27,38.45,38.51,38.55,38.72,
-38.80,39.09,39.01,39.34,39.61,39.68,39.66,39.88,40.20,40.24,
-40.34,40.53,40.64,40.80,40.88,41.08,41.25,41.42,41.45,41.68,
-41.80,42.02,42.01,42.13,42.54,42.53,42.72,42.60,43.03,43.10
-};
-
-static float sdNumAnchors[] = {
-0.82,0.86,0.94,0.98,0.98,1.02,1.10,1.11,1.12,1.12,
-1.16,1.25,1.26,1.24,1.32,1.36,1.32,1.34,1.44,1.41,
-1.47,1.50,1.48,1.54,1.53,1.60,1.62,1.62,1.61,1.72,
-1.67,1.69,1.74,1.73,1.72,1.74,1.71,1.79,1.85,1.79,
-1.93,2.01,1.98,1.98,1.97,1.91,1.93,2.03,1.95,2.06,
-2.14,2.05,2.00,2.12,2.14,2.15,2.14,2.15,2.20,2.23,
-2.27,2.26,2.26,2.26,2.30,2.26,2.22,2.27,2.38,2.32,
-2.30,2.40,2.39,2.41,2.40,2.48,2.53,2.52,2.42,2.45,
-2.49,2.57,2.48,2.48,2.60,2.54,2.65,2.67,2.61,2.63,
-2.78,2.79,2.70,2.67,2.69,2.68,2.75,2.64,2.70,2.80,
-2.83,2.80,2.73,2.71,2.83,2.92,2.93,2.80,2.83,2.93,
-2.81,3.00,2.93,2.87,2.92,2.92,3.01,2.87,2.91,3.08,
-3.07,3.18,3.02,3.04,3.09,3.15,3.09,3.08,3.14,3.05,
-3.07,3.18,3.10,3.17,3.17,3.08,3.16,3.22,3.30,3.24,
-3.23,3.31,3.35,3.39,3.34,3.31,3.41,3.23,3.34,3.37,
-3.38,3.38,3.29,3.47,3.44,3.41,3.35,3.52,3.45,3.57,
-3.51,3.45,3.46,3.30,3.47,3.54,3.45,3.45,3.53,3.53,
-3.58,3.50,3.53,3.61,3.56,3.54,3.64,3.64,3.53,3.64,
-3.78,3.69,3.70,3.69,3.78,3.74,3.71,3.86,3.68,3.62,
-3.76,3.63,3.79,3.69,3.80,3.70,3.76,3.87,3.88,3.88,
-3.95,4.02,3.75,3.87,3.88,3.92,3.88,3.92,3.94,3.92,
-3.92,4.01,4.01,4.12,3.93,4.07,3.95,4.10,3.98,3.88,
-4.04,4.09,3.96,4.12,4.10,4.23,4.10,4.12,4.26,4.08,
-4.37,4.16,4.30,4.12,4.31,4.23,4.27,4.11,4.30,4.08,
-4.17,4.08,4.16,4.13,4.22,4.23,4.39,4.26,4.22,4.16,
-4.31,4.08,4.23,4.11,4.23,4.15,4.22,4.23,4.31,4.26,
-4.37,4.42,4.42,4.36,4.50,4.40,4.28,4.27,4.51,4.37,
-4.36,4.45,4.52,4.51,4.41,4.56,4.47,4.58,4.45,4.58,
-4.48,4.53,4.68,4.61,4.70,4.54,4.76,4.55,4.74,4.58,
-0.72,0.75,0.81,0.84,0.84,0.84,0.92,0.93,1.00,0.99,
-1.04,1.01,1.06,1.07,1.15,1.14,1.18,1.19,1.19,1.22,
-1.28,1.27,1.33,1.32,1.31,1.38,1.35,1.39,1.40,1.43,
-1.42,1.47,1.41,1.48,1.53,1.54,1.58,1.59,1.55,1.55,
-1.58,1.65,1.68,1.62,1.66,1.67,1.64,1.68,1.81,1.71,
-1.72,1.79,1.72,1.80,1.86,1.74,1.90,1.84,1.92,1.88,
-1.84,1.94,1.98,1.89,1.91,1.98,1.96,1.95,1.96,1.99,
-2.02,2.09,2.08,2.10,2.08,2.02,2.08,2.13,2.19,2.14,
-2.19,2.17,2.16,2.22,2.23,2.16,2.25,2.33,2.23,2.34,
-2.28,2.29,2.36,2.29,2.22,2.41,2.27,2.36,2.34,2.39,
-2.43,2.41,2.49,2.44,2.51,2.48,2.43,2.39,2.54,2.40,
-2.47,2.42,2.56,2.58,2.53,2.49,2.47,2.62,2.57,2.64,
-2.61,2.63,2.69,2.65,2.61,2.83,2.69,2.58,2.77,2.73,
-2.67,2.67,2.75,2.78,2.67,2.65,2.73,2.75,2.78,2.79,
-2.86,2.81,2.77,2.74,2.86,2.75,2.90,2.76,2.86,2.76,
-2.90,2.88,2.85,2.78,2.90,2.92,2.89,2.84,3.11,2.99,
-3.02,2.97,2.92,2.99,2.99,3.09,2.88,2.94,3.08,3.02,
-3.02,3.08,3.15,3.10,3.14,3.12,3.15,3.11,3.08,3.16,
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-1.96,1.93,2.02,1.98,1.98,1.98,2.02,1.98,1.99,2.01,
-1.99,2.00,2.07,1.98,2.06,2.06,2.10,2.07,2.13,2.14,
-2.11,2.21,2.22,2.10,2.32,2.15,2.25,2.20,2.29,2.33,
-2.24,2.16,2.19,2.27,2.30,2.33,2.34,2.30,2.32,2.37,
-2.30,2.27,2.39,2.40,2.31,2.45,2.47,2.44,2.53,2.43,
-2.54,2.46,2.49,2.44,2.52,2.50,2.57,2.52,2.54,2.55,
-2.65,2.53,2.60,2.52,2.71,2.59,2.66,2.59,2.59,2.69,
-2.64,2.62,2.60,2.72,2.80,2.65,2.74,2.66,2.77,2.80,
-2.80,2.84,2.74,2.71,2.72,2.73,2.71,2.77,2.85,2.84,
-2.79,2.92,2.75,2.95,2.89,2.71,2.88,2.85,2.88,2.95,
-2.90,2.95,2.95,2.90,2.93,2.95,3.02,3.01,2.93,2.97,
-2.96,2.94,3.06,3.14,2.90,3.01,3.03,3.07,3.17,3.02,
-2.99,3.14,3.08,3.16,3.12,3.19,3.09,3.13,3.18,3.23,
-3.20,3.13,3.15,3.16,3.22,3.24,3.26,3.19,3.20,3.28,
-3.20,3.14,3.30,3.23,3.29,3.38,3.33,3.34,3.16,3.36,
-3.33,3.31,3.31,3.34,3.42,3.37,3.37,3.45,3.48,3.43,
-3.39,3.33,3.43,3.41,3.41,3.39,3.40,3.38,3.54,3.46,
-3.55,3.56,3.58,3.56,3.66,3.61,3.35,3.49,3.40,3.59,
-3.53,3.60,3.73,3.45,3.63,3.56,3.62,3.70,3.65,3.62,
-3.54,3.65,3.69,3.71,3.66,3.60,3.66,3.51,3.63,3.77,
-3.70,3.83,3.74,3.80,3.81,3.76,3.68,3.77,3.80,3.59,
-3.85,3.81,3.74,3.73,3.76,3.73,3.85,3.95,3.69,3.85,
-3.92,3.89,3.70,3.82,3.84,3.86,3.80,3.82,3.69,3.68,
-0.79,0.79,0.86,0.86,0.90,0.92,0.95,0.99,1.02,1.03,
-1.02,1.07,1.07,1.13,1.12,1.18,1.17,1.21,1.25,1.28,
-1.23,1.27,1.28,1.30,1.33,1.32,1.34,1.39,1.43,1.40,
-1.47,1.47,1.48,1.45,1.55,1.51,1.53,1.51,1.55,1.59,
-1.54,1.62,1.61,1.71,1.69,1.62,1.68,1.72,1.79,1.76,
-1.68,1.82,1.80,1.75,1.88,1.69,1.86,1.91,1.90,1.87,
-1.84,1.89,1.90,1.95,1.95,1.92,1.92,2.04,1.97,2.00,
-2.03,1.99,1.99,2.08,1.98,2.08,2.05,2.11,2.01,2.07,
-2.13,2.13,2.22,2.19,2.22,2.11,2.22,2.19,2.15,2.20,
-2.20,2.15,2.31,2.29,2.26,2.29,2.32,2.42,2.26,2.29,
-2.25,2.32,2.38,2.36,2.37,2.34,2.28,2.31,2.52,2.44,
-2.49,2.36,2.46,2.48,2.49,2.47,2.52,2.50,2.61,2.44,
-2.59,2.56,2.52,2.58,2.56,2.44,2.61,2.56,2.49,2.55,
-2.59,2.70,2.57,2.80,2.52,2.68,2.67,2.75,2.62,2.82,
-2.61,2.72,2.76,2.71,2.77,2.84,2.78,2.80,2.89,2.80,
-2.78,2.84,2.80,2.80,2.83,2.86,2.85,2.90,3.00,2.95,
-2.74,2.77,2.89,2.93,3.01,2.80,3.00,2.99,3.01,2.89,
-2.96,2.99,3.00,3.01,3.09,3.01,3.04,2.95,3.06,2.99,
-3.05,3.12,3.13,3.09,3.12,3.02,3.21,3.03,3.04,3.09,
-3.12,3.17,3.19,3.07,3.21,3.19,3.21,3.18,3.14,3.17,
-3.14,3.26,3.15,3.19,3.12,3.25,3.28,3.43,3.18,3.34,
-3.35,3.31,3.24,3.30,3.24,3.25,3.39,3.31,3.21,3.31,
-3.25,3.51,3.32,3.42,3.44,3.38,3.42,3.46,3.50,3.39,
-3.49,3.44,3.29,3.49,3.40,3.36,3.45,3.51,3.47,3.55,
-3.57,3.49,3.21,3.42,3.60,3.53,3.50,3.51,3.52,3.58,
-3.60,3.55,3.55,3.72,3.58,3.69,3.59,3.61,3.57,3.64,
-3.62,3.72,3.74,3.60,3.68,3.75,3.72,3.74,3.73,3.79,
-3.66,3.76,3.78,3.69,3.68,3.70,3.58,3.67,3.67,3.67,
-3.93,3.67,3.67,3.83,3.79,3.76,3.83,3.69,3.92,3.88,
-0.77,0.79,0.85,0.82,0.88,0.95,0.92,0.98,1.00,1.02,
-1.03,1.02,1.11,1.10,1.10,1.16,1.19,1.17,1.19,1.22,
-1.25,1.25,1.26,1.34,1.33,1.35,1.38,1.34,1.38,1.44,
-1.42,1.44,1.46,1.43,1.49,1.49,1.51,1.50,1.56,1.56,
-1.58,1.61,1.55,1.71,1.66,1.67,1.67,1.70,1.70,1.71,
-1.71,1.75,1.68,1.71,1.73,1.82,1.78,1.80,1.82,1.78,
-1.83,1.82,1.88,1.85,1.88,1.86,1.92,1.98,1.93,1.96,
-1.98,2.00,1.99,2.08,2.05,2.07,2.10,2.13,2.08,2.14,
-2.10,2.06,2.08,2.13,2.08,2.18,2.12,2.11,2.22,2.23,
-2.14,2.18,2.24,2.32,2.27,2.21,2.21,2.28,2.34,2.30,
-2.22,2.27,2.39,2.37,2.39,2.38,2.41,2.34,2.39,2.44,
-2.42,2.36,2.45,2.46,2.41,2.44,2.49,2.47,2.41,2.49,
-2.53,2.47,2.42,2.52,2.42,2.52,2.56,2.55,2.56,2.59,
-2.69,2.68,2.61,2.70,2.61,2.57,2.68,2.67,2.65,2.73,
-2.58,2.72,2.73,2.79,2.61,2.79,2.75,2.72,2.88,2.84,
-2.60,2.74,2.74,2.82,2.76,2.70,2.81,2.78,2.85,2.82,
-2.76,2.81,2.93,2.92,2.95,2.84,2.94,2.85,2.98,2.92,
-2.95,2.95,2.94,3.05,2.87,2.99,3.02,2.96,2.88,3.02,
-2.96,2.89,2.91,3.02,3.02,3.11,3.06,3.03,3.09,3.07,
-3.17,3.14,3.23,3.16,3.05,3.15,3.11,3.12,3.18,3.09,
-3.18,3.08,3.21,3.10,3.19,3.34,3.32,3.17,3.18,3.21,
-3.18,3.15,3.16,3.27,3.22,3.28,3.29,3.32,3.18,3.22,
-3.16,3.32,3.46,3.19,3.24,3.31,3.31,3.34,3.39,3.44,
-3.31,3.57,3.54,3.39,3.37,3.43,3.53,3.44,3.50,3.41,
-3.30,3.43,3.49,3.43,3.39,3.44,3.49,3.45,3.47,3.67,
-3.45,3.55,3.44,3.40,3.61,3.58,3.64,3.46,3.54,3.53,
-3.53,3.55,3.38,3.43,3.61,3.57,3.68,3.75,3.59,3.59,
-3.73,3.62,3.68,3.74,3.73,3.70,3.71,3.70,3.66,3.72,
-3.73,3.73,3.80,3.82,3.68,3.62,3.80,3.81,3.75,3.71,
-0.78,0.82,0.82,0.84,0.94,0.89,0.96,0.97,1.02,0.97,
-1.05,1.02,1.04,1.11,1.09,1.15,1.17,1.20,1.21,1.22,
-1.23,1.24,1.16,1.36,1.29,1.33,1.34,1.39,1.40,1.37,
-1.42,1.44,1.40,1.46,1.47,1.49,1.57,1.49,1.51,1.54,
-1.63,1.60,1.62,1.59,1.69,1.70,1.64,1.67,1.64,1.74,
-1.69,1.72,1.74,1.79,1.76,1.77,1.77,1.77,1.87,1.78,
-1.89,1.83,1.87,1.89,1.90,1.93,1.94,1.94,1.85,1.90,
-1.93,1.94,1.98,2.02,1.89,2.00,2.03,2.12,1.99,2.05,
-2.08,2.06,2.09,2.13,2.07,2.12,2.10,2.21,2.18,2.22,
-2.14,2.16,2.22,2.24,2.13,2.28,2.20,2.19,2.13,2.25,
-2.24,2.26,2.27,2.22,2.20,2.30,2.48,2.36,2.34,2.38,
-2.33,2.43,2.46,2.39,2.46,2.46,2.47,2.41,2.50,2.43,
-2.50,2.49,2.57,2.61,2.51,2.54,2.56,2.63,2.51,2.60,
-2.49,2.55,2.56,2.60,2.61,2.69,2.70,2.56,2.63,2.72,
-2.59,2.58,2.76,2.68,2.66,2.75,2.64,2.69,2.71,2.77,
-2.71,2.66,2.75,2.72,2.80,2.82,2.78,2.74,2.74,2.84,
-2.81,2.86,2.79,2.85,2.83,2.92,2.78,2.97,2.87,2.88,
-2.90,2.97,2.85,2.92,2.85,3.03,2.94,2.85,2.98,2.95,
-2.95,3.09,2.99,3.06,2.97,3.09,2.95,3.16,3.12,3.01,
-2.98,3.07,3.02,3.16,3.09,3.14,3.05,3.04,3.07,3.19,
-3.03,3.12,3.09,3.13,3.23,3.26,3.27,3.04,3.29,3.18,
-3.14,3.17,3.28,3.10,3.27,3.28,3.28,3.36,3.26,3.25,
-3.24,3.32,3.39,3.28,3.42,3.30,3.24,3.36,3.35,3.31,
-3.37,3.40,3.31,3.35,3.22,3.37,3.40,3.22,3.35,3.47,
-3.38,3.44,3.49,3.39,3.43,3.51,3.59,3.49,3.56,3.49,
-3.43,3.43,3.36,3.48,3.46,3.41,3.48,3.60,3.53,3.49,
-3.37,3.60,3.64,3.61,3.60,3.63,3.50,3.68,3.57,3.65,
-3.70,3.66,3.61,3.72,3.71,3.51,3.63,3.72,3.56,3.60,
-3.51,3.57,3.51,3.62,3.83,3.72,3.69,3.69,3.74,3.70
-};
-
-static float meanNumAnchorBases[] = {
-10.29,11.18,13.18,13.19,14.50,15.10,17.15,18.04,18.97,20.38,
-21.16,22.65,23.08,24.30,25.73,25.98,27.35,28.95,29.31,30.26,
-31.76,32.39,32.52,32.71,34.88,37.36,38.05,37.55,40.19,40.75,
-41.26,41.60,44.11,45.51,45.16,47.33,47.20,47.78,49.74,51.59,
-53.24,54.20,54.79,53.94,54.59,55.70,57.46,60.50,58.15,60.08,
-61.16,62.98,64.37,65.53,65.88,67.93,68.35,70.37,68.62,70.53,
-72.95,74.36,75.36,76.09,77.96,78.37,81.21,78.20,81.19,81.89,
-83.12,83.09,84.48,86.07,87.22,88.51,89.30,89.85,91.09,93.30,
-91.48,94.63,96.35,96.40,99.79,97.00,99.45,101.28,102.48,102.75,
-104.36,103.84,107.19,108.70,106.95,107.46,110.29,110.16,113.95,113.67,
-112.26,115.17,115.21,116.09,118.59,118.83,119.42,122.30,120.64,121.45,
-124.31,125.48,125.83,126.51,127.48,128.37,130.53,129.25,131.98,134.67,
-133.11,137.08,138.88,137.42,141.38,137.93,139.34,141.34,143.58,142.55,
-147.15,148.06,147.04,147.26,148.81,151.30,149.67,150.13,153.82,154.43,
-155.18,152.88,159.45,158.69,160.62,159.25,162.38,163.32,164.43,163.90,
-165.40,166.39,169.36,167.88,169.54,169.72,172.42,172.38,173.05,172.16,
-176.13,174.65,179.64,178.83,181.02,180.45,184.05,185.48,184.06,185.26,
-185.76,188.14,187.23,187.82,187.99,192.09,193.41,194.47,192.96,195.94,
-197.08,199.81,199.05,198.55,199.11,199.79,200.00,202.18,205.11,203.98,
-207.51,205.21,210.19,207.32,211.09,211.90,211.65,215.12,217.09,218.79,
-215.54,219.63,218.29,220.24,223.97,220.52,223.12,225.35,225.65,223.31,
-226.18,229.32,229.35,231.02,230.20,233.15,233.75,235.31,233.53,237.98,
-238.21,240.25,238.85,240.20,243.91,243.01,244.59,245.77,245.08,248.13,
-248.87,247.74,248.74,253.32,250.74,255.15,254.54,255.99,257.96,257.46,
-256.46,257.33,261.37,260.70,261.65,264.06,265.57,262.46,267.27,271.55,
-270.74,266.35,272.21,271.36,274.50,276.81,273.01,279.42,277.33,281.16,
-278.39,279.82,280.25,280.24,283.61,283.22,284.77,287.10,287.86,289.02,
-290.12,291.62,295.28,289.63,293.72,294.00,296.16,296.72,294.73,299.37,
-300.36,300.62,305.97,304.85,304.27,302.67,306.11,304.61,311.61,306.50,
-7.70,8.64,9.28,10.05,10.91,11.72,12.83,13.15,15.72,14.63,
-15.80,16.35,16.86,17.78,19.65,20.37,21.10,21.39,22.06,22.09,
-23.73,23.95,25.68,26.19,27.62,27.80,27.93,29.09,30.92,30.47,
-32.38,33.22,32.79,33.34,34.00,35.87,36.73,37.09,37.98,37.93,
-39.15,40.07,40.79,42.63,42.95,44.60,43.83,45.34,45.25,46.94,
-46.50,48.07,47.88,49.90,50.21,49.20,51.13,53.20,53.90,53.92,
-55.20,56.36,57.64,58.16,58.19,58.70,59.98,60.69,61.13,61.11,
-63.45,65.45,64.04,64.16,64.49,66.96,67.83,67.81,67.72,69.77,
-70.60,71.91,74.29,72.17,72.55,75.15,75.14,76.49,76.23,78.90,
-79.02,79.24,80.13,79.14,81.39,83.81,84.35,83.68,87.47,86.30,
-86.12,85.33,87.64,90.09,90.73,89.78,90.95,91.08,95.40,94.00,
-92.38,93.32,96.94,96.51,98.39,96.99,98.08,96.53,99.73,99.84,
-100.73,103.12,105.10,103.36,104.98,107.06,105.04,106.83,106.87,107.64,
-111.29,110.27,112.43,111.98,111.08,114.28,114.74,115.45,115.57,117.44,
-115.45,118.37,117.38,116.51,124.46,121.92,120.76,120.31,124.78,123.56,
-123.50,126.16,127.15,127.68,127.64,128.42,129.45,130.45,132.56,131.88,
-134.59,132.58,135.16,135.46,136.24,138.12,138.00,136.35,139.56,141.55,
-138.99,144.63,145.19,142.78,146.65,143.70,142.96,146.41,147.81,148.22,
-150.48,151.96,150.97,150.41,151.26,152.69,154.02,157.21,155.36,155.66,
-156.38,156.13,158.68,159.25,158.82,157.97,160.47,163.47,163.21,161.61,
-162.17,162.55,163.27,167.11,167.53,166.55,168.82,172.27,171.29,170.15,
-170.39,175.73,173.97,174.81,174.96,174.38,178.36,178.32,179.73,177.92,
-179.63,182.32,182.26,181.45,183.47,181.80,186.21,187.16,186.16,185.81,
-187.68,185.02,189.16,192.16,191.64,192.83,191.94,193.87,195.65,197.51,
-195.94,198.70,196.89,198.05,197.44,199.74,200.91,200.47,202.94,201.34,
-202.85,203.83,205.62,204.65,204.62,208.53,209.32,211.16,207.54,212.60,
-213.26,211.60,211.44,213.94,214.66,218.64,217.47,217.15,218.54,219.57,
-220.16,217.85,220.89,220.62,220.32,220.56,224.14,223.76,224.37,225.64,
-225.56,232.40,228.57,229.66,227.33,231.09,231.39,231.64,230.48,236.08,
-5.76,6.68,7.52,7.87,8.03,8.84,9.38,10.38,10.93,11.38,
-11.65,12.99,12.46,13.30,14.49,16.07,14.73,15.79,16.66,17.23,
-17.95,18.04,20.23,18.78,19.62,20.44,20.46,21.57,21.35,23.23,
-24.05,24.83,24.01,25.05,25.99,26.26,26.70,27.55,29.16,29.25,
-29.57,30.87,31.04,31.17,31.15,32.22,32.92,32.33,33.67,34.09,
-34.68,35.77,37.22,36.10,37.66,37.52,38.84,41.16,39.49,39.74,
-41.39,41.62,43.77,42.24,44.38,44.92,45.40,44.94,46.35,48.09,
-46.01,47.04,49.30,48.54,48.62,50.13,49.48,50.91,52.51,53.43,
-53.22,52.91,53.96,56.33,55.70,55.45,55.53,57.06,58.14,58.79,
-57.91,59.87,59.21,61.27,62.02,63.65,63.14,64.14,66.11,64.66,
-63.48,64.95,65.70,66.63,67.51,68.27,67.66,69.93,68.93,69.62,
-71.13,71.71,73.39,74.06,74.16,73.51,73.58,76.27,76.42,75.72,
-77.65,78.67,79.32,79.18,79.20,78.92,79.07,81.50,81.18,81.27,
-80.61,84.06,83.59,82.03,85.02,85.57,86.43,88.74,87.43,86.53,
-88.22,88.02,90.55,89.79,89.35,93.02,92.95,90.79,92.14,92.57,
-94.29,94.26,94.92,96.21,97.84,97.47,97.88,98.92,98.83,99.67,
-98.70,100.44,100.64,102.63,103.11,103.00,104.21,102.15,103.84,105.05,
-106.03,105.33,109.18,109.37,107.52,110.02,112.99,110.00,111.68,111.06,
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-1789.16,1787.42,1797.24,1790.92,1803.02,1803.52,1816.68,1828.18,1823.55,1838.21,
-68.99,75.57,80.82,86.39,91.67,99.06,102.30,108.58,117.14,122.17,
-127.44,133.27,139.30,143.97,152.44,155.55,161.26,170.53,176.49,183.08,
-183.71,193.35,197.53,205.81,209.55,213.62,221.84,225.77,233.83,239.10,
-244.26,249.69,258.58,261.63,266.87,274.37,279.90,285.98,291.94,300.05,
-304.72,304.30,313.04,325.61,331.15,331.91,338.36,345.82,350.81,355.48,
-365.73,368.85,374.88,381.62,387.03,394.34,399.29,405.11,409.69,416.55,
-423.32,425.48,430.28,443.46,444.62,447.68,455.30,461.95,469.82,479.98,
-479.95,484.89,491.84,498.03,500.41,505.68,519.77,522.03,534.53,533.48,
-538.12,547.28,551.86,557.16,567.70,569.11,577.79,584.70,588.92,587.71,
-602.16,605.32,613.42,615.45,622.44,631.36,637.46,641.84,647.23,656.75,
-662.56,666.19,668.35,677.06,678.55,686.28,689.35,702.39,703.64,709.12,
-713.71,724.59,730.66,735.96,743.50,747.14,756.93,758.39,763.28,772.58,
-775.21,779.52,785.22,794.44,801.78,809.25,812.23,820.58,822.03,827.71,
-837.10,837.78,849.69,854.62,861.62,865.66,873.10,881.54,874.84,885.98,
-893.25,897.05,902.98,907.95,915.75,920.00,929.47,936.71,939.17,948.95,
-945.55,959.81,965.54,966.75,984.45,984.39,983.05,993.55,1001.31,1002.78,
-1012.24,1018.17,1020.99,1026.12,1035.86,1038.41,1045.79,1048.62,1060.47,1068.34,
-1074.84,1081.18,1082.22,1084.84,1093.66,1105.88,1100.95,1109.86,1122.07,1126.34,
-1125.95,1137.75,1141.15,1149.25,1141.95,1156.50,1163.11,1158.37,1172.70,1182.43,
-1195.40,1198.24,1199.93,1205.77,1218.15,1225.35,1223.14,1233.94,1236.52,1243.63,
-1249.65,1253.21,1262.41,1268.67,1272.06,1277.40,1281.37,1290.43,1292.42,1293.99,
-1308.36,1308.62,1317.03,1324.92,1324.75,1335.07,1343.75,1345.07,1359.97,1357.57,
-1371.87,1372.16,1379.59,1380.49,1395.82,1396.15,1398.93,1407.69,1414.57,1419.62,
-1425.56,1428.14,1430.42,1443.91,1450.36,1455.25,1455.42,1458.54,1472.66,1476.97,
-1485.09,1485.00,1497.87,1500.93,1507.19,1512.30,1514.73,1522.77,1531.75,1542.85,
-1546.05,1544.58,1561.06,1563.94,1568.85,1570.72,1577.80,1583.11,1586.49,1591.42,
-1601.22,1606.07,1616.84,1626.82,1627.35,1631.48,1635.82,1644.55,1652.59,1656.79,
-1656.38,1663.88,1676.16,1680.95,1683.76,1683.31,1693.91,1708.35,1711.41,1706.64,
-1720.50,1723.85,1730.71,1730.99,1744.97,1751.33,1759.00,1757.40,1768.76,1774.65,
-66.00,70.54,76.11,85.05,86.87,96.40,98.33,104.78,111.11,119.07,
-120.15,128.55,134.35,141.05,144.15,152.94,157.62,163.61,169.06,171.47,
-177.80,187.09,190.74,197.50,202.54,206.76,214.29,219.74,224.63,231.59,
-238.07,242.65,247.23,253.61,259.14,263.07,273.34,276.50,283.56,287.93,
-292.55,299.88,304.41,308.73,314.75,320.52,326.35,333.38,339.38,344.53,
-348.90,354.20,362.06,364.99,368.84,379.10,385.64,392.61,396.29,399.23,
-406.23,412.29,420.65,423.89,431.49,436.15,442.89,445.90,453.14,461.19,
-462.66,472.61,473.33,482.76,492.88,489.87,497.27,501.14,507.42,516.29,
-523.26,524.57,531.21,542.22,545.29,546.17,552.36,562.58,560.24,568.63,
-576.16,577.52,590.92,594.30,600.04,614.98,611.34,616.64,625.86,627.12,
-639.53,638.94,648.14,651.96,652.85,666.46,668.31,671.31,681.99,687.33,
-690.92,693.63,703.71,711.04,706.26,719.41,724.04,734.11,739.27,739.61,
-750.48,756.44,760.80,767.62,777.68,773.27,785.83,784.38,791.48,801.79,
-800.93,805.99,816.07,822.75,820.99,835.18,836.47,847.53,845.43,854.50,
-863.32,874.84,875.50,876.08,881.49,886.58,892.57,906.55,910.96,909.52,
-921.38,919.58,928.89,942.47,941.40,945.97,957.58,951.39,964.66,968.97,
-978.63,976.65,983.72,996.95,999.18,1005.76,1012.90,1015.21,1019.70,1035.65,
-1028.42,1037.27,1038.72,1048.43,1051.30,1059.47,1067.89,1070.06,1081.93,1089.63,
-1088.31,1097.71,1101.47,1107.32,1115.18,1115.37,1124.96,1133.60,1134.28,1140.71,
-1148.55,1155.00,1155.74,1162.02,1167.21,1171.55,1181.79,1176.55,1199.13,1198.18,
-1199.69,1211.15,1217.21,1211.54,1229.53,1231.73,1237.83,1243.45,1246.79,1253.45,
-1255.22,1266.87,1270.53,1272.34,1290.92,1295.04,1295.43,1298.63,1302.07,1307.07,
-1320.93,1326.69,1323.76,1331.58,1339.15,1339.72,1350.64,1359.56,1370.62,1370.72,
-1371.77,1375.06,1379.63,1391.66,1394.92,1402.73,1408.33,1415.74,1418.01,1421.34,
-1435.18,1443.03,1445.00,1439.17,1451.48,1458.72,1468.56,1470.58,1481.48,1478.91,
-1493.60,1493.41,1497.24,1504.36,1505.64,1520.55,1524.90,1531.80,1528.04,1533.72,
-1540.61,1550.32,1551.69,1561.01,1572.25,1579.08,1576.55,1584.57,1595.91,1594.76,
-1593.01,1604.16,1612.66,1614.56,1632.09,1626.81,1636.59,1640.22,1643.61,1653.83,
-1664.35,1663.02,1669.93,1675.42,1687.93,1689.50,1689.51,1694.24,1707.42,1709.69
-};
-
-static float sdNumAnchorBases[] = {
-10.47,11.01,11.78,12.26,12.43,13.04,13.75,14.08,14.11,14.49,
-14.74,15.81,15.99,15.62,16.58,17.02,16.57,17.20,18.15,17.63,
-18.48,19.41,18.70,19.14,19.41,20.03,20.56,20.43,20.46,21.47,
-21.07,21.28,21.95,22.04,21.45,21.87,21.85,22.52,23.14,22.68,
-24.44,24.88,25.07,24.79,24.77,24.21,24.11,25.63,24.57,25.71,
-26.63,25.26,25.82,26.59,27.08,27.18,26.79,27.40,27.87,28.39,
-28.63,28.69,28.37,28.13,29.13,28.40,28.26,28.58,30.29,29.36,
-29.27,30.63,30.50,30.40,30.47,31.36,31.66,32.16,30.65,31.06,
-31.33,33.04,31.60,31.30,32.57,32.25,33.19,34.46,33.39,33.76,
-35.66,35.45,34.05,33.60,34.05,33.54,35.39,33.48,33.98,35.37,
-35.47,35.37,34.47,34.45,35.48,37.37,36.96,35.51,35.45,36.88,
-36.00,37.86,37.11,36.21,36.95,37.47,37.76,36.66,36.94,39.30,
-38.64,40.25,37.89,39.25,39.20,39.72,38.75,38.20,39.80,38.60,
-39.18,39.95,39.50,40.05,39.19,39.39,39.75,40.84,41.96,40.90,
-41.09,41.94,42.65,42.19,42.44,41.95,43.42,40.38,41.79,42.58,
-42.63,43.22,41.99,44.15,43.54,42.93,42.62,44.10,43.52,45.30,
-44.53,43.04,43.82,41.83,44.01,45.10,43.07,43.83,44.61,44.22,
-45.09,44.35,43.61,45.44,44.24,45.08,46.18,46.11,44.42,46.81,
-47.87,46.86,47.20,46.83,47.57,47.77,46.85,48.27,47.12,45.91,
-47.64,46.51,46.94,46.54,47.73,46.77,47.58,48.01,49.24,48.48,
-49.64,50.33,47.30,49.43,49.17,49.16,49.40,49.20,50.15,50.35,
-50.16,50.48,50.41,52.25,49.77,51.13,49.52,51.88,49.93,49.93,
-51.53,51.99,50.03,52.41,52.12,52.67,51.51,52.13,53.48,51.00,
-55.47,53.08,54.04,52.05,54.49,53.65,54.21,52.09,54.54,52.10,
-53.39,52.05,53.08,52.88,53.47,54.10,55.17,53.77,53.75,52.87,
-54.31,51.63,54.04,51.98,52.86,52.60,53.18,53.72,55.21,53.85,
-55.10,55.41,55.97,54.85,57.14,55.80,54.56,54.35,57.05,55.40,
-54.66,56.53,57.00,56.78,56.06,57.99,56.74,57.98,56.36,57.59,
-57.44,56.94,58.87,58.33,59.83,56.46,59.84,58.13,60.17,58.25,
-9.56,10.26,11.00,11.51,11.35,11.61,12.45,12.73,13.85,13.28,
-13.99,13.89,14.51,14.99,15.52,15.43,15.91,16.43,16.34,16.38,
-17.26,17.17,18.18,17.89,17.91,18.79,18.28,18.89,19.11,19.44,
-19.34,20.24,19.36,20.00,20.52,21.07,21.31,21.57,20.92,21.12,
-21.64,22.34,23.25,22.31,22.61,23.07,22.42,23.03,24.49,23.28,
-23.62,24.21,23.22,24.50,25.41,23.47,25.75,25.26,26.43,25.67,
-25.17,26.18,26.84,26.07,26.25,26.91,26.77,26.50,26.73,27.25,
-27.76,28.47,28.64,28.50,28.44,27.56,28.56,28.85,29.96,29.16,
-29.70,29.35,29.16,30.31,30.32,29.47,30.77,31.91,30.42,31.73,
-31.24,31.25,32.16,30.70,29.87,32.96,31.23,32.38,31.45,32.33,
-33.01,32.50,33.86,33.05,34.16,34.10,33.54,32.66,34.69,32.55,
-33.77,32.95,34.95,35.38,34.65,33.64,33.58,35.00,35.10,35.93,
-35.53,35.73,36.55,36.10,35.79,38.67,36.78,35.08,37.44,36.84,
-36.39,35.96,37.65,37.51,36.47,36.38,37.70,37.51,37.72,38.30,
-38.36,37.93,38.11,37.37,39.07,37.42,39.56,37.40,38.95,37.25,
-39.43,39.32,38.83,37.60,39.77,39.52,39.34,39.11,42.60,40.24,
-40.91,40.61,39.90,40.65,40.49,41.66,39.34,40.09,42.12,41.02,
-41.20,41.84,42.77,42.42,43.18,42.32,42.25,42.62,42.26,43.06,
-44.71,44.38,43.06,41.01,42.74,43.44,45.33,40.56,43.72,42.62,
-44.02,44.73,43.79,41.65,43.55,43.57,44.97,43.39,43.64,45.97,
-43.90,43.80,44.26,45.03,46.56,44.30,45.31,47.23,46.31,44.83,
-44.93,46.23,46.43,45.11,46.11,46.02,46.77,46.56,46.11,44.88,
-46.49,44.97,46.18,46.67,47.59,46.20,45.87,47.94,47.13,47.84,
-47.02,47.81,47.10,49.44,47.11,47.08,48.83,47.29,49.14,49.03,
-48.90,48.86,48.03,47.36,49.04,48.95,49.14,48.17,48.15,50.56,
-50.42,47.08,49.83,50.17,50.29,50.88,51.74,51.25,51.04,51.66,
-49.98,51.01,49.78,51.07,50.31,52.12,52.07,50.89,51.93,52.22,
-50.90,49.80,51.78,51.46,51.85,52.67,51.15,53.96,53.38,53.17,
-51.70,53.75,52.70,53.35,54.86,52.85,53.49,53.79,55.73,53.41,
-8.69,9.29,9.82,10.40,10.37,10.74,10.97,12.08,12.15,12.39,
-12.49,13.37,12.76,13.16,13.99,14.71,14.19,14.55,14.92,14.75,
-15.45,14.99,16.85,15.16,16.58,16.37,16.64,17.00,17.21,17.92,
-17.36,17.82,17.82,18.42,19.03,18.92,19.18,19.72,19.80,19.52,
-20.78,20.42,20.34,20.73,21.22,20.80,21.00,20.59,21.84,20.55,
-22.01,21.36,21.84,21.27,22.67,22.46,22.23,22.35,23.01,23.21,
-23.70,23.97,23.89,23.05,24.39,24.13,23.86,24.10,25.42,26.32,
-24.67,25.54,25.76,26.04,25.12,25.55,26.16,25.96,26.15,26.44,
-27.04,26.08,26.38,27.94,27.95,27.48,28.91,28.04,26.95,28.03,
-28.06,28.15,27.83,28.55,28.90,29.44,28.93,29.26,29.03,29.20,
-29.47,30.00,28.76,31.08,29.00,29.51,30.36,29.94,30.07,29.81,
-30.77,31.59,31.37,31.80,32.17,32.31,33.49,32.86,32.30,32.92,
-32.15,33.49,33.59,32.62,33.99,33.24,31.62,34.42,33.03,33.84,
-32.10,34.86,32.33,32.96,34.94,32.93,34.62,34.88,33.83,35.01,
-34.46,35.90,34.49,33.69,34.40,35.77,35.23,35.97,35.11,36.22,
-35.81,35.74,36.77,35.59,36.07,35.45,36.83,35.85,37.41,35.37,
-35.89,36.75,35.54,36.98,35.41,38.07,36.69,36.67,39.06,38.60,
-37.77,38.04,38.13,37.74,37.76,39.67,37.92,38.63,37.85,39.22,
-38.83,38.73,38.44,38.46,38.85,39.29,38.90,40.86,37.43,39.20,
-38.83,39.62,40.43,41.14,39.82,39.52,39.78,40.80,41.11,40.18,
-39.97,40.05,40.96,41.72,40.55,41.80,40.45,40.50,40.48,40.82,
-41.87,41.41,43.18,42.56,41.71,43.47,41.45,42.56,41.75,41.98,
-41.38,42.93,41.69,43.82,41.82,44.09,42.65,43.07,44.55,44.37,
-43.73,43.09,42.87,42.68,44.39,44.78,44.53,43.78,43.71,43.75,
-44.69,44.83,45.66,45.52,44.70,42.64,46.14,45.22,44.08,45.28,
-46.20,46.36,46.60,45.22,45.23,46.88,45.12,45.55,45.94,45.77,
-45.08,47.70,47.10,45.16,46.24,46.30,48.71,44.74,46.16,46.23,
-49.22,48.37,49.13,46.88,47.71,46.29,49.22,47.38,47.71,47.29,
-46.92,48.50,49.40,47.63,47.81,47.61,49.05,47.33,49.09,48.72,
-8.02,9.03,8.96,9.19,9.76,10.10,10.52,10.25,10.66,11.13,
-11.88,11.55,11.99,11.76,12.80,12.32,12.18,13.14,13.76,13.83,
-14.01,14.37,14.77,14.15,15.29,15.29,15.88,14.86,15.89,17.12,
-16.18,16.06,15.60,16.65,16.74,17.46,17.49,17.53,17.67,18.14,
-18.54,18.00,18.25,18.11,19.00,18.33,19.43,18.97,19.80,18.99,
-19.29,19.50,20.15,20.15,20.47,20.81,20.83,20.53,20.31,20.75,
-21.63,21.19,21.30,22.40,22.34,22.76,22.49,22.53,23.64,22.75,
-21.91,23.19,22.61,22.27,23.28,22.80,23.82,24.02,24.65,24.39,
-24.57,24.14,25.94,24.98,24.92,24.56,25.23,24.95,24.63,24.85,
-26.19,25.60,26.20,25.71,27.19,25.00,27.19,26.25,26.55,25.75,
-27.27,27.36,27.38,26.79,26.66,28.48,27.73,27.38,27.59,27.52,
-27.48,28.11,29.52,29.32,28.55,27.46,28.02,29.49,29.03,28.86,
-28.01,29.29,29.70,29.49,29.57,28.89,30.14,30.05,29.55,29.46,
-30.51,30.64,29.75,30.29,31.83,31.25,30.85,30.20,30.58,30.41,
-32.38,31.78,32.15,32.48,32.08,32.22,31.49,31.54,31.31,32.19,
-31.45,32.27,33.73,32.72,33.20,31.46,32.63,32.15,32.84,32.11,
-33.79,34.11,33.85,32.58,34.70,33.39,33.26,33.73,32.08,36.08,
-34.24,34.35,34.55,35.32,33.89,33.98,33.69,35.67,33.21,33.27,
-34.18,36.49,34.81,35.64,35.40,35.15,35.07,35.48,35.97,35.60,
-34.97,36.79,38.13,36.25,36.20,37.01,34.80,35.88,35.97,36.29,
-36.45,36.39,37.32,38.23,38.10,37.44,37.20,37.77,36.99,37.42,
-38.40,36.59,35.61,39.24,38.46,37.78,37.20,37.93,38.11,38.18,
-39.07,39.71,38.84,37.75,40.45,39.63,39.36,39.70,39.06,38.06,
-40.69,38.95,40.75,39.81,38.19,39.11,39.41,39.81,39.71,38.80,
-39.59,40.75,41.73,40.73,40.05,40.37,41.04,40.51,38.26,39.18,
-39.82,39.30,41.84,42.37,42.42,40.89,41.78,41.47,41.65,41.37,
-41.39,39.79,42.37,43.24,43.60,42.35,43.18,43.15,40.88,41.83,
-41.43,40.46,42.80,42.29,41.16,42.19,45.37,42.82,43.56,43.49,
-42.83,42.40,42.81,43.31,42.89,42.77,45.01,43.54,43.29,43.03,
-7.17,7.75,7.57,8.13,8.50,8.79,9.66,9.41,10.40,10.53,
-10.47,10.40,11.07,10.76,11.46,11.11,11.78,11.60,12.30,12.34,
-12.56,12.34,13.27,13.45,13.95,12.46,14.63,14.36,15.16,14.39,
-14.05,15.01,14.95,14.83,15.99,15.05,15.71,15.84,15.62,16.59,
-16.16,16.09,16.28,16.59,16.51,16.46,16.88,16.72,17.33,17.86,
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-109.85,113.10,112.23,109.72,111.94,113.73,113.55,108.71,112.32,111.10,
-115.29,116.44,117.04,117.96,110.54,114.02,114.92,116.56,118.31,119.67,
-114.59,113.30,119.13,116.20,114.33,118.37,116.17,122.87,116.69,119.60,
-122.21,118.53,115.21,124.30,121.20,123.83,123.06,122.06,120.36,119.05,
-120.74,123.03,125.51,124.44,121.47,123.77,123.84,123.71,119.65,124.97,
-123.11,126.26,130.56,122.92,125.60,129.52,126.61,127.46,131.10,127.14,
-123.96,121.82,128.71,128.22,127.73,123.29,130.06,134.08,129.99,134.65,
-130.96,129.56,130.86,124.83,134.81,133.56,129.82,128.73,135.25,129.51,
-132.05,128.24,127.19,124.63,134.01,130.53,133.15,135.62,135.53,131.90,
-134.43,130.84,139.00,134.91,139.50,142.51,134.94,131.09,131.75,134.35,
-136.27,137.18,141.53,141.95,144.69,132.68,139.84,139.42,138.14,140.61,
-32.56,33.78,34.40,35.26,36.89,37.98,39.92,39.63,40.88,38.80,
-44.34,41.43,41.30,43.13,44.34,45.41,47.62,48.66,49.39,47.81,
-48.61,49.53,48.52,52.05,51.20,52.22,50.65,53.52,54.80,55.07,
-55.10,54.90,55.15,56.51,58.41,59.16,60.96,59.95,57.81,61.74,
-62.85,62.61,62.53,62.07,66.00,65.67,64.88,66.97,66.94,67.98,
-65.10,69.09,67.27,67.74,65.91,70.75,71.25,71.07,71.09,69.64,
-72.31,71.65,70.26,74.12,74.00,75.32,74.69,74.36,72.52,75.59,
-76.18,78.10,77.59,78.98,75.59,76.98,79.45,83.27,77.44,80.27,
-80.38,77.46,79.43,82.25,81.55,81.23,81.24,86.26,83.55,86.09,
-85.69,85.16,87.15,87.02,82.29,84.94,85.36,85.18,87.82,87.93,
-88.63,87.98,88.81,86.28,84.82,88.52,92.73,94.47,93.04,93.47,
-93.42,92.59,95.44,92.25,96.62,94.60,96.60,96.35,99.72,95.62,
-97.16,96.53,96.91,97.07,98.21,97.24,96.49,100.91,96.51,99.24,
-98.93,95.39,101.25,102.29,99.22,104.09,103.30,101.05,101.45,101.80,
-100.09,101.10,105.86,103.40,103.87,104.29,102.40,105.46,105.01,106.80,
-104.76,102.67,104.84,109.24,108.00,110.64,108.25,106.28,103.07,111.12,
-108.53,106.61,104.90,112.56,109.56,112.56,107.99,109.76,111.88,107.66,
-113.42,114.14,109.06,113.78,111.60,115.14,115.21,109.81,111.06,115.63,
-115.40,117.98,115.55,116.75,116.37,116.10,119.78,118.33,120.86,118.94,
-120.01,116.34,121.32,120.29,121.30,123.21,115.70,119.25,117.94,119.76,
-118.91,120.00,122.10,121.63,124.11,123.75,126.05,117.82,126.20,121.50,
-121.64,122.51,124.65,116.36,125.67,123.12,120.58,123.72,122.23,124.26,
-128.57,128.47,127.19,128.18,126.31,124.79,126.36,124.76,128.86,124.83,
-130.10,128.93,131.75,132.86,127.38,132.50,128.23,127.54,131.49,130.07,
-131.14,132.10,133.72,130.69,129.55,130.86,137.71,131.30,137.55,135.08,
-135.05,128.49,136.52,134.24,138.05,138.98,135.00,140.70,128.21,133.84,
-131.77,138.31,133.84,134.99,141.56,142.82,135.64,140.69,137.72,136.90,
-141.85,141.14,140.50,141.03,145.70,134.28,141.08,143.15,137.94,135.65,
-143.94,139.25,135.97,142.05,146.51,140.13,144.63,139.89,145.76,143.92
-};
-#endif
diff --git a/libcpp/alignment/statistics/LookupAnchorDistribution.cpp b/libcpp/alignment/statistics/LookupAnchorDistribution.cpp
deleted file mode 100644
index ebab522..0000000
--- a/libcpp/alignment/statistics/LookupAnchorDistribution.cpp
+++ /dev/null
@@ -1,58 +0,0 @@
-#include "statistics/LookupAnchorDistribution.hpp"
-
-int LookupAnchorDistribution(int readLength, int minMatchLength,
- int accuracy, float &mn, float &sdn, float &mnab,
- float &sdnab) {
-
- int kIndex, accIndex, lengthIndex;
- int returnValue = 0;
-
- // Major index is by accuracy
- if (accuracy < anchorReadAccuracies[0]) {
- returnValue = -2;
- accuracy = anchorReadAccuracies[0];
- }
- else if (accuracy >= anchorReadAccuracies[1]) {
- returnValue = 2;
- accuracy = anchorReadAccuracies[1] - anchorReadAccuracies[2];
- }
-
- accIndex = ( ((int)accuracy) - anchorReadAccuracies[0]) / anchorReadAccuracies[2];
-
- // middle index is by k
- if (minMatchLength < anchorMinKValues[0]) {
- returnValue = -1; // signal too low
- minMatchLength = anchorMinKValues[0];
- }
- else if (minMatchLength >= anchorMinKValues[1]) {
- returnValue = 1; // signal too high
- minMatchLength = anchorMinKValues[1] - anchorMinKValues[2]; // max match length
- }
-
- kIndex = (minMatchLength - anchorMinKValues[0])/ anchorMinKValues[2];
-
- // last index is by read length
- if (readLength < anchorReadLengths[0]){
- returnValue = -3;
- readLength = anchorReadLengths[0];
- }
- else if (readLength >= anchorReadLengths[1]) {
- returnValue = 3;
- readLength = anchorReadLengths[1] - anchorReadLengths[2]; // max read length
- }
-
- lengthIndex = (readLength - anchorReadLengths[0]) / anchorReadLengths[2];
-
-
- int nLengths = (anchorReadLengths[1] - anchorReadLengths[0]) / anchorReadLengths[2];
- int nAccuracies = (anchorReadAccuracies[1] - anchorReadAccuracies[0]) / anchorReadAccuracies[2];
- int nAnchors = (anchorMinKValues[1] - anchorMinKValues[0]) / anchorMinKValues[2];
- int index = accIndex*(nLengths*nAnchors) + kIndex*nLengths + lengthIndex;
-
- mn = meanNumAnchors[index];
- sdn = sdNumAnchors[index];
- mnab = meanNumAnchorBases[index];
- sdnab = sdNumAnchorBases[index];
-
- return returnValue;
-}
diff --git a/libcpp/alignment/statistics/LookupAnchorDistribution.hpp b/libcpp/alignment/statistics/LookupAnchorDistribution.hpp
deleted file mode 100644
index cfc9e35..0000000
--- a/libcpp/alignment/statistics/LookupAnchorDistribution.hpp
+++ /dev/null
@@ -1,10 +0,0 @@
-#ifndef _BLASR_LOOKUP_ANCHOR_DISTRIBUTION_HPP_
-#define _BLASR_LOOKUP_ANCHOR_DISTRIBUTION_HPP_
-
-#include "statistics/AnchorDistributionTable.hpp" // not ported
-
-int LookupAnchorDistribution(int readLength, int minMatchLength,
- int accuracy, float &mn, float &sdn, float &mnab,
- float &sdnab);
-
-#endif
diff --git a/libcpp/alignment/statistics/StatUtils.cpp b/libcpp/alignment/statistics/StatUtils.cpp
deleted file mode 100644
index cc6bf79..0000000
--- a/libcpp/alignment/statistics/StatUtils.cpp
+++ /dev/null
@@ -1,45 +0,0 @@
-#include "StatUtils.hpp"
-
-void InitializeRandomGenerator(int value) {
- srandom((unsigned) value);
-}
-
-
-unsigned int RandomUnsignedInt(unsigned int randMax) {
- //
- // step 1, pack an unsigned integer with a random value, this
- //
- unsigned int randVal = RAND_MAX * (1.0*random())/RAND_MAX;
-
- // step 2,
- unsigned int lastBit = random() % 2;
- lastBit = lastBit << ( __WORDSIZE/2-1);
- // This should never overflow, add a 31-bit number into a 32.
- randVal+= lastBit;
- double fpRandVal = 1.0*randVal;
- return (randMax * fpRandVal / UINT_MAX);
-}
-
-unsigned int RandomInt(int randMax) {
- int randVal = (randMax * ((1.0*random()) / RAND_MAX));
- return std::min(randMax-1, randVal);
-}
-
-unsigned int RandomInt(unsigned int min, unsigned int max) {
- return RandomInt(max - min) + min;
-}
-
-float Random() {
- return (RandomInt(0,RAND_MAX)*1.0)/RAND_MAX;
-}
-
-bool FindQNorm(float prob, float & nStdDev) {
- if (prob < 0.5 or prob > 1.0) {
- return false;
- }
- else {
- nStdDev = qnorm[(int)((prob - 0.50) * 500)];
- return true;
- }
-}
-
diff --git a/libcpp/alignment/statistics/StatUtils.hpp b/libcpp/alignment/statistics/StatUtils.hpp
deleted file mode 100644
index 40ba2a5..0000000
--- a/libcpp/alignment/statistics/StatUtils.hpp
+++ /dev/null
@@ -1,165 +0,0 @@
-#ifndef _BLASR_STAT_UTILS_HPP_
-#define _BLASR_STAT_UTILS_HPP_
-
-#include <math.h>
-#include <stdlib.h>
-#include <limits.h>
-#include <time.h>
-#include <vector>
-#include <algorithm>
-#include <assert.h>
-
-static const long FactorialTableLength = 21;
-
-static const long long FactorialTable[] = {
- 1L, //0
- 1L, //1
- 2L, //2
- 6L, //3
- 24L,//4
- 120L, //5
- 720L, //6
- 5040L, //7
- 40320L,//8
- 362880L, //9
- 3628800L,//10
- 39916800L,//11
- 479001600L,//12
- 6227020800LL,//13
- 87178291200LL,//14
- 1307674368000LL,//15
- 20922789888000LL,//16
- 355687428096000LL,//17
- 6402373705728000LL,//18
- 121645100408832000LL,//19
- 2432902008176640000LL//20
-};
-
-static const float qnorm[] = {
- 0.00, 0.00250, 0.00501, 0.00751, 0.0100248, 0.0125393, 0.0150457,
- 0.0175408, 0.0200506, 0.0225647, 0.0250611, 0.0275717,
- 0.0300891, 0.0325931, 0.0351088, 0.0376059, 0.0401181,
- 0.0426244, 0.0451313, 0.0476466, 0.0501537, 0.0526685,
- 0.0551768, 0.0576842, 0.0601966, 0.0627038, 0.0652137,
- 0.0677392, 0.0702467, 0.0727575, 0.0752699, 0.0777852,
- 0.080295, 0.0828113, 0.0853292, 0.0878418, 0.0903688,
- 0.0928765, 0.095392, 0.0979195, 0.10043, 0.102954,
- 0.105478, 0.107994, 0.110512, 0.113035, 0.115563,
- 0.118083, 0.120607, 0.123137, 0.125664, 0.128186,
- 0.130713, 0.133244, 0.135772, 0.138305, 0.140837,
- 0.143367, 0.145904, 0.14843, 0.150967, 0.153507,
- 0.15604, 0.158573, 0.161116, 0.163651, 0.166199,
- 0.168748, 0.171287, 0.173822, 0.176371, 0.178922,
- 0.181467, 0.184019, 0.186569, 0.189112, 0.19167,
- 0.194223, 0.196777, 0.199337, 0.201891, 0.204451,
- 0.207017, 0.209579, 0.212134, 0.214704, 0.217263,
- 0.219839, 0.222406, 0.224971, 0.227549, 0.230116,
- 0.232695, 0.235260, 0.237849, 0.240428, 0.243002,
- 0.245581, 0.248173, 0.250756, 0.25334, 0.255933,
- 0.258520, 0.261118, 0.26371, 0.266315, 0.268900,
- 0.271509, 0.274117, 0.276717, 0.279314, 0.281921,
- 0.284532, 0.287145, 0.289754, 0.292374, 0.294996,
- 0.29761, 0.300232, 0.302859, 0.305487, 0.308105,
- 0.310732, 0.313366, 0.316003, 0.318635, 0.321276,
- 0.323913, 0.326563, 0.329201, 0.331857, 0.334502,
- 0.337157, 0.339807, 0.342461, 0.345122, 0.347787,
- 0.350451, 0.353119, 0.355785, 0.358454, 0.361132,
- 0.363806, 0.366484, 0.36917, 0.371855, 0.374543,
- 0.377232, 0.379927, 0.382624, 0.385328, 0.388027,
- 0.39072, 0.393437, 0.396148, 0.398857, 0.401579,
- 0.404289, 0.407016, 0.409731, 0.412465, 0.415197,
- 0.417922, 0.420666, 0.423403, 0.426148, 0.428892,
- 0.431646, 0.434391, 0.437152, 0.439914, 0.442672,
- 0.44544, 0.448219, 0.450981, 0.45376, 0.45654,
- 0.459323, 0.462117, 0.464905, 0.467698, 0.470491,
- 0.473297, 0.476105, 0.478915, 0.48172, 0.484549,
- 0.487361, 0.490189, 0.493015, 0.495853, 0.498682,
- 0.501528, 0.504372, 0.507226, 0.510075, 0.512938,
- 0.515798, 0.518651, 0.521522, 0.524401, 0.527279,
- 0.530169, 0.533049, 0.53594, 0.53883, 0.541737,
- 0.544649, 0.547551, 0.550462, 0.553383, 0.556308,
- 0.559237, 0.562176, 0.565104, 0.568053, 0.570997,
- 0.573953, 0.576911, 0.579874, 0.582846, 0.585819,
- 0.588790, 0.591776, 0.594768, 0.597768, 0.600759,
- 0.60376, 0.606775, 0.60979, 0.612817, 0.615842,
- 0.618879, 0.621914, 0.624957, 0.62800, 0.631069,
- 0.63412, 0.637195, 0.640264, 0.643347, 0.646437,
- 0.649525, 0.652621, 0.655723, 0.658838, 0.661952,
- 0.665073, 0.668203, 0.671345, 0.674482, 0.677636,
- 0.680795, 0.683962, 0.68713, 0.690304, 0.69349,
- 0.696681, 0.699881, 0.703089, 0.706308, 0.709528,
- 0.712753, 0.715985, 0.719224, 0.722473, 0.725735,
- 0.729009, 0.73227, 0.73555, 0.738844, 0.74214,
- 0.745449, 0.748769, 0.752081, 0.75541, 0.758751,
- 0.762107, 0.765458, 0.768822, 0.772195, 0.775574,
- 0.778965, 0.782367, 0.785774, 0.789192, 0.792612,
- 0.796053, 0.799507, 0.802953, 0.80642, 0.809898,
- 0.813384, 0.816873, 0.820371, 0.823897, 0.827412,
- 0.830958, 0.83449, 0.838056, 0.841624, 0.84519,
- 0.848787, 0.852385, 0.855992, 0.859611, 0.86325,
- 0.866898, 0.870544, 0.874213, 0.877899, 0.881584,
- 0.885292, 0.889005, 0.892736, 0.896476, 0.900224,
- 0.903991, 0.907766, 0.91156, 0.915364, 0.91918,
- 0.92301, 0.926854, 0.93071, 0.93458, 0.938479,
- 0.94237, 0.946296, 0.950225, 0.954165, 0.958123,
- 0.962092, 0.966083, 0.970097, 0.97411, 0.978152,
- 0.98220, 0.986279, 0.990355, 0.994453, 0.99857,
- 1.00271, 1.00686, 1.01103, 1.01522, 1.01942,
- 1.02365, 1.02789, 1.03215, 1.03643, 1.04073,
- 1.04504, 1.04938, 1.05374, 1.05812, 1.06251,
- 1.06693, 1.07137, 1.07583, 1.08031, 1.08482,
- 1.08934, 1.09389, 1.09846, 1.10306, 1.10768,
- 1.11232, 1.11698, 1.12167, 1.12639, 1.13113,
- 1.13589, 1.14068, 1.14550, 1.15034, 1.15522,
- 1.16011, 1.16504, 1.17000, 1.17498, 1.18000,
- 1.18504, 1.19011, 1.19522, 1.20035, 1.20552,
- 1.21072, 1.21596, 1.22122, 1.22652, 1.23186,
- 1.23723, 1.24264, 1.24808, 1.25356, 1.25908,
- 1.26464, 1.27023, 1.27587, 1.28155, 1.28727,
- 1.29303, 1.29883, 1.30468, 1.31057, 1.31651,
- 1.32250, 1.32853, 1.33462, 1.34075, 1.34693,
- 1.35317, 1.35946, 1.36580, 1.37220, 1.37865,
- 1.38517, 1.39174, 1.39837, 1.40507, 1.41183,
- 1.41865, 1.42554, 1.43250, 1.43953, 1.44663,
- 1.45380, 1.46105, 1.46838, 1.47579, 1.48328,
- 1.49085, 1.49851, 1.50626, 1.51410, 1.52203,
- 1.53006, 1.53819, 1.54643, 1.55477, 1.56322,
- 1.57178, 1.58046, 1.58926, 1.59819, 1.60724,
- 1.61643, 1.62576, 1.63523, 1.64485, 1.65462,
- 1.66456, 1.67466, 1.68494, 1.69539, 1.70604,
- 1.71688, 1.72793, 1.73919, 1.75068, 1.76241,
- 1.77438, 1.78661, 1.79911, 1.81191, 1.82500,
- 1.83842, 1.85217, 1.86629, 1.88079, 1.89569,
- 1.91103, 1.92683, 1.94313, 1.95996, 1.97736,
- 1.99539, 2.01409, 2.03352, 2.05374, 2.07485,
- 2.09692, 2.12007, 2.14441, 2.17009, 2.19728,
- 2.22621, 2.25712, 2.29036, 2.32634, 2.36561,
- 2.40891, 2.45726, 2.51214, 2.57582, 2.65206,
- 2.74778, 2.87816, 3.09023, 10000};
-
-
-inline int Choose(int a, int b);
-
-void InitializeRandomGenerator(int value);
-
-template<typename T>
-void MeanVar(std::vector<T> &values, float &mean, float &var);
-
-inline void InitializeRandomGeneratorWithTime() {
- time_t t;
- srandom((unsigned) time(&t));
-}
-
-unsigned int RandomUnsignedInt(unsigned int randMax);
-
-unsigned int RandomInt(int randMax);
-
-unsigned int RandomInt(unsigned int min, unsigned int max);
-
-float Random();
-
-bool FindQNorm(float prob, float &nStdDev);
-
-#include "StatUtilsImpl.hpp"
-
-#endif
diff --git a/libcpp/alignment/statistics/StatUtilsImpl.hpp b/libcpp/alignment/statistics/StatUtilsImpl.hpp
deleted file mode 100644
index 3d1cc76..0000000
--- a/libcpp/alignment/statistics/StatUtilsImpl.hpp
+++ /dev/null
@@ -1,57 +0,0 @@
-#ifndef _BLASR_STAT_UTILS_IMPL_HPP_
-#define _BLASR_STAT_UTILS_IMPL_HPP_
-
-#include <vector>
-#include <time.h>
-
-inline int Choose(int a, int b) {
- // A quick choose for small values.
- assert(a >= b);
- if (a < FactorialTableLength and b < FactorialTableLength) {
- return (FactorialTable[a] /
- (FactorialTable[b] * FactorialTable[a-b]));
- } else {
- //
- // Less quick choose for numerically stable values.
- //
- unsigned long al =a, bl=b, fact=0;
- fact = al;
- //
- // The full value of b! must be able to be computed.
- //
- if (b >= FactorialTableLength) {
- return 0;
- }
- while (al > bl) {
- --al;
- if (ULONG_MAX / al < fact) {
- // there is overflow in the computation of a!/(a-b)!
- return 0;
- }
- else {
- fact = fact * al;
- }
- }
- return fact / FactorialTable[b];
- }
-}
-
-
-template<typename T>
-void MeanVar(std::vector<T> &values, float &mean, float &var) {
- T sum = 0;
- T sumsq = 0;
- int i;
- if (values.size() == 0) {
- mean = 0; var = 0;
- return;
- }
- for (i = 0; i < values.size(); i++) {
- sum += values[i];
- sumsq += values[i]*values[i];
- }
- mean = (1.0*sum) / values.size();
- var = sumsq / values.size() - (mean*mean);
-}
-
-#endif
diff --git a/libcpp/alignment/statistics/VarianceAccumulator.hpp b/libcpp/alignment/statistics/VarianceAccumulator.hpp
deleted file mode 100644
index 068bc62..0000000
--- a/libcpp/alignment/statistics/VarianceAccumulator.hpp
+++ /dev/null
@@ -1,28 +0,0 @@
-#ifndef _BLASR_VARIANCE_ACCUMULATOR_HPP_
-#define _BLASR_VARIANCE_ACCUMULATOR_HPP_
-
-template<typename T>
-class VarianceAccumulator {
-public:
- int nSamples;
- T sumSqVal;
- T sumVal;
- T maxVal;
- T minVal;
-
- VarianceAccumulator<T>();
-
- T GetMean();
-
- T GetVariance();
-
- void Reset();
-
- float GetNStdDev(T value);
-
- void Append(T v);
-};
-
-#include "statistics/VarianceAccumulatorImpl.hpp"
-
-#endif
diff --git a/libcpp/alignment/statistics/VarianceAccumulatorImpl.hpp b/libcpp/alignment/statistics/VarianceAccumulatorImpl.hpp
deleted file mode 100644
index 98bda35..0000000
--- a/libcpp/alignment/statistics/VarianceAccumulatorImpl.hpp
+++ /dev/null
@@ -1,60 +0,0 @@
-#ifndef _BLASR_VARIANCE_ACCUMULATOR_IMPL_HPP_
-#define _BLASR_VARIANCE_ACCUMULATOR_IMPL_HPP_
-
-template<typename T>
-VarianceAccumulator<T>::
-VarianceAccumulator() {
- Reset();
-}
-
-template<typename T>
-void VarianceAccumulator<T>::Reset() {
- sumSqVal = 0;
- sumVal = 0;
- nSamples = 0;
- maxVal = minVal = 0;
-}
-
-template<typename T>
-T VarianceAccumulator<T>::
-GetMean() {return ((1.0)*sumVal)/nSamples;}
-
-template<typename T>
-T VarianceAccumulator<T>::
-GetVariance() {
- return (1.0*sumSqVal)/nSamples - GetMean()*GetMean();
-}
-
-template<typename T>
-float VarianceAccumulator<T>::
-GetNStdDev(T value) {
- T variance = GetVariance();
- T mean = GetMean();
- if (variance > 0) {
- return fabs(value - mean)/(sqrt(variance));
- }
- else {
- return 0;
- }
-}
-
-template<typename T>
-void VarianceAccumulator<T>::
-Append(T v) {
- if (nSamples == 0) {
- maxVal = minVal = v;
- }
- else {
- if (maxVal < v) {
- maxVal = v;
- }
- if (minVal > v) {
- minVal = v;
- }
- }
- sumSqVal += v*v;
- sumVal += v;
- nSamples++;
-}
-
-#endif
diff --git a/libcpp/alignment/statistics/cdfs.cpp b/libcpp/alignment/statistics/cdfs.cpp
deleted file mode 100644
index ab37322..0000000
--- a/libcpp/alignment/statistics/cdfs.cpp
+++ /dev/null
@@ -1,53 +0,0 @@
-#include "cdfs.hpp"
-
-float NormalCDF(float mu, float sigmaSq, float x) {
- float nStdDev = (x - mu)/sqrt(sigmaSq);
- if ((int) nStdDev <= -10.0) return 0;
- if ((int) nStdDev >= 10.0) return 1;
-
- int cdfindex = 1000 + 100*nStdDev;
- assert(cdfindex >= 0);
- assert(cdfindex <= 2000);
- if (cdfindex == 2000) {
- return 1;
- }
- // cout << "nstdev: " << nStdDev << " mu " << mu
- // << " sigma " << sigmaSq << " x " << x
- // << " norm cdf index: " << cdfindex << endl;
- return NormCDFTable[cdfindex];
-}
-
-
-float PoissonCDF(float lambda, int a, int b) {
- float cdf = 0;
- int i;
- for (i = a; i <= b; i++ ){
- // cout << "poiss " << lambda << ", " << i
- // << " " << Poisson(lambda, i) << endl;
- cdf += Poisson(lambda, i);
- }
- return cdf;
-}
-
-
-float PoissonCDF(float lambda, int a) {
-
- float cdf = 0;
- int i;
- float p;
- float epsilon =0.000000000001;
- if (lambda > (int)(FactorialTableLength*2/3)) {
- // lambda is too large, use normal approximation.
- // cout << "using table: lambda: " << lambda
- // << " a: " << a << endl;
- return NormalCDF(lambda, lambda, a);
- }
-
- for (i = 0; i <= a; i++ ){
- p = Poisson(lambda, i);
- if (p < epsilon and i > (int) lambda) break;
- // cout << "p: " << p << endl;
- cdf += p;
- }
- return cdf;
-}
diff --git a/libcpp/alignment/statistics/cdfs.hpp b/libcpp/alignment/statistics/cdfs.hpp
deleted file mode 100644
index b7ac3d2..0000000
--- a/libcpp/alignment/statistics/cdfs.hpp
+++ /dev/null
@@ -1,418 +0,0 @@
-#ifndef _BLASR_CDFS_HPP_
-#define _BLASR_CDFS_HPP_
-
-#include "pdfs.hpp"
-
-static const float NormCDFTable[2000] = {
- 7.61985302416053e-24, 8.42908720044307e-24, 9.32333910390851e-24, 1.03114418389443e-23, 1.14031357813280e-23,
- 1.26091606702069e-23, 1.39413569342072e-23, 1.54127771659480e-23, 1.70378087485724e-23, 1.88323087358676e-23,
- 2.08137521949321e-23, 2.30013953380610e-23, 2.54164548995384e-23, 2.80823053544230e-23, 3.10246957313482e-23,
- 3.42719879411367e-23, 3.78554187290007e-23, 4.18093875618591e-23, 4.61717729854569e-23, 5.09842802303871e-23,
- 5.62928231137653e-23, 6.21479435763827e-23, 6.860527251602e-23, 7.57260359288958e-23, 8.3577610755683e-23,
- 9.22341352493942e-23, 1.01777179142962e-22, 1.12296479398304e-22, 1.23890747870050e-22, 1.36668557820343e-22,
- 1.50749316881020e-22, 1.6626433478118e-22, 1.83357994947588e-22, 2.02189039948453e-22, 2.22931981695015e-22,
- 2.45778648347233e-22, 2.70939880997893e-22, 2.98647394442484e-22, 3.29155817689778e-22, 3.62744931340731e-22,
- 3.99722120572624e-22, 4.40425064223392e-22, 4.85224682392038e-22, 5.34528367069058e-22, 5.88783522602465e-22,
- 6.48481445307726e-22, 7.14161574262827e-22, 7.86416148313604e-22, 8.65895307572446e-22, 9.53312681249342e-22,
- 1.04945150753626e-21, 1.15517133550207e-21, 1.27141536357825e-21, 1.39921847426015e-21, 1.53971603015202e-21,
- 1.69415350248814e-21, 1.86389700981111e-21, 2.05044485163175e-21, 2.25544012968370e-21, 2.48068455788088e-21,
- 2.72815357134612e-21, 3.00001285497641e-21, 3.29863642301526e-21, 3.62662639309896e-21, 3.98683461131598e-21,
- 4.38238629906651e-21, 4.81670590802906e-21, 5.29354538645474e-21, 5.81701507843054e-21, 6.39161749781974e-21,
- 7.02228424044163e-21, 7.71441632185196e-21, 8.4739282539989e-21, 9.30729620224586e-21, 1.02216105949631e-20,
- 1.12246335913280e-20, 1.23248618493586e-20, 1.35315950758093e-20, 1.48550108826456e-20, 1.63062465217032e-20,
- 1.78974881201405e-20, 1.96420680947798e-20, 2.15545714837844e-20, 2.36509519997439e-20, 2.59486586796199e-20,
- 2.84667740846022e-20, 3.12261650872937e-20, 3.42496473753623e-20, 3.75621649004811e-20, 4.1190985609727e-20,
- 4.51659149143546e-20, 4.95195284787818e-20, 5.42874260516386e-20, 5.95085082117206e-20, 6.52252780657133e-20,
- 7.1484170112697e-20, 7.83359086839063e-20, 8.5835898576284e-20, 9.4044650726485e-20, 1.03028246019560e-19,
- 1.12858840595384e-19, 1.23615216307614e-19, 1.35383380306580e-19, 1.48257218061103e-19, 1.62339204507009e-19,
- 1.77741178414554e-19, 1.94585185505699e-19, 2.13004396328083e-19, 2.33144105408587e-19, 2.55162818769100e-19,
- 2.79233437493965e-19, 3.05544545696482e-19, 3.34301811945149e-19, 3.65729513983357e-19, 4.00072197414327e-19,
- 4.37596479930904e-19, 4.78593013653989e-19, 5.23378619209301e-19, 5.7229860632712e-19, 6.25729297000645e-19,
- 6.84080768593555e-19, 7.47799835754742e-19, 8.1737329158706e-19, 8.93331430237564e-19, 9.76251874938821e-19,
- 1.06676373754749e-18, 1.16555213780823e-18, 1.27336311293298e-18, 1.39100895064098e-18, 1.51937398157053e-18,
- 1.65942086996478e-18, 1.81219744477020e-18, 1.97884411678722e-18, 2.16060193129749e-18, 2.35882130968722e-18,
- 2.57497153801189e-18, 2.81065106523422e-18, 3.06759867904084e-18, 3.34770563273514e-18, 3.65302880274925e-18,
- 3.98580496284818e-18, 4.34846626815861e-18, 4.74365704977974e-18, 5.17425202897168e-18, 5.64337606881557e-18,
- 6.15442559085038e-18, 6.71109179457108e-18, 7.31738582887958e-18, 7.97766607668324e-18, 8.69666772689607e-18,
- 9.47953482220332e-18, 1.03318549861686e-17, 1.12596970496900e-17, 1.22696518145366e-17, 1.33688762108225e-17,
- 1.45651411259094e-17, 1.58668832044827e-17, 1.72832609435602e-17, 1.88242154320746e-17, 2.05005361125985e-17,
- 2.23239319728804e-17, 2.43071086073182e-17, 2.64638516234818e-17, 2.88091169065084e-17, 3.13591282948427e-17,
- 3.41314832645815e-17, 3.71452672668869e-17, 4.04211774137699e-17, 4.39816562623235e-17, 4.78510365064786e-17,
- 5.20556974489026e-17, 5.66242341940844e-17, 6.15876405773299e-17, 6.69795069237318e-17, 7.2836233816555e-17,
- 7.91972631464248e-17, 8.61053278116287e-17, 9.36067215463159e-17, 1.01751590467945e-16, 1.10594248058595e-16,
- 1.20193515427359e-16, 1.30613088843666e-16, 1.41921936684837e-16, 1.54194728106090e-16, 1.67512295918692e-16,
- 1.81962136352663e-16, 1.97638948585499e-16, 2.14645217138836e-16, 2.33091840481832e-16, 2.5309880943477e-16,
- 2.74795939239823e-16, 2.98323659460026e-16, 3.23833866183229e-16, 3.51490841347056e-16, 3.81472244365282e-16,
- 4.13970181627315e-16, 4.49192359862693e-16, 4.87363329813632e-16, 5.28725827143121e-16, 5.73542218025806e-16,
- 6.22096057427178e-16, 6.74693768675356e-16, 7.31666453572489e-16, 7.93371842982395e-16, 8.60196398570778e-16,
- 9.32557577168123e-16, 1.01090627007634e-15, 1.09572943055325e-15, 1.18755290368805e-15, 1.28694447393013e-15,
- 1.39451714665926e-15, 1.51093268139136e-15, 1.63690539550678e-15, 1.77320625877395e-15, 1.92066730042609e-15,
- 2.08018635213939e-15, 2.25273215196613e-15, 2.43934983610145e-15, 2.64116684731894e-15, 2.85939929100417e-15,
- 3.0953587719587e-15, 3.35045974754833e-15, 3.62622743534104e-15, 3.92430631613157e-15, 4.24646927619696e-15,
- 4.59462743577860e-15, 4.97084071416196e-15, 5.37732918533406e-15, 5.81648528206159e-15, 6.29088691036376e-15,
- 6.80331154077401e-15, 7.35675134750924e-15, 7.9544294717215e-15, 8.59981749040868e-15, 9.29665417833992e-15,
- 1.00489656565263e-14, 1.08610870273690e-14, 1.17376856036716e-14, 1.26837858462427e-14, 1.37047961328694e-14,
- 1.48065374900481e-14, 1.59952744280531e-14, 1.72777480297408e-14, 1.86612114539743e-14, 2.01534680257531e-14,
- 2.17629120970858e-14, 2.34985728754111e-14, 2.53701614299986e-14, 2.73881211013013e-14, 2.95636815537589e-14,
- 3.19089167291090e-14, 3.44368069749374e-14, 3.71613056420548e-14, 4.00974104643949e-14, 4.32612400565811e-14,
- 4.66701158871906e-14, 5.03426501101292e-14, 5.42988396625522e-14, 5.85601670654849e-14, 6.3149708392861e-14,
- 6.80922489062002e-14, 7.34144068857165e-14, 7.91447662244323e-14, 8.53140183899803e-14, 9.19551143994013e-14,
- 9.91034274954757e-14, 1.0679692725923e-13, 1.15076365942292e-13, 1.23985477855031e-13, 1.33571192702046e-13,
- 1.43883863815759e-13, 1.54977512301920e-13, 1.66910088177930e-13, 1.79743749656217e-13, 1.93545161800965e-13,
- 2.08385815867207e-13, 2.24342370717358e-13, 2.41497017801669e-13, 2.59937871286364e-13, 2.79759385016643e-13,
- 3.01062798111745e-13, 3.23956611106135e-13, 3.48557094675241e-13, 3.7498883311623e-13, 4.03385304894755e-13,
- 4.33889502717806e-13, 4.66654595751316e-13, 5.01844636769645e-13, 5.3963531720292e-13, 5.80214773238327e-13,
- 6.23784446333159e-13, 6.70560001711864e-13, 7.20772308646748e-13, 7.74668486563648e-13, 8.32513021270262e-13,
- 8.94588955876992e-13, 9.6119916126894e-13, 1.03266769129427e-12, 1.10934122815914e-12, 1.19159062386450e-12,
- 1.27981254388584e-12, 1.37443121968512e-12, 1.47590031705553e-12, 1.58470492773607e-12, 1.70136369219568e-12,
- 1.82643106197697e-12, 1.96049971050927e-12, 2.10420310185185e-12, 2.25821822741171e-12, 2.42326852129899e-12,
- 2.60012696563817e-12, 2.78961939784764e-12, 2.99262803263505e-12, 3.21009521223458e-12, 3.44302739923701e-12,
- 3.69249942723561e-12, 3.95965902543588e-12, 4.24573163435442e-12, 4.55202553076802e-12, 4.8799372811693e-12,
- 5.23095754414459e-12, 5.60667724331564e-12, 6.00879413378503e-12, 6.43911978639591e-12, 6.89958701556968e-12,
- 7.39225777801782e-12, 7.91933157124842e-12, 8.48315436250203e-12, 9.08622808056533e-12, 9.7312207048268e-12,
- 1.04209769879652e-11, 1.11585298507993e-11, 1.19471124900909e-11, 1.27901712424794e-11, 1.36913792502502e-11,
- 1.46546509773028e-11, 1.56841576264994e-11, 1.67843435125431e-11, 1.79599434476731e-11, 1.92160012007750e-11,
- 2.05578890939952e-11, 2.19913288046425e-11, 2.35224134440417e-11, 2.51576309891186e-11, 2.69038891468201e-11,
- 2.87685417360433e-11, 3.07594166765647e-11, 3.28848456795426e-11, 3.51536957395174e-11, 3.75754025334884e-11,
- 4.01600058385912e-11, 4.29181870861797e-11, 4.58613091767249e-11, 4.90014586869096e-11, 5.23514906076399e-11,
- 5.59250757594271e-11, 5.97367510397311e-11, 6.38019726654473e-11, 6.81371725827341e-11, 7.27598182259036e-11,
- 7.76884758170981e-11, 8.29428774090212e-11, 8.85439918840776e-11, 9.45141001349502e-11, 1.00876874663930e-10,
- 1.07657463851216e-10, 1.14882581156030e-10, 1.22580599528633e-10, 1.30781651326424e-10, 1.39517734043067e-10,
- 1.48822822176231e-10, 1.58732985576987e-10, 1.69286514642305e-10, 1.80524052731342e-10, 1.92488736206550e-10,
- 2.05226342521894e-10, 2.18785446802903e-10, 2.33217587386751e-10, 2.48577440815301e-10, 2.6492300679994e-10,
- 2.82315803704329e-10, 3.00821075119684e-10, 3.20508008137342e-10, 3.41449963954737e-10, 3.63724721484069e-10,
- 3.87414734667567e-10, 4.12607404239677e-10, 4.3939536471467e-10, 4.67876787418161e-10, 4.98155700423128e-10,
- 5.30342326294884e-10, 5.64553438595807e-10, 6.00912738148843e-10, 6.39551250109663e-10, 6.80607742950414e-10,
- 7.24229170513764e-10, 7.70571138354246e-10, 8.19798395645136e-10, 8.72085353992974e-10, 9.27616634569113e-10,
- 9.86587645037698e-10, 1.04920518783315e-09, 1.11568810141717e-09, 1.18626793622573e-09, 1.26118966710109e-09,
- 1.34071244409187e-09, 1.42511038359657e-09, 1.51467340192265e-09, 1.60970809343425e-09, 1.71053865556700e-09,
- 1.81750786309943e-09, 1.93097809418531e-09, 2.05133241077260e-09, 2.17897569616056e-09, 2.31433585257856e-09,
- 2.45786506180803e-09, 2.61004111201292e-09, 2.77136879409463e-09, 2.94238137104436e-09, 3.12364212393002e-09,
- 3.31574597832617e-09, 3.51932121517463e-09, 3.73503127024975e-09, 3.96357662659765e-09, 4.20569680452203e-09,
- 4.46217245390161e-09, 4.73382755384558e-09, 5.02153172492455e-09, 5.3262026594555e-09, 5.64880867557094e-09,
- 5.99037140106353e-09, 6.35196859327198e-09, 6.73473710155753e-09, 7.13987597921841e-09, 7.56864975199771e-09,
- 8.02239185066354e-09, 8.50250821547506e-09, 9.01048108069906e-09, 9.54787294770427e-09, 1.01163307555414e-08,
- 1.07175902583109e-08, 1.13534806190322e-08, 1.20259292301549e-08, 1.27369667712999e-08, 1.34887325152785e-08,
- 1.42834798939228e-08, 1.51235823357610e-08, 1.60115393880909e-08, 1.69499831365509e-08, 1.79416849358471e-08,
- 1.89895624658877e-08, 2.00966871281765e-08, 2.12662917979592e-08, 2.25017789482686e-08, 2.38067291627004e-08,
- 2.51849100544611e-08, 2.66402856099673e-08, 2.81770259760399e-08, 2.97995177105363e-08, 3.15123745170822e-08,
- 3.33204484854287e-08, 3.5228841859843e-08, 3.72429193588712e-08, 3.93683210707590e-08, 4.16109759498197e-08,
- 4.3977115940059e-08, 4.64732907534413e-08, 4.91063833312853e-08, 5.18836260184242e-08, 5.48126174809566e-08,
- 5.79013403996459e-08, 6.1158179972306e-08, 6.4591943259825e-08, 6.82118794118624e-08, 7.20277008096596e-08,
- 7.60496051648871e-08, 8.02882986149588e-08, 8.47550198568288e-08, 8.94615653629075e-08, 9.44203157244297e-08,
- 9.96442631693347e-08, 1.05147040303541e-07, 1.10942950126346e-07, 1.17046997372632e-07, 1.23474921236516e-07,
- 1.30243229533202e-07, 1.37369234357842e-07, 1.44871089302508e-07, 1.52767828294566e-07, 1.61079406122137e-07,
- 1.6982674071476e-07, 1.79031757249834e-07, 1.8871743415806e-07, 1.98907851103713e-07, 2.09628239018370e-07,
- 2.20905032269544e-07, 2.327659230486e-07, 2.4523991806537e-07, 2.58357397639973e-07, 2.72150177285582e-07,
- 2.86651571879194e-07, 3.01896462520848e-07, 3.17921366185283e-07, 3.34764508273617e-07, 3.52465898176424e-07,
- 3.71067407963333e-07, 3.90612854318327e-07, 4.11148083843931e-07, 4.32721061861702e-07, 4.55381964840732e-07,
- 4.79183276590321e-07, 5.04179888357536e-07, 5.30429202975094e-07, 5.57991243209782e-07, 5.86928764466638e-07,
- 6.17307372009198e-07, 6.49195642861335e-07, 6.82665252561663e-07, 7.177911069469e-07, 7.54651479146372e-07,
- 7.93328151975595e-07, 8.3390656592291e-07, 8.76475972929203e-07, 9.21129596167143e-07, 9.67964796032733e-07,
- 1.01708324256870e-06, 1.06859109454593e-06, 1.12259918543618e-06, 1.17922321651640e-06, 1.23858395735247e-06,
- 1.30080745391728e-06, 1.36602524460614e-06, 1.43437458442013e-06, 1.50599867759616e-06, 1.58104691897051e-06,
- 1.65967514437147e-06, 1.74204589034466e-06, 1.82832866352416e-06, 1.91870021997090e-06, 2.01334485480934e-06,
- 2.11245470250285e-06, 2.21623004811754e-06, 2.32487964993441e-06, 2.43862107377942e-06, 2.55768103945153e-06,
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- 0.999516575857616, 0.999533520143892, 0.999549912759408, 0.999565770079618, 0.99958110805055,
- 0.999595942198136, 0.999610287637418, 0.9996241590816, 0.999637570850967, 0.999650536881662,
- 0.999663070734323, 0.99967518560258, 0.999686894321419, 0.999698209375391, 0.99970914290671,
- 0.999719706723184, 0.999729912306036, 0.999739770817572, 0.99974929310872, 0.999758489726432,
- 0.999767370920964, 0.999775946653009, 0.999784226600705, 0.99979222016652, 0.999799936483993,
- 0.999807384424364, 0.999814572603067, 0.999821509386095, 0.999828202896254, 0.99983466101928,
- 0.999840891409842, 0.999846901497426, 0.999852698492093, 0.999858289390124, 0.999863680979554,
- 0.99986887984558, 0.999873892375862, 0.999878724765715, 0.999883383023185, 0.999887872974018,
- 0.999892200266523, 0.999896370376326, 0.999900388611024, 0.99990426011473, 0.999907989872526,
- 0.9999115827148, 0.999915043321502, 0.999918376226297, 0.999921585820616, 0.999924676357621,
- 0.999927651956075, 0.99993051660412, 0.99993327416297, 0.999935928370511, 0.999938482844817,
- 0.999940941087581, 0.999943306487466, 0.999945582323366, 0.999947771767598, 0.999949877889004,
- 0.999951903655982, 0.999953851939444, 0.999955725515688, 0.999957527069211, 0.99995925919544,
- 0.999960924403402, 0.99996252511831, 0.999964063684097, 0.999965542365885, 0.99996696335237,
- 0.999968328758167, 0.999969640626073, 0.999970900929288, 0.99997211157356, 0.99997327439928,
- 0.999974391183526, 0.999975463642034, 0.999976493431131, 0.999977482149611, 0.999978431340552,
- 0.999979342493088, 0.999980217044132, 0.99998105638005, 0.999981861838282, 0.999982634708926,
- 0.99998337623627, 0.99998408762028, 0.999984770018052, 0.99998542454521, 0.999986052277273,
- 0.999986654250984, 0.999987231465586, 0.999987784884075, 0.999988315434405, 0.999988824010668,
- 0.999989311474225, 0.999989778654816, 0.999990226351627, 0.99999065533433, 0.999991066344087,
- 0.999991460094529, 0.999991837272697, 0.999992198539962, 0.999992544532909, 0.999992875864198,
- 0.9999931931234, 0.9999934968778, 0.999993787673173, 0.999994066034554, 0.999994332466958,
- 0.999994587456092, 0.999994831469043, 0.999995064954938, 0.999995288345588, 0.999995502056111,
- 0.99999570648553, 0.999995902017353, 0.99999608902014, 0.99999626784804, 0.99999643884132,
- 0.999996602326875, 0.999996758618713, 0.999996908018431, 0.999997050815677, 0.999997187288588,
- 0.99999731770422, 0.99999744231896, 0.999997561378926, 0.99999767512035, 0.999997783769952,
- 0.999997887545298, 0.999997986655145, 0.99999808129978, 0.999998171671336, 0.99999825795411,
- 0.999998340324856, 0.99999841895308, 0.999998494001322, 0.999998565625416, 0.999998633974755,
- 0.999998699192546, 0.999998761416043, 0.999998820776783, 0.999998877400815, 0.999998931408906,
- 0.999998982916757, 0.999999032035204, 0.999999078870404, 0.999999123524027, 0.999999166093434,
- 0.999999206671848, 0.99999924534852, 0.999999282208893, 0.999999317334747, 0.999999350804357,
- 0.999999382692628, 0.999999413071236, 0.999999442008757, 0.999999469570797, 0.999999495820112,
- 0.999999520816723, 0.999999544618035, 0.999999567278938, 0.999999588851916, 0.999999609387146,
- 0.999999628932592, 0.999999647534102, 0.999999665235492, 0.999999682078634, 0.999999698103538,
- 0.999999713348428, 0.999999727849823, 0.999999741642602, 0.999999754760082, 0.999999767234077,
- 0.999999779094968, 0.999999790371761, 0.99999980109215, 0.999999811282566, 0.999999820968243,
- 0.99999983017326, 0.999999838920594, 0.999999847232172, 0.99999985512891, 0.999999862630766,
- 0.99999986975677, 0.999999876525079, 0.999999882953003, 0.99999988905705, 0.99999989485296,
- 0.999999900355737, 0.999999905579684, 0.999999910538435, 0.99999991524498, 0.999999919711701,
- 0.999999923950395, 0.9999999279723, 0.99999993178812, 0.999999935408057, 0.99999993884182,
- 0.99999994209866, 0.999999945187383, 0.999999948116374, 0.999999950893617, 0.99999995352671,
- 0.999999956022884, 0.999999958389024, 0.99999996063168, 0.99999996275708, 0.999999964771158,
- 0.999999966679551, 0.999999968487626, 0.999999970200482, 0.999999971822974, 0.999999973359714,
- 0.99999997481509, 0.99999997619327, 0.999999977498221, 0.999999978733708, 0.999999979903313,
- 0.999999981010438, 0.999999982058315, 0.999999983050017, 0.99999998398846, 0.999999984876418,
- 0.99999998571652, 0.999999986511268, 0.999999987263033, 0.99999998797407, 0.99999998864652,
- 0.99999998928241, 0.99999998988367, 0.999999990452127, 0.999999990989519, 0.999999991497492,
- 0.999999991977608, 0.99999999243135, 0.999999992860124, 0.999999993265263, 0.999999993648031,
- 0.999999994009629, 0.99999999435119, 0.999999994673797, 0.999999994978468, 0.999999995266172,
- 0.999999995537828, 0.999999995794303, 0.999999996036423, 0.999999996264969, 0.999999996480679,
- 0.999999996684254, 0.999999996876358, 0.999999997057619, 0.999999997228631, 0.99999999738996,
- 0.999999997542135, 0.999999997685664, 0.999999997821024, 0.999999997948668, 0.999999998069022,
- 0.999999998182492, 0.999999998289461, 0.999999998390292, 0.999999998485327, 0.99999999857489,
- 0.999999998659288, 0.99999999873881, 0.999999998813732, 0.999999998884312, 0.999999998950795,
- 0.999999999013412, 0.999999999072383, 0.999999999127915, 0.999999999180202, 0.999999999229429,
- 0.99999999927577, 0.999999999319392, 0.99999999936045, 0.999999999399087, 0.999999999435447,
- 0.999999999469658, 0.999999999501844, 0.999999999532123, 0.999999999560605, 0.999999999587393,
- 0.999999999612585, 0.999999999636275, 0.99999999965855, 0.999999999679492, 0.99999999969918,
- 0.999999999717684, 0.999999999735077, 0.999999999751423, 0.999999999766782, 0.999999999781215,
- 0.999999999794774, 0.999999999807511, 0.999999999819476, 0.999999999830714, 0.999999999841267,
- 0.999999999851177, 0.999999999860482, 0.999999999869218, 0.99999999987742, 0.999999999885117,
- 0.999999999892343, 0.999999999899123, 0.999999999905486, 0.999999999911456, 0.999999999917057,
- 0.999999999922311, 0.99999999992724, 0.999999999931863, 0.999999999936198, 0.999999999940263,
- 0.999999999944075, 0.999999999947649, 0.999999999950999, 0.999999999954139, 0.999999999957082,
- 0.99999999995984, 0.999999999962425, 0.999999999964846, 0.999999999967115, 0.99999999996924,
- 0.999999999971231, 0.999999999973096, 0.999999999974842, 0.999999999976478, 0.999999999978009,
- 0.999999999979442, 0.999999999980784, 0.99999999998204, 0.999999999983216, 0.999999999984316,
- 0.999999999985345, 0.999999999986309, 0.99999999998721, 0.999999999988053, 0.999999999988841,
- 0.999999999989579, 0.999999999990269, 0.999999999990914, 0.999999999991517, 0.99999999999208,
- 0.999999999992608, 0.9999999999931, 0.99999999999356, 0.999999999993991, 0.999999999994393,
- 0.99999999999477, 0.99999999999512, 0.999999999995448, 0.999999999995754, 0.99999999999604,
- 0.999999999996308, 0.999999999996557, 0.99999999999679, 0.999999999997007, 0.99999999999721,
- 0.9999999999974, 0.999999999997577, 0.999999999997742, 0.999999999997896, 0.99999999999804,
- 0.999999999998174, 0.999999999998299, 0.999999999998415, 0.999999999998524, 0.999999999998626,
- 0.99999999999872, 0.999999999998808, 0.99999999999889, 0.999999999998967, 0.999999999999039,
- 0.999999999999105, 0.999999999999167, 0.999999999999225, 0.99999999999928, 0.99999999999933,
- 0.999999999999376, 0.99999999999942, 0.99999999999946, 0.999999999999498, 0.999999999999533,
- 0.999999999999566, 0.999999999999597, 0.999999999999625, 0.999999999999651, 0.999999999999676,
- 0.999999999999699, 0.99999999999972, 0.99999999999974, 0.999999999999759, 0.999999999999776,
- 0.999999999999792, 0.999999999999806, 0.99999999999982, 0.999999999999833, 0.999999999999845,
- 0.999999999999856, 0.999999999999866, 0.999999999999876, 0.999999999999885, 0.999999999999893,
- 0.9999999999999, 0.999999999999908, 0.999999999999915, 0.99999999999992, 0.999999999999927,
- 0.999999999999932, 0.999999999999937, 0.999999999999941, 0.999999999999946, 0.99999999999995,
- 0.999999999999953, 0.999999999999957, 0.99999999999996, 0.999999999999963, 0.999999999999966,
- 0.999999999999968, 0.99999999999997, 0.999999999999973, 0.999999999999975, 0.999999999999976,
- 0.999999999999978, 0.99999999999998, 0.999999999999981, 0.999999999999983, 0.999999999999984,
- 0.999999999999985, 0.999999999999986, 0.999999999999987, 0.999999999999988, 0.99999999999999,
- 0.99999999999999, 0.99999999999999, 0.999999999999991, 0.999999999999992, 0.999999999999993,
- 0.999999999999993, 0.999999999999994, 0.999999999999994, 0.999999999999995, 0.999999999999995,
- 0.999999999999995, 0.999999999999996, 0.999999999999996, 0.999999999999996, 0.999999999999997,
- 0.999999999999997, 0.999999999999997, 0.999999999999997, 0.999999999999998, 0.999999999999998,
- 0.999999999999998, 0.999999999999998, 0.999999999999998, 0.999999999999998, 0.999999999999998,
- 0.999999999999999, 0.999999999999999, 0.999999999999999, 0.999999999999999, 0.999999999999999,
- 1, 1, 1, 1, 1,
- 1, 1, 1, 1, 1,
- 1, 1, 1, 1, 1,
- 1, 1, 1, 1, 1,
- 1, 1, 1, 1, 1,
- 1, 1, 1, 1, 1,
- 1, 1, 1, 1, 1,
- 1, 1, 1, 1, 1,
- 1, 1, 1, 1, 1,
- 1, 1, 1, 1, 1,
- 1, 1, 1, 1, 1,
- 1, 1, 1, 1, 1,
- 1, 1, 1, 1, 1,
- 1, 1, 1, 1, 1,
- 1, 1, 1, 1, 1,
- 1, 1, 1, 1, 1,
- 1, 1, 1, 1, 1,
- 1, 1, 1, 1, 1,
- 1, 1, 1, 1, 1,
- 1, 1, 1, 1, 1,
- 1, 1, 1, 1, 1,
- 1, 1, 1, 1, 1,
- 1, 1, 1, 1, 1,
- 1, 1, 1, 1, 1,
- 1, 1, 1, 1, 1,
- 1, 1, 1, 1, 1,
- 1, 1, 1, 1, 1,
- 1, 1, 1, 1, 1,
- 1, 1, 1, 1, 1,
- 1, 1, 1, 1, 1,
- 1, 1, 1, 1, 1,
- 1, 1, 1, 1, 1,
- 1, 1, 1, 1, 1,
- 1, 1, 1, 1, 1,
- 1, 1, 1, 1, 1,
- 1, 1, 1, 1, 1,
- 1, 1, 1, 1, 1,
- 1, 1, 1, 1, 1,
- 1, 1, 1, 1, 1,
- 1, 1, 1, 1, 1,
- 1, 1, 1, 1, 1,
-};
-
-// Normal cumulative distribution function
-float NormalCDF(float mu, float sigmaSq, float x);
-
-// Poisson cumulative distribution function
-float PoissonCDF(float lambda, int a, int b);
-
-// Poisson cumulative distribution function
-float PoissonCDF(float lambda, int a);
-
-#endif
diff --git a/libcpp/alignment/statistics/pdfs.cpp b/libcpp/alignment/statistics/pdfs.cpp
deleted file mode 100644
index 1e066d1..0000000
--- a/libcpp/alignment/statistics/pdfs.cpp
+++ /dev/null
@@ -1,36 +0,0 @@
-#include "pdfs.hpp"
-
-float Binomial(float p, int x, int n) {
- return pow(p,n) * pow(1-p,x-n) * Choose(x,n);
-}
-
-float Poisson(float lambda, int n) {
- if (n < FactorialTableLength) {
- float lambdaToN = pow(lambda, n);
- if (lambdaToN == HUGE_VALF)
- return 1;
- return (pow(lambda, n) * exp(-lambda)) / FactorialTable[n];
- }
- else {
- return 0;
- }
-}
-
-float Gamma(float lambda, float t, int n) {
- if (n <= FactorialTableLength) {
- return (pow(lambda, n) * pow(t,n-1) * exp(-lambda*t)) / FactorialTable[n-1];
- }
- else {
- return 0;
- }
-}
-
-float Exponential(float lambda, int t) {
- return lambda * exp(-lambda*t);
-}
-
-float Normal(float mu, float sigma, float x) {
- assert(0);
- return 0;
-}
-
diff --git a/libcpp/alignment/statistics/pdfs.hpp b/libcpp/alignment/statistics/pdfs.hpp
deleted file mode 100644
index 5f760c6..0000000
--- a/libcpp/alignment/statistics/pdfs.hpp
+++ /dev/null
@@ -1,18 +0,0 @@
-#ifndef _BLASR_PDFS_HPP_
-#define _BLASR_PDFS_HPP_
-
-#include <math.h>
-#include <assert.h>
-#include "StatUtils.hpp"
-
-float Binomial(float p, int x, int n);
-
-float Poisson(float lambda, int n);
-
-float Gamma(float lambda, float t, int n);
-
-float Exponential(float lambda, int t);
-
-float Normal(float mu, float sigma, float x);
-
-#endif
diff --git a/libcpp/alignment/suffixarray/LCPTable.hpp b/libcpp/alignment/suffixarray/LCPTable.hpp
deleted file mode 100644
index 85037f2..0000000
--- a/libcpp/alignment/suffixarray/LCPTable.hpp
+++ /dev/null
@@ -1,182 +0,0 @@
-#ifndef _BLASR_LCP_TABLE_HPP_
-#define _BLASR_LCP_TABLE_HPP_
-
-#include <map>
-#include <fstream>
-
-template <typename T>
-class LCPTable {
- //
- // Change the following TWO type defs if
- // the max LCP is changed.
- //
- typedef short SignedPrefixLength;
- typedef unsigned short PrefixLength;
- typedef std::map<int, int> LongPrefixMap;
- PrefixLength maxPrefixLength;
- LongPrefixMap llongPrefixMap, rlongPrefixMap;
- int tableLength;
- public:
- PrefixLength *llcp, *rlcp;
- LCPTable() {
- tableLength =0;
- llcp = rlcp = NULL;
- }
-
- LCPTable(T* data, unsigned int pTableLength) {
- Init(data, pTableLength);
- }
-
- inline int LengthLongestCommonPrefix(T* a, int alen, T* b, int blen) {
- int i;
- for (i = 0 ; i < alen and i < blen; i++ )
- if (a[i] != b[i])
- break;
- return i;
- }
-
- void Init(T* data, unsigned int pTableLength, unsigned int *index) {
- tableLength = pTableLength;
- maxPrefixLength = (PrefixLength) (SignedPrefixLength(-1));
- llcp = new PrefixLength[tableLength];
- rlcp = new PrefixLength[tableLength];
- std::fill(llcp, llcp + tableLength, 0);
- std::fill(rlcp, rlcp + tableLength, 0);
- FillTable(data, index);
- }
-
- int SetL(int index, int length) {
- assert(index >= 0);
- assert(index < tableLength);
- if (index >= maxPrefixLength) {
- llcp[index] = maxPrefixLength;
- llongPrefixMap[index] = length;
- }
- else {
- llcp[index] = length;
- }
- return llcp[index];
- }
-
- int SetR(int index, int length) {
- assert(index >= 0);
- assert(index < tableLength);
- if (index >= maxPrefixLength) {
- rlcp[index] = maxPrefixLength;
- rlongPrefixMap[index] = length;
- }
- else {
- rlcp[index] = length;
- }
- return rlcp[index];
- }
-
-
- int GetL(int index) {
- if (llcp[index] == maxPrefixLength) {
- assert(llongPrefixMap.find(index) != llongPrefixMap.end());
- return llongPrefixMap[index];
- }
- else {
- return llcp[index];
- }
- }
-
- int GetR(int index) {
- if (rlcp[index] == maxPrefixLength) {
- assert(rlongPrefixMap.find(index) != llongPrefixMap.end());
- return rlongPrefixMap[index];
- }
- else {
- return rlcp[index];
- }
- }
-
-
- ~LCPTable() {
- /*
- if (llcp != NULL)
- delete[] llcp;
- llcp = NULL;
- if (rlcp != NULL)
- delete[] rlcp;
- rlcp = NULL;
- */
- // the two maps automatically go away.
- }
-
- void WriteLCPTable(std::ofstream &out) {
- out.write((char*) &tableLength, sizeof(tableLength));
- out.write((char*) llcp, sizeof(PrefixLength)*tableLength);
- out.write((char*) rlcp, sizeof(PrefixLength)*tableLength);
- typename LongPrefixMap::iterator llcpTableIt, llcpTableEnd;
- int llongPrefixMapSize = llongPrefixMap.size();
- out.write((char*) &llongPrefixMapSize, sizeof(llongPrefixMapSize));
- for((llcpTableIt = llongPrefixMap.begin(),
- llcpTableEnd = llongPrefixMap.end());
- llcpTableIt != llcpTableEnd;
- ++llcpTableIt) {
- out.write((char*) &llcpTableIt->first, sizeof(typename LongPrefixMap::key_type));
- out.write((char*) &llcpTableIt->second, sizeof(typename LongPrefixMap::mapped_type));
- }
- typename LongPrefixMap::iterator rlcpTableIt, rlcpTableEnd;
- int rlongPrefixMapSize = rlongPrefixMap.size();
- out.write((char*) &rlongPrefixMapSize, sizeof(rlongPrefixMapSize));
- for((rlcpTableIt = rlongPrefixMap.begin(),
- rlcpTableEnd = rlongPrefixMap.end());
- rlcpTableIt != rlcpTableEnd;
- ++rlcpTableIt) {
- out.write((char*) &rlcpTableIt->first, sizeof(typename LongPrefixMap::key_type));
- out.write((char*) &rlcpTableIt->second, sizeof(typename LongPrefixMap::mapped_type));
- }
- }
-
- void ReadLCPTables(std::ifstream &in) {
- in.read((char*) &tableLength, sizeof(tableLength));
- in.read((char*) &llcp, sizeof(PrefixLength)*tableLength);
- in.read((char*) &rlcp, sizeof(PrefixLength)*tableLength);
- int longPrefixMapSize;
- in.read((char*) &longPrefixMapSize, sizeof(longPrefixMapSize));
- int i;
- int index, lcpLength;
- // The rest is stored as a tree, but read and construct this on the fly.
- for (i = 0; i < longPrefixMapSize; i++) {
- in.read((char*) &index, sizeof(index));
- in.read((char*) &lcpLength, sizeof(lcpLength));
- llongPrefixMap[index] = lcpLength;
- }
-
- // Read the rlcp
- in.read((char*) &longPrefixMapSize, sizeof(longPrefixMapSize));
- for (i = 0; i < longPrefixMapSize; i++) {
- in.read((char*) &index, sizeof(index));
- in.read((char*) &lcpLength, sizeof(lcpLength));
- rlongPrefixMap[index] = lcpLength;
- }
- }
-
-
- void FillTable(T* data, unsigned int *index) {
- //
- // This assumes that the index table is now in sorted order.
- //
- FillTable(0, tableLength, data, index);
- }
-
- void FillTable(unsigned int low, unsigned int high, T* data, unsigned int *index) {
- if (low == high)
- return;
- unsigned int mid = (low + high) / 2;
- assert (mid != low);
- SetL(mid, LengthLongestCommonPrefix(&data[index[low]], tableLength - index[low],
- &data[index[mid]], tableLength - index[mid]));
- FillTable(low, mid, data, index);
- assert(mid != high);
- SetR(mid, LengthLongestCommonPrefix(&data[index[mid]], tableLength - index[mid],
- &data[index[high]], tableLength - index[high]));
- FillTable(mid+1, high, data, index);
- }
-
-};
-
-#endif // _BLASR_LCP_TABLE_HPP_
diff --git a/libcpp/alignment/suffixarray/SharedSuffixArray.hpp b/libcpp/alignment/suffixarray/SharedSuffixArray.hpp
deleted file mode 100644
index dd31437..0000000
--- a/libcpp/alignment/suffixarray/SharedSuffixArray.hpp
+++ /dev/null
@@ -1,83 +0,0 @@
-#ifndef _BLASR_SHARED_SUFFIX_ARRAY_HPP_
-#define _BLASR_SHARED_SUFFIX_ARRAY_HPP_
-
-#include <stdlib.h>
-#include <fstream>
-#include <sstream>
-#include "SuffixArray.hpp"
-#include "ipc/SharedMemoryAllocator.hpp"
-#include "tuples/DNATuple.hpp"
-#include "tuples/CompressedDNATuple.hpp"
-#include "algorithms/compare/CompareStrings.hpp"
-
-
-template<typename T,
- typename Sigma,
- typename Compare = DefaultCompareStrings<T>,
- typename Tuple = DNATuple >
-class SharedSuffixArray : public SuffixArray<T, Sigma, Compare, Tuple> {
-public:
- std::string shmIdTag;
- SAIndex *indexShared;
- int indexID;
- std::string indexHandle;
- SAIndex *lookupTableShared;
- int lookupTableID;
- std::string lookupTableHandle;
- int lookupPrefixLength;
-
- void InitShmIdTag() {
- std::stringstream tagStrm;
- tagStrm << "_" << getpid();
- shmIdTag = tagStrm.str();
- }
-
-
- void ReadSharedArray(std::ifstream &saIn) {
- std::cout << "reading a shared suffix array index." << std::endl;
- saIn.read((char*) &this->length, sizeof(int));
- indexHandle = "suffixarray.index." + shmIdTag;
- AllocateMappedShare(indexHandle, this->length + 1, indexShared, indexID);
- std::cout << "the shared index is: " << indexShared << std::endl;
- this->index = indexShared;
- std::cout << "the index used is: " << this->index << std::endl;
- this->ReadAllocatedArray(saIn);
- }
-
- void ReadSharedLookupTable(std::ifstream &saIn) {
- this->ReadLookupTableLengths(saIn);
- lookupTableHandle = "suffixarray.lookuptable." + shmIdTag;
- AllocateMappedShare(lookupTableHandle, this->lookupTableLength + 1, lookupTableShared, lookupTableID);
- this->lookupTable = lookupTableShared;
- this->ReadAllocatedLookupTable(saIn);
- }
-
- void ReadShared(std::string &inFileName) {
- std::ifstream saIn;
- InitShmIdTag();
- saIn.open(inFileName.c_str(), std::ios::binary);
- this->ReadComponentList(saIn);
- if (this->componentList[SuffixArray<T,Sigma,Compare,Tuple>::CompArray]) {
- this->ReadSharedArray(saIn);
- }
- if (this->componentList[SuffixArray<T,Sigma,Compare,Tuple>::CompLookupTable]) {
- this->ReadSharedLookupTable(saIn);
- }
- saIn.close();
- }
-
- void FreeShared() {
-
- if (this->componentList[SuffixArray<T,Sigma,Compare,Tuple>::CompArray]) {
- shm_unlink(indexHandle.c_str());
- }
- if (this->componentList[SuffixArray<T,Sigma,Compare,Tuple>::CompLookupTable]) {
- shm_unlink(lookupTableHandle.c_str());
- }
- }
-
-
-};
-
-
-#endif // _BLASR_SHARED_SUFFIX_ARRAY_HPP_
diff --git a/libcpp/alignment/suffixarray/SuffixArray.hpp b/libcpp/alignment/suffixarray/SuffixArray.hpp
deleted file mode 100644
index 907bf1b..0000000
--- a/libcpp/alignment/suffixarray/SuffixArray.hpp
+++ /dev/null
@@ -1,1197 +0,0 @@
-#ifndef _BLASR_SUFFIX_ARRAY_HPP_
-#define _BLASR_SUFFIX_ARRAY_HPP_
-
-#include <string.h>
-#include <assert.h>
-#include <iostream>
-#include <fstream>
-#include <string>
-#include <vector>
-#include "LCPTable.hpp"
-#include "defs.h"
-#include "utils.hpp"
-#include "tuples/DNATuple.hpp"
-#include "tuples/CompressedDNATuple.hpp"
-#include "qvs/QualityValue.hpp"
-#include "DNASequence.hpp"
-#include "NucConversion.hpp"
-#include "algorithms/compare/CompareStrings.hpp"
-#include "algorithms/sorting/qsufsort.hpp"
-#include "algorithms/sorting/LightweightSuffixArray.hpp"
-/*
- * Suffix array implementation, with a Manber and Meyers sort, but
- * that is typically not used.
- *
- */
-
-typedef enum E_SAType {manmy, slow, mcilroy, larsson, kark, mafe, welter} SAType;
-
-template<typename T>
-class CompareSuffixes {
-public:
- T t;
- int refLength;
- CompareSuffixes(T tref, int prefLength) {
- t = tref;
- refLength = prefLength;
- }
- int operator()(int a, int b) {
- int aSufLen = refLength - a;
- int bSufLen = refLength - b;
- int abMinLength = MIN(aSufLen, bSufLen);
- int cmpRes = memcmp(&(t[a]), &(t[b]), abMinLength);
- if (cmpRes == 0) {
- if (aSufLen < bSufLen) {
- return 1;
- }
- else {
- return 0;
- }
- }
- else {
- return cmpRes < 0;
- }
- }
-};
-
-typedef uint32_t SAIndex;
-typedef uint32_t SAIndexLength;
-
-template<typename T,
- typename Sigma,
- typename Compare = DefaultCompareStrings<T>,
- typename Tuple = DNATuple >
-class SuffixArray {
-public:
- SAIndex *index;
- bool deleteStructures;
- T* target;
- SAIndex length;
- SAIndex *startPosTable, *endPosTable;
- SAIndexLength lookupTableLength;
- SAIndex lookupPrefixLength;
- TupleMetrics tm;
- unsigned int magicNumber;
- unsigned int ckMagicNumber;
- typedef Compare CompareType;
- enum Component { CompArray, CompLookupTable, CompLCPTable};
- static const int ComponentListLength = 2;
- static const int FullSearch = -1;
- int componentList[ComponentListLength];
-
- // vector<SAIndex> leftBound, rightBound;
-
- inline int LengthLongestCommonPrefix(T *a, int alen, T *b, int blen) {
- int i;
- for (i = 0 ; i < alen and i < blen; i++ )
- if (a[i] != b[i])
- break;
- return i;
- }
-
- SuffixArray() {
- // Not necessarily using the lookup table.
- // The magic number is linked with a version
- magicNumber = 0xacac0001;
- startPosTable = endPosTable = NULL;
- lookupPrefixLength = 0;
- lookupTableLength = 0;
- deleteStructures = true;
- ckMagicNumber = 0;
- length = 0;
- int i;
- for (i = 0; i < ComponentListLength; i++) {
- componentList[i] = false;
- }
- // Must create a suffix array, but for now make it null.
- target = NULL;
- index = NULL;
- }
- ~SuffixArray() {
- if (deleteStructures == false) {
- //
- // It is possible this class is referencing another structrue. In
- // this case, do not try and delete in the destructor.
- //
- return;
- }
- if (startPosTable != NULL) {
- delete[] startPosTable;
- }
- if (endPosTable != NULL) {
- delete[] endPosTable;
- }
- if (index != NULL) {
- delete[] index;
- }
- }
-
- int StringLessThanEqual(T *a, int aLen, T *b, int bLen) {
- return Compare::LessThanEqual(a, aLen, b, bLen);
- }
-
- int StringEquals(T *a, int aLen, T *b, int bLen) {
- return Compare::Equal(a, aLen, b, bLen);
- }
- int StringLessThan(T *a, int aLen, T *b, int bLen) {
- return Compare::LessThan(a, aLen, b, bLen);
- }
-
- void InitAsciiCharDNAAlphabet(std::vector<int> &dnaAlphabet) {
- int i;
- for (i = 0; i < 127; i++) {
- dnaAlphabet.push_back(i);
- }
- }
-
- void InitTwoBitDNAAlphabet(std::vector<int> &dnaAlphabet) {
- dnaAlphabet.push_back(0);
- dnaAlphabet.push_back(1);
- dnaAlphabet.push_back(2);
- dnaAlphabet.push_back(3);
- }
-
- void InitThreeBitDNAAlphabet(std::vector<int> &dnaAlphabet) {
- //
- // This is initialized to have ACTG-0123, N=4, and EOF=5
- //
- dnaAlphabet.push_back(0);
- dnaAlphabet.push_back(1);
- dnaAlphabet.push_back(2);
- dnaAlphabet.push_back(3);
- dnaAlphabet.push_back(4);
- dnaAlphabet.push_back(5);
- }
-
- void PrintSuffices(T *target, int targetLength, int maxPrintLength) {
- std::string seq;
- seq.resize(maxPrintLength+1);
- SAIndex i, s;
- seq[maxPrintLength] = '\0';
- for (i = 0; i < length; i++) {
- DNALength suffixLength = maxPrintLength;
- if (index[i] + maxPrintLength > length) {
- suffixLength = length - index[i];
- }
- std::cout << index[i] << " " << suffixLength << " ";
- seq.resize(suffixLength);
- for (s = 0; s < suffixLength; s++ ){
- seq[s] = TwoBitToAscii[target[index[i] + s]];
- }
- seq[suffixLength] = '\0';
- std::cout << seq << std::endl;
- }
- }
-
- void BuildLookupTable(T *target, SAIndexLength targetLength, int prefixLengthP) {
-
- //
- // pprefixLength is the length used to lookup the index boundaries
- // given a string.
- //
-
- SAIndexLength i;
- tm.tupleSize = lookupPrefixLength = prefixLengthP;
- tm.InitializeMask();
- lookupTableLength = 1 << (2*lookupPrefixLength);
-
- if (startPosTable) {delete [] startPosTable;}
- startPosTable = ProtectedNew<SAIndex>(lookupTableLength);
-
- if (endPosTable) {delete [] endPosTable;}
- endPosTable = ProtectedNew<SAIndex>(lookupTableLength);
- deleteStructures = true;
-
- Tuple curPrefix, nextPrefix;
- SAIndex tablePrefixIndex = 0;
-
- for (i = 0; i < lookupTableLength; i++) {
- startPosTable[i] = endPosTable[i] = 0;
- }
- i = 0;
- VectorIndex tablePos;
- SAIndex indexPos;
- indexPos = 0;
- do {
- // Advance to the first position that may be translated into a tuple.
- if (targetLength < lookupPrefixLength)
- break;
- while(indexPos < targetLength - lookupPrefixLength + 1 and
- index[indexPos] + lookupPrefixLength > targetLength) {
- indexPos++;
- }
- if (indexPos >= targetLength - lookupPrefixLength + 1) {
- break;
- }
- while (indexPos < targetLength - lookupPrefixLength + 1 and
- curPrefix.FromStringLR((Nucleotide*) &target[index[indexPos]], tm) == 0) {
- ++indexPos;
- }
-
- startPosTable[curPrefix.tuple] = indexPos;
- indexPos++;
- while(indexPos < targetLength - lookupPrefixLength + 1 and
- index[indexPos] + lookupPrefixLength < targetLength) {
- nextPrefix.tuple = 0;
- nextPrefix.FromStringLR((Nucleotide*) &target[index[indexPos]], tm);
- if (nextPrefix.tuple != curPrefix.tuple) {
- break;
- }
- else {
- indexPos++;
- }
- }
- endPosTable[curPrefix.tuple] = indexPos;
- }
- while ((indexPos < targetLength - lookupPrefixLength + 1) and
- (uint32_t(curPrefix.tuple) < uint32_t(lookupTableLength - 1)));
- }
-
- void AllocateSuffixArray(SAIndexLength stringLength) {
- assert(index == NULL or not deleteStructures);
- index = ProtectedNew<SAIndex>(stringLength + 1);
- deleteStructures = true;
- length = stringLength;
- }
-
- void LarssonBuildSuffixArray(T* target, SAIndexLength targetLength, Sigma &alphabet) {
- assert(index == NULL or not deleteStructures);
- index = ProtectedNew<SAIndex>(targetLength+1);
- deleteStructures = true;
- SAIndex *p = ProtectedNew<SAIndex>(targetLength+1);
- SAIndexLength i;
- for (i = 0; i < targetLength; i++) { index[i] = target[i] + 1;}
- SAIndexLength maxVal = 0;
- for (i = 0; i < targetLength; i++) { maxVal = index[i] > maxVal ? index[i] : maxVal;}
- index[targetLength] = 0;
- LarssonSuffixSort<SAIndex, UINT_MAX> sorter;
- sorter(index, p, ((SAIndex) targetLength), ((SAIndex) maxVal+1), (SAIndex) 1 );
- for (i = 0; i < targetLength; i++ ){ index[i] = p[i+1];};
- length = targetLength;
- delete[] p;
- }
-
- void LightweightBuildSuffixArray(T*target, SAIndexLength targetLength, int diffCoverSize=2281) {
- assert(index == NULL or not deleteStructures);
- index = ProtectedNew<SAIndex>(targetLength+1);
- deleteStructures = true;
- length = targetLength;
- DNALength pos;
- for (pos = 0; pos < targetLength; pos++) {
- target[pos]++;
- }
- LightweightSuffixSort(target, targetLength, index, diffCoverSize);
- for (pos = 0; pos < targetLength; pos++) {
- target[pos]--;
- }
-
- }
-
- void MMBuildSuffixArray(T* target, SAIndexLength targetLength, Sigma &alphabet) {
- /*
- * Manber and Myers suffix array construction.
- */
- length = targetLength;
- VectorIndex a;
- std::vector<int> prm;
- std::vector<int> bucket;
- std::vector<int> count;
- // To be changed to bit vectors
- std::vector<bool> bh, b2h;
- bucket.resize(alphabet.size());
-
- prm.resize(targetLength);
- count.resize(targetLength);
- bh.resize(targetLength+1);
- b2h.resize(targetLength+1);
- std::fill(bh.begin(), bh.end(), false);
- std::fill(b2h.begin(), b2h.end(), false);
- std::fill(count.begin(), count.end(), 0);
- assert(index == NULL or not deleteStructures);
- index = ProtectedNew<SAIndex>(targetLength);
- //index = new SAIndex[targetLength];
- deleteStructures = true;
- for (a = 0; a < alphabet.size(); a++ ) {
- bucket[a] = -1;
- }
-
- SAIndexLength i;
- for (i = 0; i < targetLength; i++) {
- index[i] = bucket[target[i]];
- bucket[target[i]] = i;
- }
-
- int j;
- SAIndex c;
- std::fill(prm.begin(), prm.end(), -1);
- //
- // Prepare the buckets.
- //
- c = 0;
- int b;
- for (a = 0; a < alphabet.size(); a++) {
- b = bucket[alphabet[a]]; // position of last suffix starting with 'a'
- while (b != -1) {
- j = index[b];
- prm[b] = c;
- if (b == bucket[a]) {
- bh[c] = true;
- }
- else {
- bh[c] = false;
- }
- c = c + 1;
- b = j;
- }
- }
- b2h[targetLength] = bh[targetLength] = true;
- // fill the index with positions sorted by the first character.
- for (i = 0; i < targetLength; i++) {
- index[prm[i]] = i;
- }
-
- SAIndex h;
- h = 1;
- SAIndex l, r;
-
- while (h < targetLength) {
- // re-order the buckets;
- l = 0;
- int bstart;
- while (l < targetLength) {
- bstart = l;
- r = l + 1;
- count[l] = 0;
- // bh[l] = 0;
- while (bh[r] == false) {r++;} // find the begining of the next bucket.
- while (l < r) {
- assert(l < targetLength);
- prm[index[l]] = bstart;
- l++;
- }
- }
-
- SAIndex d = targetLength - h;
- SAIndex e = prm[d];
-
- /*
- * Phase 1: Set up the buckets in the index and bh list.
- */
-
- //
- // suffix d needs to be moved to the front of it's bucket.
- // d should exist in the bucket starting at prm[d]
- SAIndex i;
-
- l = 0;
- r = 1;
-
- //
- // Move each d that is h backwards up in it's 2h bucket.
- //
-
- d = targetLength - h;
- e = prm[d];
- bh[e] = true; // e is bstart, the beginning of the bucket.
- prm[d] = e + count[e];
- count[e] = count[e] + 1;
- b2h[prm[d]] = true;
-
- for (c = 0; c < targetLength; c++ ){
- // d is T_i
- d = index[c] - h;
- if (index[c] >= h and d < targetLength) {
- e = prm[d];
- prm[d] = e + count[e];
- count[e] = count[e] + 1;
- b2h[prm[d]] = true;
- }
- }
-
-
- //
- // Fix the bucket boundaries.
- //
-
- l = 0;
-
-
- while(l < targetLength) {
-
- // First assign b2h to be 1 on the entire portion of the
- // current bucket (from l ... bh[c]==true).
- for (c = l; c == l or bh[c] == false; c++) {
- d = index[c] - h;
- if (d < targetLength) {
- b2h[prm[d]] = true;
- }
- }
-
- //
- // Mark the start boundaries of the 2h bucket.
- //
- for (c = l; c == l or bh[c] == false; c++) {
- d = index[c] - h;
- if (d < targetLength) {
- if (b2h[prm[d]] == true) {
- j = prm[d] + 1;
- // advance j to the next bucket.
- while (!(bh[j] == true or b2h[j] == false)) {
- j++;
- }
-
- e = j;
- SAIndex f;
- for (f = prm[d] + 1; f <= e - 1; f++) {
- b2h[f] = false;
- }
- }
- }
- }
- l = c;
- }
-
- for (i = 0; i < targetLength; i++) {
- index[prm[i]] = i;
- }
-
- for (i = 0 ; i < targetLength; i++) {
- if (b2h[i] == true and bh[i] == false) {
- bh[i] = b2h[i];
- }
- }
- h <<= 1;
- }
- }
-
- void BuildSuffixArray(T* target, SAIndex targetLength, Sigma &alphabet) {
- length = targetLength;
- assert(index == NULL or not deleteStructures);
- index = ProtectedNew<SAIndex>(length);
- deleteStructures = true;
- CompareSuffixes<T*> cmp(target, length);
- SAIndex i;
- for (i = 0; i < length; i++ ){
- index[i] = i;
- }
- std::sort(index, index + length, cmp);
- }
-
- void WriteArray(std::ofstream &out) {
- out.write((char*) &length, sizeof(int));
- out.write((char*) index, sizeof(int) * (length));
- }
-
- void WriteLookupTable(std::ofstream &out) {
-
- out.write((char*) &lookupTableLength, sizeof(SAIndex));
- out.write((char*) &lookupPrefixLength, sizeof(SAIndex));
- out.write((char*) startPosTable, sizeof(SAIndex) * (lookupTableLength));
- out.write((char*) endPosTable, sizeof(SAIndex) * (lookupTableLength));
- }
-
- void WriteComponentList(std::ofstream &out) {
- //
- // First build the component list.
- //
- if (index != NULL)
- componentList[CompArray] = 1;
- else
- componentList[CompArray] = 0;
-
- if (startPosTable != NULL)
- componentList[CompLookupTable] = 1;
- else
- componentList[CompLookupTable] = 0;
-
- out.write((char*) componentList, sizeof(int) * ComponentListLength);
- }
-
- void WriteLCPTable(std::ofstream &out) {
- std::cout << "NOT YET IMPLEMENTED." << std::endl;
- exit(1);
- }
-
- void Write(std::string &outFileName) {
-
- //
- // The suffix array is written in 2 or more parts:
- // 1 - a preamble listing the components of the
- // array that are written
- // 2 - The components.
- //
- //
- std::ofstream suffixArrayOut;
- suffixArrayOut.open(outFileName.c_str(), std::ios::binary);
- if (!suffixArrayOut.good()) {
- std::cout << "Could not open " << outFileName << std::endl;
- exit(1);
- }
- WriteMagicNumber(suffixArrayOut);
- // write the preamble
- WriteComponentList(suffixArrayOut);
-
- // write the components
- if (componentList[CompArray]) {
- WriteArray(suffixArrayOut);
- }
- if (componentList[CompLookupTable]) {
- WriteLookupTable(suffixArrayOut);
- }
- suffixArrayOut.close();
- }
- void WriteMagicNumber(std::ofstream &out) {
- out.write((char*) &magicNumber, sizeof(int));
- }
-
- int ReadMagicNumber(std::ifstream &in) {
- in.read((char*) &ckMagicNumber, sizeof(int));
- if (ckMagicNumber != magicNumber) {
- return 0;
- }
- else {
- return 1;
- }
- }
-
- void ReadComponentList(std::ifstream &in) {
- in.read((char*) componentList, sizeof(int) * ComponentListLength);
- }
-
- void ReadAllocatedArray(std::ifstream &in) {
- in.read((char*) index, sizeof(int) * length);
- }
-
- void LightReadArray(std::ifstream &in) {
- in.read((char*) &length, sizeof(int));
- // skip the actual array
- in.seekg(length*sizeof(int), std::ios_base::cur);
- }
-
- void ReadArray(std::ifstream &in) {
- in.read((char*) &length, sizeof(int));
- assert(index == NULL or not deleteStructures);
- index = ProtectedNew<SAIndex>(length);
- deleteStructures = true;
- ReadAllocatedArray(in);
- }
-
- void ReadAllocatedLookupTable(std::ifstream &in) {
- in.read((char*) startPosTable, sizeof(int) * (lookupTableLength));
- in.read((char*) endPosTable, sizeof(int) * (lookupTableLength));
- }
-
- void ReadLookupTableLengths(std::ifstream &in) {
- in.read((char*) &lookupTableLength, sizeof(int));
- in.read((char*) &lookupPrefixLength, sizeof(int));
- }
-
- void ReadLookupTable(std::ifstream &in) {
- ReadLookupTableLengths(in);
- tm.Initialize(lookupPrefixLength);
- assert(startPosTable == NULL or not deleteStructures);
- assert(endPosTable == NULL or not deleteStructures);
- startPosTable = ProtectedNew<SAIndex>(lookupTableLength);
- endPosTable = ProtectedNew<SAIndex>(lookupTableLength);
- deleteStructures = true;
- ReadAllocatedLookupTable(in);
- }
-
- void ReadLCPTable(std::ifstream &in) {
- std::cout <<" NOT YET IMPLEMENTED!!!" << std::endl;
- exit(1);
- }
-
- bool LightRead(std::string &inFileName) {
- std::ifstream saIn;
- saIn.open(inFileName.c_str(), std::ios::binary);
- int hasMagicNumber;
- hasMagicNumber = ReadMagicNumber(saIn);
- if (hasMagicNumber == 1) {
- ReadComponentList(saIn);
- LightReadArray(saIn);
- ReadLookupTable(saIn);
- saIn.close();
- return true;
- }
- else {
- saIn.close();
- return false;
- }
- }
-
- bool Read(std::string &inFileName) {
- std::ifstream saIn;
- saIn.open(inFileName.c_str(), std::ios::binary);
- int hasMagicNumber;
- hasMagicNumber = ReadMagicNumber(saIn);
- if (hasMagicNumber == 1) {
- ReadComponentList(saIn);
- if (componentList[CompArray]) {
- ReadArray(saIn);
- }
- if (componentList[CompLookupTable]) {
- ReadLookupTable(saIn);
- }
- saIn.close();
- return true;
- }
- else {
- saIn.close();
- return false;
- }
- }
-
- int SearchLCP(T* target, T* query, DNALength queryLength, SAIndex &low, SAIndex &high, DNALength &lcpLength, DNALength maxlcp) {
- // cout << "searching lcp with query of length: " << queryLength << endl;
- lcpLength = 0;
- if (startPosTable != NULL and
- queryLength >= lookupPrefixLength) {
- Tuple lookupTuple;
- int left, right;
- // just in case this was changed.
- lookupTuple.FromStringLR(query, tm);
- left = startPosTable[lookupTuple.tuple];
- right = endPosTable[lookupTuple.tuple];
- //
- // When left == right, the k-mer in the read did not exist in the
- // genome. Don't even try and map it in this case.
- //
- if (left == right) {
- low = high = 0;
- return 0;
- }
-
- //
- // Otherwise, the sequence of length 'lookupPrefixLength' was found
- // in the genome. The bounds of this prefix in the suffix array
- // are stored in the lookup tables, so begin the binary search there.
- //
- lcpLength = lookupPrefixLength;
- low = left, high = right;
- }
- else {
- low = 0; high = length - 1;
- lcpLength = 0;
- }
- int prevLow = low;
- int prevHigh = high;
- int prevLCPLength = lcpLength - 1;
-
- // When the boundaries and the string share a prefix, it is not necessary
- // to use this as a comparison in further lcp searches.
- prevLCPLength = lcpLength;
-
- Search(target, query, queryLength, low, high, low, high, 0);
-
- DNALength lowLCP = lookupPrefixLength, highLCP = lookupPrefixLength;
- while (lowLCP < queryLength and index[low]+lowLCP < length and
- target[index[low] + lowLCP] == query[lowLCP]) lowLCP++;
-
- while (highLCP < queryLength and index[high]+highLCP < length and
- target[index[high] + highLCP] == query[highLCP]) highLCP++;
-
- DNALength minLCP = highLCP;
- if (lowLCP < highLCP ) {
- minLCP = lowLCP;
- }
-
- while (minLCP >= (lookupPrefixLength -2 )and
- low > 0 and high < (length - minLCP) and high - low < 10) {
- while(low > 0 and StringEquals(&target[index[low]], minLCP, &target[index[high]], minLCP)) low--;
- while(high > 0 and StringEquals(&target[index[low]], minLCP, &target[index[high]], minLCP)) high++;
- --minLCP;
- }
-
- //
- // The LCP is not an exact match to the end of the string.
- //
-
- prevLow = low;
- prevHigh = high;
-
- low = prevLow; high = prevHigh;
- if (low < high and high - low < 100) {
- return queryLength;
- }
- else {
- high = low - 1;
- lcpLength = 0;
- }
- return lcpLength;
- }
-
- int Search(T* target, T* query, DNALength queryLength, SAIndex left, SAIndex right, SAIndex &low, SAIndex &high, unsigned int offset=0) {
- if (offset >= queryLength) {
- return high - low;
- }
- SearchLow(target, query, queryLength, left, right, low, offset);
- SearchHigh(target, query, queryLength, left, right, high, offset);
- return high - low;
- }
-
- int Search(T* target, T* query, DNALength queryLength, SAIndex &low, SAIndex &high, int offset = 0) {
-
- int left = 0;
- int right = length - 1;
- //
- // Constrain the lookup if a lookup table exists.
- //
- if (startPosTable != NULL and
- queryLength >= lookupPrefixLength) {
- Tuple lookupTuple;
- lookupTuple.FromStringLR(query, tm);
- left = startPosTable[lookupTuple.tuple];
- right = endPosTable[lookupTuple.tuple];
- }
- return Search(target, query, queryLength, left, right, low, high, offset);
- }
-
-
- long SearchLeftBound(T* target, long targetLength, DNALength targetOffset, T queryChar, long l, long r) {
- long ll, lr;
- ll = l;
- lr = r;
- long m;
- long targetSufLen = 0;
- while (ll < lr) {
- m = (ll + lr) / 2;
- targetSufLen = targetLength - index[m];
- if (targetSufLen == targetOffset) {
- ll =m + 1;
- continue;
- }
- //
- // The suffix at index[m] is shorter than the lengths of the
- // two sequences being compared. With the Larsson
- // implementation, that means that the target suffix is lex-less
- // than the read.
- int comp;
- if (targetSufLen < targetOffset) {
- comp = -1;
- }
- else {
- //
- // There is enough sequence to compare the target suffix with
- // the query suffix.
- //
- assert(index[m]+targetOffset < targetLength);
-
- /*
- if (ThreeBit[target[index[m]+targetOffset]] >= 4 or
- ThreeBit[queryChar] >= 4) {
- lr = ll;
- break;
- }
- */
- comp = Compare::Compare(target[index[m]+targetOffset], queryChar);
-
- }
- if (comp < 0) {
- ll = m + 1;
- }
- else {
- lr = m;
- }
- }
- return ll;
- }
-
- long SearchRightBound(T* target, long targetLength, DNALength targetOffset,
- T queryChar, long l, long r) {
- long rl, rr;
- rl = l;
- rr = r;
- long m;
- long targetSufLen;
- while (rl < rr) {
- m = (rl + rr) / 2;
- targetSufLen = targetLength - index[m];
- if (targetSufLen == targetOffset) {
- rr = m;
- break;
- }
- if (targetSufLen < targetOffset) {
- rr = m ;
- }
- else {
- /*
- * Do not try and map stretches of N. These do not add
- * infomrative anchors.
- */
- /*
- if (ThreeBit[target[index[m]+targetOffset]] >= 4 or
- ThreeBit[queryChar] >= 4) {
- rl = rr;
- break;
- }
- */
- int comp = Compare::Compare(target[index[m] + targetOffset], queryChar);
- if (comp <= 0) {
- rl = m + 1;
- }
- else {
- rr = m ;
- }
- }
- }
- return rr;
- }
-
- /*
- * Search the suffix array for the bounds l and r that specify the
- * indices in the suffix array that have the longest common prefix
- * between the read and the genome.
- */
-
- int SearchLCPBounds(T*target, long targetLength, T*query, DNALength queryLength, SAIndex &l, SAIndex &r, DNALength &refOffset, DNALength &queryOffset) {
- // l = 0; r = targetLength;
- for (; refOffset < targetLength and queryOffset < queryLength and l < r; queryOffset++, refOffset++) {
- std::cout << "bounds: " << l << ", " << r << std::endl;
- //
- // Band l by the character at query[offset]
- //
-
- l = SearchLeftBound(target, targetLength, refOffset, query[queryOffset], l, r);
-
- //
- // If the current search is past the end of the suffix array, it
- // will be impossible to extend.
- //
- if (index[l] + refOffset >= targetLength or
- Compare::Compare(target[index[l] + refOffset], query[queryOffset]) != 0) {
- break;
- }
-
- r = SearchRightBound(target, targetLength, refOffset, query[queryOffset], l, r);
- if (Compare::Compare(query[queryOffset], target[index[l]+refOffset]) != 0 or
- Compare::Compare(query[queryOffset], target[index[r]+refOffset]) != 0) {
- break;
- }
- }
- return refOffset;
- }
-
-
- int StoreLCPBounds(T *target, long targetLength,
- T *query, long queryLength,
- SAIndex &low, SAIndex &high) {
-
- DNALength targetOffset = 0;
- DNALength queryOffset = 0;
-
- DNALength lcpLength = 0;
- low = 0; high = targetLength;
- for (; index[low] + targetOffset < targetLength and
- targetOffset < targetLength and
- queryOffset < queryLength and
- low < high ;
- targetOffset++, queryOffset++, lcpLength++) {
- //
- // Band l by the character at query[offset]
- //
-
- low = SearchLeftBound(target, targetLength, targetOffset, query[queryOffset], low, high);
-
- //
- // If the current search is past the end of the suffix array, it
- // will be impossible to extend.
- //
- if (index[low] + targetOffset > targetLength or
- Compare::Compare(target[index[low] + targetOffset], query[queryOffset]) != 0 or
- ThreeBit[query[queryOffset]] > 3) {
- break;
- }
-
- high = SearchRightBound(target, targetLength, targetOffset, query[queryOffset], low, high);
-
- }
- return lcpLength;
-
- }
-
- int CountNumBranches(T* target, DNALength targetLength, DNALength targetOffset, SAIndex low, SAIndex high) {
- //
- // look to see how many different characters start suffices between
- // low and high at targetOffset
- //
-
- // Check some easy boundary conditions.
- //
-
- // 1. No branches (indices do not define any subset of the suffix
- // array).
- if (high <= low) {
- return 0;
- }
- // 2. One branch,
- if (target[index[low] + targetOffset ] == target[index[high-1] + targetOffset]) {
- return 1;
- }
- int numBranches = 1;
- // More than one branch.
- while ( low < high ) {
- //
- // Find the band where the suffices share the same chatacter
- // 'targetOffset' bases into the suffix as the first suffix in
- // the band given to this function.
- //
- SAIndex curCharHigh = high;
- curCharHigh = SearchRightBound(target, targetLength, targetOffset, target[index[low]+targetOffset], low, high);
- if (curCharHigh != high) {
- ++numBranches;
- }
- low = curCharHigh;
- }
- return numBranches;
- }
-
-
- int StoreLCPBounds(T *target, long targetLength, // The string which the suffix array is built on.
- T *query, DNALength queryLength, // The query string. search starts at pos 0 in this string
- bool useLookupTable, // Should the indices of the first k bases be determined by a lookup table?
- int maxMatchLength, // Stop extending match at lcp length = maxMatchLength,
- // Vectors containing lcpLeft and lcpRight from 0 ... lcpLength.
- std::vector<SAIndex> &lcpLeftBounds, std::vector<SAIndex> &lcpRightBounds,
- bool stopOnceUnique=false) {
-
- //
- // Precondition: target[l][0] >= query[offset]
- //
- long l, r;
-
- l = 0; r = targetLength;
- DNALength lcpLength = 0;
- Tuple lookupTuple;
- lookupTuple.tuple = -1;
-
- /*
- * Various parameters may make the search through the SA not use
- * the full binary search. If priorLCP is > 0, the search for an
- * LCP is limited to lcpLeftBounds[priorLCP] and lcpRightBounds[priorLCP].
- * This is the case when continuing a search using branched
- * re-uses previous lcp searches.
- */
-
- if (useLookupTable and
- startPosTable != NULL) {
- // just in case this was changed.
- if (lookupTuple.FromStringLR(query, tm)) {
- l = startPosTable[lookupTuple.tuple];
- r = endPosTable[lookupTuple.tuple];
- lcpLength = lookupPrefixLength;
- }
- else {
- //
- // Not able to find a match for this sequence, so do not
- // register a hit.
- //
- l = 0;
- r = 0;
- lcpLength = 0;
- return 0;
- }
- //
- // the values of startPosTable and endPosTable are the same when
- // there are no matches. When they are not equal, a valid range
- // has been found, so store this.
- //
- if (l < r) {
- VectorIndex off_i;
- VectorIndex boundLength = lcpLeftBounds.size();
- lcpLeftBounds.push_back(l);
- lcpRightBounds.push_back(r);
- }
- else {
- //
- // No exact match found in the lookup table, do not bother
- // searching, and return 0 lcp length.
- //
- return 0;
- }
- }
-
- //
- // Search the suffix array for the longest common prefix between
- // the read and the genome.
- //
- while( l < r and
- lcpLength < queryLength // stop searching when the end of
- // the query is reached.
- ) {
-
- //
- // If there is only one match in the suffix array, and and not
- // extending matches as far as possible (stopping the search once
- // they are unique), halt the search.
- if (stopOnceUnique and l == r - 1) {
- break;
- }
-
- //
- // If there is a maximal match length and it is reached, stop
- // searchign as well.
- //
- if (maxMatchLength and lcpLength >= maxMatchLength) {
- break;
- }
-
- //
- // If the match extends into one or more N's, stop. The reason
- // for this is that sometimes people will set up genome databases
- // by appending a stretch of N's between matches (although they
- // should just use a multi-fasta file). Since the reads also
- // have stretches of N's, this tends to slow the search down
- // dramatically.
- if (ThreeBit[target[index[l] + lcpLength]] >= 4) {
- break;
- }
-
- //
- // Find the bounds in the suffix array matching query[0... lcp]
- // and target.
- //
-
- l = SearchLeftBound(target, targetLength, lcpLength, query[lcpLength], l, r);
- r = SearchRightBound(target, targetLength, lcpLength, query[lcpLength], l, r);
-
-
- //
- // If the current search is past the end of the suffix array, it
- // will be impossible to extend.
- //
- if (l == r or // if this point is reached, stop loop now since
- // otherwise the lcp length will be incremented by
- // 1, which will give one longer than the actual
- // LCP length.
- index[l] + lcpLength >= targetLength or // This shouldn't
- // happen
- // End on a mismatch.
- ThreeBit[query[lcpLength]] >= 4 or
- Compare::Compare(target[index[l] + lcpLength], query[lcpLength]) != 0
-
- ) {
- break;
- }
-
-
-
- //
- // Store the bounds for the current offset. These are used later
- // to expand the search if necessary.
- //
- lcpLeftBounds.push_back(l);
- lcpRightBounds.push_back(r);
- lcpLength++;
-
-
- }
- return lcpLength;
- }
-
-
- int SearchLow(T *target, T *query, DNALength queryLength, SAIndex l, SAIndex r, SAIndex &low, unsigned int offset=0) {
-
- long midPos;
- int high;
- int numSteps = 0;
- //
- // Boundary conditions, the string is either before (lexicographically) the text
- // or after.
- //
- if (StringLessThanEqual(&query[offset],
- queryLength-offset,
- &target[index[l]+offset],
- length - index[l]-offset)) {
- low = l;
- return low;
- }
- else if (StringLessThan(&target[index[r]+offset],
- length - index[r] - offset ,
- &query[offset],
- queryLength - offset)) {
- low = length;
- return low;
- }
-
- //
- // The string fits somewhere in the text.
- //
- low = l;
- high = r;
- long diff = ((long) high) - ((long) low);
- while (diff > 1) {
- ++numSteps;
- midPos = ((long) high) + ((long) low);
- midPos = midPos / 2;
- if (StringLessThanEqual(&query[offset], queryLength-offset, &target[index[midPos]+offset], length - index[midPos]-offset)) {
- high = midPos;
- }
- else {
- low = midPos;
- }
- diff = ((long) high) - ((long) low);
- }
-
- //
- // The search is for the least position such that the query is greater than or equal to the text.
- // High tracks the positions that may be equal to the query, and low is strictly less than the query.
- // At the end of the search, high is either pointing to the query, or the first element where the query
- // could be placed before high without changing the order of target.
- //
- low = high;
- diff = ((long) high) - ((long) low);
- return low;
- // cout << "search low took: " << numSteps << endl;
- }
-
-
- int SearchHigh(T *target, T *query, DNALength queryLength, SAIndex l, SAIndex r, SAIndex &high, unsigned int offset=0) {
-
- //
- // Find the last position where the query is less than the target.
- //
- long midPos;
- int low;
- int numSteps = 0;
- //
- // Boundary conditions, the string is either before (lexicographically) the text
- // or after.
- //
- if (StringLessThan(&target[index[r]+offset], length - index[r] - offset, &query[offset], queryLength-offset)) {
- high = -1;
- return high;
- }
-
- //
- // The string fits somewhere in the text.
- //
- low = l;
- high = r;
- long diff = ((long) high) - ((long) low);
- while (diff > 1) {
- ++numSteps;
- midPos = ((long) high) + ((long) low);
- midPos = midPos / 2;
- if (StringLessThan(&query[offset], queryLength - offset, &target[index[midPos]+offset], length - index[midPos] - offset)) {
- high = midPos;
- }
- else {
- low = midPos;
- }
- diff = ((long) high) - ((long) low);
- }
-
- //
- // The search is for the last position where the query is less than or equal to the text. High is
- // strictly greater than or the query. Low is less than or equal to the query. At the end, low will be
- // the last spot where query could be inserted after and not wreck the ordering of the array.
- //
- high = low;
- // cout << "search high took: " << numSteps << " steps." << endl;
- }
-};
-
-
-
-#endif // _BLASR_SUFFIX_ARRAY_HPP_
diff --git a/libcpp/alignment/suffixarray/SuffixArrayTypes.hpp b/libcpp/alignment/suffixarray/SuffixArrayTypes.hpp
deleted file mode 100644
index a9047dc..0000000
--- a/libcpp/alignment/suffixarray/SuffixArrayTypes.hpp
+++ /dev/null
@@ -1,17 +0,0 @@
-#ifndef _BLASR_SUFFIX_ARRAY_TYPES_HPP_
-#define _BLASR_SUFFIX_ARRAY_TYPES_HPP_
-
-#include <vector>
-#include "SuffixArray.hpp"
-#include "SharedSuffixArray.hpp"
-
-#include "CompressedSequence.hpp"
-#include "Compare4BitCompressed.hpp"
-#include "FASTASequence.hpp"
-
-typedef SuffixArray<Nucleotide, std::vector<int> > DNASuffixArray;
-typedef SuffixArray<Nucleotide, std::vector<int>,
- Compare4BitCompressed<Nucleotide>,
- CompressedDNATuple<FASTASequence> > CompressedDNASuffixArray;
-
-#endif // _BLASR_SUFFIX_ARRAY_TYPES_HPP_
diff --git a/libcpp/alignment/suffixarray/ssort.hpp b/libcpp/alignment/suffixarray/ssort.hpp
deleted file mode 100644
index 0a6f9b8..0000000
--- a/libcpp/alignment/suffixarray/ssort.hpp
+++ /dev/null
@@ -1,449 +0,0 @@
-/****************************************************************
-Copyright (C) Lucent Technologies 1997
-All Rights Reserved
-
-Permission to use, copy, modify, and distribute this software and
-its documentation for any purpose and without fee is hereby
-granted, provided that the above copyright notice appear in all
-copies and that both that the copyright notice and this
-permission notice and warranty disclaimer appear in supporting
-documentation, and that the name Lucent Technologies or any of
-its entities not be used in advertising or publicity pertaining
-to distribution of the software without specific, written prior
-permission.
-
-LUCENT DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE,
-INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS.
-IN NO EVENT SHALL LUCENT OR ANY OF ITS ENTITIES BE LIABLE FOR ANY
-SPECIAL, INDIRECT OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
-WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER
-IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION,
-ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF
-THIS SOFTWARE.
-****************************************************************/
-/*
- Suffix sort
- Peter M. McIlroy
- M. Douglas McIlroy
-
-Prototype
- int ssort(int a[], int s[]);
-
-Purpose
- Return in a[] a suffix array for the original
- contents of a[]. (The original values in a[]
- are typically serial numbers of distinct tokens
- in some list.) Optionally return in s[] an
- array of shared lengths between adjacent sorted
- suffixes.
-
-Precondition
- Array a[] holds n values, with n>=1. Exactly k
- distinct values, in the range 0..k-1, are present.
- Value 0, an endmark, appears exactly once, at a[n-1].
- Pointer s is 0 or points to an array of n elements.
-
-Postcondition
- Array a[] is a copy of the internal array p[]
- that records the sorting permutation: if i<j
- then the original suffix a[p[i]..n-1] is
- lexicographically less than a[p[j]..n-1].
-
- If s is nonzero, its elements are filled in with
- "shared lengths": s[i] is the length of the agreeing
- prefixes of a[p[i-1]..n-1] and a[p[i]..n-1].
- s[0] is 0.
-
-Return value
- 0 success
- 1 out of space; data unchanged
- 2 bad data; data may be changed
-
-Cost
- Sorting takes time O(n log m), where m is the longest
- duplicate (possibly overlapped) substring, and uses n words
- of temporary memory. There are at most log n passes,
- each involving essentially 5 serial and 6 random
- traversals of size-n arrays (a[] and p[]). Shared
- lengths cost an extra n words of temporary memory;
- for time cost see comment with function shared() below.
-
- A tradeoff desribed after step (3) below saves
- about 20% in time at the cost of another n words.
-
-Terminology
- "The h-gram at a[i]" is the string a[i], a[i+1], ...,
- a[i+h-1], with subscripts taken mod n, except that
- when h=0 the "0-gram" at a[i] is a[i]. (More succinctly,
- the h-gram at a[i] is a[i], ..., a[i+max(h,1)-1].)
- "The h-successor of the h-gram at a[i]" is the h-gram
- at a[i+h].
-
-Method
- Order 2h-grams by doing steps (1)-(5) below
- for h = 0, 1, 2, 4, ... Because of the unique endmark,
- ordering n-grams (or longer grams) is exactly the same as
- ordering the suffixes of a[].
-
- This is a fillip on radix sort. The i-th stage of a
- traditional radix sort distributes on the i-th "character"
- counting from the right of the keys, thus arranging the keys
- so that their i-character suffixes are in lexicographic order.
- Here, instead, we distribute on h-gram prefixes of 2h-grams,
- where h = 2^i, thus arranging 2h-grams in order. Each
- h-gram is coded into one element of a[].
- This is possible within a constant word width because
- there are only n h-grams for any h. With 2^i-grams being
- placed in order at stage i, and each stage taking time O(n),
- sorting is complete after log n stages for a total
- time of O(n log n).
-
- The method for shared lengths is given with the
- shared-length code far below.
-
-History
- The general radix-sorting notion is due to Manber and
- Myers, SODA '91, who used a big-endian radix sort. They
- also made the observation that by cleverly multiplexing
- uses of the two arrays, one can get by with O(1) extra
- space beyond arrays a[] and p[]. The circular-array idea,
- which greatly simplifies the program, is due to P. McIlroy.
- Steps (1) and (2) below are based on M&M's method for
- the first cycle (h=0); they do something entirely different
- for the h-gram doubling cycles and develop in a[] the
- inverse of permutation p[].
-
- The state of the art has improved since this code was
- written. A variant developed independently by (at least)
- Larssen at Lund, Sadakane at Tokyo and Quinlan at Bell Labs
- is several times as fast; see Larssen and Sadakane
- LU-CS-TR:99-214, Dept. of CS, Lund Univ. Sweden.
-
-Data used in the sort
- a[] array of h-gram codes.
- al[] linked-list area, overlaid on a[].
- p[] permutation.
- pl[] list heads, overlaid on p[].
- s[] array of shared lengths (optional).
- q[] tree of bucket refinements, for calculating s[].
- ORIG mark at the end of lists, originally on p[].
- BUCK mark at start of "buckets", stretches of p[]
- that point to identical codes in a[].
-
- Were the overlaid arrays pulled apart, the algorithm would
- simplify only slightly, mainly by dropping the inner loop from
- steps (1) and (2).
-
-Description of steps, except for optional shared lengths
-
-(0) (0a) Initialize p[] to contain the identity permutation.
- (0b) Place mark ORIG on every element of p[].
-
-State before step 1
- Each element a[i] encodes the h-gram at a[i].
- The h-grams are coded 0,..,k-1 in increasing
- lexicographic order. When h>0, permutation p[]
- lists h-grams in lexicographic order: if i<j then
- a[p[i]] <= a[p[j]]. When h=0, p[] contains
- the input order 0,..,n-1.
-
-(1) Construct in al[] linked lists of like-valued
- codes in a[] ordered in reverse of the order
- of their h-successors as given by p[].
- (Done by iterating over elements of a[] in p[]-order
- and operating on their h-predecessors.)
-
- Place in pl[j] the head of the list of elements with
- value j. Thus, if a[7]=a[3]=a[9]=2, and these
- elements were visited in this order according to p[],
- then pl[2]=9, al[9]=3, al[3]=7. The list is developed
- by pushing previous contents of pl[j] onto the list.
- In particular the original content of pl[j] (which
- was p[j]) gets pushed to the end of the list (al[7]
- in the example), still bearing the mark ORIG. The mark
- serves both to note the end of the list and to flag the
- fact that this element contains a quantity of a different
- kind.
-
- During step (1), a[] contains three kinds of data:
- unprocessed elements of a[], list links of al[]
- and list ends, marked ORIG, that contain original
- data from p[]. p[] contains two kinds of data:
- elements of p[], marked ORIG, and elements of pl[].
-
- The elements of p[] that have been displaced by pl[]
- are retrieved by chasing the lists; this is done by
- a for loop. Each list will be chased at most once in
- step (1) and once in step (2) and the total size of
- all lists will never exceed n, so the overhead of list
- chasing is at most linear in n.
-
-State before step (2)
- Array a[] has been wiped out and replaced by
- the lists of al[], which together with pl[] give
- exactly the same information. The first k elements
- of p[] are occupied by pl[] and the remaining elements
- are occupied by ORIG-marked elements of p[].
-
-(2) Make p[] point to the (former) elements of a[]
- in order of increasing value. This is done in reverse:
- biggest values first, and for each value running out the
- list created in (1), which is already in reverse order.
- New values fill in the size-n array p[] from the top,
- while the size-k array pl[] of list heads shrinks
- toward the bottom. Because no list is empty, the
- two uses of p[] cannot collide.
-
- Place mark BUCK at each bucket start, namely the
- element of p[] last transferred from each list.
-
-State before step 3
- Permutation p[] lists h-grams in lexicographic order.
- It is bucketed by h-grams. Within each bucket h-grams
- are ordered by their h-successors.
-
-(3) Reconstruct codes in a[] from the buckets. The
- element of a[] pointed to from the first bucket is 0;
- the elements pointed to from the second bucket are 1;
- and so on.
-
- This step would be unnecessary if al[] did not share
- storage with a[]. Then steps (2) and (4) could
- be combined.
-
-State before step 4
- Permutation p[] is as before step 3, and code array
- a[] is as before step 1.
-
-(4) Refine buckets by values of h-successors in a[] by
- placing a BUCK mark on each p[i] where the h-successors
- of a[p[i]] and a[p[i-1]] differ.
-
-State before step 5
- Array p[] holds an ordered, bucketed list of 2h-grams.
-
-(5) Recode a[] according to the new buckets, exactly as
- a[] was reconstructed in step (3). Count the
- buckets to determine a new value of k. If k==n, every
- bucket is a singleton and sorting is complete.
-
-
-Bad input
- Code that invokes finish() is solely defensive. It
- could be dropped if you like to live dangerously.
-*/
-
-#include <stdlib.h>
-
-enum {
- ORIG = ~(~0u>>1), /* sign bit */
- BUCK = ~(~0u>>1)
-};
-
-void shared(SAIndex a[], SAIndex n, SAIndex p[], SAIndex q[], SAIndex s[], int h);
-
-#define pred(i, h) ((t=(i)-(h))<0? t+n: t)
-#define succ(i, h) ((t=(i)+(h))>=n? t-n: t)
-
-inline int
-ssort(SAIndex a[], SAIndex s[])
-{
- SAIndex h, i, j, l, n, t;
- SAIndex k = 0; /* initialized for lint */
- SAIndex *p = 0;
- int result = 0;
- SAIndex *q = 0;
-# define al a
-# define pl p
-# define finish(r) if(1){result=r; goto out;}else
-
- for(j=n=0; a[n]>0; n++) /* find n */
- if(a[n] > j)
- j = a[n]; /* and max element */
- if(a[n++]<0 || j>=n)
- finish(2);
- // p = malloc(n*sizeof(int));
- p = new SAIndex[n];
- if(p == 0)
- finish(1);
-
- for(i=0; i<n; i++) /* (0) initialize */
- p[i] = i | ORIG;
-
- if(s) { /* shared lengths */
- // q = malloc(n*sizeof(int));
- q = new SAIndex[n];
- if(q == 0)
- finish(1);
- }
-
- for(h = 0; ; h = h==0? 1: 2*h) {
- for(i=0; i<n; i++) { /* (1) link */
- for(j=p[i]; !(j&ORIG); j=al[j]);
- j = pred(j&~ORIG, h);
- l = a[j];
- al[j] = pl[l];
- pl[l] = j;
- }
-
- if(h == 0) { /* find k */
- for(k=0; k<n; k++)
- if(pl[k]&ORIG)
- break;
-
- for(i=k; i<n; i++) /* check input */
- if(!(pl[i]&ORIG))
- finish(2);
- }
-
- for(i=n; --k>=0; ) { /* (2) order */
- j = pl[k];
- do
- p[--i] = j;
- while(!((j=al[j]) & ORIG));
- p[i] |= BUCK;
- }
-
- for(i=0; i<n; i++) { /* (3) reconstruct */
- if(p[i] & BUCK)
- k++;
- a[p[i]&~BUCK] = k;
- }
-
- for(i=0, j=-1; i<n; i++, j=l) { /* (4) refine */
- l = a[succ(p[i]&~BUCK, h)];
- if(l != j)
- p[i] |= BUCK;
-
- }
- if(s)
- shared(a, n, p, q, s, h);
-
- for(i=0, k=-1; i<n; i++) { /* (5) recode */
- if(p[i] & BUCK)
- k++;
- a[p[i]&~BUCK] = k;
- p[i] |= ORIG; /* (0b) reinitialize */
- }
- if(++k >= n)
- break;
- }
-
- for(i=0; i<n; i++)
- a[i] = p[i] & ~ORIG;
-
-out:
- delete [] p;
- delete [] q;
- return result;
-}
-
-/* shareda.c: shared lengths for suffix arrays by ancestor tree
-
- a[] temporary space, used for pointers to containing buckets
- n, p[], s[], h as in ssort()
- q[] tree of bucket heads
-
- Array q holds a tree of bucket heads. Initially q[0]
- is 0 and q[i] = -1 for i>0. For each new bucket i
- created in the current pass, q[i] is (notionally)
- made to point to the previous bucket, j. The shared
- length between the i-1st and i-th smallest suffix
- is stored in s[i]. The shared length between two
- arbitrary buckets is the minimum of the stored
- shared lengths on the paths to their nearest common
- ancestor (excluding that ancestor).
-
- For efficient search, paths are compressed by making
- each bucket point to the next bucket on the path to
- the root with a strictly smaller stored shared length.
- This may change the identity of the nearest common
- ancestor, but does not affect shared lengths.
-
-Cost
- There are 3 serial passes and 1 random pass over
- size-n arrays per call, plus the inner loops of steps
- (2) and (3), each of which is executed n times fpr
- each call of ssort(). The asymptotic worst case has
- not been analyzed, however the code has always been
- seen to be at least as fast as a guaranteed O(n log n)
- method that takes twice as much code. (That method
- keeps in element i of an integer array the minimum
- value of s[] over the largest aligned power-of-2
- interval beginning at i.)
-
-(0) On the first pass, with h=0, the shared length between
- buckets is zero, and every bucket bcomes a child of the
- root node, 0.
-
-(1) On subsequent passes the old bucket that each potential
- new bucket refines is remembered in a[]. Array a[]
- is ordered by substring places, while q[] is ordered
- by substring values.
-
- If the values placed in a[] were kept in another array,
- the loops of shared() could be combined with loops of
- lssort().
-
-(2) When an h-gram bucket is split, the shared lengths between
- adjacent subbuckets is h+u, where u is the shared length
- between the h-successors that differed (causing the split).
- To find u, we locate the nearest common ancestor.
-
- The common ancestor is found by searching the path from
- the higher-numbered bucket, k1, until reaching a bucket
- whose number does not exceed that of the lower-numbered
- bucket, k0. This method is justified by two observations.
- All the new subbuckets have strictly longer shared lengths
- than all the old buckets. All the subbuckets of a
- bucket fall between the bucket head and its next higher
- numbered sibling.
-
-(3) After new buckets have been processed, the tree q is
- updated. New buckets are recognized by having mark
- BUCK and q[i]<0.
-*/
-
-inline void
-shared(SAIndex a[], SAIndex n, SAIndex p[], SAIndex q[], SAIndex s[], int h)
-{
- SAIndex i, j, k0, k1, t, u;
- if(h == 0) { /* (0) initialize */
- for(i=0; i<n; i++)
- if(p[i]&BUCK)
- q[i] = s[i] = 0;
- else
- q[i] = -1;
- return;
- }
-
- for(i=j=0; i<n; i++) { /* (1) get parents */
- if(q[i] >= 0)
- j = i;
- a[p[i]&~BUCK] = j;
- }
-
- for(i=0; i<n; i++) { /* (2) find lengths */
- if(!(p[i]&BUCK))
- continue;
- k0 = j; /* k0=garbage if i=0 */
- k1 = j = a[succ(p[i]&~BUCK, h)];
- if(q[i] >= 0)
- continue;
- for(u=n; k1>k0; k1=q[k1])
- if(s[k1] < u)
- u = s[k1];
- s[i] = h + u;
- }
-
- for(i=0; i<n; i++) /* (3) update tree */
- if(p[i]&BUCK) {
- if(q[i] < 0)
- for(t=j; ;t=q[t]) {
- q[i] = t;
- if(s[i] > s[t])
- break;
- }
- j = i;
- }
-}
diff --git a/libcpp/alignment/tuples/BaseTuple.cpp b/libcpp/alignment/tuples/BaseTuple.cpp
deleted file mode 100644
index fefbab7..0000000
--- a/libcpp/alignment/tuples/BaseTuple.cpp
+++ /dev/null
@@ -1,53 +0,0 @@
-#include <stdint.h>
-#include "Types.h"
-#include "TupleMask.h"
-#include "TupleMetrics.hpp"
-#include "BaseTuple.hpp"
-
-ULong BaseTuple::HashPowerOfFour(int nBases, TupleMetrics &tm) {
- //
- // When the hash can fit inside the entire tuple, just return the
- // tuple.
- //
- if (tm.tupleSize > nBases) {
- return tuple;
- }
- else {
- return ((tuple & TupleMask[nBases]) + (tuple % 1063)) % (1 << (nBases*2));
- }
-}
-
-int BaseTuple::operator<(const BaseTuple &rhs) const {
- return tuple < rhs.tuple;
-}
-
-int BaseTuple::operator==(const BaseTuple &rhs) const {
- return tuple == rhs.tuple;
-}
-
-int BaseTuple::operator!= (const BaseTuple &rhs) const {
- return tuple != rhs.tuple;
-}
-
-BaseTuple BaseTuple::ShiftLeft(TupleMetrics &tm, ULong shift) {
- tuple = tuple << shift;
- tuple = tuple & tm.tupleMask;
- return *this;
-}
-
-BaseTuple BaseTuple::ShiftRight(ULong shift) {
- tuple = tuple >> shift;
- return *this;
-}
-
-BaseTuple BaseTuple::Append(ULong val, TupleMetrics &tm, ULong nBits) {
- tuple = tuple << nBits;
- tuple = tuple & tm.tupleMask;
- tuple = tuple + val;
- return *this;
-}
-
-long BaseTuple::ToLongIndex() {
- long tempTuple = tuple;
- return tempTuple;
-}
diff --git a/libcpp/alignment/tuples/BaseTuple.hpp b/libcpp/alignment/tuples/BaseTuple.hpp
deleted file mode 100644
index 0a6a9ea..0000000
--- a/libcpp/alignment/tuples/BaseTuple.hpp
+++ /dev/null
@@ -1,27 +0,0 @@
-#ifndef _BLASR_BASE_TUPLE_HPP_
-#define _BLASR_BASE_TUPLE_HPP_
-
-#include "tuples/TupleMetrics.hpp"
-
-class BaseTuple {
-public:
- ULong tuple;
-
- ULong HashPowerOfFour(int nBases, TupleMetrics &tm);
-
- int operator<(const BaseTuple &rhs) const;
-
- int operator==(const BaseTuple &rhs) const;
-
- int operator!= (const BaseTuple &rhs) const;
-
- BaseTuple ShiftLeft(TupleMetrics &tm, ULong shift=1L);
-
- BaseTuple ShiftRight(ULong shift=1L);
-
- BaseTuple Append(ULong val, TupleMetrics &tm, ULong nBits);
-
- long ToLongIndex();
-};
-
-#endif
diff --git a/libcpp/alignment/tuples/CompressedDNATuple.hpp b/libcpp/alignment/tuples/CompressedDNATuple.hpp
deleted file mode 100644
index c60a838..0000000
--- a/libcpp/alignment/tuples/CompressedDNATuple.hpp
+++ /dev/null
@@ -1,63 +0,0 @@
-#ifndef _BLASR_COMPRESSED_DNA_TUPLE_HPP_
-#define _BLASR_COMPRESSED_DNA_TUPLE_HPP_
-
-#include "DNATuple.hpp"
-#include "CompressedSequence.hpp"
-
-template<typename T_Sequence>
-class CompressedDNATuple : public DNATuple {
- static const unsigned char mask = 0xf;
- public:
- int FromStringLR(Nucleotide *strPtr, TupleMetrics &tm) {
- //
- // Make sure the sequence contains all valid characters.
- //
-
- if (!CompressedSequence<T_Sequence>::Only4BitACTG(strPtr, tm.tupleSize))
- return 0;
-
- if (tm.tupleSize == 0)
- return 1;
-
- tuple = 0;
- Nucleotide *p;
- Nucleotide *endPtr = &strPtr[tm.tupleSize - 1];
- for (p = strPtr; p != endPtr; p++) {
- tuple += TwoBit[*p & mask];
- tuple <<=2;
- }
- //
- // The tuple size is guaranteed to be at least
- // 1, so it's safe to add the last value.
- // This cannot be in the previous loop since
- // the shift shouldn't happen.
- tuple += TwoBit[*p & mask];
- return 1;
- }
-
-
- int FromStringRL(Nucleotide *strPtr, TupleMetrics &tm) {
-
- if (!CompressedSequence<T_Sequence>::Only4BitACTG((CompressedNucleotide*)strPtr, tm.tupleSize))
- return 0;
-
- if (tm.tupleSize == 0)
- return 1;
-
- tuple = 0;
- Nucleotide *p;
- for (p = strPtr + tm.tupleSize - 1; p > strPtr; p--) {
- tuple += TwoBit[*p & mask];
- tuple <<=2;
- }
- //
- // The tuple size is guaranteed to be at least
- // 1, so it's safe to add the last value.
- // This cannot be in the previous loop since
- // the shift shouldn't happen.
- tuple += TwoBit[*p & mask];
- return 1;
- }
-};
-
-#endif // _BLASR_COMPRESSED_DNA_TUPLE_HPP_
diff --git a/libcpp/alignment/tuples/CountedTuple.h b/libcpp/alignment/tuples/CountedTuple.h
deleted file mode 100644
index acb997e..0000000
--- a/libcpp/alignment/tuples/CountedTuple.h
+++ /dev/null
@@ -1,16 +0,0 @@
-#ifndef COUNTED_TUPLE_H_
-#define COUNTED_TUPLE_H_
-
-#include "tuples/DNATuple.h"
-
-class CountedDNATuple : public DNATuple {
- public:
- int count;
- int IncrementCount() {
- count = count + 1;
- }
-
-};
-
-
-#endif
diff --git a/libcpp/alignment/tuples/DNATuple.cpp b/libcpp/alignment/tuples/DNATuple.cpp
deleted file mode 100644
index cf779dd..0000000
--- a/libcpp/alignment/tuples/DNATuple.cpp
+++ /dev/null
@@ -1,94 +0,0 @@
-#include "tuples/DNATuple.hpp"
-
-
-int DNATuple::FromStringRL(Nucleotide *strPtr, TupleMetrics &tm) {
-
- //
- // Tuples are created with the right-most character
- // in the most significant bit in the sequence.
- //
- DNASequence tmpSeq;
- tmpSeq.seq = strPtr;
- tmpSeq.length = tm.tupleSize;
- if (!OnlyACTG(tmpSeq))
- return 0;
-
- if (tm.tupleSize == 0)
- return 1;
-
- tuple = 0;
- Nucleotide *p;
- for (p = strPtr + tm.tupleSize - 1; p > strPtr; p--) {
- tuple += TwoBit[*p];
- tuple <<=2;
- }
- //
- // The tuple size is guaranteed to be at least
- // 1, so it's safe to add the last value.
- // This cannot be in the previous loop since
- // the shift shouldn't happen.
- tuple += TwoBit[*p];
- return 1;
-}
-
-
-int DNATuple::MakeRC(DNATuple &dest, TupleMetrics &tm) {
- int i;
- ULong tempTuple = tuple;
- dest.tuple = 0;
- ULong mask = 0x3;
- if (tm.tupleSize == 0)
- return 0;
- for (i = 0; i < tm.tupleSize - 1; i++ ) {
- dest.tuple += (~tempTuple & mask);
- tempTuple >>= 2;
- dest.tuple <<= 2;
- }
- dest.tuple += (~tempTuple & mask);
- return 1;
-}
-
-std::string DNATuple::ToString(TupleMetrics &tm) {
- int i;
- std::string s;
- ULong tempTuple = tuple;
- for (i = 0;i < tm.tupleSize;i++) {
- s.insert(s.begin(), TwoBitToAscii[tempTuple & 3]);
- tempTuple = tempTuple >> 2;
- }
- return s;
-}
-
-bool
-CompareByTuple::operator()(const DNATuple &lhs, const DNATuple &rhs)
-const {
- return lhs.tuple < rhs.tuple;
-}
-
-int PositionDNATuple::operator==(const DNATuple &pTuple) const {
- return tuple == pTuple.tuple;
-}
-
-PositionDNATuple::PositionDNATuple() : DNATuple() {
- pos = -1;
-}
-
-PositionDNATuple::PositionDNATuple(PositionDNATuple &tupleP, DNALength posP) {
- tuple = tupleP.tuple;
- pos = posP;
-}
-
-
-int
-OrderPositionDNATuplesByPosition::operator()(
- const PositionDNATuple &lhs, const PositionDNATuple &rhs)
-const {
- return lhs.pos < rhs.pos;
-}
-
-int
-OrderPositionDNATuplesByTuple::operator()(
- const PositionDNATuple &lhs, const PositionDNATuple &rhs)
-const {
- return lhs.tuple < rhs.tuple;
-}
diff --git a/libcpp/alignment/tuples/DNATuple.hpp b/libcpp/alignment/tuples/DNATuple.hpp
deleted file mode 100644
index 57a12ff..0000000
--- a/libcpp/alignment/tuples/DNATuple.hpp
+++ /dev/null
@@ -1,103 +0,0 @@
-#ifndef _BLASR_DNA_TUPLE_HPP_
-#define _BLASR_DNA_TUPLE_HPP_
-
-#include <cassert>
-#include <vector>
-#include <stdint.h>
-#include <ostream>
-#include <string>
-#include "Types.h"
-#include "SeqUtils.hpp"
-#include "DNASequence.hpp"
-#include "NucConversion.hpp"
-#include "tuples/BaseTuple.hpp"
-#include "tuples/TupleMetrics.hpp"
-#include "tuples/TupleList.hpp"
-#include "tuples/TupleOperations.h"
-
-class DNATuple : public BaseTuple {
-public:
- DNALength pos;
-
- inline int FromStringLR(Nucleotide *strPtr, TupleMetrics &tm);
-
- int FromStringRL(Nucleotide *strPtr, TupleMetrics &tm);
-
- inline int ShiftAddRL(Nucleotide nuc, TupleMetrics &tm);
-
- int MakeRC(DNATuple &dest, TupleMetrics &tm);
-
- std::string ToString(TupleMetrics &tm);
-};
-
-class CompareByTuple {
-public:
- bool operator()(const DNATuple &lhs, const DNATuple &rhs) const;
-};
-
-
-class CountedDNATuple : public DNATuple {
-public:
- int count;
-};
-
-class PositionDNATuple : public DNATuple {
-public:
- PositionDNATuple& operator=(const PositionDNATuple &rhs) {
- pos = rhs.pos;
- tuple = rhs.tuple;
- return *this;
- }
-
- int operator<(const PositionDNATuple & pTuple) const {
- if (tuple < pTuple.tuple)
- return 1;
- else if (tuple == pTuple.tuple)
- return pos < pTuple.pos;
- else
- return 0;
- }
-
- int operator==(const PositionDNATuple &pTuple) const {
- return tuple == pTuple.tuple and pos == pTuple.pos;
- }
-
- int operator<(const DNATuple &pTuple) const {
- return (tuple < pTuple.tuple);
- }
-
- int operator==(const DNATuple &pTuple) const;
-
- int operator!=(const DNATuple &pTuple) const {
- return tuple != pTuple.tuple;
- }
-
- PositionDNATuple();
-
- PositionDNATuple(PositionDNATuple &tupleP, DNALength posP);
-
-};
-
-class OrderPositionDNATuplesByPosition {
-public:
- int operator()(const PositionDNATuple &lhs, const PositionDNATuple &rhs) const;
-};
-
-class OrderPositionDNATuplesByTuple {
-public:
- int operator()(const PositionDNATuple &lhs, const PositionDNATuple &rhs) const;
-};
-
-
-template<typename Sequence>
-int SearchSequenceForTuple(Sequence &seq, TupleMetrics &tm, DNATuple &queryTuple);
-
-template<typename Sequence>
-int SequenceToTupleList(Sequence &seq, TupleMetrics &tm, TupleList<DNATuple> &tupleList);
-
-template<typename Sequence>
-int SequenceToTupleList(Sequence &seq, TupleMetrics &tm, TupleList<PositionDNATuple> &tupleList);
-
-#include "DNATupleImpl.hpp"
-
-#endif // _BLASR_DNA_TUPLE_HPP_
diff --git a/libcpp/alignment/tuples/DNATupleImpl.hpp b/libcpp/alignment/tuples/DNATupleImpl.hpp
deleted file mode 100644
index 4ba748e..0000000
--- a/libcpp/alignment/tuples/DNATupleImpl.hpp
+++ /dev/null
@@ -1,200 +0,0 @@
-#include <cassert>
-#include "NucConversion.hpp"
-
-inline int DNATuple::FromStringLR(Nucleotide *strPtr, TupleMetrics &tm) {
- DNASequence tmpSeq;
- tmpSeq.seq = strPtr;
- tmpSeq.length = tm.tupleSize;
- if (!OnlyACTG(tmpSeq))
- return 0;
-
- if (tm.tupleSize == 0)
- return 1;
-
- tuple = 0;
- Nucleotide *p;
- Nucleotide *endPtr = &strPtr[tm.tupleSize - 1];
- for (p = strPtr; p != endPtr; p++) {
- // If it is not possible to convert this string, return null.
- if (ThreeBit[*p] > 3) {
- return 0;
- }
- tuple += TwoBit[*p];
- tuple <<=2;
- }
- //
- // The tuple size is guaranteed to be at least
- // 1, so it's safe to add the last value.
- // This cannot be in the previous loop since
- // the shift shouldn't happen.
- tuple += TwoBit[*p];
- return 1;
-}
-
-
-inline int DNATuple::ShiftAddRL(Nucleotide nuc, TupleMetrics &tm) {
- if (ThreeBit[nuc] > 3) {
- return 0;
- }
- else {
- tuple >>= 2;
- tuple += (TwoBit[nuc] << ((tm.tupleSize-1)*2));
- return 1;
- }
-}
-
-
-template<typename Sequence>
-int SearchSequenceForTuple(Sequence &seq, TupleMetrics &tm, DNATuple &queryTuple) {
- DNALength p;
- PositionDNATuple tempTuple, upperTuple;
-
- p = 0;
- DNALength cur = 0;
- DNALength curValidEnd = 0;
-
- //
- // Construct the mask-off bit pair for the shifted tuple.
- //
- PositionDNATuple maskLeftTuple;
- maskLeftTuple.tuple = 3;
- maskLeftTuple.tuple = maskLeftTuple.tuple << 2*tm.tupleSize;
- maskLeftTuple.tuple = ~maskLeftTuple.tuple;
- PositionDNATuple testTuple;
- while (curValidEnd < seq.length) {
- //
- // Search for the next available window that can be translated into a tuple.
- //
- cur = curValidEnd;
- while(curValidEnd < seq.length and IsACTG[seq.seq[curValidEnd]]) {
- curValidEnd++;
- }
- if (curValidEnd - cur >= tm.tupleSize) {
- //
- // Found a span that does not have N's in it,
- //
- assert (tempTuple.FromStringRL(&(seq.seq[cur]), tm) == 1);
- p = cur;
- if (tempTuple.tuple == queryTuple.tuple) {
- return 1;
- }
- for (p++; p < curValidEnd - tm.tupleSize + 1; p++) {
- tempTuple.tuple >>=2;
- // tempTuple.tuple &= maskLeftTuple.tuple;
- upperTuple.tuple = TwoBit[seq.seq[p+tm.tupleSize-1]];
- upperTuple.tuple = upperTuple.tuple << (2 * (tm.tupleSize-1));
- tempTuple.tuple += upperTuple.tuple;
- if (tempTuple.tuple == queryTuple.tuple) {
- return 1;
- }
- }
- }
- else {
- ++curValidEnd;
- }
- }
-}
-
-
-template<typename Sequence>
-int SequenceToTupleList(Sequence &seq, TupleMetrics &tm, TupleList<DNATuple> &tupleList) {
- DNALength p;
- PositionDNATuple tempTuple, upperTuple;
-
- p = 0;
- DNALength cur = 0;
- DNALength curValidEnd = 0;
-
- //
- // Construct the mask-off bit pair for the shifted tuple.
- //
- PositionDNATuple maskLeftTuple;
- maskLeftTuple.tuple = 3;
- maskLeftTuple.tuple = maskLeftTuple.tuple << 2*tm.tupleSize;
- maskLeftTuple.tuple = ~maskLeftTuple.tuple;
- PositionDNATuple testTuple;
- while (curValidEnd < seq.length) {
- //
- // Search for the next available window that can be translated into a tuple.
- //
- cur = curValidEnd;
- while(curValidEnd < seq.length and IsACTG[seq.seq[curValidEnd]]) {
- curValidEnd++;
- }
- if (curValidEnd - cur >= tm.tupleSize) {
- //
- // Found a span that does not have N's in it,
- //
- assert (tempTuple.FromStringRL(&(seq.seq[cur]), tm) == 1);
- p = cur;
- tupleList.Append(tempTuple);
- for (p++; p < curValidEnd - tm.tupleSize + 1; p++) {
- tempTuple.tuple >>=2;
- // tempTuple.tuple &= maskLeftTuple.tuple;
- upperTuple.tuple = TwoBit[seq.seq[p+tm.tupleSize-1]];
- upperTuple.tuple = upperTuple.tuple << (2 * (tm.tupleSize-1));
- tempTuple.tuple += upperTuple.tuple;
- //testTuple.FromStringRL(&seq.seq[p], tm);
- //assert(testTuple.tuple == tempTuple.tuple);
- tupleList.Append(tempTuple);
- }
- }
- else {
- ++curValidEnd;
- }
- }
- return tupleList.size();
-}
-
-
-template<typename Sequence>
-int SequenceToTupleList(Sequence &seq, TupleMetrics &tm, TupleList<PositionDNATuple> &tupleList) {
- DNALength p;
- PositionDNATuple tempTuple, upperTuple;
-
- p = 0;
- DNALength cur = 0;
- DNALength curValidEnd = 0;
-
- //
- // Construct the mask-off bit pair for the shifted tuple.
- //
- PositionDNATuple maskLeftTuple;
- maskLeftTuple.tuple = 3;
- maskLeftTuple.tuple = maskLeftTuple.tuple << 2*tm.tupleSize;
- maskLeftTuple.tuple = ~maskLeftTuple.tuple;
- PositionDNATuple testTuple;
- while (curValidEnd < seq.length) {
- //
- // Search for the next available window that can be translated into a tuple.
- //
- cur = curValidEnd;
- while(curValidEnd < seq.length and IsACTG[seq.seq[curValidEnd]]) {
- curValidEnd++;
- }
- if (curValidEnd - cur >= tm.tupleSize) {
- //
- // Found a span that does not have N's in it,
- //
- assert (tempTuple.FromStringRL(&(seq.seq[cur]), tm) == 1);
- p = cur;
- tempTuple.pos = p;
- tupleList.Append(tempTuple);
- for (p++; p < curValidEnd - tm.tupleSize + 1; p++) {
- tempTuple.tuple >>=2;
- // tempTuple.tuple &= maskLeftTuple.tuple;
- upperTuple.tuple = TwoBit[seq.seq[p+tm.tupleSize-1]];
- upperTuple.tuple = upperTuple.tuple << (2 * (tm.tupleSize-1));
- tempTuple.tuple += upperTuple.tuple;
- tempTuple.pos = p;
- //testTuple.FromStringRL(&seq.seq[p], tm);
- //assert(testTuple.tuple == tempTuple.tuple);
- tupleList.Append(tempTuple);
- }
- }
- else {
- ++curValidEnd;
- }
- }
- return tupleList.size();
-}
diff --git a/libcpp/alignment/tuples/DNATupleList.h b/libcpp/alignment/tuples/DNATupleList.h
deleted file mode 100644
index a5b0dae..0000000
--- a/libcpp/alignment/tuples/DNATupleList.h
+++ /dev/null
@@ -1,53 +0,0 @@
-#ifndef TUPLES_DNA_TUPLE_LIST_H_
-#define TUPLES_DNA_TUPLE_LIST_H_
-
-#include <vector>
-#include "DNATuple.h"
-
-
-
-
-
-template<typename Sequence>
- DNALength StoreTuplePosList(Sequence seq, TupleMetrics &tm, vector<PositionDNATuple> &tupleList) {
- //
- // Do this faster later on with a suffix tree -- faster than n log n construction time.
- //
- DNALength s;
-
- PositionDNATuple tempTuple;
- for (s = 0; s < seq.length - tm.tupleSize + 1; s++) {
- if (tempTuple.FromStringLR(&(seq.seq[s]), tm)) {
- tempTuple.pos = s;
- tupleList.push_back(tempTuple);
- }
- }
-
- std::sort(tupleList.begin(), tupleList.end());
-
- //
- // Be nice and leave the pos list in ascending sorted order,
- // even though the top of this function does not specify it.
- //
-
- return tupleList.size();
-}
-
-
-void WriteTuplePosList(vector<PositionDNATuple> &tupleList, int tupleSize, ofstream &out) {
- DNALength tupleListLength = tupleList.size();
- out.write((char*) &tupleSize, sizeof(tupleSize));
- out.write((char*) &tupleListLength, sizeof(DNALength));
- out.write((char*) &tupleList[0], sizeof(PositionDNATuple) * tupleList.size());
-}
-
-void ReadTuplePosList(ifstream &in, vector<PositionDNATuple> &tupleList, int &tupleSize) {
- DNALength tupleListLength;
- in.read((char*) &tupleSize, sizeof(int));
- in.read((char*) &tupleListLength, sizeof(DNALength));
- tupleList.resize(tupleListLength);
- in.read((char*) &tupleList[0], sizeof(PositionDNATuple) * tupleListLength);
-}
-
-
-#endif
diff --git a/libcpp/alignment/tuples/HashedTupleList.hpp b/libcpp/alignment/tuples/HashedTupleList.hpp
deleted file mode 100644
index 8695844..0000000
--- a/libcpp/alignment/tuples/HashedTupleList.hpp
+++ /dev/null
@@ -1,61 +0,0 @@
-#ifndef _BLASR_HASHED_TUPLE_LIST_HPP_
-#define _BLASR_HASHED_TUPLE_LIST_HPP_
-
-#include "tuples/TupleList.hpp"
-#include "tuples/TupleMetrics.hpp"
-#include "DNASequence.hpp"
-
-template<typename T_Tuple>
-class HashedTupleList {
-public:
- long mask;
- std::vector<TupleList<T_Tuple> > hashTable;
- int hashLength;
- int hashTableLength;
- typedef T_Tuple Tuple;
-
- //
- // Provide a default constructor with a small
- // tuple size for testing.
- //
- HashedTupleList();
-
- void Initialize(int _hashLength);
-
- HashedTupleList(int _hashLength);
-
- void clear();
-
- void Clear();
-
- void Sort();
-
- void Append(T_Tuple tuple);
-
- void Insert(T_Tuple tuple);
-
- int Find(T_Tuple tuple);
-
- void Print();
-
- //
- // Provide a version of find that stores easy access to
- // the original tuple.
- //
- int Find(T_Tuple tuple, int &hashValue, int &index);
-
- void FindAll(T_Tuple &tuple,
- typename std::vector<T_Tuple>::const_iterator &firstPos,
- typename std::vector<T_Tuple>::const_iterator &endPos);
-
- int GetHashLength();
-};
-
-
-template<typename T_Tuple>
-void SequenceToHash(DNASequence &seq, HashedTupleList<T_Tuple> &hash,
- TupleMetrics &tm);
-
-#include "tuples/HashedTupleList.hpp"
-
-#endif
diff --git a/libcpp/alignment/tuples/HashedTupleListImpl.hpp b/libcpp/alignment/tuples/HashedTupleListImpl.hpp
deleted file mode 100644
index 41d9832..0000000
--- a/libcpp/alignment/tuples/HashedTupleListImpl.hpp
+++ /dev/null
@@ -1,144 +0,0 @@
-#ifndef _BLASR_HASHED_TUPLE_LIST_IMPL_HPP_
-#define _BLASR_HASHED_TUPLE_LIST_IMPL_HPP_
-
-template<typename T_Tuple>
-HashedTupleList<T_Tuple>::
-HashedTupleList() {
- Initialize(5);
-}
-
-template<typename T_Tuple>
-HashedTupleList<T_Tuple>::
-HashedTupleList(int _hashLength) {
- Initialize(_hashLength);
- cout << hashTable.size() << endl;
-}
-
-template<typename T_Tuple>
-void HashedTupleList<T_Tuple>::
-Initialize(int _hashLength) {
- mask = 0;
- int i;
- hashLength = _hashLength;
- hashTable.resize(1L << (hashLength*2));
- hashTableLength = hashTable.size();
-
- for (i = 0; i < hashLength; i++ ){
- mask = mask << 2L;
- mask = mask + 3L;
- }
-}
-
-template<typename T_Tuple>
-void HashedTupleList<T_Tuple>::
-clear() {
- // Synonym.
- Clear();
-}
-
-template<typename T_Tuple>
-void HashedTupleList<T_Tuple>::
-Clear() {
- int i;
- for (i = 0; i < hashTableLength; i++ ){
- hashTable[i].tupleList.clear();
- }
-}
-
-
-template<typename T_Tuple>
-void HashedTupleList<T_Tuple>::
-Sort() {
- int i;
- for (i = 0; i < hashTableLength; i++ ){
- sort(hashTable[i].tupleList.begin(),
- hashTable[i].tupleList.end());
- }
-}
-
-template<typename T_Tuple>
-void HashedTupleList<T_Tuple>::
-Append(T_Tuple tuple) {
- int hashValue = tuple.tuple & mask;
- std::cout << "htl adding " << tuple.tuple << std::endl;
- hashTable[hashValue].tupleList.push_back(tuple);
-}
-
-
-template<typename T_Tuple>
-void HashedTupleList<T_Tuple>::
-Insert(T_Tuple tuple) {
- std::cout << "htl adding " << tuple.tuple << std::endl;
- int hashValue = tuple.tuple & mask;
- hashTable[hashValue].Insert(tuple);
-}
-
-template<typename T_Tuple>
-int HashedTupleList<T_Tuple>::
-Find(T_Tuple tuple) {
- int hashValue, index;
- return Find(tuple, hashValue, index);
-}
-
-
-template<typename T_Tuple>
-void HashedTupleList<T_Tuple>::
-Print() {
- int i;
- for (i = 0; i < hashTableLength; i++ ){
- hashTable[i].Print();
- }
-}
-
-//
-// Provide a version of find that stores easy access to
-// the original tuple.
-//
-template<typename T_Tuple>
-int HashedTupleList<T_Tuple>::
-Find(T_Tuple tuple, int &hashValue, int &index) {
- hashValue = tuple.tuple & mask;
- if (hashTable[hashValue].size()) {
- return ((index = hashTable[hashValue].Find(tuple)) != -1);
- }
- else {
- return 0;
- }
-}
-
-
-template<typename T_Tuple>
-void HashedTupleList<T_Tuple>::
-FindAll(T_Tuple &tuple,
- typename vector<T_Tuple>::const_iterator &firstPos,
- typename vector<T_Tuple>::const_iterator &endPos ) {
- int hashValue;
- hashValue = tuple.tuple & mask;
- hashTable[hashValue].FindAll(tuple, firstPos, endPos);
-}
-
-
-template<typename T_Tuple>
-int HashedTupleList<T_Tuple>::
-GetHashLength() {
- return hashLength;
-}
-
-
-template<typename T_Tuple>
-void SequenceToHash(DNASequence &seq, HashedTupleList<T_Tuple> &hash,
- TupleMetrics &tm) {
-
- int i;
- T_Tuple tuple;
- int res = 0;
- for (i = 0; i < seq.length - hash.hashLength + 1; i++ ) {
- if ((res and
- (res = tuple.ShiftAddRL(seq.seq[i+tm.tupleSize-1], tm))) or
- (!res and (res = tuple.FromStringRL(&seq.seq[i], tm)))) {
- hash.Insert(tuple);
- }
- }
-}
-
-#endif
diff --git a/libcpp/alignment/tuples/TupleCountTable.hpp b/libcpp/alignment/tuples/TupleCountTable.hpp
deleted file mode 100644
index 603ccd9..0000000
--- a/libcpp/alignment/tuples/TupleCountTable.hpp
+++ /dev/null
@@ -1,33 +0,0 @@
-#ifndef _BLASR_TUPLE_COUNT_TABLE_HPP_
-#define _BLASR_TUPLE_COUNT_TABLE_HPP_
-
-#include <algorithm>
-#include <fstream>
-#include <iostream>
-#include <assert.h>
-#include "tuples/TupleMetrics.hpp"
-using namespace std;
-
-template<typename TSequence, typename TTuple>
-class TupleCountTable {
-public:
- int *countTable;
- int countTableLength;
- int nTuples;
- TupleMetrics tm;
- bool deleteStructures;
- void InitCountTable(TupleMetrics &ptm);
-
- TupleCountTable();
- ~TupleCountTable();
- void Free();
-
- void IncrementCount(TTuple &tuple);
- void AddSequenceTupleCountsLR(TSequence &seq);
- void Write(ofstream &out);
- void Read(ifstream &in);
-};
-
-#include "tuples/TupleCountTableImpl.hpp"
-
-#endif
diff --git a/libcpp/alignment/tuples/TupleCountTableImpl.hpp b/libcpp/alignment/tuples/TupleCountTableImpl.hpp
deleted file mode 100644
index 805dc66..0000000
--- a/libcpp/alignment/tuples/TupleCountTableImpl.hpp
+++ /dev/null
@@ -1,101 +0,0 @@
-#ifndef _BLASR_TUPLE_COUNT_TABLE_IMPL_HPP_
-#define _BLASR_TUPLE_COUNT_TABLE_IMPL_HPP_
-
-using namespace std;
-
-template<typename TSequence, typename TTuple>
-void TupleCountTable<TSequence, TTuple>::InitCountTable(TupleMetrics &ptm) {
- Free();
- tm = ptm;
- tm.InitializeMask();
- assert(tm.tupleSize > 0);
- // create the mask just in case the ptm is not initialized
- // properly.
- countTableLength = 4;
- countTableLength = countTableLength << ((tm.tupleSize - 1)*2);
-
- assert(countTableLength > 0);
- countTable = new int[countTableLength];
- deleteStructures = true;
- fill(&countTable[0], &countTable[countTableLength], 0);
- nTuples = 0;
-}
-
-
-template<typename TSequence, typename TTuple>
-TupleCountTable<TSequence, TTuple>::TupleCountTable() {
- countTable = NULL;
- countTableLength = 0;
- nTuples = 0;
- deleteStructures = false;
-}
-
-
-template<typename TSequence, typename TTuple>
-TupleCountTable<TSequence, TTuple>::~TupleCountTable() {
- Free();
-}
-
-template<typename TSequence, typename TTuple>
-void TupleCountTable<TSequence, TTuple>::Free() {
- if (deleteStructures == false) {
- //
- // Do not delete this if it is referencing another structure
- //
- return;
- }
- if (countTable != NULL) {
- delete [] countTable;
- countTable = NULL;
- }
- countTableLength = nTuples = 0;
-}
-
-
-template<typename TSequence, typename TTuple>
-void TupleCountTable<TSequence, TTuple>::IncrementCount(
- TTuple &tuple) {
- long tupleIndex = tuple.ToLongIndex();
- assert(tupleIndex < countTableLength);
- countTable[tupleIndex]++;
- ++nTuples;
-}
-
-
-template<typename TSequence, typename TTuple>
-void TupleCountTable<TSequence, TTuple>::AddSequenceTupleCountsLR(
- TSequence &seq) {
- VectorIndex i;
- TTuple tuple;
- if (seq.length>= tm.tupleSize) {
- for (i = 0; i < seq.length - tm.tupleSize + 1; i++ ) {
- if (tuple.FromStringLR(&seq.seq[i], tm)) {
- IncrementCount(tuple);
- }
- }
- }
-}
-
-
-template<typename TSequence, typename TTuple>
-void TupleCountTable<TSequence, TTuple>::Write(ofstream &out) {
- out.write((char*) &countTableLength, sizeof(int));
- out.write((char*) &nTuples, sizeof(int));
- out.write((char*) &tm.tupleSize, sizeof(int));
- out.write((char*) countTable, sizeof(int) * countTableLength);
-}
-
-
-template<typename TSequence, typename TTuple>
-void TupleCountTable<TSequence, TTuple>::Read(ifstream &in) {
- Free(); // Clear before reusing this object.
- in.read((char*) &countTableLength, sizeof(int));
- in.read((char*) &nTuples, sizeof(int));
- in.read((char*) &tm.tupleSize, sizeof(int));
- tm.InitializeMask();
- countTable = new int[countTableLength];
- deleteStructures = true;
- in.read((char*) countTable, sizeof(int) * countTableLength);
-}
-
-#endif
diff --git a/libcpp/alignment/tuples/TupleList.hpp b/libcpp/alignment/tuples/TupleList.hpp
deleted file mode 100644
index 2f9eef0..0000000
--- a/libcpp/alignment/tuples/TupleList.hpp
+++ /dev/null
@@ -1,64 +0,0 @@
-#ifndef _BLASR_TUPLE_LIST_HPP_
-#define _BLASR_TUPLE_LIST_HPP_
-
-#include <stdint.h>
-#include <algorithm>
-#include <string>
-#include <iostream>
-#include <fstream>
-#include <vector>
-
-#include "Types.h"
-#include "tuples/TupleMetrics.hpp"
-
-template<typename T>
-class TupleList {
- int listLength;
- TupleMetrics tm;
- public:
- typedef T Tuple;
- std::vector<T> tupleList;
-
- TupleList();
-
- void Reset();
-
- T &operator[](int index);
-
- void GetTupleMetrics(TupleMetrics &ptm);
-
- void SetTupleMetrics(TupleMetrics &ptm);
-
- int size();
-
- int GetLength();
-
- int InitFromFile(std::string &fileName);
-
- void clear();
-
- int WriteToFile(std::string &fileName);
-
- //
- // Find one instance of a match.
- //
- int Find(T& tuple);
-
- //
- // Find the boundaries of all instances of a match.
- //
- void FindAll(T &tuple,
- typename std::vector<T>::const_iterator &firstPos,
- typename std::vector<T>::const_iterator &endPos );
-
- void Append( T&tuple);
-
- void Insert(T&tuple);
-
- void Sort();
-
- void Print();
-};
-
-#include "TupleListImpl.hpp"
-#endif // _BLASR_TUPLE_LIST_HPP_
diff --git a/libcpp/alignment/tuples/TupleListImpl.hpp b/libcpp/alignment/tuples/TupleListImpl.hpp
deleted file mode 100644
index fdbf91f..0000000
--- a/libcpp/alignment/tuples/TupleListImpl.hpp
+++ /dev/null
@@ -1,134 +0,0 @@
-
-template<typename T>
-TupleList<T>::TupleList() {
- listLength = 0;
-}
-
-template<typename T>
-void TupleList<T>::Reset() {
- std::vector<T>().swap(tupleList);
-}
-
-template<typename T>
-T& TupleList<T>::operator[](int index) {
- return tupleList[index];
-}
-
-template<typename T>
-void TupleList<T>::GetTupleMetrics(TupleMetrics &ptm) {
- ptm = tm;
-}
-
-template<typename T>
-void TupleList<T>::SetTupleMetrics(TupleMetrics &ptm) {
- tm = ptm;
-}
-
-template<typename T>
-int TupleList<T>::size() {
- return tupleList.size();
-}
-
-template<typename T>
-int TupleList<T>::GetLength() {
- return tupleList.size();
-}
-
-template<typename T>
-int TupleList<T>::InitFromFile(std::string &fileName) {
- std::ifstream listIn;
- listIn.open(fileName.c_str(), std::ios_base::binary);
- if (!listIn)
- return 0;
- listIn.read((char*) &listLength, sizeof(int));
- listIn.read((char*) &tm.tupleSize, sizeof(int));
- tm.InitializeMask();
- //list = new T[listLength];
- tupleList.resize(listLength);
- listIn.read((char*) &tupleList[0], sizeof(T) * listLength);
- return 1;
-}
-
-template<typename T>
-void TupleList<T>::clear() {
- tupleList.clear();
- listLength = 0;
-}
-
-template<typename T>
-int TupleList<T>::WriteToFile(std::string &fileName) {
- std::ofstream listOut;
- listOut.open(fileName.c_str(), std::ios_base::binary);
- if (!listOut)
- return 0;
- listLength = tupleList.size();
- std::cout << "writing tuple lis of length " << listLength << std::endl;
- listOut.write((char*) &listLength, sizeof(int));
- listOut.write((char*) &tm.tupleSize, sizeof(int));
- listOut.write((char*) &tupleList[0], sizeof(T)*listLength);
- return 1;
-}
-
-//
-// Find one instance of a match.
-//
-template<typename T>
-int TupleList<T>::Find( T& tuple) {
- typename std::vector<T>::const_iterator begin, end, matchIt;
- begin = tupleList.begin();
- end = tupleList.end();
- matchIt = lower_bound(begin, end, tuple);
- if (*matchIt != tuple) {
- return -1;
- }
- else {
- return matchIt - tupleList.begin();
- }
-}
-
-//
-// Find the boundaries of all instances of a match.
-//
-template<typename T>
-void TupleList<T>::FindAll(T &tuple,
- typename std::vector<T>::const_iterator &firstPos,
- typename std::vector<T>::const_iterator &endPos ) {
- firstPos = lower_bound(tupleList.begin(), tupleList.end(), tuple);
- typename std::vector<T>::const_iterator firstPos2;
- endPos = tupleList.end();
- endPos = upper_bound(firstPos, endPos, tuple);
- while (endPos != tupleList.end()) {
- if (*endPos != tuple) {
- return;
- }
- else {
- endPos++;
- }
- }
-}
-
-template<typename T>
-void TupleList<T>::Append( T&tuple) {
- tupleList.push_back(tuple);
-}
-
-template<typename T>
-void TupleList<T>::Insert(T&tuple) {
- // insert and maintain order.
- typename std::vector<T>::iterator pos;
- pos = std::lower_bound(tupleList.begin(), tupleList.end(), tuple);
- tupleList.insert(pos, tuple);
-}
-
-template<typename T>
-void TupleList<T>::Sort() {
- sort(tupleList.begin(), tupleList.end());
-}
-
-template<typename T>
-void TupleList<T>::Print() {
- int i;
- for (i = 0; i< tupleList.size(); i++) {
- std::cout << tupleList[i].tuple << std::endl;
- }
-}
diff --git a/libcpp/alignment/tuples/TupleMask.h b/libcpp/alignment/tuples/TupleMask.h
deleted file mode 100644
index f731db1..0000000
--- a/libcpp/alignment/tuples/TupleMask.h
+++ /dev/null
@@ -1,13 +0,0 @@
-#ifndef TUPLES_TUPLE_MASK
-#define TUPLES_TUPLE_MASK
-//
-// Each f is conveniently 2 bases.
-//
-//
-static unsigned long TupleMask[] = {0, 0xf, 0xff, 0xfff, 0xffff, 0xfffff, 0xffffff, // 0 - 6
- 0xfffffff, 0xfffffff, 0xffffffff, 0xfffffffff, // 7 - 9
- 0xffffffffff, 0xfffffffffff, 0xffffffffffff, // 10-12
- 0xfffffffffffff, 0xffffffffffffff, 0xfffffffffffffff, // 13-15
- 0xffffffffffffffff}; // 16
-
-#endif
diff --git a/libcpp/alignment/tuples/TupleMatching.hpp b/libcpp/alignment/tuples/TupleMatching.hpp
deleted file mode 100644
index dd8c01e..0000000
--- a/libcpp/alignment/tuples/TupleMatching.hpp
+++ /dev/null
@@ -1,25 +0,0 @@
-#ifndef _BLASR_TUPLE_MATCHING_HPP_
-#define _BLASR_TUPLE_MATCHING_HPP_
-
-#include "tuples/TupleMetrics.hpp"
-#include "tuples/TupleList.hpp"
-#include "tuples/BaseTuple.hpp"
-#include "tuples/DNATuple.hpp"
-#include "tuples/TupleMatching.hpp"
-
-template<typename Sequence, typename T_TupleList>
-int SequenceToTupleList(
- Sequence &seq, TupleMetrics &tm, T_TupleList &tupleList);
-
-template<typename TSequence, typename TMatch, typename T_TupleList>
-int StoreMatchingPositions(
- TSequence &querySeq, TupleMetrics &tm, T_TupleList &targetTupleList,
- std::vector<TMatch> &matchSet);
-
-template<typename Sequence, typename Tuple>
-int StoreUniqueTuplePosList(Sequence seq, TupleMetrics &tm,
- std::vector<int> &uniqueTuplePosList);
-
-#include "TupleMatchingImpl.hpp"
-
-#endif // _BLASR_TUPLE_MATCHING_HPP_
diff --git a/libcpp/alignment/tuples/TupleMatchingImpl.hpp b/libcpp/alignment/tuples/TupleMatchingImpl.hpp
deleted file mode 100644
index c89a247..0000000
--- a/libcpp/alignment/tuples/TupleMatchingImpl.hpp
+++ /dev/null
@@ -1,106 +0,0 @@
-#include <vector>
-#include <algorithm>
-#include <utility>
-#include <iostream>
-#include <stdint.h>
-#include "Types.h"
-#include "NucConversion.hpp"
-#include "DNASequence.hpp"
-#include "SeqUtils.hpp"
-
-using namespace std;
-
-template<typename Sequence, typename T_TupleList>
-int SequenceToTupleList(Sequence &seq, TupleMetrics &tm, T_TupleList &tupleList) {
- int s;
- typename T_TupleList::Tuple tempTuple;
- if (seq.size() < tm.tupleSize) {
- return 1;
- }
-
- // Otherwise, there is at least one tuple
-
- tupleList.Append(tempTuple);
- int res = 0;
- for (s = 0; s < seq.length - tm.tupleSize + 1; s++ ) {
- if ((res and (res = tempTuple.ShiftAddRL(seq.seq[s+tm.tupleSize-1], tm))) or
- (!res and (res = tempTuple.FromStringRL(&seq.seq[s], tm)))) {
- tempTuple.ShiftAddRL(seq.seq[s + tm.tupleSize - 1], tm);
- tempTuple.pos = s;
- tupleList.Append(tempTuple);
- }
- }
- return 1;
-}
-
-
-template<typename TSequence, typename TMatch, typename T_TupleList>
-int StoreMatchingPositions(TSequence &querySeq, TupleMetrics &tm, T_TupleList &targetTupleList, vector<TMatch> &matchSet) {
- DNALength s;
- // TQueryTuple queryTuple;
- typename T_TupleList::Tuple queryTuple;
- queryTuple.pos = 0;
- if (querySeq.length >= tm.tupleSize) {
- int res = 0;
- for (s = 0; s < querySeq.length - tm.tupleSize + 1; s++) {
- if ((res and (res = queryTuple.ShiftAddRL(querySeq.seq[s+tm.tupleSize-1], tm))) or
- (!res and (res = queryTuple.FromStringRL(&querySeq.seq[s], tm)))) {
- int targetListIndex = 0;
- typename vector<typename T_TupleList::Tuple>::const_iterator curIt, endIt;
- targetTupleList.FindAll(queryTuple, curIt, endIt);
-
- for(; curIt != endIt; curIt++) {
- matchSet.push_back(TMatch(s, (*curIt).pos));
- ++targetListIndex;
- }
- }
- }
- }
- return matchSet.size();
-}
-
-
-template<typename Sequence, typename Tuple>
-int StoreUniqueTuplePosList(Sequence seq, TupleMetrics &tm, vector<int> &uniqueTuplePosList) {
- //
- // Do this faster later on with a suffix tree -- faster than n log n construction time.
- //
- int s;
- vector<pair<Tuple, int> > tuples;
- Tuple tempTuple;
- for (s = 0; s < seq.length - tm.tupleSize + 1; s++) {
- tempTuple.FromStringRL(&(seq.seq[s]), tm);
- tuples.push_back(make_pair(tempTuple, s));
- }
- std::sort(tuples.begin(), tuples.end());
- int curUnique = 0, curPos = 0;
-
- //
- // Filter out the repetitive tuples.
- //
-
- while ( curPos < tuples.size() ) {
- int nextPos = curPos;
-
- while (nextPos < tuples.size() and tuples[nextPos] == tuples[curPos])
- nextPos++;
- if (nextPos - curPos == 1) {
- tuples[curUnique].first == tuples[curPos].first;
- uniqueTuplePosList.push_back(tuples[curUnique].second);
- ++curUnique;
- ++curPos;
- }
- else {
- curPos = nextPos;
- }
- }
-
- //
- // Be nice and leave the pos list in ascending sorted order,
- // even though the top of this function does not specify it.
- //
- std::sort(uniqueTuplePosList.begin(), uniqueTuplePosList.end());
- return uniqueTuplePosList.size();
-}
-
-
diff --git a/libcpp/alignment/tuples/TupleMetrics.cpp b/libcpp/alignment/tuples/TupleMetrics.cpp
deleted file mode 100644
index 5b00a7b..0000000
--- a/libcpp/alignment/tuples/TupleMetrics.cpp
+++ /dev/null
@@ -1,16 +0,0 @@
-#include <stdint.h>
-#include "TupleMask.h"
-#include "TupleMetrics.hpp"
-
-TupleMetrics::TupleMetrics() {
- tupleSize = tupleMask = 0;
-}
-
-void TupleMetrics::InitializeMask() {
- tupleMask = TupleMask[tupleSize];
-}
-
-void TupleMetrics::Initialize(int pTupleSize) {
- tupleSize = pTupleSize;
- InitializeMask();
-}
diff --git a/libcpp/alignment/tuples/TupleMetrics.hpp b/libcpp/alignment/tuples/TupleMetrics.hpp
deleted file mode 100644
index 841aaf2..0000000
--- a/libcpp/alignment/tuples/TupleMetrics.hpp
+++ /dev/null
@@ -1,19 +0,0 @@
-#ifndef _BLASR_TUPLE_METRICS_HPP_
-#define _BLASR_TUPLE_METRICS_HPP_
-
-#include "Types.h"
-
-class TupleMetrics {
-public:
- unsigned int tupleSize;
- ULong tupleMask;
-
- TupleMetrics();
-
- void InitializeMask();
-
- void Initialize(int pTupleSize);
-};
-
-
-#endif //_BLASR_TUPLE_METRICS_HPP_
diff --git a/libcpp/alignment/tuples/TupleOperations.h b/libcpp/alignment/tuples/TupleOperations.h
deleted file mode 100644
index 2c7d13e..0000000
--- a/libcpp/alignment/tuples/TupleOperations.h
+++ /dev/null
@@ -1,7 +0,0 @@
-#ifndef TUPLE_OPERATIONS_H_
-#define TUPLE_OPERATIONS_H_
-
-
-#endif
-
-
diff --git a/libcpp/alignment/tuples/TupleTranslations.h b/libcpp/alignment/tuples/TupleTranslations.h
deleted file mode 100644
index a96cf15..0000000
--- a/libcpp/alignment/tuples/TupleTranslations.h
+++ /dev/null
@@ -1,4 +0,0 @@
-#ifndef TUPLE_OPERATIONS_H_
-#define TUPLE_OPERATIONS_H_
-
-
diff --git a/libcpp/alignment/tuples/tuple.h b/libcpp/alignment/tuples/tuple.h
deleted file mode 100644
index 5063f08..0000000
--- a/libcpp/alignment/tuples/tuple.h
+++ /dev/null
@@ -1,82 +0,0 @@
-#ifndef TUPLE_H_
-#define TUPLE_H_
-
-#include <vector>
-#include <utility>
-
-#include "Types.h"
-#include "tuples/TupleMetrics.hpp"
-
-template<typename Sequence, typename Tuple>
- BuildTupleList(Sequence seq, vector<Tuple> &tupleList) {
- BuildTupleList(seq, 0, seq.length, tupleList);
- }
-
-template<typename Sequence, typename Tuple>
- BuildTupleList(Sequence seq, int seqStart, int length, vector<Tuple> &tupleList) {
-
- }
-
-template<typename Sequence, typename CountedTuple>
- BuildCountedTupleList(Sequence seq, int seqStart, int length, TupleMetrics &tm, vector<CountedTuple> &tupleList) {
- int s;
- CountedTuple tuple;
- for (s = 0; s < seq.length - tm.tupleSize + 1; s++) {
- }
- }
-
-
-template<typename Sequence, typename Tuple>
- StoreUniqueTuplePosList(Sequence seq, TupleMetrics &tm, vector<int> &uniqueTuplePosList) {
- //
- // Do this faster later on with a suffix tree -- faster than n log n construction time.
- //
- int s;
- vector<pair<Tuple, int> > tuples;
- Tuple tempTuple;
- for (s = 0; s < seq.length; s++) {
- tempTuple.FromStringLR(&(seq.seq[s]), tm);
- tuples.push_back(make_pair(tempTuple, s));
- }
- std::sort(tuples.begin(), tuples.end());
- int curUnique = 0, curPos = 0;
-
- //
- // Filter out the repetitive tuples.
- //
-
- while ( curPos < tuples.size() ) {
- int nextPos = curPos;
-
- while (nextPos < tuples.size() and tuples[nextPos] == tuples[curPos])
- nextPos++;
- if (nextPos - curPos == 1) {
- tuples[curUnique].first == tuples[curPos].first;
- uniqueTuplePosList.push_back(tuples[curUnique].second);
- ++curUnique;
- ++curPos;
- }
- else {
- curPos = nextPos;
- }
- }
-
- //
- // Be nice and leave the pos list in ascending sorted order,
- // even though the top of this function does not specify it.
- //
- std::sort(uniqueTuplePosList.begin(), uniqueTuplePosList.end());
- }
-
-
-
-
-
-
-
-
-
-
-
-
-#endif
diff --git a/libcpp/alignment/utils/FileOfFileNames.cpp b/libcpp/alignment/utils/FileOfFileNames.cpp
deleted file mode 100644
index da738bd..0000000
--- a/libcpp/alignment/utils/FileOfFileNames.cpp
+++ /dev/null
@@ -1,102 +0,0 @@
-#include "utils/FileOfFileNames.hpp"
-#include "HDFNewBasReader.hpp"
-#include <cstdlib>
-
-void
-FileOfFileNames::StoreFileOrFileList(std::string fileName,
- std::vector<std::string> &fofnList) {
-
- std::vector<std::string> tmpList;
- if (IsFOFN(fileName)) {
- FOFNToList(fileName, tmpList);
- }
- else {
- tmpList.push_back(fileName);
- }
- for (int i = 0; i < int(tmpList.size()); i++) {
- if (FileOfFileNames::IsFOFN(tmpList[i])) {
- std::cout << "ERROR. Nested File of File Names are not allowed. "
- << std::endl;
- exit(1);
- } else if (FileOfFileNames::IsBasH5(tmpList[i])) {
- std::vector<std::string> baxFNs = FileOfFileNames::Bas2Bax(tmpList[i]);
- fofnList.insert(fofnList.end(), baxFNs.begin(), baxFNs.end());
- } else {
- fofnList.push_back(tmpList[i]);
- }
- }
-}
-
-void
-FileOfFileNames::FOFNToList(std::string &fofnFileName,
- std::vector<std::string> &fofnList) {
- std::ifstream fofnIn;
- CrucialOpen(fofnFileName, fofnIn);
- while(fofnIn) {
- std::string name;
- getline(fofnIn, name);
- if (name.size() > 0) {
- fofnList.push_back(name);
- }
- }
-}
-
-bool
-FileOfFileNames::IsFOFN(std::string &fileName) {
- std::string::size_type dotPos = fileName.rfind(".");
- if (dotPos != std::string::npos) {
- std::string extension;
- extension.assign(fileName, dotPos+1, fileName.size() - (dotPos+1));
- if (extension == "fofn") {
- return true;
- }
- }
- return false;
-}
-
-bool
-FileOfFileNames::IsBasH5(std::string & fileName) {
- // Return true if file ends with bas.h5
- if (fileName.size() > 6) {
- if (fileName.rfind("bas.h5") == fileName.size() - 6) {
- return true;
- }
- }
- return false;
-}
-
-std::vector<std::string>
-FileOfFileNames::Bas2Bax(std::string & basFN) {
- // There are two types of bas.h5 files.
- // Before SMRT 2.0, bas.h5 files contain all the /PulseData data,
- // in this case, return the bas.h5.
- // After SMRT 2.0, bas.h5 files have been changed to only contain
- // paths to bax.h5 files (in the /MultiPart/Parts group), while
- // all base calls and QVs are in bax.h5 files. In this case,
- // return path to the bax.h5 files. Assumption is that bax.h5
- // files are in the same directory as bas.h5 file.
- vector<string> baxFNs;
- HDFNewBasReader reader;
- if (reader.Initialize(basFN) != 0) {
- baxFNs = reader.GetBaxFileNames();
- } else {
- baxFNs.push_back(basFN);
- }
- reader.Close();
- return baxFNs;
-}
-
-
-int
-FileOfFileNames::ExpandFileNameList(std::vector<std::string> &fileNames) {
- int rfn;
- std::vector<std::string> expandedFileNames;
- for (rfn = 0; rfn < fileNames.size(); rfn++) {
- std::vector<std::string> tmpList;
- FileOfFileNames::StoreFileOrFileList(fileNames[rfn], tmpList);
- expandedFileNames.insert(expandedFileNames.end(),
- tmpList.begin(), tmpList.end());
- }
- fileNames = expandedFileNames;
- return fileNames.size();
-}
diff --git a/libcpp/alignment/utils/FileOfFileNames.hpp b/libcpp/alignment/utils/FileOfFileNames.hpp
deleted file mode 100644
index 2aef7c6..0000000
--- a/libcpp/alignment/utils/FileOfFileNames.hpp
+++ /dev/null
@@ -1,27 +0,0 @@
-#ifndef _BLASR_FILE_OF_FILE_NAMES_HPP_
-#define _BLASR_FILE_OF_FILE_NAMES_HPP_
-
-#include <iostream>
-#include <string>
-#include <vector>
-#include <fstream>
-#include "utils.hpp"
-
-class FileOfFileNames {
-public:
- static void StoreFileOrFileList(std::string fileName,
- std::vector<std::string> &fofnList);
-
- static void FOFNToList(std::string &fofnFileName,
- std::vector<std::string> &fofnList);
-
- static bool IsFOFN(std::string &fileName);
-
- static bool IsBasH5(std::string &fileName);
-
- static std::vector<std::string> Bas2Bax(std::string &basFN);
-
- static int ExpandFileNameList(std::vector<std::string> &fileNames);
-};
-
-#endif
diff --git a/libcpp/alignment/utils/FileUtils.cpp b/libcpp/alignment/utils/FileUtils.cpp
deleted file mode 100644
index 84813e8..0000000
--- a/libcpp/alignment/utils/FileUtils.cpp
+++ /dev/null
@@ -1,61 +0,0 @@
-#include "utils/FileUtils.hpp"
-
-using namespace std;
-
-bool FileExists(string &fileName) {
- FILE *fp = fopen(fileName.c_str(),"r");
- if( fp ) {
- // exists
- fclose(fp);
- return true;
- }
- else {
- return false;
- }
-}
-
-void CriticalOpenRead(string &fileName, ifstream &file, std::ios::openmode mode) {
- file.open(fileName.c_str(), mode | std::ios::in);
- if (!file.good()) {
- cerr << "Could not open file:" << fileName << endl;
- exit(1);
- }
-}
-
-int OpenRead(string &fileName, ifstream &file, std::ios::openmode mode) {
- file.open(fileName.c_str(), mode | std::ios::in);
- return file.good();
-}
-
-
-void CriticalOpenWrite(string &fileName, ofstream &file, std::ios::openmode mode) {
- file.open(fileName.c_str(), mode | std::ios::out);
- if (!file.good()) {
- cerr << "Could not open file: " << fileName << endl;
- exit(1);
- }
-}
-
-int OpenWrite(string &fileName, ofstream &file, std::ios::openmode mode) {
- file.open(fileName.c_str(), mode | std::ios::out);
- return file.good();
-}
-
-
-int CountLinesInFile(string fileName) {
- char* filePtr;
- long fileSize;
- int fileDes;
- fileDes = open(fileName.c_str(), O_RDONLY);
- fileSize = lseek(fileDes, 0, SEEK_END);
- lseek(fileDes, 0, SEEK_SET);
- filePtr = (char*) mmap(0, fileSize, PROT_READ, MAP_PRIVATE, fileDes, 0);
- long pos;
- int numLines = 0;
- for (pos = 0; pos < fileSize; pos++, filePtr++) {
- if (*filePtr == '\n') {
- numLines++;
- }
- }
- return numLines;
-}
diff --git a/libcpp/alignment/utils/FileUtils.hpp b/libcpp/alignment/utils/FileUtils.hpp
deleted file mode 100644
index 7457b33..0000000
--- a/libcpp/alignment/utils/FileUtils.hpp
+++ /dev/null
@@ -1,27 +0,0 @@
-#ifndef _BLASR_FILE_UTILS_HPP_
-#define _BLASR_FILE_UTILS_HPP_
-
-#include <iostream>
-#include <fstream>
-#include <string>
-#include "sys/fcntl.h"
-#include "sys/mman.h"
-#include <sys/types.h> // for lseek
-#include <unistd.h> // for lseek
-#include <stdio.h>
-
-using namespace std;
-
-bool FileExists(string &fileName);
-
-void CriticalOpenRead(string &fileName, ifstream &file, std::ios::openmode mode=std::ios::in);
-
-int OpenRead(string &fileName, ifstream &file, std::ios::openmode mode=std::ios::in);
-
-void CriticalOpenWrite(string &fileName, ofstream &file, std::ios::openmode mode=std::ios::out);
-
-int OpenWrite(string &fileName, ofstream &file, std::ios::openmode mode=std::ios::out);
-
-int CountLinesInFile(string fileName);
-
-#endif
diff --git a/libcpp/alignment/utils/LogUtils.cpp b/libcpp/alignment/utils/LogUtils.cpp
deleted file mode 100644
index 018d7bc..0000000
--- a/libcpp/alignment/utils/LogUtils.cpp
+++ /dev/null
@@ -1,55 +0,0 @@
-#include "LogUtils.hpp"
-
-double LogSumOfTwo(double value1, double value2) {
- //
- // value1 and value2 are in log space already.
- //
- double minValue, maxValue;
- minValue = value1, maxValue = value2;
-
- if (maxValue < minValue) {
- minValue = value2; maxValue = value1;
- }
-
- // convert to log10
- minValue *= LOG10;
- maxValue *= LOG10;
-
- double difference = minValue - maxValue;
-
- if (difference < LOG_EPSILON) {
- return maxValue / LOG10;
- }
- else if (difference < LOG_EPSILON2) {
- return (maxValue + exp(difference))/LOG10;
- }
- else {
- float expv = exp(difference);
- float log1pv = log1p(expv);
- return (maxValue + log1pv)/LOG10;
- }
-}
-
-double LogSumOfThree(double value1, double value2, double value3) {
- double minValue, maxValue, middleValue;
- if (value1 > value2 and value2 > value3) {
- maxValue = value1; middleValue = value2; minValue = value3;
- }
- else if (value1 > value3 and value3 > value2) {
- maxValue = value1; middleValue = value3; minValue = value2;
- }
- else if (value2 > value1 and value1 > value3) {
- maxValue = value2; middleValue = value1; minValue = value3;
- }
- else if (value2 > value3 and value3 > value1) {
- maxValue = value2; middleValue = value3; minValue = value1;
- }
- else if (value3 > value1 and value1 > value2) {
- maxValue = value3; middleValue = value1; minValue = value2;
- }
- else {
- maxValue = value3; middleValue = value2; minValue = value1;
- }
- return LogSumOfTwo(maxValue, LogSumOfTwo(middleValue, minValue));
-}
-
diff --git a/libcpp/alignment/utils/LogUtils.hpp b/libcpp/alignment/utils/LogUtils.hpp
deleted file mode 100644
index 16f2ecd..0000000
--- a/libcpp/alignment/utils/LogUtils.hpp
+++ /dev/null
@@ -1,15 +0,0 @@
-#ifndef _BLASR_UTILS_SUM_OF_LOG_HPP_
-#define _BLASR_UTILS_SUM_OF_LOG_HPP_
-
-#include <math.h>
-
-#define LOG_EPSILON -30
-#define LOG_EPSILON2 -8
-#define LOG_EPSILON4 (logEpsilon/4.0)
-#define LOG10 2.3025850929
-
-double LogSumOfTwo(double value1, double value2);
-
-double LogSumOfThree(double value1, double value2, double value3);
-
-#endif // _BLASR_UTILS_SUM_OF_LOG_HPP_
diff --git a/libcpp/alignment/utils/PhredUtils.cpp b/libcpp/alignment/utils/PhredUtils.cpp
deleted file mode 100644
index b2653d0..0000000
--- a/libcpp/alignment/utils/PhredUtils.cpp
+++ /dev/null
@@ -1,13 +0,0 @@
-#include <math.h>
-#include "PhredUtils.hpp"
-
-double InversePhred(double phred) {
- float num = 1;
- float denom = (1+pow(10,phred/10));
- return num/denom;
-}
-
-double Phred(double pvalue) {
- double v = log10(pvalue);
- return -10*v;
-}
diff --git a/libcpp/alignment/utils/PhredUtils.hpp b/libcpp/alignment/utils/PhredUtils.hpp
deleted file mode 100644
index c90dbdd..0000000
--- a/libcpp/alignment/utils/PhredUtils.hpp
+++ /dev/null
@@ -1,8 +0,0 @@
-#ifndef _BLASR_UTILS_PHRED_UTILS_HPP_
-#define _BLASR_UTILS_PHRED_UTILS_HPP_
-
-double InversePhred(double phred);
-
-double Phred(double pvalue);
-
-#endif // _BLASR_UTILS_PHRED_UTILS_HPP_
diff --git a/libcpp/alignment/utils/RangeUtils.cpp b/libcpp/alignment/utils/RangeUtils.cpp
deleted file mode 100644
index 90a1458..0000000
--- a/libcpp/alignment/utils/RangeUtils.cpp
+++ /dev/null
@@ -1,107 +0,0 @@
-
-#include <stdexcept>
-
-#include "RangeUtils.hpp"
-
-using namespace std;
-
-Range::Range(UInt pStart) {
- start = end = pStart;
-}
-Range::Range(UInt pStart, UInt pEnd) {
- start = pStart;
- end = pEnd;
- if (start > end) {
- cout << "ERROR: start of a range should be less than the end."
- << endl;
- exit(1);
- }
-}
-
-bool Range::contains(const UInt & query) {
- return (start <= query && query <= end);
-}
-bool Range::operator < (const Range & pRange) const {
- if (start == pRange.start) {
- return (end > pRange.end);
- }
- return (start < pRange.start);
-}
-
-//
-// Input is a comma-delimited string of ranges.
-// e.g. 1,2,3,10-20
-bool ParseRanges(string & rangesStr, vector<Range> & ranges) {
- ranges.clear();
- bool parseSucceed = true;
- vector<string> strList;
- ParseSeparatedList(rangesStr, strList, ',');
- for(int i=0; i<int(strList.size()); i++) {
- string & str = strList[i];
- if(str.find('-') == string::npos) {
- ranges.push_back(Range(atoi(str.c_str())));
- } else {
- vector<string> start_end;
- ParseSeparatedList(str, start_end, '-');
- if (start_end.size() != 2) {
- parseSucceed = false;
- break;
- }
- ranges.push_back(Range(atoi(start_end[0].c_str()),
- atoi(start_end[1].c_str())));
- }
- }
- if (parseSucceed) {
- sort(ranges.begin(), ranges.end());
- } else {
- ranges.clear();
- }
- return parseSucceed;
-}
-
-Ranges::Ranges(string rangesStr) {
- if (!ParseRanges(rangesStr, ranges))
- throw std::invalid_argument("bad range");
-}
-
-bool Ranges::setRanges(string rangesStr) {
- return ParseRanges(rangesStr, ranges);
-}
-
-int Ranges::size() {
- return ranges.size();
-}
-
-UInt Ranges::max() {
- if (size() == 0) {
- cout << "ERROR, could not determine the maximum value "
- << "of an empty Ranges object." << endl;
- exit(1);
- }
- return ranges.back().end;
-}
-
-bool Ranges::contains(const UInt & query) {
- if (ranges.size() == 0) return false;
- vector<Range> searchRanges;
- searchRanges.push_back(Range(0, ranges.size()-1));
- while (searchRanges.size() > 0) {
- Range searchRange = searchRanges.back();
- searchRanges.pop_back();
- UInt mid = (searchRange.start + searchRange.end) / 2;
- if (ranges[mid].contains(query)) {
- return true;
- }
- if (mid > 0 && searchRange.start <= mid - 1) {
- searchRanges.push_back(Range(searchRange.start,
- mid - 1));
- }
- if (ranges[mid].start <= query and
- searchRange.end >= mid + 1) {
- searchRanges.push_back(Range(mid + 1,
- searchRange.end));
- }
- }
- return false;
-}
-
diff --git a/libcpp/alignment/utils/RangeUtils.hpp b/libcpp/alignment/utils/RangeUtils.hpp
deleted file mode 100644
index b0a41ba..0000000
--- a/libcpp/alignment/utils/RangeUtils.hpp
+++ /dev/null
@@ -1,56 +0,0 @@
-/*
- * ============================================================================
- *
- * Filename: RangeUtils.h
- *
- * Description: Parse a list of ranges separated by commas.
- * Designed for specifying a set of holeNumbers to analyze.
- *
- * Version: 1.0
- * Created: 05/02/2013 12:51:27 PM
- * Revision: none
- * Compiler: gcc
- *
- * Author: Yuan Li (yli), yli at pacificbiosciences.com
- * Company: Pacific Biosciences
- *
- * ============================================================================
- */
-#include <stdlib.h>
-#include <algorithm>
-#include "StringUtils.hpp"
-#include "Types.h"
-
-class Range {
-public:
- UInt start; // Start position of a range, inclusive
- UInt end; // End position of a range, inclusive
-
- Range(UInt pStart);
-
- Range(UInt pStart, UInt pEnd);
-
- bool contains(const UInt & query);
-
- bool operator < (const Range & pRange) const;
-};
-
-// Input is a comma-delimited string of ranges.
-// e.g. 1,2,3,10-20
-bool ParseRanges(string & rangesStr, vector<Range> & ranges);
-
-class Ranges {
-public:
- std::vector<Range> ranges;
- Ranges(std::string rangesStr="");
-
- bool setRanges(std::string rangesStr);
-
- int size();
-
- UInt max();
-
- bool contains(const UInt & query);
-};
-
-
diff --git a/libcpp/alignment/utils/RegionUtils.cpp b/libcpp/alignment/utils/RegionUtils.cpp
deleted file mode 100644
index 0448f2e..0000000
--- a/libcpp/alignment/utils/RegionUtils.cpp
+++ /dev/null
@@ -1,302 +0,0 @@
-#include "utils/RegionUtils.hpp"
-
-// General functions.
-bool LookupHQRegion(int holeNumber, RegionTable ®ionTable,
- int &start, int &end, int &score) {
-
- int regionLowIndex, regionHighIndex;
- regionLowIndex = regionHighIndex = 0;
-
- regionTable.LookupRegionsByHoleNumber(holeNumber,
- regionLowIndex, regionHighIndex);
-
- bool readHasGoodRegion = true;
- int regionIndex = regionLowIndex;
- while (regionIndex < regionHighIndex and
- regionTable.GetType(regionIndex) != HQRegion) {
- regionIndex++;
- }
-
- if (regionIndex == regionHighIndex) {
- start = end = score = 0;
- return false;
- }
- else {
- start = regionTable.GetStart(regionIndex);
- end = regionTable.GetEnd(regionIndex);
- score = regionTable.GetScore(regionIndex);
- return true;
- }
-}
-
-// Functions of class CompareRegionIndicesByStart.
-int CompareRegionIndicesByStart::
-operator()(const int a, const int b) const {
- if (regionTablePtr->GetStart(a) == regionTablePtr->GetStart(b)) {
- return (regionTablePtr->GetEnd(a) < regionTablePtr->GetEnd(b));
- }
- else {
- return (regionTablePtr->GetStart(a) < regionTablePtr->GetStart(b));
- }
-}
-
-// General functions.
-int SortRegionIndicesByStart(RegionTable ®ionTable,
- std::vector<int> &indices) {
-
- CompareRegionIndicesByStart cmpFctr;
- cmpFctr.regionTablePtr = ®ionTable;
- std::sort(indices.begin(), indices.end(), cmpFctr);
- return indices.size();
-}
-
-
-// Functions of OrderRegionsByReadStart:
-int OrderRegionsByReadStart::
-operator()(const ReadInterval &lhs, const ReadInterval &rhs) const {
- return lhs.start < rhs.start;
-}
-
-
-// General functions.
-int FindRegionIndices(unsigned int holeNumber, RegionTable *regionTablePtr,
- int ®ionLowIndex, int ®ionHighIndex) {
-
- int regionIndex;
- regionLowIndex = regionHighIndex = 0;
-
- regionTablePtr->LookupRegionsByHoleNumber(holeNumber,
- regionLowIndex, regionHighIndex);
-
- return regionHighIndex - regionLowIndex;
-}
-
-
-int FindRegionIndices(SMRTSequence &read, RegionTable *regionTablePtr,
- int ®ionLowIndex, int ®ionHighIndex) {
- return FindRegionIndices(read.zmwData.holeNumber,
- regionTablePtr, regionLowIndex, regionHighIndex);
-}
-
-
-//
-// Collect region indices for either all region types, or just a few specific region types.
-//
-//
-int CollectRegionIndices(SMRTSequence &read, RegionTable ®ionTable,
- std::vector<int> ®ionIndices, RegionType *regionTypes,
- int numRegionTypes) {
-
- int regionLow, regionHigh;
- int prevNumRegionIndices = regionIndices.size();
- if (FindRegionIndices(read, ®ionTable, regionLow, regionHigh)) {
- int i;
- for (i = regionLow; i < regionHigh; i++) {
- if (regionTypes == NULL) {
- regionIndices.push_back(i);
- }
- else {
- int t;
- for (t = 0; t < numRegionTypes; t++) {
- if (regionTable.GetType(i) == regionTypes[t]) {
- regionIndices.push_back(i);
- break;
- }
- }
- }
- }
- }
- return regionIndices.size() - prevNumRegionIndices;
-}
-
-
-// Given a vecotr of ReadInterval objects and their corresponding
-// directions, intersect each object with an interval
-// [hqStart, hqEnd), if there is no intersection or the intersected
-// interval is less than minIntervalLength, remove this object and
-// their corresponding directions; otherwise, replace this object
-// with the intersected interval and keep their directions.
-// Return index of the (left-most) longest subread interval in the
-// updated vector.
-int GetHighQualitySubreadsIntervals(
- std::vector<ReadInterval> & subreadIntervals,
- std::vector<int> & subreadDirections,
- int hqStart, int hqEnd, int minIntervalLength) {
-
- // Avoid using vector.erase() when possible, as it is slow.
- int ret = -1;
- int maxLength = 0;
- assert(subreadIntervals.size() == subreadDirections.size());
- std::vector<ReadInterval> subreadIntervals2;
- std::vector<int> subreadDirections2;
- for(int i = 0; i < int(subreadIntervals.size()); i++) {
- int & thisStart = subreadIntervals[i].start;
- int & thisEnd = subreadIntervals[i].end;
- int & thisScore = subreadIntervals[i].score;
-
- if (thisStart >= hqEnd or thisEnd <= hqStart) {
- continue;
- }
- if (thisStart < hqStart and thisEnd > hqStart) {
- thisStart = hqStart;
- }
- if (thisStart < hqEnd and thisEnd > hqEnd ) {
- thisEnd = hqEnd;
- }
- if (thisEnd - thisStart >= minIntervalLength) {
- if (maxLength < thisEnd - thisStart) {
- ret = subreadIntervals2.size();
- maxLength = thisEnd - thisStart;
- }
- subreadIntervals2.push_back(subreadIntervals[i]);
- subreadDirections2.push_back(subreadDirections[i]);
- }
- }
- subreadIntervals = subreadIntervals2;
- subreadDirections = subreadDirections2;
- return ret;
-}
-
-
-// Given a vector of subreads and a vector of adapters, return
-// indices of all fullpass subreads in the input subreads vector.
-std::vector<int>
-GetFullPassSubreadIndices(std::vector<ReadInterval> & subreadIntervals,
- std::vector<ReadInterval> & adapterIntervals) {
- std::vector<int> indices; // Indices of fullpass subread.
- for(int i = 0; i < subreadIntervals.size(); i++) {
- ReadInterval & subread = subreadIntervals[i];
- bool ladapter = false, radapter = false;
- for(int j = 0; j < adapterIntervals.size(); j++) {
- ReadInterval & adapter = adapterIntervals[j];
- if (abs(subread.start - adapter.end) < 10) {
- ladapter = true;
- } else if(abs(subread.end - adapter.start) < 10) {
- radapter = true;
- }
- if (ladapter && radapter) {
- indices.push_back(i);
- break;
- }
- }
- }
- return indices;
-}
-
-bool cmp_index_len_pair(std::pair<int, int> x, std::pair<int, int> y) {
- if (x.second == y.second) {
- return x.first < y.first;
- } else
- return x.second < y.second;
-}
-
-// Given a vector of subreads and a vector of adapters, return
-// index of the (left-most) longest subread which has both
-// adapters before & after itself. If no full-pass subread available,
-// return -1;
-int GetLongestFullSubreadIndex(std::vector<ReadInterval> & subreadIntervals,
- std::vector<ReadInterval> & adapterIntervals) {
-
- std::vector<int> indices = GetFullPassSubreadIndices(subreadIntervals, adapterIntervals);
- if (indices.size() == 0)
- return -1;
- std::vector<std::pair<int, int>> indices_lens;
-
- for (int i = 0; i < indices.size(); i++) {
- ReadInterval & subread = subreadIntervals[indices[i]];
- indices_lens.push_back(std::make_pair(indices[i], subread.end - subread.start));
- }
-
- std::sort(indices_lens.begin(), indices_lens.end(), cmp_index_len_pair);
- return indices_lens[int(indices_lens.size()-1)].first;
-}
-
-
-// Given a vector of subreads and a vector of adapters, return
-// index of the typical fullpass subread which can represent subreads
-// of this zmw.
-// * if there is no fullpass subread, return -1;
-// * if number of fullpass subreads is less than 4, return index of the
-// left-most longest subread
-// * if number of fullpass subreads is greater than or equal 4,
-// * if length of the longest read does not exceed
-// meanLength + 1.96 * deviationLength
-// then, return index of the longest left-most subread
-// * otherwise, return index of the second longest left-most subread
-int GetTypicalFullSubreadIndex(std::vector<ReadInterval> & subreadIntervals,
- std::vector<ReadInterval> & adapterIntervals) {
-
- std::vector<int> indices = GetFullPassSubreadIndices(subreadIntervals, adapterIntervals);
- if (indices.size() == 0)
- return -1; // no full-pass subread in this zmw
- std::vector<std::pair<int, int>> indices_lens;
- std::vector<int> lengths;
-
- for (int i = 0; i < indices.size(); i++) {
- ReadInterval & subread = subreadIntervals[indices[i]];
- indices_lens.push_back(std::make_pair(indices[i], subread.end - subread.start));
- lengths.push_back(subread.end - subread.start);
- }
-
- std::sort(indices_lens.begin(), indices_lens.end(), cmp_index_len_pair);
-
- int longestIndex = indices_lens[int(indices_lens.size()-1)].first;
- int secondLongestIndex = (indices_lens.size() <= 1)?(-1): (indices_lens[int(indices_lens.size()-2)].first);
-
- if (indices.size() < 4) {
- // very few fullpass subreads, use the longest subread anyway.
- return longestIndex;
- } else {
- // if length of the longest falls out of 95% CI of all other
- // fullpass subreads, use the second longest.
- sort(lengths.begin(), lengths.end());
- float meanLength, varLength;
- MeanVar(lengths, meanLength, varLength);
- if (lengths[int(lengths.size()-1)] > meanLength + 1.96 * sqrt(varLength)) {
- return secondLongestIndex;
- } else {
- return longestIndex;
- }
- }
-}
-
-
-// Given a vector of subreads and a vector of adapters, return
-// index of the median length subread which has both
-// adapters before & after itself. If no full-pass subreads are
-// available, return -1.
-int GetMedianLengthFullSubreadIndex(
- std::vector<ReadInterval> & subreadIntervals,
- std::vector<ReadInterval> & adapterIntervals) {
-
- std::vector<int> indices = GetFullPassSubreadIndices(subreadIntervals, adapterIntervals);
- if (indices.size() == 0)
- return -1;
- std::vector<std::pair<int, int>> indices_lens;
-
- for (int i = 0; i < indices.size(); i++) {
- ReadInterval & subread = subreadIntervals[indices[i]];
- indices_lens.push_back(std::make_pair(indices[i], subread.end - subread.start));
- }
- std::sort(indices_lens.begin(), indices_lens.end(), cmp_index_len_pair);
- return indices_lens[int(indices_lens.size()/2)].first;
-}
-
-// Create a vector of n directions consisting of interleaved 0 and 1s.
-void CreateDirections(std::vector<int> & directions, const int & n) {
- directions.clear();
- directions.resize(n);
- for(int i = 0; i < n; i++) {
- directions[i] = i % 2;
- }
-}
-
-// Flop all directions in the given vector, if flop is true.
-void UpdateDirections(std::vector<int> & directions, bool flop) {
- if (not flop) return;
- for (int i = 0; i < int(directions.size()); i++) {
- assert(directions[i] == 0 or directions[i] == 1);
- directions[i] = (directions[i] == 0)?1:0;
- }
-}
-
diff --git a/libcpp/alignment/utils/RegionUtils.hpp b/libcpp/alignment/utils/RegionUtils.hpp
deleted file mode 100644
index f5fb870..0000000
--- a/libcpp/alignment/utils/RegionUtils.hpp
+++ /dev/null
@@ -1,132 +0,0 @@
-#ifndef _BLASR_REGION_UTILS_HPP_
-#define _BLASR_REGION_UTILS_HPP_
-
-#include <algorithm>
-#include <cmath>
-#include "SMRTSequence.hpp"
-#include "statistics/StatUtils.hpp"
-#include "reads/ReadInterval.hpp"
-#include "reads/RegionTable.hpp"
-
-bool LookupHQRegion(int holeNumber, RegionTable ®ionTable,
- int &start, int &end, int &score);
-
-template<typename T_Sequence>
-bool MaskRead(T_Sequence &fastaRead, ZMWGroupEntry &zmwData,
- RegionTable ®ionTable);
-
-
-template<typename T_Sequence>
-bool GetReadTrimCoordinates(T_Sequence &fastaRead,
- ZMWGroupEntry &zmwData, RegionTable ®ionTable,
- DNALength &readStart ,DNALength &readEnd, int &score);
-
-template<typename T_Sequence>
-bool TrimRead(T_Sequence &fastaRead, ZMWGroupEntry &zmwData,
- RegionTable ®ionTable, T_Sequence &trimmedRead);
-
-
-class CompareRegionIndicesByStart {
-public:
- RegionTable *regionTablePtr;
- int operator()(const int a, const int b) const;
-};
-
-
-int SortRegionIndicesByStart(RegionTable ®ionTable,
- std::vector<int> &indices);
-
-class OrderRegionsByReadStart {
-public:
- int operator()(const ReadInterval &lhs, const ReadInterval &rhs) const;
-};
-
-int FindRegionIndices(unsigned int holeNumber, RegionTable *regionTablePtr,
- int ®ionLowIndex, int ®ionHighIndex);
-
-int FindRegionIndices(SMRTSequence &read, RegionTable *regionTablePtr,
- int ®ionLowIndex, int ®ionHighIndex);
-
-//
-// Collect region indices for either all region types, or just a few
-// specific region types.
-//
-int CollectRegionIndices(SMRTSequence &read, RegionTable ®ionTable,
- std::vector<int> ®ionIndices, RegionType *regionTypes=NULL,
- int numRegionTypes = 0);
-
-
-template<typename T_Sequence>
-void CollectSubreadIntervals(T_Sequence &read, RegionTable *regionTablePtr,
- std::vector<ReadInterval> &subreadIntervals, bool byAdapter=false);
-
-// Get all adapter intervals of a ZMW.
-// Input:
-// read - read.zmwData.holeNumber specifies the zmw.
-// regionTablePtr - a pointer to a region table.
-// Output:
-// adapterIntervals - where to assign all adapter intervals of the zmw
-template<typename T_Sequence>
-void CollectAdapterIntervals(T_Sequence &read, RegionTable *regionTablePtr,
- std::vector<ReadInterval> &adapterIntervals);
-
-// Given a vecotr of ReadInterval objects and their corresponding
-// directions, intersect each object with an interval
-// [hqStart, hqEnd), if there is no intersection or the intersected
-// interval is less than minIntervalLength, remove this object and
-// their corresponding directions; otherwise, replace this object
-// with the intersected interval and keep their directions.
-// Return index of the (left-most) longest subread interval in the
-// updated vector.
-int GetHighQualitySubreadsIntervals(
- std::vector<ReadInterval> & subreadIntervals,
- std::vector<int> & subreadDirections,
- int hqStart, int hqEnd, int minIntervalLength = 0);
-
-// Given a vector of subreads and a vector of adapters, return
-// indices of all full-pass subreads.
-std::vector<int> GetFullPassSubreadIndices(
- std::vector<ReadInterval> & subreadIntervals,
- std::vector<ReadInterval> & adapterIntervals);
-
-// Given a vector of subreads and a vector of adapters, return
-// index of the (left-most) longest subread which has both
-// adapters before & after itself. If no full-pass subreads are
-// available, return -1.
-int GetLongestFullSubreadIndex(
- std::vector<ReadInterval> & subreadIntervals,
- std::vector<ReadInterval> & adapterIntervals);
-
-// Given a vector of subreads and a vector of adapters, return
-// index of the median length subread which has both
-// adapters before & after itself. If no full-pass subreads are
-// available, return -1.
-int GetMedianLengthFullSubreadIndex(
- std::vector<ReadInterval> & subreadIntervals,
- std::vector<ReadInterval> & adapterIntervals);
-
-
-// Given a vector of subreads and a vector of adapters, return
-// index of the typical fullpass subread which can represent subreads
-// of this zmw.
-// * if there is no fullpass subread, return -1;
-// * if number of fullpass subreads is less than 4, return index of the
-// left-most longest subread
-// * if number of fullpass subreads is greater than or equal 4,
-// * if length of the longest read does not exceed
-// meanLength + 1.96 * deviationLength
-// then, return index of the longest left-most subread
-// * otherwise, return index of the second longest left-most subread
-int GetTypicalFullSubreadIndex(
- std::vector<ReadInterval> & subreadIntervals,
- std::vector<ReadInterval> & adapterIntervals);
-
-// Create a vector of n directions consisting of interleaved 0 and 1s.
-void CreateDirections(std::vector<int> & directions, const int & n);
-
-// Flop all directions in the given vector, if flop is true.
-void UpdateDirections(std::vector<int> & directions, bool flop = false);
-
-#include "utils/RegionUtilsImpl.hpp"
-
-#endif
diff --git a/libcpp/alignment/utils/RegionUtilsImpl.hpp b/libcpp/alignment/utils/RegionUtilsImpl.hpp
deleted file mode 100644
index fc4b859..0000000
--- a/libcpp/alignment/utils/RegionUtilsImpl.hpp
+++ /dev/null
@@ -1,215 +0,0 @@
-#ifndef _BLASR_REGION_UTILS_IMPL_HPP
-#define _BLASR_REGION_UTILS_IMPL_HPP
-
-
-template<typename T_Sequence>
-bool MaskRead(T_Sequence &fastaRead, ZMWGroupEntry &zmwData,
- RegionTable ®ionTable) {
- int regionIndex;
- int regionLowIndex, regionHighIndex;
- regionLowIndex = regionHighIndex = 0;
-
- regionTable.LookupRegionsByHoleNumber(zmwData.holeNumber,
- regionLowIndex, regionHighIndex);
-
- bool readHasGoodRegion = true;
-
- DNALength readPos;
-
- regionIndex = regionLowIndex;
- int lastHQRegionIndex;
-
- int hqRegionStart=0, hqRegionEnd=0, hqRegionScore = 0;
- readHasGoodRegion = LookupHQRegion(zmwData.holeNumber,
- regionTable, hqRegionStart, hqRegionEnd, hqRegionScore);
-
- //
- // Mask off the low quality portion of this read.
- //
- for (readPos = 0; (readPos < hqRegionStart and
- readPos < fastaRead.length); readPos++) {
- fastaRead.seq[readPos] = 'N';
- }
-
- for (readPos = hqRegionEnd; readPos < fastaRead.length; readPos++) {
- fastaRead.seq[readPos] = 'N';
- }
-
- //
- // Look to see if there is region information provided, but the
- // entire read is bad.
- //
- if (hqRegionEnd == hqRegionStart) {
- //
- // This read is entirely bad, flag that.
- //
- readHasGoodRegion = false;
- }
-
- return readHasGoodRegion;
-}
-
-
-template<typename T_Sequence>
-bool GetReadTrimCoordinates(T_Sequence &fastaRead,
- ZMWGroupEntry &zmwData, RegionTable ®ionTable,
- DNALength &readStart ,DNALength &readEnd, int &score) {
-
- int regionIndex;
- int regionLowIndex, regionHighIndex;
- regionLowIndex = regionHighIndex = 0;
-
- regionTable.LookupRegionsByHoleNumber(zmwData.holeNumber,
- regionLowIndex, regionHighIndex);
-
- bool readHasGoodRegion = true;
-
- DNALength readPos;
-
- regionIndex = regionLowIndex;
- int lastHQRegionIndex;
-
- while (regionIndex < regionHighIndex and
- regionTable.GetType(regionIndex) != HQRegion) {
- regionIndex++;
- }
-
- if (regionIndex < regionHighIndex ) {
- readStart = regionTable.GetStart(regionIndex);
- readEnd = regionTable.GetEnd(regionIndex);
- score = regionTable.GetScore(regionIndex);
- return true;
- }
- else {
- readStart = 0;
- readEnd = fastaRead.length;
- return false;
- }
-}
-
-
-template<typename T_Sequence>
-bool TrimRead(T_Sequence &fastaRead, ZMWGroupEntry &zmwData,
- RegionTable ®ionTable, T_Sequence &trimmedRead) {
-
- DNALength readStart, readEnd;
-
- GetReadTrimCoordinates(fastaRead, zmwData, regionTable,
- readStart, readEnd);
-
- if (readEnd - readStart > 0) {
- trimmedRead.CopySubsequence((FASTQSequence&)fastaRead,
- readStart, readEnd);
- // signal that the read has a good region.
- return true;
- }
- else {
- //
- // There is no information for this read. Make it skipped.
- //
- trimmedRead.seq = NULL;
- trimmedRead.CopyTitle(fastaRead.title);
- // signal this read has no good region.
- return false;
- }
-}
-
-template<typename T_Sequence>
-void CollectSubreadIntervals(T_Sequence &read, RegionTable *regionTablePtr,
- std::vector<ReadInterval> &subreadIntervals, bool byAdapter) {
-
- int regionIndex;
- int regionLowIndex, regionHighIndex;
- regionLowIndex = regionHighIndex = 0;
-
- regionTablePtr->LookupRegionsByHoleNumber(read.zmwData.holeNumber,
- regionLowIndex, regionHighIndex);
-
- if (byAdapter == false) {
- // read subreads (insert) directly from region table.
- for (regionIndex = regionLowIndex;
- regionIndex < regionHighIndex; regionIndex++) {
- if (regionTablePtr->GetType(regionIndex) == Insert) {
-
- RegionAnnotation & ra = regionTablePtr->table[regionIndex];
- subreadIntervals.push_back(ReadInterval(
- ra.row[RegionAnnotation::RegionStart],
- ra.row[RegionAnnotation::RegionEnd],
- ra.row[RegionAnnotation::RegionScore]));
- }
- }
- }
- else { // Determine subreads according to adapters only.
- std::vector<int> adapterIntervalIndices;
- for (regionIndex = regionLowIndex;
- regionIndex < regionHighIndex; regionIndex++) {
- if (regionTablePtr->GetType(regionIndex) == Adapter) {
- adapterIntervalIndices.push_back(regionIndex);
- }
- }
- // Sort indices so that the intervals appear in order on the read.
- SortRegionIndicesByStart(*regionTablePtr, adapterIntervalIndices);
- int curIntervalStart = 0;
- int i;
- if (adapterIntervalIndices.size() == 0) {
- // no adapter, this zmw has only one subread (pass)
- subreadIntervals.push_back(ReadInterval(0, read.length));
- }
- else {
- // The first subread covers [0, RegionStart of first adapter)
- subreadIntervals.push_back(ReadInterval(0,
- regionTablePtr->table[adapterIntervalIndices[0]].
- row[RegionAnnotation::RegionStart]));
-
- // The subread[i] covers (RegionEnd of i-1-th adapter, RegionStart of i-th adapter)
- for (i = 0; i + 1 < adapterIntervalIndices.size(); i++) {
- subreadIntervals.push_back(ReadInterval(
- regionTablePtr->table[adapterIntervalIndices[i]].
- row[RegionAnnotation::RegionEnd],
- regionTablePtr->table[adapterIntervalIndices[i+1]].
- row[RegionAnnotation::RegionStart]));
- }
- // The last subread covers (RegionEnd of last adapter, end of read)
- subreadIntervals.push_back(
- ReadInterval(regionTablePtr->table[
- adapterIntervalIndices[adapterIntervalIndices.size()-1]].
- row[RegionAnnotation::RegionEnd],
- read.length));
- }
- }
- sort(subreadIntervals.begin(), subreadIntervals.end(),
- OrderRegionsByReadStart());
-}
-
-
-// Get all adapter intervals of a ZMW.
-// Input:
-// read - read.zmwData.holeNumber specifies the zmw.
-// regionTablePtr - a pointer to a region table.
-// Output:
-// adapterIntervals - where to assign all adapter intervals of the zmw
-template<typename T_Sequence>
-void CollectAdapterIntervals(T_Sequence &read,
- RegionTable *regionTablePtr,
- std::vector<ReadInterval> &adapterIntervals) {
-
- assert(regionTablePtr != NULL);
- int regionLowIndex = 0, regionHighIndex = 0;
-
- regionTablePtr->LookupRegionsByHoleNumber(read.zmwData.holeNumber,
- regionLowIndex, regionHighIndex);
-
- for (int regionIndex = regionLowIndex;
- regionIndex < regionHighIndex; regionIndex++) {
-
- if (regionTablePtr->GetType(regionIndex) == Adapter) {
- RegionAnnotation & ra = regionTablePtr->table[regionIndex];
- adapterIntervals.push_back(ReadInterval(
- ra.row[RegionAnnotation::RegionStart],
- ra.row[RegionAnnotation::RegionEnd],
- ra.row[RegionAnnotation::RegionScore]));
- }
- }
-}
-
-#endif
diff --git a/libcpp/alignment/utils/SimpleXMLUtils.hpp b/libcpp/alignment/utils/SimpleXMLUtils.hpp
deleted file mode 100644
index 020a4bb..0000000
--- a/libcpp/alignment/utils/SimpleXMLUtils.hpp
+++ /dev/null
@@ -1,99 +0,0 @@
-#ifndef _BLASR_SIMPLE_XML_UTILS_HPP_
-#define _BLASR_SIMPLE_XML_UTILS_HPP_
-
-#include <string>
-#include <sstream>
-
-/*
- * WARNING !!! The functions here use TONS of temoprary variables and are
- * very slow. Do not use for high-throughput xml generation.
- */
-
-/*
- * none of this is really used... just the keyword value pair items.
- */
-
-template<typename T_String, typename T_Value>
-int OutputKeywordValuePair(T_String title, T_Value value, std::ostream out) {
- out << title << "=\"" << value << "\" ";
- return out.good();
-}
-
-template<typename T_String>
-int OutputBeginElement(T_String title, std::ostream out) {
- out << "<" << title << " ";
- return 1;
-}
-
-template<typename T_String>
-int OutputEndElement(T_String title, std::ostream out) {
- out << "/" << title;
- return 1;
-}
-
-template<typename T_String>
-int OutputElement(T_String title, std::ostream out) {
- out << "<" << title << " ";
- return 1;
-}
-
-inline
-void OutputEnd(std::ostream out) {
- out << "/>";
-}
-
-template<typename T_String, typename T_Value>
-T_String CreateKeywordValuePair(T_String title, T_Value value) {
- T_String keywordPair;
- std::stringstream sstrm;
- sstrm << title << "=\"" << value << "\"";
- keywordPair = sstrm.str();
- return keywordPair;
-}
-
-template<typename T_String>
-T_String BeginDataEntry(T_String id, T_String data) {
- T_String entry;
- entry += "<";
- entry += id;
- entry += " ";
- entry += data;
- entry += ">";
- return entry;
-}
-
-template<typename T_String>
-T_String EndDataEntry(T_String id) {
- T_String entry;
- entry = "<" + id + ">/";
- return entry;
-}
-
-
-template<typename T_String>
-T_String CreateDataEntry(T_String id, T_String data) {
- T_String entry;
- entry += "<";
- entry += id;
- entry += " ";
- entry += data;
- entry += " />";
- return entry;
-}
-
-
-template<typename T_String>
- T_String CreateStartEntry(T_String id, T_String data) {
- T_String entry;
- entry = "<" + id + " " + data + ">";
- return entry;
-}
-
-template<typename T_String>
-T_String CreateEndEntry(T_String id) {
- T_String entry;
- entry = "<" + id + "/>";
- return entry;
-}
-
-#endif
diff --git a/libcpp/alignment/utils/TimeUtils.cpp b/libcpp/alignment/utils/TimeUtils.cpp
deleted file mode 100644
index 94f7851..0000000
--- a/libcpp/alignment/utils/TimeUtils.cpp
+++ /dev/null
@@ -1,20 +0,0 @@
-#include <sstream>
-#include <time.h>
-#include <iomanip> // std::setfill setd::setw
-#include "utils/TimeUtils.hpp"
-
-std::string GetTimestamp() {
- time_t timer;
- time(&timer); // t is an integer type
- // Prepare timestamp in the format : 2012-04-05T09:26:02.689093
- std::stringstream timeStrm;
- struct tm t;
- localtime_r(&timer, &t);
- timeStrm << t.tm_year + 1900 << "-"
- << std::setfill('0') << std::setw(2) << t.tm_mon + 1 << "-"
- << std::setfill('0') << std::setw(2) << t.tm_mday << "T"
- << std::setfill('0') << std::setw(2) << t.tm_hour << ":"
- << std::setfill('0') << std::setw(2) << t.tm_min << ":"
- << std::setfill('0') << std::setw(2) << t.tm_sec;
- return timeStrm.str();
-}
diff --git a/libcpp/alignment/utils/TimeUtils.hpp b/libcpp/alignment/utils/TimeUtils.hpp
deleted file mode 100644
index 543d929..0000000
--- a/libcpp/alignment/utils/TimeUtils.hpp
+++ /dev/null
@@ -1,7 +0,0 @@
-#ifndef _BLASR_TIME_UTILS_HPP_
-#define _BLASR_TIME_UTILS_HPP_
-
-#include <string>
-std::string GetTimestamp();
-
-#endif
diff --git a/libcpp/configure.py b/libcpp/configure.py
deleted file mode 100755
index b147c09..0000000
--- a/libcpp/configure.py
+++ /dev/null
@@ -1,268 +0,0 @@
-#!/usr/bin/env python
-"""Configure the build.
-
-- Fetch HDF5 headers.
-- Create libconfig.h
-- Create defines.mk
-
-This is not used by './unittest/'.
-"""
-import commands
-import contextlib
-import os
-import sys
-
-def log(msg):
- sys.stderr.write(msg)
- sys.stderr.write('\n')
-
-def shell(cmd):
- log(cmd)
- status, output = commands.getstatusoutput(cmd)
- if status:
- raise Exception('%d <- %r' %(status, cmd))
- return output
-
-def update_content(fn, content):
- current_content = open(fn).read() if os.path.exists(fn) else None
- if content != current_content:
- log('writing to %r' %fn)
- log('"""\n' + content + '"""')
- open(fn, 'w').write(content)
-
-def compose_libconfig(pbbam=False):
- if pbbam:
- content = """
-#define USE_PBBAM
-"""
- else:
- content = """
-"""
- return content
-
-def compose_defines_with_hdf(HDF5_INCLUDE, HDF5_LIB):
- """We have to use := for HDF5_LIB b/c blasr
- is using it to mean the directory, not the file,
- and it's in the environment.
- """
- thisdir = os.path.dirname(os.path.abspath(__file__))
- return """
-HDF5_INCLUDE:=%(HDF5_INCLUDE)s
-HDF5_LIB:=%(HDF5_LIB)s
-#CPPFLAGS+=-I../pbdata -I../hdf -I../alignment
-LIBPBDATA_INCLUDE ?=../pbdata
-LIBPBIHDF_INCLUDE ?=../hdf
-LIBBLASR_INCLUDE ?=../alignment
-LIBPBDATA_LIB ?=../pbdata/libpbdata.so
-LIBPBIHDF_LIB ?=../hdf/libpbihdf.so
-LIBBLASR_LIB ?=../alignment/libblasr.so
-"""%(dict(
- thisdir=thisdir,
- HDF5_INCLUDE=HDF5_INCLUDE,
- HDF5_LIB=HDF5_LIB))
-
-
-def compose_defines_with_hdf_headers(HDF_HEADERS):
- thisdir = os.path.dirname(os.path.abspath(__file__))
- return """
-HDF_HEADERS:=%(HDF_HEADERS)s
-#HDF5_INCLUDE?=${HDF_HEADERS}/src
-CPPFLAGS+=-I${HDF_HEADERS}/src -I${HDF_HEADERS}/c++/src
-CPPFLAGS+=-I../pbdata -I../hdf -I../alignment
-LIBPBDATA_LIB ?=../pbdata/libpbdata.so
-LIBPBIHDF_LIB ?=../pbdata/libpbihdf.so
-LIBBLASR_LIB ?=../pbdata/libblasr.so
-"""%(dict(thisdir=thisdir, HDF_HEADERS=HDF_HEADERS))
-
-def compose_defines():
- """
- Note that our local 'hdf' subdir will not even build
- in this case.
- """
- thisdir = os.path.dirname(os.path.abspath(__file__))
- return """
-LIBPBDATA_INCLUDE ?=../pbdata
-LIBPBIHDF_INCLUDE ?=../hdf
-LIBBLASR_INCLUDE ?=../alignment
-LIBPBDATA_LIB ?=%(thisdir)s/pbdata/libpbdata.so
-LIBPBIHDF_LIB ?=%(thisdir)s/pbdata/libpbihdf.so
-LIBBLASR_LIB ?=%(thisdir)s/pbdata/libblasr.so
-nohdf ?=1
-"""%(dict(thisdir=thisdir))
-
-def get_OS_STRING():
- G_BUILDOS_CMD = """bash -c 'set -e; set -o pipefail; id=$(lsb_release -si | tr "[:upper:]" "[:lower:]"); rel=$(lsb_release -sr); case $id in ubuntu) printf "$id-%04d\n" ${rel/./};; centos) echo "$id-${rel%%.*}";; *) echo "$id-$rel";; esac' 2>/dev/null"""
- return shell(G_BUILDOS_CMD)
-def get_PREBUILT():
- cmd = 'cd ../../../../prebuilt.out 2>/dev/null && pwd || echo -n notfound'
- return shell(cmd)
-def get_BOOST_INCLUDE(env):
- key_bi = 'BOOST_INCLUDE'
- key_br = 'BOOST_ROOT'
- if key_bi in env:
- return env[key_bi]
- if key_br in env:
- return env[key_br]
- return '${PREBUILT}/boost/boost_1_55_0'
-
-def get_PBBAM(env, prefix):
- """
- key = 'PBBAM'
- if key in env:
- return env[key]
- cmd = 'cd $(THIRD_PARTY_PREFIX)/../staging/PostPrimary/pbbam 2>/dev/null && pwd || echo -n notfound' %(
- THIRD_PARTY_PREFIX=prefix)
- return shell(cmd)
- """
-def get_HTSLIB(env, prefix):
- """
- key = 'HTSLIB'
- if key in env:
- return env[key]
- cmd = 'cd $(THIRD_PARTY_PREFIX)/../staging/PostPrimary/htslib 2>/dev/null && pwd || echo -n notfound' %(
- THIRD_PARTY_PREFIX=prefix)
- return shell(cmd)
- """
-def ifenvf(env, key, func):
- if key in env:
- return env[key]
- else:
- return func()
-def setifenvf(envout, envin, key, func):
- envout[key] = ifenvf(envin, key, func)
-def setifenv(envout, envin, key, val):
- envout[key] = envin.get(key, val)
-def setenv(envout, key, val):
- envout[key] = val
-def update_env_if(envout, envin, keys):
- for key in keys:
- if key in envin:
- envout[key] = envin[key]
-def compose_defs_env(env):
- # We disallow env overrides for anything with a default from GNU make.
- nons = ['CXX', 'CC', 'AR'] # 'SHELL'?
- ovr = ['%-20s ?= %s' %(k, v) for k,v in env.items() if k not in nons]
- nonovr = ['%-20s := %s' %(k, v) for k,v in env.items() if k in nons]
- return '\n'.join(ovr + nonovr + [''])
-def compose_defines_pacbio(envin):
- """
- This is used by mobs via buildcntl.sh.
- """
- env = dict()
- setenv(env, 'SHELL', 'bash')
- setifenvf(env, envin, 'OS_STRING', get_OS_STRING)
- setifenvf(env, envin, 'PREBUILT', get_PREBUILT)
- setifenv(env, envin, 'LIBPBDATA_INCLUDE', '../pbdata')
- setifenv(env, envin, 'LIBPBIHDF_INCLUDE', '../hdf')
- setifenv(env, envin, 'LIBBLASR_INCLUDE', '../alignment')
- setifenv(env, envin, 'LIBPBDATA_LIB', '../pbdata/libpbdata.so')
- setifenv(env, envin, 'LIBPBIHDF_LIB', '../hdf/libpbihdf.so')
- setifenv(env, envin, 'LIBBLASR_LIB', '../alignment/libblasr.so')
- if 'nohdf' in envin:
- env['nohdf'] = envin['nohdf']
- # Otherwise, do not define it at all.
- nondefaults = set([
- 'CXX', 'AR',
- 'HDF5_INCLUDE', 'HDF5_LIB',
- 'PBBAM_INCLUDE', 'PBBAM_LIB',
- 'HTSLIB_INCLUDE', 'HTSLIB_LIB',
- 'BOOST_INCLUDE',
- 'ZLIB_LIB',
- ])
- update_env_if(env, envin, nondefaults)
- return compose_defs_env(env)
-
-
- at contextlib.contextmanager
-def cd(nwd):
- cwd = os.getcwd()
- log('cd %r -> %r' %(cwd, nwd))
- os.chdir(nwd)
- yield
- os.chdir(cwd)
- log('cd %r <- %r' %(cwd, nwd))
-
-def fetch_hdf5_headers():
- """Fetch into ./hdf/HEADERS directory.
- Return actual directory path, relative to subdirs.
- """
- version = 'hdf5-1.8.12-headers'
- if not os.path.isdir(os.path.join('hdf', version)):
- with cd('hdf'):
- cmd = 'curl -k -L https://www.dropbox.com/s/8971bcyy5o42rxb/hdf5-1.8.12-headers.tar.bz2\?dl\=0 | tar xjf -'
- shell(cmd)
- return os.path.join('../hdf', version) # Relative path might help caching.
-
-def update(content_defines_mk, content_libconfig_h):
- """ Write these relative to the same directory as *this* file.
- """
- thisdir = os.path.dirname(os.path.abspath(__file__))
- fn_defines_mk = os.path.join(thisdir, 'defines.mk')
- update_content(fn_defines_mk, content_defines_mk)
- fn_libconfig_h = os.path.join(thisdir, 'pbdata', 'libconfig.h')
- update_content(fn_libconfig_h, content_libconfig_h)
-
-def configure_nopbbam():
- """Use HDF5 from env-vars.
- This is the path used by blasr in a GitHub build, for now.
- """
- HDF5_INCLUDE = os.environ.get('HDF5_INCLUDE')
- if not HDF5_INCLUDE:
- HDF5_INCLUDE = os.environ['HDF5_INC']
- HDF5_LIB = os.environ['HDF5_LIB']
- content1 = compose_defines_with_hdf(HDF5_INCLUDE, HDF5_LIB)
- content2 = compose_libconfig(pbbam=False)
- update(content1, content2)
-
-def configure_nopbbam_skip_hdf():
- """Fetch HDF5 headers.
- We lack HDF5 libs, so we cannot build our hdf/ subdir.
- But the others are fine.
- """
- HDF_HEADERS = fetch_hdf5_headers()
- content1 = compose_defines_with_hdf_headers(HDF_HEADERS)
- content2 = compose_libconfig(pbbam=False)
- update(content1, content2)
-
-def configure_nopbbam_nohdf5():
- content1 = compose_defines()
- content2 = compose_libconfig(pbbam=False)
- update(content1, content2)
-
-def configure_pacbio(envin):
- content1 = compose_defines_pacbio(envin)
- content2 = compose_libconfig(pbbam=True)
- update(content1, content2)
-
-def get_make_style_env(envin, args):
- envout = dict()
- for arg in args:
- if '=' in arg:
- k, v = arg.split('=')
- envout[k] = v
- envout.update(envin)
- return envout
-
-def main(prog, *args):
- """We are still deciding what env-vars to use, if any.
- """
- if 'NOPBBAM' in os.environ:
- if 'NOHDF' in os.environ:
- configure_nopbbam_nohdf5()
- else:
- if 'HDF5_LIB' in os.environ:
- assert 'HDF5_INC' in os.environ or 'HDF5_INCLUDE' in os.environ, 'Hey! You have HDF5_LIB but not HDF5_INCLUDE!'
- if 'HDF5_INC' not in os.environ:
- print "NOT1"
- if 'HDF5_INCLUDE' not in os.environ:
- print "NOT2"
- configure_nopbbam()
- else:
- configure_nopbbam_skip_hdf()
- else:
- envin = get_make_style_env(os.environ, args)
- configure_pacbio(envin)
-
-
-if __name__=="__main__":
- main(*sys.argv)
diff --git a/libcpp/hdf/BufferedHDF2DArray.cpp b/libcpp/hdf/BufferedHDF2DArray.cpp
deleted file mode 100644
index 204d4d7..0000000
--- a/libcpp/hdf/BufferedHDF2DArray.cpp
+++ /dev/null
@@ -1,79 +0,0 @@
-#include "BufferedHDF2DArray.hpp"
-/*
- *
- * Implementation of a 2-D array for IO from an HDF array.
- * This is templated, but specialized for a few data types, so that
- * the HDF data types do not need to be specified by somebody when reading.
- *
- * Currently no support exists for reading non-contiguous blocks of data, and
- * the main intended use is to read in increments of rows.
-
- int main(int argc, char* argv[]) {
- if (argc < 1) {
- cout << "usage: testHDFReading hdfFile" << endl;
- exit(0);
- }
-
- string hdfFileName = argv[1];
-
- H5File hdfFile;
- hdfFile.openFile(hdfFileName.c_str(), H5F_ACC_RDONLY, H5P_DEFAULT);
- BufferedHDF2DArray<uint16_t> xyArray;
- xyArray.Initialize(hdfFile, "PulseData/BaseCalls/ZMW/HoleXY");
- int curX = 0;
- xyArray.Read(curX, curX + 1, 0, 2, holeXY);
-
- or, to read a row:
- xyArray.Read(curX, curX+1, holeXY);
-
- */
-
-UInt GetDatasetNDim(H5::CommonFG &parentGroup, std::string datasetName) {
- HDFData tmpDataset;
- tmpDataset.InitializeDataset(parentGroup, datasetName);
- H5::DataSpace dataspace = tmpDataset.dataset.getSpace();
- UInt nDims = dataspace.getSimpleExtentNdims();
- dataspace.close();
- tmpDataset.dataset.close();
- return nDims;
-}
-
-#define DEFINE_TYPED_WRITE_ROW(T, Pred) template<>\
-void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, const H5::DataSpace &memorySpace, const H5::DataSpace &fileSpace) {\
- dataset.write(data, Pred, memorySpace, fileSpace);\
-}
-
-DEFINE_TYPED_WRITE_ROW(int, H5::PredType::NATIVE_INT)
-DEFINE_TYPED_WRITE_ROW(unsigned int, H5::PredType::NATIVE_UINT)
-DEFINE_TYPED_WRITE_ROW(unsigned char, H5::PredType::NATIVE_UINT8)
-DEFINE_TYPED_WRITE_ROW(uint16_t, H5::PredType::NATIVE_UINT16)
-DEFINE_TYPED_WRITE_ROW(int16_t, H5::PredType::NATIVE_INT16)
-DEFINE_TYPED_WRITE_ROW(float, H5::PredType::NATIVE_FLOAT)
-
-
-#define DEFINE_TYPED_READ_ROW(T, Pred) template<>\
-void BufferedHDF2DArray<T>::Read(int startX, int endX, int startY, int endY, T* dest) {\
- Read(startX, endX, startY, endY, Pred, dest);\
-}
-
-DEFINE_TYPED_READ_ROW(int, H5::PredType::NATIVE_INT)
-DEFINE_TYPED_READ_ROW(unsigned int, H5::PredType::NATIVE_UINT)
-DEFINE_TYPED_READ_ROW(char, H5::PredType::NATIVE_INT8)
-DEFINE_TYPED_READ_ROW(unsigned char, H5::PredType::NATIVE_UINT8)
-DEFINE_TYPED_READ_ROW(uint16_t, H5::PredType::NATIVE_UINT16)
-DEFINE_TYPED_READ_ROW(int16_t, H5::PredType::NATIVE_INT16)
-DEFINE_TYPED_READ_ROW(float, H5::PredType::NATIVE_FLOAT)
-
-#define DEFINE_TYPED_CREATE_ROW(T, Pred) template<>\
-void BufferedHDF2DArray<T>::TypedCreate(H5::DataSpace &fileSpace, H5::DSetCreatPropList &cparms) {\
- dataset = container->createDataSet(datasetName.c_str(), Pred, fileSpace, cparms);\
-}
-
-DEFINE_TYPED_CREATE_ROW(int, H5::PredType::NATIVE_INT)
-DEFINE_TYPED_CREATE_ROW(unsigned int, H5::PredType::NATIVE_UINT)
-DEFINE_TYPED_CREATE_ROW(char, H5::PredType::NATIVE_INT8)
-DEFINE_TYPED_CREATE_ROW(unsigned char, H5::PredType::NATIVE_UINT8)
-DEFINE_TYPED_CREATE_ROW(uint16_t, H5::PredType::NATIVE_UINT16)
-DEFINE_TYPED_CREATE_ROW(int16_t, H5::PredType::NATIVE_INT16)
-DEFINE_TYPED_CREATE_ROW(float, H5::PredType::NATIVE_FLOAT)
-
diff --git a/libcpp/hdf/BufferedHDF2DArray.hpp b/libcpp/hdf/BufferedHDF2DArray.hpp
deleted file mode 100644
index 36a4a33..0000000
--- a/libcpp/hdf/BufferedHDF2DArray.hpp
+++ /dev/null
@@ -1,158 +0,0 @@
-#ifndef _BLASR_HDF_BUFFERED_HDF_2D_ARRAY_HPP_
-#define _BLASR_HDF_BUFFERED_HDF_2D_ARRAY_HPP_
-
-#include <cstdlib>
-#include <iostream>
-#include <string>
-
-#include "H5Cpp.h"
-
-#include "Types.h"
-#include "HDFConfig.hpp"
-#include "HDFData.hpp"
-#include "HDFGroup.hpp"
-#include "HDFWriteBuffer.hpp"
-
-/*
- *
- * Implementation of a 2-D array for IO from an HDF array.
- * This is templated, but specialized for a few data types, so that
- * the HDF data types do not need to be specified by somebody when reading.
- *
- * Currently no support exists for reading non-contiguous blocks of data, and
- * the main intended use is to read in increments of rows.
-
- int main(int argc, char* argv[]) {
- if (argc < 1) {
- cout << "usage: testHDFReading hdfFile" << endl;
- exit(0);
- }
-
- std::string hdfFileName = argv[1];
-
- H5File hdfFile;
- hdfFile.openFile(hdfFileName.c_str(), H5F_ACC_RDONLY, H5P_DEFAULT);
- BufferedHDF2DArray<uint16_t> xyArray;
- xyArray.Initialize(hdfFile, "PulseData/BaseCalls/ZMW/HoleXY");
- int curX = 0;
- xyArray.Read(curX, curX + 1, 0, 2, holeXY);
-
- or, to read a row:
- xyArray.Read(curX, curX+1, holeXY);
-
- *
- */
-template<typename T>
-class BufferedHDF2DArray : public HDFData, public HDFWriteBuffer<T> {
-
-private:
- hsize_t nDims;
- hsize_t *dimSize;
- int maxDims;
- int rowLength, colLength;
-
-public:
-
- BufferedHDF2DArray(H5::CommonFG *_container, std::string _datasetName);
-
- BufferedHDF2DArray();
-
- unsigned int GetNRows();
-
- unsigned int GetNCols();
-
- void Close();
-
- ~BufferedHDF2DArray();
-
- int InitializeForReading(HDFGroup &group, std::string datasetName);
-
- /*
- * Initialize HDF2D for reading. No write buffer initialization is
- * required. The assumption is that the dataspace is in two
- * dimensions, and this exits without grace if it is not.
- */
- int Initialize(HDFGroup &group, std::string datasetName, unsigned int _rowLength=0,
- int _bufferSize=0, bool createIfMissing=true);
-
- int size();
-
- /*
- * Read rows in the range (startX, endX] in to dest.
- */
-
- void Read(int startX, int endX, H5::DataType typeID, T*dest);
-
- void Read(int startX, int endX, T*dest);
-
- /*
- * This is the non-specialized definition. Since this should only
- * operate on specialized types, report an error and bail.
- */
- void Read(int startX, int endX, int startY, int endY, T* dest);
-
- void Read(int startX, int endX, int startY, int endY, H5::DataType typeID,
- T *dest);
-
- void Create(H5::CommonFG *_container, std::string _datasetName, unsigned int _rowLength);
-
- void TypedCreate(H5::DataSpace &fileSpace, H5::DSetCreatPropList &cparms);
-
- // Append
- void TypedWriteRow(const T*, const H5::DataSpace &memoryDataSpace,
- const H5::DataSpace &fileDataSpace);
-
- /*
- * This code is copied directly form BufferedHDFArray. I'm not sure
- * how to set up the objects nicely to share the code between the
- * two since the Flush() function is different. There probably is a
- * design pattern or simply better way to engineer this, but for now
- * it's 15 lines of code.
- */
- void WriteRow(const T *data, int dataLength, int destRow=-1);
-
- void Flush(int destRow = -1);
-};
-
-UInt GetDatasetNDim(H5::CommonFG &parentGroup, std::string datasetName);
-
-#define DECLARE_TYPED_WRITE_ROW(T, Pred) template<>\
-void BufferedHDF2DArray<T>::TypedWriteRow(const T *data, \
- const H5::DataSpace &memorySpace, const H5::DataSpace &fileSpace) ;
-
-
-DECLARE_TYPED_WRITE_ROW(int, H5::PredType::NATIVE_INT)
-DECLARE_TYPED_WRITE_ROW(unsigned int, H5::PredType::NATIVE_UINT)
-DECLARE_TYPED_WRITE_ROW(unsigned char, H5::PredType::NATIVE_UINT8)
-DECLARE_TYPED_WRITE_ROW(uint16_t, H5::PredType::NATIVE_UINT16)
-DECLARE_TYPED_WRITE_ROW(int16_t, H5::PredType::NATIVE_INT16)
-DECLARE_TYPED_WRITE_ROW(float, H5::PredType::NATIVE_FLOAT)
-
-
-#define DECLARE_TYPED_READ_ROW(T, Pred) template<>\
-void BufferedHDF2DArray<T>::Read(int startX, int endX, int startY, int endY, T* dest);
-
-
-DECLARE_TYPED_READ_ROW(int, H5::PredType::NATIVE_INT)
-DECLARE_TYPED_READ_ROW(unsigned int, H5::PredType::NATIVE_UINT)
-DECLARE_TYPED_READ_ROW(char, H5::PredType::NATIVE_INT8)
-DECLARE_TYPED_READ_ROW(unsigned char, H5::PredType::NATIVE_UINT8)
-DECLARE_TYPED_READ_ROW(uint16_t, H5::PredType::NATIVE_UINT16)
-DECLARE_TYPED_READ_ROW(int16_t, H5::PredType::NATIVE_INT16)
-DECLARE_TYPED_READ_ROW(float, H5::PredType::NATIVE_FLOAT)
-
-#define DECLARE_TYPED_CREATE_ROW(T, Pred)template<>\
-void BufferedHDF2DArray<T>::TypedCreate(H5::DataSpace &fileSpace, \
- H5::DSetCreatPropList &cparms) ;
-
-DECLARE_TYPED_CREATE_ROW(int, H5::PredType::NATIVE_INT)
-DECLARE_TYPED_CREATE_ROW(unsigned int, H5::PredType::NATIVE_UINT)
-DECLARE_TYPED_CREATE_ROW(char, H5::PredType::NATIVE_INT8)
-DECLARE_TYPED_CREATE_ROW(unsigned char, H5::PredType::NATIVE_UINT8)
-DECLARE_TYPED_CREATE_ROW(uint16_t, H5::PredType::NATIVE_UINT16)
-DECLARE_TYPED_CREATE_ROW(int16_t, H5::PredType::NATIVE_INT16)
-DECLARE_TYPED_CREATE_ROW(float, H5::PredType::NATIVE_FLOAT)
-
-#include "BufferedHDF2DArrayImpl.hpp"
-
-#endif
diff --git a/libcpp/hdf/BufferedHDF2DArrayImpl.hpp b/libcpp/hdf/BufferedHDF2DArrayImpl.hpp
deleted file mode 100644
index 49336ef..0000000
--- a/libcpp/hdf/BufferedHDF2DArrayImpl.hpp
+++ /dev/null
@@ -1,379 +0,0 @@
-#ifndef _BLASR_HDF_BUFFERED_HDF_2D_ARRAY_IMPL_HPP_
-#define _BLASR_HDF_BUFFERED_HDF_2D_ARRAY_IMPL_HPP_
-
-#include <cstring>
-#include <cassert>
-
-template<typename T>
-BufferedHDF2DArray<T>::BufferedHDF2DArray(H5::CommonFG *_container,
- std::string _datasetName) : HDFData(_container, _datasetName) {}
-
-template<typename T>
-BufferedHDF2DArray<T>::BufferedHDF2DArray() : HDFData() {
- maxDims = 0;
- nDims = 2;
- dimSize =NULL;
- rowLength = -1;
- colLength = -1;
-}
-
-template<typename T>
-unsigned int BufferedHDF2DArray<T>::GetNRows() {
- return rowLength;
-}
-
-template<typename T>
-unsigned int BufferedHDF2DArray<T>::GetNCols() {
- return colLength;
-}
-
-template<typename T>
-void BufferedHDF2DArray<T>::Close() {
-
- //
- // Clean up the write buffer.
- //
- // Flush();
- if (dimSize != NULL) {
- delete[] dimSize;
- dimSize = NULL;
- }
- this->HDFWriteBuffer<T>::Free();
-}
-
-template<typename T>
-BufferedHDF2DArray<T>::~BufferedHDF2DArray() {
- Close();
-}
-
-template<typename T>
-int BufferedHDF2DArray<T>::InitializeForReading(HDFGroup& group, std::string datasetName)
-{
- return Initialize(group, datasetName, 0, 0, false);
-}
-
-/*
- * Initialize HDF2D for reading. No write buffer initialization is
- * required. The assumption is that the dataspace is in two
- * dimensions, and this exits without grace if it is not.
- */
-template<typename T>
-int BufferedHDF2DArray<T>::Initialize(HDFGroup &group, std::string datasetName,
- unsigned int _rowLength, int _bufferSize, bool createIfMissing) {
-
- bool groupContainsDataset = group.ContainsObject(datasetName);
- if (groupContainsDataset == false) {
- //
- // Do some error checking.
- //
- if (createIfMissing == false) {
- std::cout << "ERROR! Could not open dataset " << datasetName << std::endl;
- exit(1);
- }
- if (_rowLength == 0) {
- std::cout << "ERROR! Improper usage of BufferedHDF2DArray::Initialize. The 2D Array "<<std::endl
- << "is being created but is given a number of columns of 0." << std::endl;
- exit(1);
- }
- Create(&group.group, datasetName, _rowLength);
- }
- else {
- InitializeDataset(group.group, datasetName);
- try {
- dataspace = dataset.getSpace();
- }
- catch(H5::DataSetIException &e) {
- std::cout << e.getDetailMsg() << std::endl;
- exit(1);
- }
-
- maxDims = MAX_DIMS;
- try {
- nDims = dataspace.getSimpleExtentNdims();
- /*
- * Prevent abuse of this class for multidimensional IO.
- */
- if (nDims != 2) {
- std::cout << "ERROR in HDF format: dataset: " << datasetName << " should be 1-D, but it is not." << std::endl;
- exit(1);
- }
-
- /*
- * Load in the size of this dataset, and make a map to the whole thing.
- */
- if (dimSize) {
- delete [] dimSize;
- }
- dimSize = new hsize_t[nDims];
- dataspace.getSimpleExtentDims(dimSize);
- rowLength = dimSize[0];
- colLength = dimSize[1];
- if (rowLength == 0) {
- dataspace.close();
- return 1;
- }
- fullSourceSpace = H5::DataSpace(2, dimSize);
- dataspace.close();
- }
- catch(H5::Exception &e) {
- std::cout << e.getDetailMsg() << std::endl;
- exit(1);
- }
- }
- return 1;
-}
-
-template<typename T>
-int BufferedHDF2DArray<T>::size() {
- // Why assert nDims == 1 for 2D Array?
- assert(nDims == 1);
- dataspace.getSimpleExtentDims(dimSize);
- return dimSize[0];
-}
-
-/*
- * Read rows in the range (startX, endX] in to dest.
- */
-template<typename T>
-void BufferedHDF2DArray<T>::Read(int startX, int endX, H5::DataType typeID, T*dest) {
- Read(startX, endX, 0, dimSize[1], typeID, dest);
-}
-
-template<typename T>
-void BufferedHDF2DArray<T>::Read(int startX, int endX, T*dest) {
- Read(startX, endX, 0, dimSize[1], dest);
-}
-/*
- * This is the non-specialized definition. Since this should only
- * operate on specialized types, report an error and bail.
- */
-template<typename T>
-void BufferedHDF2DArray<T>::Read(int startX, int endX, int startY, int endY, T* dest) {
- assert("ERROR, calling Read with an unsupported type. Use Read(startx,endx, starty,endy,datatype, dest) instead." == 0);
- exit(1);
-}
-
-template<typename T>
-void BufferedHDF2DArray<T>::Read(int startX, int endX, int startY, int endY, H5::DataType typeID, T *dest) {
- hsize_t memSpaceSize[2] = {0, 0};
- memSpaceSize[0] = endX - startX;
- memSpaceSize[1] = endY - startY;
- hsize_t sourceSpaceOffset[2] = {0, 0};
- sourceSpaceOffset[0] = startX;
- sourceSpaceOffset[1] = startY;
-
- H5::DataSpace destSpace(2, memSpaceSize);
- fullSourceSpace.selectHyperslab(H5S_SELECT_SET, memSpaceSize, sourceSpaceOffset);
- dataset.read(dest, typeID, destSpace, fullSourceSpace);
- destSpace.close();
-}
-
-template<typename T>
-void BufferedHDF2DArray<T>::Create(H5::CommonFG *_container, string _datasetName, unsigned int _rowLength) {
- container = _container;
- datasetName = _datasetName;
- rowLength = (unsigned int)_rowLength;
- //
- // Make life easy if the buffer is too small to fit a row --
- // resize it so that rows may be copied and written out in an
- // atomic unit.
- //
- if (this->bufferSize < rowLength) {
- // When the buffer size is greater than 0, the write buffer
- // should exist.
- if (this->bufferSize > 0) {
- assert(this->writeBuffer != NULL);
- delete[] this->writeBuffer;
- }
- this->writeBuffer = new T[rowLength];
- this->bufferSize = rowLength;
- }
-
- hsize_t dataSize[2] = {0, hsize_t(rowLength)};
- hsize_t maxDataSize[2] = {H5S_UNLIMITED, hsize_t(rowLength)};
- H5::DataSpace fileSpace(2, dataSize, maxDataSize);
- H5::DSetCreatPropList cparms;
-
- /*
- * For some reason, chunking must be enabled when creating a dataset
- * that has an unlimited dimension. Of course, this is not
- * mentioned in the hdf5 c++ documentation, because that
- * docuemntation was written for people who enjoy learning how to
- * use an API by reading comments in source code.
- */
- hsize_t chunkDims[2] = {16384, hsize_t(rowLength)};
- cparms.setChunk( 2, chunkDims );
- TypedCreate(fileSpace, cparms);
- fileSpace.close();
-
- //
- // Set some flags that indicate this dataset is ready for writing.
- //
- fileDataSpaceInitialized = true;
- isInitialized = true;
-}
-
-template<typename T>
-void BufferedHDF2DArray<T>::TypedCreate(H5::DataSpace &fileSpace,
- H5::DSetCreatPropList &cparms) {
-
- assert("Error, calling HDF2DArray<T>::TypedCreate on an unsupported type. A specialization must be written in HDF2DArray.h" == 0);
-}
-
-// Append
-template<typename T>
-void TypedWriteRow(const T*, const H5::DataSpace &memoryDataSpace,
- const H5::DataSpace &fileDataSpace) {
-
- assert("Error, calling HDF2DArray<T>::TypedWriteRow on an unsupported type. A specialization must be written in HDF2DArray.h" == 0);
-}
-
-
-/*
- * This code is copied directly form BufferedHDFArray. I'm not sure
- * how to set up the objects nicely to share the code between the
- * two since the Flush() function is different. There probably is a
- * design pattern or simply better way to engineer this, but for now
- * it's 15 lines of code.
- */
-
-template<typename T>
-void BufferedHDF2DArray<T>::WriteRow(const T *data, int dataLength, int destRow) {
- // Fill the buffer with data. When there is overflow, write
- // that out to disk.
- //
- int dataIndex = 0;
- int bufferCapacity;
- int bufferFillSize = 0;
- bool flushBuffer;
- while(dataIndex < dataLength) {
- //
- // Compute the capacity of this buffer to fit an integral number
- // of rows into it.
- //
- bufferCapacity = (this->bufferSize / rowLength)*rowLength - this->bufferIndex;
- flushBuffer = false;
- if (bufferCapacity > dataLength - dataIndex) {
- bufferFillSize = dataLength - dataIndex;
- }
- else {
- bufferFillSize = bufferCapacity;
- flushBuffer = true;
- }
- memcpy((void*) &this->writeBuffer[this->bufferIndex], (void*) &data[dataIndex], sizeof(T)*bufferFillSize);
- dataIndex += bufferFillSize;
- this->bufferIndex += bufferFillSize;
- if (flushBuffer) {
- Flush(destRow);
- }
- //
- // When not appending, increment the position of where the data
- // is to be written.
- //
- if (destRow != -1) {
- destRow += this->bufferIndex / rowLength;
- }
- }
-}
-
-template<typename T>
-void BufferedHDF2DArray<T>::Flush(int destRow) {
-
- //
- // A default writeRow of -1 implies append
- //
- int numRowsToCreate; // FIXME(yli): why is numRowsToCreate assigned but not used?
- int numDataRows;
- //
- // this->bufferIndex points after the end of the last data in the
- // buffer (full rows), so this->bufferIndex / rowLength is the
- // number of number of rows to create.
- //
- numDataRows = this->bufferIndex / rowLength;
-
- if (destRow < 0) {
- numRowsToCreate = this->bufferIndex / rowLength;
- }
- else {
- numRowsToCreate = this->bufferIndex / rowLength + destRow;
- }
- if (numDataRows > 0) {
- assert(fileDataSpaceInitialized);
-
- H5::DataSpace fileSpace;
- fileSpace = dataset.getSpace();
-
- //
- // Load the current size of the array on disk.
- //
- hsize_t fileArraySize[2], fileArrayMaxSize[2], blockStart[2];
- fileSpace.getSimpleExtentDims(fileArraySize, fileArrayMaxSize);
-
- // Save this for later to determine the offsets
- blockStart[0] = fileArraySize[0];
- blockStart[1] = fileArraySize[1];
-
- //
- // Calculate the number of rows to create. This is dependent
- // on the current file size, the destination of where the data
- // will go, and how much to write.
- //
-
- if (destRow == -1) {
- fileArraySize[0] += numDataRows;
- }
- else {
- // If the data cannot fit in the current file size, extend
- // it, otherwise, do not toch the file array size.
- if (destRow + numDataRows > fileArraySize[0]) {
- fileArraySize[0] = destRow + numDataRows;
- }
- }
-
- //
- // Make room in the file for the array.
- //
- dataset.extend(fileArraySize);
-
- H5::DataSpace extendedSpace = dataset.getSpace();
- //
- // Store the newly dimensioned dataspaces.
- //
- fileSpace.getSimpleExtentDims(fileArraySize, fileArrayMaxSize);
- //int extendedSize = extendedSpace.getSimpleExtentNpoints(); // FIXME(yli): should this be used??
- //
- // Configure the proper addressing to append to the array.
- //
- hsize_t dataSize[2];
- dataSize[0] = numDataRows;
- dataSize[1] = rowLength;
- hsize_t offset[2];
- //
- // Determine which row to write to.
- //
- if (destRow == -1) {
- offset[0] = blockStart[0];
- }
- else {
- offset[0] = destRow;
- }
- offset[1] = 0;
- extendedSpace.selectHyperslab(H5S_SELECT_SET, dataSize, offset);
- H5::DataSpace memorySpace(2, dataSize);
-
- //
- // Finally, write out the data.
- // This uses a generic function which is specialized with
- // templates later on to t
- // memorySpace addresses the entire array in linear format
- // fileSpace addresses the last dataLength blocks of dataset.
- //
- TypedWriteRow(this->writeBuffer, memorySpace, extendedSpace);
- memorySpace.close();
- extendedSpace.close();
- fileSpace.close();
- }
- this->ResetWriteBuffer();
-}
-
-#endif // _BLASR_HDF_BUFFERED_HDF_2D_ARRAY_IMPL_HPP_
diff --git a/libcpp/hdf/BufferedHDFArray.cpp b/libcpp/hdf/BufferedHDFArray.cpp
deleted file mode 100644
index a23f6f8..0000000
--- a/libcpp/hdf/BufferedHDFArray.cpp
+++ /dev/null
@@ -1,92 +0,0 @@
-#include "BufferedHDFArray.hpp"
-
-/*
- *
- * Implementation of a 1-D array for IO from an HDF array.
- * This is templated, but specialized for a few data types, so that
- * the HDF data types do not need to be specified by anybody.
- *
- * Two examples of the usage of this class follow:
- *
- * HDFArray<int> nElemArray;
- * nElemArray.Initialize(hdfFile, "PulseData/BaseCalls/ZMW/NumEvent");
- * nElemArray.Read(i, i+1, &nElem);
- *
- * HDFArray<unsigned char> qualArray;
- * qualArray.Initialize(hdfFile, "PulseData/BaseCalls/QualityValue");
- * qualArray.Read(cur, cur + nElem, qual);
- *
- */
-
-//
-// Type specializations for some standard types. Use the macro for
-// vanilla specializations (that only require the HDF type ID to be
-// specified).
-//
-#define DEFINE_TYPED_READ_ARRAY(T, Pred) template<> \
- void BufferedHDFArray<T>::Read(UInt start, UInt end, T* dest) { \
- Read(start,end, Pred, dest); \
- }
-
-DEFINE_TYPED_READ_ARRAY(int, H5::PredType::NATIVE_INT)
-DEFINE_TYPED_READ_ARRAY(char, H5::PredType::NATIVE_INT8)
-DEFINE_TYPED_READ_ARRAY(unsigned char, H5::PredType::NATIVE_UINT8)
-DEFINE_TYPED_READ_ARRAY(unsigned int, H5::PredType::NATIVE_UINT)
-DEFINE_TYPED_READ_ARRAY(uint16_t, H5::PredType::NATIVE_UINT16)
-DEFINE_TYPED_READ_ARRAY(float, H5::PredType::NATIVE_FLOAT)
-DEFINE_TYPED_READ_ARRAY(char*, H5::PredType::C_S1)
-
-
-#define DEFINE_TYPED_READ_DATASET(T, Pred) template<> \
- void BufferedHDFArray<T>::ReadDataset(std::vector<T> &dest) { \
- dest.resize(arrayLength); \
- Read(0, arrayLength, Pred, &dest[0]); \
-}
-
-DEFINE_TYPED_READ_DATASET(int, H5::PredType::NATIVE_INT)
-DEFINE_TYPED_READ_DATASET(char, H5::PredType::NATIVE_INT8)
-DEFINE_TYPED_READ_DATASET(unsigned char, H5::PredType::NATIVE_UINT8)
-DEFINE_TYPED_READ_DATASET(unsigned int, H5::PredType::NATIVE_UINT)
-DEFINE_TYPED_READ_DATASET(uint16_t, H5::PredType::NATIVE_UINT16)
-DEFINE_TYPED_READ_DATASET(float, H5::PredType::NATIVE_FLOAT)
-DEFINE_TYPED_READ_DATASET(char*, H5::PredType::C_S1)
-
-
-#define DEFINE_TYPED_CREATE_ARRAY(T, Pred) template<> \
- void BufferedHDFArray<T>::TypedCreate(H5::DataSpace &fileSpace, H5::DSetCreatPropList &cparms) { \
- T zero; zero = 0;\
- cparms.setFillValue(Pred, &zero);\
- dataset = container->createDataSet(datasetName.c_str(), Pred, fileSpace, cparms); \
-}
-
-DEFINE_TYPED_CREATE_ARRAY(int, H5::PredType::NATIVE_INT)
-DEFINE_TYPED_CREATE_ARRAY(char, H5::PredType::NATIVE_INT8)
-DEFINE_TYPED_CREATE_ARRAY(char*, H5::StrType(0,H5T_VARIABLE))
-DEFINE_TYPED_CREATE_ARRAY(unsigned char, H5::PredType::NATIVE_UINT8)
-DEFINE_TYPED_CREATE_ARRAY(unsigned int, H5::PredType::NATIVE_UINT)
-DEFINE_TYPED_CREATE_ARRAY(float, H5::PredType::NATIVE_FLOAT)
-DEFINE_TYPED_CREATE_ARRAY(uint16_t, H5::PredType::NATIVE_UINT16)
-
-template<>
-void BufferedHDFArray<string>::TypedCreate(H5::DataSpace &space, H5::DSetCreatPropList &cparms) {
- H5::StrType varStrType(0,H5T_VARIABLE);
- dataset = container->createDataSet(datasetName.c_str(), varStrType, space, cparms);
-}
-
-
-#define DEFINE_TYPED_WRITE_ARRAY(T, Pred) template<> \
-void BufferedHDFArray<T>::TypedWrite(const T *data, \
- const H5::DataSpace &memorySpace, const H5::DataSpace &fileSpace) { \
- dataset.write(data, Pred, memorySpace, fileSpace); \
-}
-
-DEFINE_TYPED_WRITE_ARRAY(int, H5::PredType::NATIVE_INT)
-DEFINE_TYPED_WRITE_ARRAY(unsigned int, H5::PredType::NATIVE_UINT)
-DEFINE_TYPED_WRITE_ARRAY(unsigned char, H5::PredType::NATIVE_UINT8)
-DEFINE_TYPED_WRITE_ARRAY(char, H5::PredType::NATIVE_INT8)
-DEFINE_TYPED_WRITE_ARRAY(float, H5::PredType::NATIVE_FLOAT)
-DEFINE_TYPED_WRITE_ARRAY(uint16_t, H5::PredType::NATIVE_UINT16)
-DEFINE_TYPED_WRITE_ARRAY(char*, H5::StrType(0,H5T_VARIABLE))
-DEFINE_TYPED_WRITE_ARRAY(std::string, H5::StrType(0,H5T_VARIABLE))
-
-
diff --git a/libcpp/hdf/BufferedHDFArray.hpp b/libcpp/hdf/BufferedHDFArray.hpp
deleted file mode 100644
index cb1037e..0000000
--- a/libcpp/hdf/BufferedHDFArray.hpp
+++ /dev/null
@@ -1,207 +0,0 @@
-#ifndef _BLASR_BUFFERED_HDF_ARRAY_HPP_
-#define _BLASR_BUFFERED_HDF_ARRAY_HPP_
-
-#include <cassert>
-#include <cstdint>
-#include <string>
-#include <vector>
-
-// HDF5 library includes
-#include "hdf5.h"
-#include "H5Cpp.h"
-
-#include "Types.h"
-#include "HDFConfig.hpp"
-#include "HDFData.hpp"
-#include "HDFGroup.hpp"
-#include "HDFWriteBuffer.hpp"
-#include "HDFFile.hpp"
-#include "DNASequence.hpp"
-#include "FASTQSequence.hpp"
-
-/*
- *
- * Implementation of a 1-D array for IO from an HDF array.
- * This is templated, but specialized for a few data types, so that
- * the HDF data types do not need to be specified by anybody.
- *
- * Two examples of the usage of this class follow:
- *
- * HDFArray<int> nElemArray;
- * nElemArray.Initialize(hdfFile, "PulseData/BaseCalls/ZMW/NumEvent");
- * nElemArray.Read(i, i+1, &nElem);
- *
- * HDFArray<unsigned char> qualArray;
- * qualArray.Initialize(hdfFile, "PulseData/BaseCalls/QualityValue");
- * qualArray.Read(cur, cur + nElem, qual);
- *
- */
-
-template<typename T>
-class BufferedHDFArray : public HDFData, public HDFWriteBuffer<T> {
-public:
- hsize_t nDims;
- hsize_t *dimSize;
- int maxDims;
- UInt arrayLength;
-
- /*
- * Constructor meant to be used for data that will be written.
- * This allocates the write buffer.
- */
- BufferedHDFArray(int pBufferSize=1024);
-
- BufferedHDFArray(H5::CommonFG* _container, std::string _datasetName);
-
- ~BufferedHDFArray();
-
- void SetBufferSize(int _bufferSize);
-
- void Write(const T *data, UInt dataLength, bool append=true,
- UInt writePos = 0);
-
- void Flush(bool append=true, UInt writePos = 0);
-
- void TypedWrite(const char **data, const H5::DataSpace &memorySpace,
- const H5::DataSpace &extendedSpace);
-
- void TypedWrite(const T*data, const H5::DataSpace &memorySpace,
- const H5::DataSpace &extendedSpace);
-
- void TypedCreate(H5::DataSpace &fileSpace, H5::DSetCreatPropList &cparms);
-
- void Create(HDFGroup &parentGroup, std::string _datasetName);
-
- void Create(H5::CommonFG* _container, std::string _datasetName);
-
- /*
- * Initialize for reading.
- *
- * Open a dataset in an hdf file. Only call this on datasets that
- * exist, since this currently handles errors with opening datasets
- * by ungracefully exiting the program.
- */
-
- int InitializeForReading(HDFGroup &parentGroup,
- const std::string datasetName);
-
- int Initialize(HDFGroup &parentGroup, const std::string &datasetName);
-
- int Initialize(HDFGroup &parentGroup, const std::string &datasetName,
- bool createIfMissing, UInt newArrayLength=0);
-
- int UpdateH5Dataspace();
-
- int Resize(UInt newArrayLength);
-
- void Close();
-
- UInt size();
-
- /*
- * Unspecialized form of read.
- * Read cannot be called on a type T* that does not have a
- * specialized template definition. This is all determined at
- * compile time. To ensure this, the following
- * default definition is provided that gives a nasty warning and
- * exits the code.
- */
-
- virtual void Read(UInt start, UInt end, T* dest);
-
- /*
- * Read in type T from the opened dataset from the interval (start,
- * end].
- */
- void ReadDataset(std::vector<T> &dest);
-
- void Read(UInt start, UInt end, H5::DataType typeID, T* dest);
-
- void ReadCharArray(UInt start, UInt end, std::string* dest);
-};
-
-/*
- * Type specializations for some standard types. Use the macro for
- * vanilla specializations (that only require the HDF type ID to be
- * specified).
- */
-#define DECLARE_TYPED_READ_ARRAY(T, Pred) template<> \
-void BufferedHDFArray<T>::Read(UInt start, UInt end, T* dest);
-
-DECLARE_TYPED_READ_ARRAY(int, H5::PredType::NATIVE_INT)
-DECLARE_TYPED_READ_ARRAY(char, H5::PredType::NATIVE_INT8)
-DECLARE_TYPED_READ_ARRAY(unsigned char, H5::PredType::NATIVE_UINT8)
-DECLARE_TYPED_READ_ARRAY(unsigned int, H5::PredType::NATIVE_UINT)
-DECLARE_TYPED_READ_ARRAY(uint16_t, H5::PredType::NATIVE_UINT16)
-DECLARE_TYPED_READ_ARRAY(float, H5::PredType::NATIVE_FLOAT)
-DECLARE_TYPED_READ_ARRAY(char*, H5::PredType::C_S1)
-
-
-#define DECLARE_TYPED_READ_DATASET(T, Pred) template<> \
-void BufferedHDFArray<T>::ReadDataset(vector<T> &dest);
-
-DECLARE_TYPED_READ_DATASET(int, H5::PredType::NATIVE_INT)
-DECLARE_TYPED_READ_DATASET(char, H5::PredType::NATIVE_INT8)
-DECLARE_TYPED_READ_DATASET(unsigned char, H5::PredType::NATIVE_UINT8)
-DECLARE_TYPED_READ_DATASET(unsigned int, H5::PredType::NATIVE_UINT)
-DECLARE_TYPED_READ_DATASET(uint16_t, H5::PredType::NATIVE_UINT16)
-DECLARE_TYPED_READ_DATASET(float, H5::PredType::NATIVE_FLOAT)
-DECLARE_TYPED_READ_DATASET(char*, H5::PredType::C_S1)
-
-
-#define DECLARE_TYPED_CREATE_ARRAY(T, Pred) template <> \
-void BufferedHDFArray<T>::TypedCreate(H5::DataSpace &fileSpace, \
- H5::DSetCreatPropList &cparms);
-
-DECLARE_TYPED_CREATE_ARRAY(int, H5::PredType::NATIVE_INT)
-DECLARE_TYPED_CREATE_ARRAY(char, H5::PredType::NATIVE_INT8)
-DECLARE_TYPED_CREATE_ARRAY(char*, H5::StrType(0,H5T_VARIABLE))
-DECLARE_TYPED_CREATE_ARRAY(unsigned char, H5::PredType::NATIVE_UINT8)
-DECLARE_TYPED_CREATE_ARRAY(unsigned int, H5::PredType::NATIVE_UINT)
-DECLARE_TYPED_CREATE_ARRAY(float, H5::PredType::NATIVE_FLOAT)
-DECLARE_TYPED_CREATE_ARRAY(uint16_t, H5::PredType::NATIVE_UINT16)
-
-template<>
-void BufferedHDFArray<std::string>::TypedCreate(H5::DataSpace &space, H5::DSetCreatPropList &cparms);
-
-#define DECLARE_TYPED_WRITE_ARRAY(T, Pred) template <> \
-void BufferedHDFArray<T>::TypedWrite(const T *data, \
- const H5::DataSpace &memorySpace, const H5::DataSpace &fileSpace);
-
-DECLARE_TYPED_WRITE_ARRAY(int, H5::PredType::NATIVE_INT)
-DECLARE_TYPED_WRITE_ARRAY(unsigned int, H5::PredType::NATIVE_UINT)
-DECLARE_TYPED_WRITE_ARRAY(unsigned char, H5::PredType::NATIVE_UINT8)
-DECLARE_TYPED_WRITE_ARRAY(char, H5::PredType::NATIVE_INT8)
-DECLARE_TYPED_WRITE_ARRAY(float, H5::PredType::NATIVE_FLOAT)
-DECLARE_TYPED_WRITE_ARRAY(uint16_t, H5::PredType::NATIVE_UINT16)
-DECLARE_TYPED_WRITE_ARRAY(char*, H5::StrType(0,H5T_VARIABLE))
-DECLARE_TYPED_WRITE_ARRAY(std::string, H5::StrType(0,H5T_VARIABLE))
-
-//
-// This is a nonstandard definition because it requires the creation
-// of a special datatype for variable length string type.
-//
-//
-// Use this as the base class for other lists.
-//
-typedef BufferedHDFArray<void> BaseHDFArray;
-
-#define DEFINE_TYPED_CLASS(CLASS_NAME, TEMPLATE_TYPE) \
-class CLASS_NAME : public BufferedHDFArray< TEMPLATE_TYPE > { \
-public: \
- void Read(UInt start, UInt end, TEMPLATE_TYPE *dest) { \
- BufferedHDFArray<TEMPLATE_TYPE>::Read(start, end, dest); \
- } \
-};
-
-DEFINE_TYPED_CLASS(HDFIntArray, int)
-DEFINE_TYPED_CLASS(HDFUIntArray, unsigned int)
-DEFINE_TYPED_CLASS(HDFUCharArray, unsigned char)
-DEFINE_TYPED_CLASS(HDFCharArray, char)
-DEFINE_TYPED_CLASS(HDFUShortArray, uint16_t )
-//DEFINE_TYPED_CLASS(HDFStringArray, std::string)
-DEFINE_TYPED_CLASS(HDFFloatArray, float)
-
-#include "BufferedHDFArrayImpl.hpp"
-
-#endif
diff --git a/libcpp/hdf/BufferedHDFArrayImpl.hpp b/libcpp/hdf/BufferedHDFArrayImpl.hpp
deleted file mode 100644
index 9f890ca..0000000
--- a/libcpp/hdf/BufferedHDFArrayImpl.hpp
+++ /dev/null
@@ -1,435 +0,0 @@
-#ifndef _BLASR_HDF_BUFFERED_HDF_ARRAY_IMPL_HPP_
-#define _BLASR_HDF_BUFFERED_HDF_ARRAY_IMPL_HPP_
-
-#include <cstdlib>
-#include <iostream>
-#include <cstring>
-#include "BufferedHDFArray.hpp"
-
-template<typename T>
-BufferedHDFArray<T>::BufferedHDFArray(int pBufferSize) : HDFData() {
- nDims = 0;
- maxDims = 0;
- arrayLength = 0;
- dimSize = NULL;
- this->bufferIndex = 0;
- this->InitializeBuffer(pBufferSize);
-}
-
-template<typename T>
-BufferedHDFArray<T>::BufferedHDFArray(H5::CommonFG* _container,
- std::string _datasetName) : HDFData(_container, _datasetName) {
- // no-op
-}
-
-template<typename T>
-BufferedHDFArray<T>::~BufferedHDFArray() {
- //
- // Clean up the write buffer.
- //
- if (dimSize != NULL) {
- delete[] dimSize;
- dimSize = NULL;
- }
- this->Free();
-}
-
-template<typename T>
-void BufferedHDFArray<T>::SetBufferSize(int _bufferSize) {
- this->InitializeBuffer(_bufferSize);
-}
-
-template<typename T>
-void BufferedHDFArray<T>::Write(const T *data, UInt dataLength, bool append,
- UInt writePos) {
-
- // Fill the buffer with data. When there is overflow, write
- // that out to disk.
- //
- UInt dataIndex = 0;
- int bufferCapacity;
- int bufferFillSize = 0;
- bool flushBuffer;
- while(dataIndex < dataLength) {
- bufferCapacity = this->bufferSize - this->bufferIndex;
- flushBuffer = false;
- if (bufferCapacity > dataLength - dataIndex) {
- bufferFillSize = dataLength - dataIndex;
- }
- else {
- bufferFillSize = bufferCapacity;
- flushBuffer = true;
- }
- memcpy((void*) &this->writeBuffer[this->bufferIndex], (void*) &data[dataIndex], sizeof(T)*bufferFillSize);
- dataIndex += bufferFillSize;
- this->bufferIndex += bufferFillSize;
- if (flushBuffer) {
- Flush(append, writePos);
- }
- }
-}
-
-template<typename T>
-void BufferedHDFArray<T>::Flush(bool append, UInt writePos) {
- //
- // Flush contents of current buffer to the file.
- //
- if (this->WriteBufferEmpty()) {
- //
- // There is no data in the buffer, so nothing can be written.
- // HDF does not support empty arrays (as far as I can tell), so
- // don't even bother trying to create the dataspace.
- //
- return;
- }
-
- // fetch the current size of the dataspace
- if (fileDataSpaceInitialized == false) {
- std::cout << "ERROR, trying to flush a dataset that has not been ";
- std::cout << "created or initialized" << std::endl;
- exit(1);
- fileDataSpaceInitialized = true;
- }
-
- H5::DataSpace fileSpace;
- fileSpace = dataset.getSpace();
-
- //
- // Load the current size of the array on disk.
- //
- hsize_t fileArraySize[1], blockStart;
- fileArraySize[0] = fileSpace.getSimpleExtentNpoints();
- if (append) {
- blockStart = fileSpace.getSimpleExtentNpoints();
- fileArraySize[0] += this->bufferIndex;
- //
- // Make room in the file for the array.
- //
- dataset.extend(fileArraySize);
- }
- else {
- blockStart = writePos;
- if (blockStart + this->bufferIndex > fileArraySize[0]) {
- fileArraySize[0] = blockStart + this->bufferIndex;
- dataset.extend(fileArraySize);
- }
- }
-
- H5::DataSpace extendedSpace = dataset.getSpace();
- //int extendedSize = extendedSpace.getSimpleExtentNpoints(); // FIXME(yli): why isn't this used?
- //
- // Configure the proper addressing to append to the array.
- //
- hsize_t dataSize[1];
- hsize_t offset[1];
- dataSize[0] = this->bufferIndex;
- offset[0] = blockStart;
- extendedSpace.selectHyperslab(H5S_SELECT_SET, dataSize, offset);
- H5::DataSpace memorySpace(1, dataSize);
-
- //
- // Finally, write out the data.
- // This uses a generic function which is specialized with
- // templates later on to t
- // memorySpace addresses the entire array in linear format
- // fileSpace addresses the last dataLength blocks of dataset.
- //
- try {
- TypedWrite(this->writeBuffer, memorySpace, extendedSpace);
- }
- catch(H5::DataSetIException e) {
- std::cout <<"ERROR! Could not write HDF5 data." << std::endl;
- e.printError();
- exit(1);
- }
- memorySpace.close();
- extendedSpace.close();
- fileSpace.close();
-
- // Clear the buffer.
- this->ResetWriteBuffer();
-}
-
-template<typename T>
-void BufferedHDFArray<T>::TypedWrite(const char **data, const H5::DataSpace &memorySpace,
- const H5::DataSpace &extendedSpace) {
-
- H5::StrType varStrType(0,H5T_VARIABLE);
- dataset.write(data, varStrType, memorySpace, extendedSpace);
-}
-
-template<typename T>
-void BufferedHDFArray<T>::TypedWrite(const T* data, const H5::DataSpace &memorySpace,
- const H5::DataSpace &extendedSpace) {
-
- assert("Calling TypedWrite on an unsupported type" == 0);
-}
-
-template<typename T>
-void BufferedHDFArray<T>::TypedCreate(H5::DataSpace &fileSpace,
- H5::DSetCreatPropList &cparms) {
-
- std::cout << "DEFAULT typed create " << std::endl;
-}
-
-
-template<typename T>
-void BufferedHDFArray<T>::Create(HDFGroup &parentGroup, std::string _datasetName) {
- return Create(&parentGroup.group, _datasetName);
-}
-
-
-template<typename T>
-void BufferedHDFArray<T>::Create(H5::CommonFG* _container, std::string _datasetName) {
- //
- // Initialize where the dataset will go.
- container = _container;
- datasetName = _datasetName;
-
- hsize_t dataSize[] = {0};
- hsize_t maxDataSize[] = {H5S_UNLIMITED};
- H5::DataSpace fileSpace(1, dataSize, maxDataSize);
- H5::DSetCreatPropList cparms;
-
- /*
- * For some reason, chunking must be enabled when creating a dataset
- * that has an unlimited dimension. Of course, this is not
- * mentioned in the hdf5 c++ documentation, because that
- * docuemntation was written for people who enjoy learning how to
- * use an API by reading comments in source code.
- */
- hsize_t chunk_dims[1] = { 16384 };
- cparms.setChunk( 1, chunk_dims );
- TypedCreate(fileSpace, cparms);
-
- //
- // Since TypedCreate created an assigned a dataset, this array is
- // now initialized. Do the bookkeeping here.
- //
-
- isInitialized = true;
- fileDataSpaceInitialized = true;
- fileSpace.close();
-}
-
-
-
-/*
- * Initialize for reading.
- *
- * Open a dataset in an hdf file. Only call this on datasets that
- * exist, since this currently handles errors with opening datasets
- * by ungracefully exiting the program.
- */
-
-template<typename T>
-int BufferedHDFArray<T>::InitializeForReading(HDFGroup &parentGroup,
- const std::string datasetName) {
-
- return Initialize(parentGroup, datasetName, false);
-}
-
-template<typename T>
-int BufferedHDFArray<T>::Initialize(HDFGroup &parentGroup,
- const std::string &datasetName) {
-
- return Initialize(parentGroup, datasetName, true);
-}
-
-template<typename T>
-int BufferedHDFArray<T>::Initialize(HDFGroup &parentGroup,
- const std::string &datasetName, bool createIfMissing, UInt newArrayLength) {
- //
- // For writing to this dataset, start at the first position in the
- // write buffer.
- //
- this->bufferIndex = 0;
- //
- // It's possible that the group may be asked to initialize this
- // dataset when the dataset does not exist. Check that here.
- //
- bool parentHasObject = parentGroup.ContainsObject(datasetName);
- if ( parentHasObject and InitializeDataset(parentGroup, datasetName) == 0) {
- //
- // The parent group already contains this dataset. Try to
- // initialize this dataset and if it does not exist, flag fail.
- //
- return 0;
- }
-
- //
- // This is a hack to create in read/write mode. If the parent
- // does not have the object, try and create it. The problem with
- // trying to open a dataset in append mode is it will fail if the
- // dataset does not exist.
- //
- if (parentHasObject == false) {
- if (createIfMissing) {
- Create(parentGroup, datasetName);
- }
- else {
- //
- // Trying to open a dataset to read only, but it does not
- // exist. Bail.
- //
- return 0;
- }
- }
- int ret = UpdateH5Dataspace();
- if (newArrayLength > 0) {
- ret *= Resize(newArrayLength);
- }
- return ret;
-}
-
-template<typename T>
-int BufferedHDFArray<T>::UpdateH5Dataspace() {
- try {
- dataspace = dataset.getSpace();
- }
- catch(H5::DataSetIException &e) {
- e.printError();
- return 0;
- }
- maxDims = MAX_DIMS;
- try {
- nDims = dataspace.getSimpleExtentNdims();
- /*
- * Prevent abuse of this class for multidimensional IO.
- */
- if (nDims != 1) {
- std::cout << "ERROR in HDF format: dataset: ";
- std::cout << datasetName << " should be 1-D, but it is not.";
- std::cout << std::endl;
- exit(1);
- }
-
- /*
- * Load in the size of this dataset, and make a map to the whole thing.
- */
- if (dimSize != NULL) {
- delete [] dimSize;
- dimSize = NULL;
- }
- dimSize = new hsize_t[nDims];
-
- dataspace.getSimpleExtentDims(dimSize);
- arrayLength = dimSize[0];
- if (dimSize[0] == 0) {
- // DONT create a real dataspace if the size is 0
- // cout << "WARNING, trying to open a zero sized dataspace." << endl;
- dataspace.close();
- return 1;
- }
- fullSourceSpace = H5::DataSpace(1, dimSize);
- dataspace.close();
- }
- catch(H5::Exception& e) {
- e.printError();
- return 0;
- }
- return 1;
-}
-
-template<typename T>
-int BufferedHDFArray<T>::Resize(UInt newArrayLength) {
- //
- // Resize this dataset. May or may not allocate space in file.
- // May or may not write fill value.
- //
- try{
- H5::DataSpace fileSpace;
- fileSpace = dataset.getSpace();
-
- hsize_t fileArraySize[1];
- fileArraySize[0] = newArrayLength;
- arrayLength = newArrayLength;
- dataset.extend(fileArraySize);
- fileSpace.close();
- } catch(H5::DataSetIException &e) {
- e.printError();
- return 0;
- }
- return 1;
-}
-
-
-template<typename T>
-void BufferedHDFArray<T>::Close() {
- if (dimSize != NULL) {
- delete[] dimSize;
- dimSize = NULL;
- HDFData::Close();
- }
-}
-
-template<typename T>
-UInt BufferedHDFArray<T>::size() {
- dataspace = dataset.getSpace();
- hsize_t dimSizeArray[1];
- dataspace.getSimpleExtentDims(dimSizeArray);
- dataspace.close();
- return dimSizeArray[0];
-}
-
-/*
- * Unspecialized form of read.
- * Read cannot be called on a type T* that does not have a
- * specialized template definition. This is all determined at
- * compile time. To ensure this, the following
- * default definition is provided that gives a nasty warning and
- * exits the code.
- */
-
-template<typename T>
-void BufferedHDFArray<T>::Read(UInt start, UInt end, T* dest) {
- assert("ERROR, calling Read with an unsupported type. Use Read(start,end,datatype, dest) instead." == 0);
- exit(1); // this is in case the assert statement is removed.
-}
-
-/*
- * Read in type T from the opened dataset from the interval (start,
- * end].
- */
-
-template<typename T>
-void BufferedHDFArray<T>::ReadDataset(std::vector<T> &dest) {
- assert("ERROR, calling ReadDataset with an unsupported type.");
- exit(1); // this is in case the assert statement is removed.
-}
-
-template<typename T>
-void BufferedHDFArray<T>::Read(UInt start, UInt end, H5::DataType typeID, T *dest) {
- if (end - start == 0) {
- return;
- }
- hsize_t memSpaceSize[] = {0};
- memSpaceSize[0] = end - start;
- hsize_t sourceSpaceOffset[] = {0};
- sourceSpaceOffset[0] = start;
- H5::DataSpace destSpace(1, memSpaceSize);
- fullSourceSpace.selectHyperslab(H5S_SELECT_SET, memSpaceSize, sourceSpaceOffset);
- dataset.read(dest, typeID, destSpace, fullSourceSpace);
- destSpace.close();
-}
-
-template<typename T>
-void BufferedHDFArray<T>::ReadCharArray(UInt start, UInt end, std::string* dest) {
- hsize_t memSpaceSize[] = {0};
- memSpaceSize[0] = end - start;
- hsize_t sourceSpaceOffset[] = {0};
- sourceSpaceOffset[0] = start;
- H5::DataSpace destSpace(1, memSpaceSize);
- H5::StrType strType(0, H5T_VARIABLE);
- fullSourceSpace.selectHyperslab(H5S_SELECT_SET, memSpaceSize, sourceSpaceOffset);
- std::vector<char*> tmpStringArray;
- tmpStringArray.resize(end-start);
- dataset.read(&tmpStringArray[0], strType, destSpace, fullSourceSpace);
- UInt i;
- for (i = 0; i < tmpStringArray.size(); i++) {
- dest[i] = tmpStringArray[i];
- }
- destSpace.close();
-}
-
-#endif // _BLASR_HDF_BUFFERED_HDF_ARRAY_IMPL_HPP_
diff --git a/libcpp/hdf/DatasetCollection.cpp b/libcpp/hdf/DatasetCollection.cpp
deleted file mode 100644
index 3184e49..0000000
--- a/libcpp/hdf/DatasetCollection.cpp
+++ /dev/null
@@ -1,61 +0,0 @@
-#include "DatasetCollection.hpp"
-
-void DatasetCollection::MakeFieldRequired(std::string &fieldName) {
- includedFields[fieldName] = true;
- requiredFields[fieldName] = true;
-}
-
-void DatasetCollection::MakeFieldOptional(std::string &fieldName) {
- includedFields[fieldName] = true;
- requiredFields[fieldName] = false;
-}
-
-void DatasetCollection::InitializeAllFields(bool value) {
- size_t f;
- for (f = 0; f < fieldNames.size(); f++ ) {
- includedFields[fieldNames[f]] = value;
- }
-}
-
-void DatasetCollection::InitializeFields(std::vector<std::string> &fieldList) {
- size_t i;
- for (i = 0; i < fieldList.size(); i++) {
- includedFields[fieldList[i]] = true;
- }
-}
-
-void DatasetCollection::InitializeFields(std::vector<char*> &fieldList) {
- size_t i;
- InitializeAllFields(false);
- for (i = 0; i < fieldList.size(); i++) {
- includedFields[fieldList[i]] = true;
- }
-}
-
-int DatasetCollection::IncludeField(std::string fieldName) {
- if (includedFields.find(fieldName) == includedFields.end()) {
- return 0;
- }
- else {
- includedFields[fieldName] = true;
- }
- return 1;
-}
-
-bool DatasetCollection::FieldIsIncluded(std::string fieldName) {
- if (includedFields.find(fieldName) == includedFields.end()) {
- return false;
- }
- else {
- return includedFields[fieldName];
- }
-}
-
-bool DatasetCollection::ContainsField(std::string fieldName) {
- size_t f;
- for (f = 0; f < fieldNames.size(); f++) {
- if (fieldNames[f] == fieldName) return true;
- }
- return false;
-}
-
diff --git a/libcpp/hdf/DatasetCollection.hpp b/libcpp/hdf/DatasetCollection.hpp
deleted file mode 100644
index b3305f7..0000000
--- a/libcpp/hdf/DatasetCollection.hpp
+++ /dev/null
@@ -1,41 +0,0 @@
-#ifndef _BLASR_DATASET_COLLECTION_HPP_
-#define _BLASR_DATASET_COLLECTION_HPP_
-
-#include <map>
-#include <vector>
-#include <string>
-#include <iostream>
-#include "HDFGroup.hpp"
-#include "HDFData.hpp"
-
-
-class DatasetCollection {
-public:
- std::vector<std::string> fieldNames;
- std::map<std::string,bool> includedFields;
- std::map<std::string,bool> requiredFields;
-
- void MakeFieldRequired(std::string &fieldName);
-
- void MakeFieldOptional(string &fieldName);
-
- void InitializeAllFields(bool value);
-
- void InitializeFields(std::vector<std::string> &fieldList);
-
- void InitializeFields(std::vector<char*> &fieldList);
-
- int IncludeField(std::string fieldName);
-
- bool FieldIsIncluded(std::string fieldName);
-
- bool ContainsField(std::string fieldName);
-
- template <typename T_Dataset>
- bool InitializeDataset(HDFGroup &group, T_Dataset &dataset, std::string datasetName);
-
-};
-
-#include "DatasetCollectionImpl.hpp"
-
-#endif
diff --git a/libcpp/hdf/DatasetCollectionImpl.hpp b/libcpp/hdf/DatasetCollectionImpl.hpp
deleted file mode 100644
index 7344e9f..0000000
--- a/libcpp/hdf/DatasetCollectionImpl.hpp
+++ /dev/null
@@ -1,29 +0,0 @@
-#ifndef _BLASR_DATASET_COLLECTION_IMPL_HPP_
-#define _BLASR_DATASET_COLLECTION_IMPL_HPP_
-
-template <typename T_Dataset>
-bool DatasetCollection::InitializeDataset(HDFGroup &group,
- T_Dataset &dataset, std::string datasetName) {
-
- //
- // Perform initialization of the dataset in a way that keep track
- // of which datasets in the collection are present.
- //
- if (includedFields[datasetName]) {
- if (dataset.Initialize(group, datasetName) == false) {
- if (requiredFields[datasetName]) {
- return false;
- }
- else {
- //
- // This field was supposed to be included but it either does
- // not exist or there was a problem otherwise in creating
- // it. Don't try and read from it later on.
- //
- includedFields[datasetName] = false;
- }
- }
- }
- return true;
-}
-#endif
diff --git a/libcpp/hdf/HDF2DArray.hpp b/libcpp/hdf/HDF2DArray.hpp
deleted file mode 100644
index 1e76e6e..0000000
--- a/libcpp/hdf/HDF2DArray.hpp
+++ /dev/null
@@ -1,25 +0,0 @@
-#ifndef _BLASR_HDF_2DARRAY_HPP_
-#define _BLASR_HDF_2DARRAY_HPP_
-
-#include "BufferedHDF2DArray.hpp"
-
-template<typename T>
-class HDF2DArray : public BufferedHDF2DArray<T> {
-public:
-
- void WriteRow(const T*data, int dataLength, int destRow=-1) {
- this->writeBuffer = (T*) data;
- this->bufferIndex = dataLength;
- this->bufferSize = dataLength;
- this->Flush(destRow);
- //
- // Reset status of buffer so that no methods are tricked into
- // thinking this is a valid pointer.
- //
- this->writeBuffer = NULL;
- this->bufferIndex = 0;
- this->bufferSize = 0;
- }
-};
-
-#endif
diff --git a/libcpp/hdf/HDFAlnGroup.hpp b/libcpp/hdf/HDFAlnGroup.hpp
deleted file mode 100644
index ebdc05e..0000000
--- a/libcpp/hdf/HDFAlnGroup.hpp
+++ /dev/null
@@ -1,50 +0,0 @@
-#ifndef _BLASR_HDF_ALN_GROUP_HPP_
-#define _BLASR_HDF_ALN_GROUP_HPP_
-
-#include "HDFArray.h"
-#include "HDFGroup.h"
-
-class HDFAlnGroup {
- public:
- HDFGroup alnGroup;
- HDFArray<unsigned int> idArray;
- HDFStringArray pathArray;
-
- void Initialize(HDFGroup &parent) {
- alnGroup.Initialize(parent.group, "AlnGroup");
- idArray.Initialize(alnGroup.group, "ID");
- }
-
- void Read(AlnGroup &aln) {
- // Seem to write data in this HDFAlnGroup obj to AlnGroup & aln
- int idNElem = idArray.arrayLength;
- int pathNElem = pathArray.arrayLength;
- if (idNElem > 0) {
-
- aln.id.resize(idNElem);
- idArray.Read(0, idNElem);
-
- aln.path.resize(pathNElem);
- unsigned int i;
- for (i = 0; i < pathNElem; i++) {
- pathArray.Read(i, i+1, &aln.path[i]);
- }
- }
- }
-
- int AddPath(string &path) {
- int id;
- pathArray.Write(&path, 1);
- id = pathArray.size();
- idArray.Write(&id, 1);
- return id;
- }
-
- ~HDFAlnGroup() {
- alnGroup.Close();
- }
-
-};
-
-
-#endif
diff --git a/libcpp/hdf/HDFAlnGroupGroup.cpp b/libcpp/hdf/HDFAlnGroupGroup.cpp
deleted file mode 100644
index 959098e..0000000
--- a/libcpp/hdf/HDFAlnGroupGroup.cpp
+++ /dev/null
@@ -1,52 +0,0 @@
-#include "HDFAlnGroupGroup.hpp"
-
-using namespace std;
-
-bool HDFAlnGroupGroup::Create(HDFGroup &parent) {
- parent.AddGroup("AlnGroup");
- if (alnGroup.Initialize(parent.group, "AlnGroup") == 0) { return 0; }
- idArray.Create(alnGroup, "ID");
- pathArray.Create(alnGroup, "Path");
- return true;
-}
-
-int HDFAlnGroupGroup::AddPath(string path) {
- pathArray.Write(&path, 1);
- unsigned int id = pathArray.size();
- idArray.Write(&id, 1);
- int size = pathArray.size();
- return size;
-}
-
-int HDFAlnGroupGroup::Initialize(HDFGroup &parent) {
- if (alnGroup.Initialize(parent.group, "AlnGroup") == 0) {
- cout << "ERROR, could not open /AlnGroup group." << endl;
- exit(1);
- }
- if (idArray.Initialize(alnGroup, "ID") == 0) {
- cout << "ERROR, could not open /AlnGroup/ID." << endl;
- exit(1);
- }
- if (pathArray.Initialize(alnGroup, "Path") == 0) {
- cout << "ERROR, could not open /AlnGroup/Path." << endl;
- exit(1);
- }
- return 1;
-}
-
-void HDFAlnGroupGroup::Read(AlnGroup &aln) {
- UInt nRow = idArray.size();
- if (nRow > 0) {
- aln.id.resize(nRow);
- idArray.Read(0, nRow, &aln.id[0]);
- aln.path.resize(nRow);
- unsigned int i;
- for (i = 0; i < nRow; i++) {
- pathArray.Read(i, i+1, &aln.path[i]);
- }
- }
-}
-
-HDFAlnGroupGroup::~HDFAlnGroupGroup() {
- alnGroup.Close();
-}
diff --git a/libcpp/hdf/HDFAlnGroupGroup.hpp b/libcpp/hdf/HDFAlnGroupGroup.hpp
deleted file mode 100644
index 8045e48..0000000
--- a/libcpp/hdf/HDFAlnGroupGroup.hpp
+++ /dev/null
@@ -1,27 +0,0 @@
-#ifndef _BLASR_HDF_ALN_GROUP_HPP_
-#define _BLASR_HDF_ALN_GROUP_HPP_
-
-#include <string>
-#include "HDFArray.hpp"
-#include "HDFGroup.hpp"
-#include "saf/AlnGroup.hpp"
-
-class HDFAlnGroupGroup {
-public:
- HDFGroup alnGroup;
- HDFArray<unsigned int> idArray;
- HDFStringArray pathArray;
-
- bool Create(HDFGroup &parent);
-
- int AddPath(std::string path);
-
- int Initialize(HDFGroup &parent);
-
- void Read(AlnGroup &aln);
-
- ~HDFAlnGroupGroup();
-};
-
-
-#endif
diff --git a/libcpp/hdf/HDFAlnInfoGroup.cpp b/libcpp/hdf/HDFAlnInfoGroup.cpp
deleted file mode 100644
index 4beba5f..0000000
--- a/libcpp/hdf/HDFAlnInfoGroup.cpp
+++ /dev/null
@@ -1,102 +0,0 @@
-#include "HDFAlnInfoGroup.hpp"
-
-using namespace std;
-
-int HDFAlnInfoGroup::InitializeNumPasses() {
- numPasses.Initialize(alnInfoGroup, "NumPasses");
- return 1;
-}
-
-void HDFAlnInfoGroup::InitializeDefaultColumnNames(vector<string> &defaultColumnNames) {
- defaultColumnNames.push_back("AlnID");
- defaultColumnNames.push_back("AlnGroupID");
- defaultColumnNames.push_back("MovieID");
- defaultColumnNames.push_back("RefGroupID");
- defaultColumnNames.push_back("tStart");
- defaultColumnNames.push_back("tEnd");
- defaultColumnNames.push_back("RCRefStrand");
- defaultColumnNames.push_back("HoleNumber");
- defaultColumnNames.push_back("SetNumber");
- defaultColumnNames.push_back("StrobeNumber");
- defaultColumnNames.push_back("MoleculeID");
- defaultColumnNames.push_back("rStart");
- defaultColumnNames.push_back("rEnd");
- defaultColumnNames.push_back("MapQV");
- defaultColumnNames.push_back("nM");
- defaultColumnNames.push_back("nMM");
- defaultColumnNames.push_back("nIns");
- defaultColumnNames.push_back("nDel");
- defaultColumnNames.push_back("Offset_begin");
- defaultColumnNames.push_back("Offset_end");
- defaultColumnNames.push_back("nBackRead");
- defaultColumnNames.push_back("nReadOverlap");
-}
-
-bool HDFAlnInfoGroup::Create(HDFGroup &parent) {
- parent.AddGroup("AlnInfo");
- // Make sure it was created, and intialize this group to reference the newly created one.
- if (alnInfoGroup.Initialize(parent.group, "AlnInfo") == 0) { return 0; }
- vector<string> defaultColumnNames;
- InitializeDefaultColumnNames(defaultColumnNames);
- columnNames.Create(alnInfoGroup.group, "ColumnNames", defaultColumnNames);
-
- alnIndexArray.Create(&alnInfoGroup.group, "AlnIndex", defaultColumnNames.size());
- return true;
-}
-
-int HDFAlnInfoGroup::Initialize(HDFGroup &rootGroup) {
- if (alnInfoGroup.Initialize(rootGroup.group, "AlnInfo") == 0) { return 0; }
- if (alnIndexArray.Initialize(alnInfoGroup, "AlnIndex") == 0) { return 0; }
- /*
- * This functionality should go into the python.
- if (!alnIndexArray.ContainsAttribute("ColumnNames")) {
- try {
- vector<string> defaultColumnNames;
- InitializeDefaultColumnNames(defaultColumnNames);
- columnNames.Create(alnIndexArray.dataset, "ColumnNames", defaultColumnNames);
- }
- catch(Execption e) {
- //
- // If the dataset is not writable
- }
- }
- */
- return 1;
-}
-
-HDFAlnInfoGroup::~HDFAlnInfoGroup() {
- alnInfoGroup.Close();
-}
-
-// Return size of /AlnInfo/AlnIndex in KB
-UInt HDFAlnInfoGroup::GetAlnIndexSize() {
- return alnIndexArray.GetNRows() / 1024 * sizeof (unsigned int) * NCols;
-}
-
-void HDFAlnInfoGroup::Read(AlnInfo &alnInfo) {
-
- UInt nAlignments = alnIndexArray.GetNRows();
- alnInfo.alignments.resize(nAlignments);
- UInt alignmentIndex;
- UInt alignmentRow[NCols];
- for (alignmentIndex = 0; alignmentIndex < nAlignments; alignmentIndex++) {
- // Input the values.
- alnIndexArray.Read(alignmentIndex, alignmentIndex + 1, alignmentRow);
- alnInfo.alignments[alignmentIndex].StoreAlignmentIndex(alignmentRow, NCols);
- }
-}
-
-int HDFAlnInfoGroup::GetNAlignments() {
- return alnIndexArray.GetNRows();
-}
-
-unsigned int HDFAlnInfoGroup::WriteAlnIndex(vector<unsigned int> &aln) {
- alnIndexArray.WriteRow(&aln[0], aln.size());
- return alnIndexArray.GetNRows();
-}
-
-void HDFAlnInfoGroup::ReadCmpAlignment(UInt alignmentIndex, CmpAlignment &cmpAlignment) {
- UInt alignmentRow[NCols];
- alnIndexArray.Read(alignmentIndex, alignmentIndex + 1, alignmentRow);
- cmpAlignment.StoreAlignmentIndex(alignmentRow, NCols);
-}
diff --git a/libcpp/hdf/HDFAlnInfoGroup.hpp b/libcpp/hdf/HDFAlnInfoGroup.hpp
deleted file mode 100644
index 4941b1b..0000000
--- a/libcpp/hdf/HDFAlnInfoGroup.hpp
+++ /dev/null
@@ -1,46 +0,0 @@
-#ifndef _BLASR_HDF_ALN_INFO_GROUP_HPP_
-#define _BLASR_HDF_ALN_INFO_GROUP_HPP_
-
-#include <cinttypes>
-#include <vector>
-#include <string>
-#include "HDFGroup.hpp"
-#include "HDFAtom.hpp"
-#include "HDFArray.hpp"
-#include "HDF2DArray.hpp"
-#include "saf/AlnInfo.hpp"
-#include "alignment/CmpAlignment.hpp"
-
-class HDFAlnInfoGroup {
-public:
- HDFGroup alnInfoGroup;
- HDF2DArray<unsigned int> alnIndexArray;
- HDFArray<float> startTime;
- static const int NCols=22;
- HDFArray<unsigned int> numPasses;
- HDFAtom<vector<string> > columnNames;
- HDFAtom<int> frameRate;
-
- int Initialize(HDFGroup &rootGroup);
-
- int InitializeNumPasses();
-
- void InitializeDefaultColumnNames(std::vector<std::string> &defaultColumnNames);
-
- bool Create(HDFGroup &parent);
-
- ~HDFAlnInfoGroup();
-
- // Return size of /AlnInfo/AlnIndex in KB
- UInt GetAlnIndexSize();
-
- void Read(AlnInfo &alnInfo);
-
- int GetNAlignments();
-
- unsigned int WriteAlnIndex(std::vector<unsigned int> &aln);
-
- void ReadCmpAlignment(UInt alignmentIndex, CmpAlignment &cmpAlignment);
-};
-
-#endif
diff --git a/libcpp/hdf/HDFArray.hpp b/libcpp/hdf/HDFArray.hpp
deleted file mode 100644
index af4c66a..0000000
--- a/libcpp/hdf/HDFArray.hpp
+++ /dev/null
@@ -1,85 +0,0 @@
-#ifndef _BLASR_HDF_ARRAY_HPP_
-#define _BLASR_HDF_ARRAY_HPP_
-
-#include <assert.h>
-#include <iostream>
-
-#include "H5Cpp.h"
-
-#include "HDFConfig.hpp"
-#include "HDFData.hpp"
-#include "BufferedHDFArray.hpp"
-#include "DNASequence.hpp"
-#include "FASTQSequence.hpp"
-
-/*
- *
- * Implementation of a 1-D array for IO from an HDF array.
- * This is templated, but specialized for a few data types, so that
- * the HDF data types do not need to be specified by anybody.
- *
- * Two examples of the usage of this class follow:
- *
- * HDFArray<int> nElemArray;
- * nElemArray.Initialize(hdfFile, "PulseData/BaseCalls/ZMW/NumEvent");
- * nElemArray.Read(i, i+1, &nElem);
- *
- * HDFArray<unsigned char> qualArray;
- * qualArray.Initialize(hdfFile, "PulseData/BaseCalls/QualityValue");
- * qualArray.Read(cur, cur + nElem, qual);
- *
- */
-
-template<typename T>
-class HDFArray : public BufferedHDFArray<T> {
-public:
-
- HDFArray() : BufferedHDFArray<T>() {}
- HDFArray(H5::CommonFG* _container, std::string _datasetName) :
- BufferedHDFArray<T>(_container, _datasetName) {}
-
- /*
- * An unbuffered write is simply a write immediately followed by a flush.
- */
- void WriteToPos(const T*data, int dataLength, UInt writePos) {
- this->writeBuffer = (T*) data;
- this->bufferIndex = dataLength;
- this->bufferSize = dataLength;
- this->Flush(false, writePos);
- ResetBuffer();
- }
-
- void ResetBuffer() {
- this->writeBuffer = NULL;
- this->bufferIndex = 0;
- this->bufferSize = 0;
- }
-
- void Write(const T *data, int dataLength) {
- this->writeBuffer = (T*) data;
- this->bufferIndex = dataLength;
- this->bufferSize = dataLength;
- this->Flush();
- //
- // Reset status of buffer so that no methods are tricked into
- // thinking this is a valid pointer.
- //
- ResetBuffer();
- }
-
- ~HDFArray() {}
-};
-
-
-class HDFStringArray: public HDFArray<std::string> {
-public:
- void Read(UInt start, UInt end, std::string* dest) {
- std::vector<char*> tmpDestCharPtrs;
- if (end == start) return;
- assert(end > start);
- tmpDestCharPtrs.resize(end-start);
- // ReadCharArray(start, end, (char**) &tmpDestCharPtrs[0]);
- ReadCharArray(start, end, dest);
- }
-};
-#endif
diff --git a/libcpp/hdf/HDFAtom.cpp b/libcpp/hdf/HDFAtom.cpp
deleted file mode 100644
index ef23749..0000000
--- a/libcpp/hdf/HDFAtom.cpp
+++ /dev/null
@@ -1,159 +0,0 @@
-#include "HDFAtom.hpp"
-
-template<>
-void HDFAtom<std::string>::Create(H5::H5Location &object, std::string atomName) {
- H5::StrType strType(0, H5T_VARIABLE);
- hsize_t defaultDims[] = {1};
- H5::DataSpace defaultDataSpace(1, defaultDims);
- attribute = object.createAttribute(atomName.c_str(), strType, H5::DataSpace(H5S_SCALAR));
- initialized= true;
-}
-
-
-#define DEFINE_TYPED_CREATE_ATOM(T, predtype) template<> \
- void HDFAtom<T>::TypedCreate(H5::H5Location &object, std::string &atomName, H5::DataSpace &defaultDataSpace) { \
- attribute = object.createAttribute(atomName.c_str(), (predtype), defaultDataSpace ); \
-}
-
-
-DEFINE_TYPED_CREATE_ATOM(int, H5::PredType::NATIVE_INT)
-DEFINE_TYPED_CREATE_ATOM(unsigned int, H5::PredType::NATIVE_UINT)
-DEFINE_TYPED_CREATE_ATOM(unsigned char, H5::PredType::NATIVE_UINT8)
-DEFINE_TYPED_CREATE_ATOM(char, H5::PredType::NATIVE_INT8)
-DEFINE_TYPED_CREATE_ATOM(float, H5::PredType::NATIVE_FLOAT)
-DEFINE_TYPED_CREATE_ATOM(uint64_t, H5::PredType::STD_I64LE)
-
-
-template<>
-void HDFAtom<std::vector<int> >::Write(const std::vector<int> vect) {
- hsize_t length = vect.size();
- H5::DataType baseType = H5::PredType::NATIVE_INT;
- H5::ArrayType arrayDataType(baseType, 1, &length);
- attribute.write(arrayDataType, &((vect)[0]));
-}
-
-
-template<>
-void HDFAtom<std::string>::Write(std::string value) {
- // H5::StrType strType(0, value.size());
- H5::StrType strType(0, H5T_VARIABLE);
- attribute.write(strType, std::string(value.c_str()));
-}
-
-template<>
-void HDFAtom<uint64_t>::Write(uint64_t value) {
- attribute.write( H5::PredType::STD_I64LE, &value);
-}
-
-template<>
-void HDFAtom<int>::Write(int value) {
- attribute.write( H5::PredType::NATIVE_INT, &value);
-}
-
-template<>
-void HDFAtom<unsigned int>::Write(unsigned int value) {
- attribute.write( H5::PredType::NATIVE_INT, &value);
-}
-
-template<>
-void HDFAtom<unsigned char>::Write(unsigned char value) {
- attribute.write( H5::PredType::NATIVE_UINT8, &value);
-}
-
-template<>
-void HDFAtom<char>::Write(char value) {
- attribute.write( H5::PredType::NATIVE_INT8, &value);
-}
-
-template<>
-void HDFAtom<float>::Write(float value) {
- attribute.write( H5::PredType::NATIVE_FLOAT, &value);
-}
-
-template<>
-void HDFAtom<std::string>::Read(std::string &value) {
- /*
- * Read in a std::string that has been stored either as an array or a
- * variable length std::string. To decide which, query the
- * isVariableStr() option.
- */
- H5::StrType stringType = attribute.getStrType();
- bool stringIsVariableLength = stringType.isVariableStr();
- if (stringIsVariableLength)
- attribute.read(stringType, value);
- else {
- hsize_t stsize = attribute.getStorageSize();
- value.resize(stsize);
- // char *valueStr = new char[stsize+1];
- attribute.read(stringType, &value[0]);
- if (stsize > 0 and value[stsize-1] == '\0') {
- value.resize(stsize-1);
- }
- }
-}
-
-template<>
-void HDFAtom<int>::Read(int &value) {
- H5::DataType intType(H5::PredType::NATIVE_INT);
- attribute.read(intType, &value);
-}
-
-template<>
-void HDFAtom<uint64_t>::Read(uint64_t &value) {
- H5::DataType intType(H5::PredType::STD_I64LE);
- attribute.read(intType, &value);
-}
-
-template<>
-void HDFAtom<unsigned int>::Read(unsigned int &value) {
- H5::DataType uintType(H5::PredType::NATIVE_UINT);
- attribute.read(uintType, &value);
-}
-
-template<>
-void HDFAtom<float>::Read(float &value) {
- H5::DataType type(H5::PredType::NATIVE_FLOAT);
- attribute.read(type, &value);
-}
-
-template<>
-void HDFAtom<std::vector<std::string> >::Read(std::vector<std::string> &values) {
- std::string value;
- /*
- * This attribute is an array of std::strings. They are read in by
- * storing pointers to std::strings in memory controlled by HDF. To read
- * the std::strings, read the pointers into a temporary array, then copy
- * those std::strings to the values array. This way when the values array
- * is destroyed, it will not try and get rid of space that is under
- * HDF control.
- */
- H5::DataSpace attributeSpace = attribute.getSpace();
- hsize_t nPoints;
- nPoints = attributeSpace.getSelectNpoints();
- H5::DataType attrType = attribute.getDataType(); // necessary for attr.read()
-
- // Declare and initialize std::vector of pointers to std::string attribute list.
- std::vector<char*> ptrsToHDFControlledMemory;
- ptrsToHDFControlledMemory.resize(nPoints);
- // Copy the pointers.
- attribute.read(attrType, &ptrsToHDFControlledMemory[0]);
- // Copy the std::strings into memory the main program has control over.
- unsigned int i;
- for (i = 0; i < ptrsToHDFControlledMemory.size(); i++ ){
- values.push_back(ptrsToHDFControlledMemory[i]);
- free(ptrsToHDFControlledMemory[i]);
- }
-}
-
-// Explict instantiate classes
-template class HDFAtom<int>;
-template class HDFAtom<unsigned int>;
-template class HDFAtom<char>;
-template class HDFAtom<unsigned char>;
-template class HDFAtom<uint64_t>;
-template class HDFAtom<float>;
-template class HDFAtom< std::string >;
-template class HDFAtom< std::vector <int> >;
-template class HDFAtom< std::vector <unsigned int> >;
-template class HDFAtom< std::vector <string> >;
-
diff --git a/libcpp/hdf/HDFAtom.hpp b/libcpp/hdf/HDFAtom.hpp
deleted file mode 100644
index f8934df..0000000
--- a/libcpp/hdf/HDFAtom.hpp
+++ /dev/null
@@ -1,176 +0,0 @@
-#ifndef _BLASR_HDF_ATOM_HPP_
-#define _BLASR_HDF_ATOM_HPP_
-
-#include <cassert>
-#include <string>
-#include <vector>
-#include <cstdint>
-#include "H5Cpp.h"
-
-#include "HDFConfig.hpp"
-#include "HDFGroup.hpp"
-#include "HDFData.hpp"
-
-template<typename T>
-class HDFAtom : public HDFData {
-public:
- H5::Attribute attribute;
-
- bool initialized;
- HDFAtom() {
- initialized = false;
- }
- ~HDFAtom() {
- if (initialized) {
- attribute.close();
- }
- }
-
- H5::H5Location *GetObject() {
- return NULL;
- }
-
- int Initialize(H5::H5Location &object, std::string attributeName, bool createIfMissing=false) {
- attribute = object.openAttribute(attributeName.c_str());
- initialized = true;
- return 1;
- }
-
- int Initialize(HDFGroup &group, std::string attributeName, bool createIfMissing=false) {
- return Initialize(group.group, attributeName);
- }
-
- int Initialize(HDFData &data, std::string attributeName, bool createIfMissing=false) {
- return Initialize(data.dataset, attributeName);
- }
-
- int Initialize(H5::Group &object, std::string attributeName, bool createIfMissing=false) {
- try {
- attribute = object.openAttribute(attributeName.c_str());
- }
- catch (H5::Exception e) {
- cout << "ERROR. Could not open attribute " << attributeName << endl;
- exit(1);
- }
- initialized = true;
- return 1;
- }
-
- int Initialize(H5::H5File &hdfFile, std::string groupName, std::string attributeName) {
- HDFGroup group;
- group.Initialize(hdfFile, groupName);
- attribute = group.group.openAttribute(attributeName.c_str());
- initialized = true;
- return 1;
- }
-
- //
- // This handles creation of all non-std::string types. A specialization
- // for std::strings is provided below.
- //
- void Create(H5::H5Location &object, std::string atomName) {
- hsize_t defaultDims[] = {1};
- H5::DataSpace defaultDataSpace(1, defaultDims);
- TypedCreate(object, atomName, defaultDataSpace);
- }
-
-
- void Create(H5::H5Location &object, std::string name, std::string value) {
- H5::StrType strType(0, value.size());
- attribute = object.createAttribute(name.c_str(), strType, H5::DataSpace(0,NULL));
- initialized = true;
- attribute.write(strType, value.c_str());
- }
-
- void Create(H5::H5Location &object, std::string name, std::vector<int> &vect) {
- hsize_t length = vect.size();
- H5::ArrayType arrayDataType(H5::PredType::NATIVE_INT, 1, &length);
- attribute = object.createAttribute(name.c_str(), H5::PredType::NATIVE_INT, H5::DataSpace(1, &length));
- attribute.write(H5::PredType::NATIVE_INT, &((vect)[0]));
- }
-
- void Create(H5::H5Location &object, std::string name, std::vector<std::string> &vect) {
- hsize_t length = vect.size();
- H5::StrType strType(0,H5T_VARIABLE);
- H5::ArrayType arrayDataType(strType, 1, &length);
- attribute = object.createAttribute(name.c_str(), strType, H5::DataSpace(1, &length));
- attribute.write(strType, &((vect)[0]));
- }
-
- void TypedCreate(H5::H5Location &object, std::string &atomName, H5::DataSpace &dataSpace) {
- assert("Calling HDFAtom<T>::typedCreate on an unsupported type" == 0);
- }
-
- void Write(T value) {
- assert("Calling HDFAtom<T>::Write on an unsupported type" == 0);
- }
-
- void Read(T& value) {
- assert("Calling read on an unsupported type!" == 0);
- }
-
-};
-
-//
-// Special create for std::strings. Since this uses a H5::StrType for the
-// typename rather than specifying a H5::PredType, it mertis its own
-// function.
-//
-
-template<>
-void HDFAtom<std::string>::Create(H5::H5Location &object, std::string atomName);
-
-#define DECLARE_TYPED_CREATE_ATOM(T, predtype) template<> \
- void HDFAtom<T>::TypedCreate(H5::H5Location &object, std::string &atomName, H5::DataSpace &defaultDataSpace);
-
-DECLARE_TYPED_CREATE_ATOM(int, H5::PredType::NATIVE_INT)
-DECLARE_TYPED_CREATE_ATOM(unsigned int, H5::PredType::NATIVE_UINT)
-DECLARE_TYPED_CREATE_ATOM(unsigned char, H5::PredType::NATIVE_UINT8)
-DECLARE_TYPED_CREATE_ATOM(char, H5::PredType::NATIVE_INT8)
-DECLARE_TYPED_CREATE_ATOM(float, H5::PredType::NATIVE_FLOAT)
-DECLARE_TYPED_CREATE_ATOM(uint64_t, H5::PredType::STD_I64LE)
-
-
-template<>
-void HDFAtom<std::vector<int> >::Write(const std::vector<int> vect);
-
-template<>
-void HDFAtom<std::string>::Write(std::string value);
-
-template<>
-void HDFAtom<uint64_t>::Write(uint64_t value);
-
-template<>
-void HDFAtom<int>::Write(int value);
-
-template<>
-void HDFAtom<unsigned int>::Write(unsigned int value);
-
-template<>
-void HDFAtom<unsigned char>::Write(unsigned char value);
-
-template<>
-void HDFAtom<char>::Write(char value);
-
-template<>
-void HDFAtom<float>::Write(float value);
-
-template<>
-void HDFAtom<std::string>::Read(std::string &value);
-
-template<>
-void HDFAtom<int>::Read(int &value);
-
-template<>
-void HDFAtom<uint64_t>::Read(uint64_t &value);
-
-template<>
-void HDFAtom<unsigned int>::Read(unsigned int &value);
-
-template<>
-void HDFAtom<float>::Read(float &value);
-
-template<>
-void HDFAtom<std::vector<std::string> >::Read(std::vector<std::string> &values);
-
-#endif
diff --git a/libcpp/hdf/HDFAttributable.cpp b/libcpp/hdf/HDFAttributable.cpp
deleted file mode 100644
index da57d08..0000000
--- a/libcpp/hdf/HDFAttributable.cpp
+++ /dev/null
@@ -1,41 +0,0 @@
-#include <cassert>
-#include "HDFAttributable.hpp"
-
-using namespace std;
-using namespace H5;
-
-void CallStoreAttributeName(H5Location &obj, string attrName, void *attrList){
- ((vector<string>*)attrList)->push_back(attrName);
-}
-
-void HDFAttributable::StoreAttributeNames(H5Location &thisobject,
- std::vector<std::string> &attributeNames) {
- int nAttr = thisobject.getNumAttrs();
- unsigned int bounds[2];
- bounds[0] = 0;
- bounds[1] = nAttr;
- attributeNameList.clear();
- thisobject.iterateAttrs(&CallStoreAttributeName,
- bounds, (void*) &attributeNames);
-}
-
-H5Location* HDFAttributable::GetObject() {
- return NULL;
-}
-
-int HDFAttributable::ContainsAttribute(string attributeName) {
- size_t i;
- std::vector<std::string> tmpAttributeNames;
- try{
- H5Location *obj = GetObject();
- assert(obj != NULL);
- StoreAttributeNames(*obj, tmpAttributeNames);
- for (i = 0; i < tmpAttributeNames.size(); i++) {
- if (tmpAttributeNames[i] == attributeName) return true;
- }
- } catch (H5::Exception e) {
- //Failed to read attribute // e.printError();
- }
- return false;
-}
-
diff --git a/libcpp/hdf/HDFAttributable.hpp b/libcpp/hdf/HDFAttributable.hpp
deleted file mode 100644
index 4b223c7..0000000
--- a/libcpp/hdf/HDFAttributable.hpp
+++ /dev/null
@@ -1,23 +0,0 @@
-#ifndef _BLASR_HDF_ATTRIBUTABLE_HPP_
-#define _BLASR_HDF_ATTRIBUTABLE_HPP_
-
-#include <string>
-#include <vector>
-#include "H5Cpp.h"
-
-void CallStoreAttributeName(H5::H5Location &obj, std::string attrName, void *attrListPtr);
-
-class HDFAttributable {
-public:
- std::vector<std::string> attributeNameList;
-
- void StoreAttributeNames(H5::H5Location &thisobject,
- std::vector<std::string> &attributeNames);
-
- virtual H5::H5Location* GetObject();
-
- int ContainsAttribute(std::string attributeName);
-
-};
-
-#endif
diff --git a/libcpp/hdf/HDFBasReader.cpp b/libcpp/hdf/HDFBasReader.cpp
deleted file mode 100644
index 48e375d..0000000
--- a/libcpp/hdf/HDFBasReader.cpp
+++ /dev/null
@@ -1,46 +0,0 @@
-#include "HDFBasReader.hpp"
-
-//
-// Below is sample code for using the bas reader to read in sequences
-// from a .bas.h5 or .pls.h5 file.
-// One may select which quality value fields to read. By default,
-// none are read in. To read in the rich quality values (insertionQV,
-// deletionQV, substitutionQV, mergeQV, substitutionTag, deletionTag),
-// call InitializeDefaultIncludedFields() BEFORE initializing the
-// reader on the file name.
-//
-//#include "data/hdf/HDFBasReader.h"
-//#include "SMRTSequence.h"
-//#include <string>
-//
-//int main(int argc, char* argv[]) {
-//
-// string basFile = argv[1];
-//
-// HDFBasReader reader;
-// reader.InitializeDefaultIncludedFields();
-// reader.Initialize(basFile);
-//
-// SMRTSequence read;
-//
-// while(reader.GetNext(read)) {
-// read.PrintQualSeq(cout);
-// }
-//
-//
-// return 0;
-//}
-//
-// * If you wanted to read only fasta sequences and not fastq, use:
-//
-// FASTASequence read;
-// while (reader.GetNext(read) {
-// read.PritnSeq(cout);
-// }
-//
-
-int HDFSmrtReader::Advance(int nSteps) {
- int retVal;
- retVal = ((T_HDFBasReader<FASTQSequence>*)this)->Advance(nSteps);
- return retVal;
-}
diff --git a/libcpp/hdf/HDFBasReader.hpp b/libcpp/hdf/HDFBasReader.hpp
deleted file mode 100644
index 23fe235..0000000
--- a/libcpp/hdf/HDFBasReader.hpp
+++ /dev/null
@@ -1,1178 +0,0 @@
-#ifndef _BLASR_HDF_BAS_READER_HPP_
-#define _BLASR_HDF_BAS_READER_HPP_
-
-#include <cstdlib>
-#include <sstream>
-#include <vector>
-#include <string>
-#include <cstdint>
-
-#include "Enumerations.h"
-#include "FASTQSequence.hpp"
-#include "SMRTSequence.hpp"
-#include "VectorUtils.hpp"
-#include "ChangeListID.hpp"
-#include "reads/BaseFile.hpp"
-
-#include "HDFArray.hpp"
-#include "HDF2DArray.hpp"
-#include "HDFAtom.hpp"
-#include "HDFGroup.hpp"
-#include "HDFZMWReader.hpp"
-#include "HDFScanDataReader.hpp"
-#include "HDFPulseDataFile.hpp"
-#include "DatasetCollection.hpp"
-
-//
-// Below is sample code for using the bas reader to read in sequences
-// from a .bas.h5 or .pls.h5 file.
-// One may select which quality value fields to read. By default,
-// none are read in. To read in the rich quality values (insertionQV,
-// deletionQV, substitutionQV, mergeQV, substitutionTag, deletionTag),
-// call InitializeDefaultIncludedFields() BEFORE initializing the
-// reader on the file name.
-//
-//#include "data/hdf/HDFBasReader.h"
-//#include "SMRTSequence.h"
-//#include <string>
-//
-//int main(int argc, char* argv[]) {
-//
-// string basFile = argv[1];
-//
-// HDFBasReader reader;
-// reader.InitializeDefaultIncludedFields();
-// reader.Initialize(basFile);
-//
-// SMRTSequence read;
-//
-// while(reader.GetNext(read)) {
-// read.PrintQualSeq(cout);
-// }
-//
-//
-// return 0;
-//}
-//
-// * If you wanted to read only fasta sequences and not fastq, use:
-//
-// FASTASequence read;
-// while (reader.GetNext(read) {
-// read.PritnSeq(cout);
-// }
-//
-
-template<typename T_Sequence>
-class T_HDFBasReader : public DatasetCollection, public HDFPulseDataFile {
-public:
- DNALength curBasePos;
- int curRead;
- unsigned int nBases;
-
-
- //bool readPulseInformation;
- bool hasRegionTable;
-
- HDFArray<int> zmwXCoordArray;
- HDFArray<int> zmwYCoordArray;
- HDFArray<unsigned char> baseArray;
- HDFArray<unsigned char> deletionQVArray;
- HDFArray<unsigned char> deletionTagArray;
- HDFArray<unsigned char> insertionQVArray;
- HDFArray<unsigned char> substitutionTagArray;
- HDFArray<unsigned char> substitutionQVArray;
- HDFArray<unsigned char> mergeQVArray;
- HDFArray<unsigned char> qualArray;
- HDFArray<unsigned int> simulatedCoordinateArray;
- HDFArray<unsigned int> simulatedSequenceIndexArray;
- HDFArray<uint16_t> basWidthInFramesArray;
- HDFArray<uint16_t> preBaseFramesArray;
- HDFArray<int> pulseIndexArray;
- HDFArray<int> holeIndexArray;
-
- // useful ZMWMetrics data
- HDF2DArray<float> hqRegionSNRMatrix;
- HDFArray<float> readScoreArray;
-
- HDFGroup baseCallsGroup;
- HDFGroup zmwMetricsGroup;
- HDFGroup zmwGroup;
- // HDFArray<HalfWord> pulseWidthArray; This is deprecated
- HDFAtom<std::string> changeListIDAtom;
-
- //bool useWidthInFrames, usePulseIndex,
- bool useZmwReader;
- // bool usePulseWidth; This is deprecated
-
- std::string baseCallsGroupName;
- std::string zmwMetricsGroupName;
- bool qualityFieldsAreCritical;
-
- //bool useHoleNumbers, useHoleStatus;
- //bool usePreBaseFrames;
- bool useBasHoleXY;
- //bool useBasecall;
- //bool useQuality;
- bool readBasesFromCCS;
- ChangeListID changeList;
- QVScale qvScale;
-
- PlatformId GetPlatform() {
- return scanDataReader.platformId;
- }
-
- std::string GetMovieName() {
- return scanDataReader.GetMovieName();
- }
-
- int GetReadAt(int index, SMRTSequence &read) {
- //
- // The first time this is called there may be no table of read
- // offset positions. Check for that and build if it does not
- // exist.
- //
- if (preparedForRandomAccess == false) {
- PrepareForRandomAccess();
- }
- curRead = index;
- curBasePos = eventOffset[index];
- zmwReader.curZMW = index;
- return GetNext(read);
- }
-
- std::string GetRunCode() {
- return scanDataReader.GetRunCode();
- }
-
- T_HDFBasReader() {
- curRead = 0;
- curBasePos = 0;
- nBases = 0;
- preparedForRandomAccess = false;
- readBasesFromCCS = false;
- baseCallsGroupName = "BaseCalls";
- zmwMetricsGroupName = "ZMWMetrics";
- qualityFieldsAreCritical = true;
- useZmwReader = false;
- useBasHoleXY = true;
- hasRegionTable = false;
- qvScale = POverOneMinusP; //default 0 = POverOneMinusP
- fieldNames.push_back("Basecall");
- fieldNames.push_back("DeletionQV");
- fieldNames.push_back("DeletionTag");
- fieldNames.push_back("InsertionQV");
- fieldNames.push_back("SubstitutionTag");
- fieldNames.push_back("SubstitutionQV");
- fieldNames.push_back("QualityValue");
- fieldNames.push_back("WidthInFrames");
- fieldNames.push_back("PulseIndex");
- fieldNames.push_back("PreBaseFrames");
- fieldNames.push_back("MergeQV");
- fieldNames.push_back("SimulatedCoordinate");
- fieldNames.push_back("SimulatedSequenceIndex");
- // Useful ZMWMetrics fields
- fieldNames.push_back("HQRegionSNR");
- fieldNames.push_back("ReadScore");
- // Start out with no fields being read.
- InitializeAllFields(false);
- // Then by default always read bases.
- IncludeField("Basecall");
- }
-
-
- void InitializeDefaultCCSIncludeFields() {
- InitializeAllFields(false);
- IncludeField("Basecall");
- IncludeField("DeletionQV");
- IncludeField("DeletionTag");
- IncludeField("InsertionQV");
- IncludeField("SubstitutionQV");
- IncludeField("SubstitutionTag");
- IncludeField("QualityValue");
- }
-
- void InitializeDefaultRawBasIncludeFields() {
- IncludeField("Basecall");
- IncludeField("QualityValue");
- IncludeField("InsertionQV");
- IncludeField("DeletionQV");
- IncludeField("MergeQV");
- IncludeField("SubstitutionQV");
- IncludeField("DeletionTag");
- IncludeField("SubstitutionTag"); // used in IDSScoreFunction
- // FIXME: The following QVs are not really used by downstream
- // analysis such as Quiver, make them optional to include.
- IncludeField("WidthInFrames");
- IncludeField("PulseIndex");
- IncludeField("PreBaseFrames");
- IncludeField("HQRegionSNR");
- IncludeField("ReadScore");
- }
- void InitializeDefaultIncludedFields() {
- if (readBasesFromCCS == false) {
- InitializeDefaultRawBasIncludeFields();
- }
- else {
- InitializeDefaultCCSIncludeFields();
- }
- }
-
- void InitializeDefaultRequiredFields() {
- requiredFields["Basecall"] = true;
- }
-
- bool HasRegionTable() {
- return hasRegionTable;
- }
-
-
- bool HasSimulatedCoordinatesStored() {
- if (baseCallsGroup.ContainsObject("SimulatedCoordinate") and
- baseCallsGroup.ContainsObject("SimulatedSequenceIndex")) {
- return true;
- }
- else {
- return false;
- }
- }
-
- void SetReadBasesFromCCS() {
- InitializeDefaultCCSIncludeFields();
- readBasesFromCCS = true;
- }
-
- void GetChangeListID(std::string &changeListID) {
- if (changeListIDAtom.initialized) {
- changeListIDAtom.Read(changeListID);
- }
- else {
- changeListID = "0";
- }
- }
-
- /// Get BindingKit, SequencingKit and Base Caller Version.
- void GetChemistryTriple(std::string & bindingKit,
- std::string & sequencingKit,
- std::string & baseCallerVersion) {
- scanDataReader.ReadBindingKit(bindingKit);
- scanDataReader.ReadSequencingKit(sequencingKit);
- baseCallerVersion = changeList.GetVersion();
- }
-
- int InitializeForReadingBases() {
-
- //
- // Initialize root group + scan data information.
- //
- if (HDFPulseDataFile::Initialize(rootGroupPtr) == 0) return 0;
-
- //
- // Open the base group, this contains all the required information.
- //
-
- if (readBasesFromCCS) {
- baseCallsGroupName = "ConsensusBaseCalls";
- }
- if (pulseDataGroup.ContainsObject(baseCallsGroupName) == 0 or
- baseCallsGroup.Initialize(pulseDataGroup.group, baseCallsGroupName) == 0) {
- return 0;
- }
- if (baseCallsGroup.ContainsAttribute("ChangeListID")) {
- changeListIDAtom.Initialize(baseCallsGroup.group, "ChangeListID");
- std::string changeListIdString;
- GetChangeListID(changeListIdString);
- changeList = ChangeListID(changeListIdString);
- qvScale = changeList.DetermineQVScaleFromChangeListID();
- }
- if (pulseDataGroup.ContainsObject("Regions")) {
- hasRegionTable = true;
- }
- else {
- hasRegionTable = false;
- }
-
- //
- // Initialize read and quality arrays for reading.
- //
- if (this->InitializeSequenceFields(baseCallsGroup) == 0) {
- return 0;
- }
-
- //
- // Initialize simulated coordinate fields if they exist. They are
- // automatically opened and read from when they are in the bas.h5
- // file since they are used for debugging.
- //
-
- if (baseCallsGroup.ContainsObject("SimulatedCoordinate")) {
- includedFields["SimulatedCoordinate"] = true;
- InitializeDataset(baseCallsGroup, simulatedCoordinateArray, "SimulatedCoordinate");
- }
- else {
- includedFields["SimulatedCoordinate"] = false;
- }
-
- if (baseCallsGroup.ContainsObject("SimulatedSequenceIndex")) {
- includedFields["SimulatedSequenceIndex"] = true;
- InitializeDataset(baseCallsGroup, simulatedSequenceIndexArray, "SimulatedSequenceIndex");
- }
- else {
- includedFields["SimulatedSequenceIndex"] = false;
- }
- nBases = baseArray.arrayLength;
-
- return 1;
- }
-
-
- int InitializeCommon() {
-
- //
- // Initialize the smallest set of fields required to import bases.
- //
- if (InitializeForReadingBases() == 0) {
- return 0;
- }
-
-
- return 1;
- }
-
- template<typename T_Dataset>
- void InitializeRequiredField(HDFGroup &group, std::string arrayName, T_Dataset &field) {
- if (group.ContainsObject(arrayName)) {
- if (field.Initialize(group, arrayName) != 0) {
- return;
- }
- }
- cout << "ERROR. Could not initialize dataset " << arrayName << endl;
- exit(1);
- }
-
- template<typename T>
- int InitializeField(HDFGroup &rootGroup, std::string arrayName,
- T &field, bool &initialized) {
- initialized = false;
- if (rootGroup.ContainsObject(arrayName)) {
- if (field.Initialize(rootGroup, arrayName) != 0) {
- initialized = true;
- return true;
- }
- }
- return false;
- }
-
- template<typename T>
- int InitializeAttribute(HDFGroup &rootGroup, std::string arrayName,
- T &field, bool &initialized,
- bool fieldIsCritical = true) {
- int success = 1;
- initialized = false;
- if (rootGroup.ContainsAttribute(arrayName)) {
- if (field.Initialize(rootGroup, arrayName) == 0) {
- success = 0;
- }
- else {
- initialized = true;
- }
- }
- else {
- // the field does not exist
- success = 0;
- }
- if (fieldIsCritical) {
- return success;
- }
- else {
- return 1;
- }
- }
-
- int InitializeSequenceFields(HDFGroup &baseCallsGroup) {
- //
- // The only field that is absoultely required is Basecall
- if (baseArray.InitializeForReading(baseCallsGroup, "Basecall") == false) return 0;
- if (includedFields["QualityValue"] and qualArray.InitializeForReading(baseCallsGroup, "QualityValue") == false) return 0;
- if (includedFields["InsertionQV"] and insertionQVArray.InitializeForReading(baseCallsGroup, "InsertionQV") == false) return 0;
- if (includedFields["DeletionQV"] and deletionQVArray.InitializeForReading(baseCallsGroup, "DeletionQV") == false) return 0;
- if (includedFields["DeletionTag"] and deletionTagArray.InitializeForReading(baseCallsGroup, "DeletionTag") == false) return 0;
- if (includedFields["SubstitutionQV"] and substitutionQVArray.InitializeForReading(baseCallsGroup, "SubstitutionQV") == false) return 0;
- if (includedFields["SubstitutionTag"] and substitutionTagArray.InitializeForReading(baseCallsGroup, "SubstitutionTag") == false) return 0;
- // if (includedFields["PreBaseFrames"] and preBaseFramesArray.InitializeForReading(baseCallsGroup, "PreBaseFrames") == false) return 0;
-
- if (baseCallsGroup.ContainsObject("PreBaseFrames")) {
- if (preBaseFramesArray.InitializeForReading(baseCallsGroup, "PreBaseFrames") == false) return 0;
- } else {
- includedFields["PreBaseFrames"] = false;
- }
-
- //
- // These fields are not always present in bas.h5 files.
- //
- if (baseCallsGroup.ContainsObject("PulseIndex")) {
- if (pulseIndexArray.InitializeForReading(baseCallsGroup, "PulseIndex") == false) return 0;
- }
- else {
- includedFields["PulseIndex"] = false;
- }
-
- if (baseCallsGroup.ContainsObject("WidthInFrames")) {
- if (basWidthInFramesArray.InitializeForReading(baseCallsGroup, "WidthInFrames") == false) return 0;
- }
- else {
- includedFields["WidthInFrames"] = false;
- }
-
- if (baseCallsGroup.ContainsObject("MergeQV")) {
- if (includedFields["MergeQV"] and mergeQVArray.InitializeForReading(baseCallsGroup, "MergeQV") == false) return false;
- }
- else {
- includedFields["MergeQV"] = false;
- }
-
- if ((includedFields["HQRegionSNR"] or includedFields["ReadScore"]) and
- (baseCallsGroup.ContainsObject(zmwMetricsGroupName) == 0 or
- zmwMetricsGroup.Initialize(baseCallsGroup.group, zmwMetricsGroupName) == 0)) {
- includedFields["HQRegionSNR"] = false;
- includedFields["ReadScore"] = false;
- }
- if (includedFields["HQRegionSNR"] and (zmwMetricsGroup.ContainsObject("HQRegionSNR") == 0 or
- GetDatasetNDim(zmwMetricsGroup.group, "HQRegionSNR") != 2 or
- hqRegionSNRMatrix.InitializeForReading(zmwMetricsGroup, "HQRegionSNR") == false or
- hqRegionSNRMatrix.GetNCols() != 4)) {
- includedFields["HQRegionSNR"] = false;
- }
- if (includedFields["ReadScore"] and (zmwMetricsGroup.ContainsObject("ReadScore") == 0 or
- readScoreArray.InitializeForReading(zmwMetricsGroup, "ReadScore")) == false) {
- includedFields["ReadScore"] = false;
- }
-
- return 1;
- }
-
- int InitializeAstro() {
- useBasHoleXY = true;
- return 1;
- }
-
- int InitializeSpringfield() {
- //
- // For now, no special initialization is required.
- //
- return 1;
- }
-
- int Initialize(HDFGroup *rootGroupP) {
- rootGroupPtr= rootGroupP;
- return Initialize();
- }
-
-
- int Initialize() {
-
- // Return 0 if any of the array inializations do not work.
- if (InitializeCommon() == 0) {
- return 0;
- }
-
- // Must have zmw information.
- if (zmwReader.Initialize(&baseCallsGroup) == 0) {
- return 0;
- }
- else {
- useZmwReader = true;
- }
- //
- // Get information about the chip - how many zmw's, the hole
- // number indices to keep track of reads, etc..
- //
- nReads = zmwReader.numEventArray.arrayLength;
-
-
-
- if (scanDataReader.platformId == Astro) {
- if (InitializeAstro() == 0) {
- return 0;
- }
- }
- else if (scanDataReader.platformId == Springfield) {
- if (InitializeSpringfield() == 0) {
- return 0;
- }
- }
-
- /*
- * Initialize state variables.
- */
-
- curBasePos = 0;
- curRead = 0;
-
- /*
- * All ok, return that.
- */
- return 1;
- }
-
- int InitializeHDFFile(std::string hdfBasFileName,
- const H5::FileAccPropList & fileAccPropList = H5::FileAccPropList::DEFAULT) {
- /*
- * Initialize access to the HDF file. For reading bas files, this
- * involves:
- * - Opening the file, and initializing both base and zmw grops.
- */
- if (OpenHDFFile(hdfBasFileName, fileAccPropList) == 0) {
- return 0;
- }
-
- if (rootGroup.Initialize(hdfBasFile, "/") == 0) {
- return 0;
- }
- rootGroupPtr = &rootGroup;
- return 1;
- }
-
- int Initialize(std::string hdfBasFileName,
- const H5::FileAccPropList & fileAccPropList = H5::FileAccPropList::DEFAULT) {
- int init = InitializeHDFFile(hdfBasFileName, fileAccPropList);
- if (init == 0) return 0;
- return Initialize();
- }
-
- int GetNumReads() {
- return nReads;
- }
-
- void BuildReadTitle(std::string movieTitle, unsigned int holeNumber, std::string &readTitle, unsigned int simIndex=0, unsigned int simCoordinate=0) {
- std::stringstream readTitleStrm;
- readTitleStrm << movieTitle << "/" << holeNumber;
- readTitle = readTitleStrm.str();
- }
-
- int GetNext(FASTASequence &seq) {
- if (curRead == nReads) {
- return 0;
- }
-
- int seqLength;
- try {
- seqLength = GetNextWithoutPosAdvance(seq);
- } catch(H5::DataSetIException e) {
- cout << "ERROR, could not read base calls for FASTA Sequence "
- << seq.GetName() << endl;
- exit(1);
- }
- curBasePos += seqLength;
- seq.StorePlatformId(scanDataReader.platformId);
- return 1;
- }
-
-
- int GetNext(FASTQSequence &seq) {
- try {
- if (curRead == nReads) {
- return 0;
- }
- int seqLength = GetNextWithoutPosAdvance(seq);
- seq.length = seqLength;
-
- if (seqLength > 0 ) {
- if (includedFields["QualityValue"]) {
- seq.AllocateQualitySpace(seqLength);
- qualArray.Read((int)curBasePos, (int) curBasePos + seqLength, (unsigned char*) seq.qual.data);
- }
- }
-
- if (includedFields["DeletionQV"]) {
- GetNextDeletionQV(seq);
- }
- if (includedFields["DeletionTag"]) {
- GetNextDeletionTag(seq);
- }
- if (includedFields["InsertionQV"]) {
- GetNextInsertionQV(seq);
- }
- if (includedFields["SubstitutionQV"]) {
- GetNextSubstitutionQV(seq);
- }
- if (includedFields["SubstitutionTag"]) {
- GetNextSubstitutionTag(seq);
- }
- if (includedFields["MergeQV"]) {
- GetNextMergeQV(seq);
- }
- seq.SetQVScale(qvScale);
- curBasePos += seqLength;
- } catch(H5::DataSetIException e) {
- cout << "ERROR, could not read quality metrics for FASTQ Sequence "
- << seq.GetName() << endl;
- exit(1);
- }
- return 1;
- }
-
- //
- // Read a SMRTSequence, but only the basecalls and maybe the QVs. This
- // makes pls2fasta more efficient.
- //
- int GetNextBases(SMRTSequence &seq, bool readQVs) {
- try {
- if (curRead == nReads) {
- return 0;
- }
-
- // must be done before GetNextWithoutPosAdvance (which increments curRead)
- // get ZMWMetrics fields
- if (includedFields["HQRegionSNR"]) {
- GetNextHQRegionSNR(seq);
- }
- if (includedFields["ReadScore"]) {
- GetNextReadScore(seq);
- }
-
- int seqLength = GetNextWithoutPosAdvance(seq);
- seq.length = seqLength;
- if(readQVs) {
- if (seqLength > 0 ) {
- if (includedFields["QualityValue"]) {
- seq.AllocateQualitySpace(seqLength);
- qualArray.Read((int)curBasePos,
- (int) curBasePos + seqLength,
- (unsigned char*) seq.qual.data);
- }
- }
- }
-
- seq.SetQVScale(qvScale);
- curBasePos += seqLength;
-
- seq.subreadStart = 0;
- seq.subreadEnd = seq.length;
- zmwReader.GetNext(seq.zmwData);
- seq.xy[0] = seq.zmwData.x;
- seq.xy[1] = seq.zmwData.y;
- } catch (H5::DataSetIException e) {
- cout << "ERROR, could not read bases or QVs for SMRTSequence "
- << seq.GetName() << endl;
- exit(1);
- }
- return 1;
- }
-
- //
- // Reading of SMRT Sequences reads both the sequence fields, and the
- // fields with ZMW information for identification of this read.
- //
-
- int GetNext(SMRTSequence &seq) {
- //
- // Read in quality values.
- //
- int retVal;
-
- DNALength curBasPosCopy = curBasePos;
- //
- // Getting next advances the curBasPos to the end of
- // the current sequence.
- //
- try {
- // must check before looking at HQRegionSNR/ReadScore!!
- if (curRead == nReads) {
- return 0;
- }
-
- // get ZMWMetrics fields, must be done before GetNext
- // (which calls GetNextWithoutAdvancePos, which increments curRead)
- if (includedFields["HQRegionSNR"]) {
- GetNextHQRegionSNR(seq);
- }
- if (includedFields["ReadScore"]) {
- GetNextReadScore(seq);
- }
-
- //
- // Bail now if the file is already done
- //
- if ((retVal = this->GetNext((FASTQSequence&)seq)) == 0) {
- return 0;
- }
-
- DNALength nextBasePos = curBasePos;
- curBasePos = curBasPosCopy;
-
- if (includedFields["WidthInFrames"] ) {
- assert(nextBasePos <= basWidthInFramesArray.arrayLength);
- GetNextWidthInFrames(seq);
- }
- if (includedFields["PreBaseFrames"]) {
- GetNextPreBaseFrames(seq);
- }
- if (includedFields["PulseIndex"]) {
- GetNextPulseIndex(seq);
- }
- curBasePos = nextBasePos;
-
- //
- // By default, the subread of a read without subread information is
- // the whole read.
- //
- seq.subreadStart = 0;
- seq.subreadEnd = seq.length;
- zmwReader.GetNext(seq.zmwData);
- seq.xy[0] = seq.zmwData.x;
- seq.xy[1] = seq.zmwData.y;
- } catch(H5::DataSetIException e) {
- cout << "ERROR, could not read pulse metrics for SMRTSequence "
- << seq.GetName() << endl;
- exit(1);
- }
- return retVal;
- }
- /*
- int16_t xy[2];
- if (zmwReader.readHoleXY) {
- zmwReader.xyArray.Read(curRead, curRead+1, 0, 2, xy);
- }
- else {
- xy[0] = xy[1] = 0;
- }
- seq.StoreXY(xy);
- */
- void GetAllPulseIndex(std::vector<int> &pulseIndex) {
- CheckMemoryAllocation(pulseIndexArray.arrayLength, maxAllocNElements, "PulseIndex");
- pulseIndex.resize(pulseIndexArray.arrayLength);
- pulseIndexArray.Read(0, pulseIndexArray.arrayLength, &pulseIndex[0]);
- }
-
- void GetAllPreBaseFrames(std::vector<uint16_t> &preBaseFrames) {
- CheckMemoryAllocation(preBaseFramesArray.arrayLength, maxAllocNElements, "PreBaseFrames");
- preBaseFrames.resize(nBases);
- preBaseFramesArray.Read(0, nBases, &preBaseFrames[0]);
- }
-
- void GetAllWidthInFrames(std::vector<uint16_t> &widthInFrames) {
- CheckMemoryAllocation(basWidthInFramesArray.arrayLength, maxAllocNElements, "WidthInFrames");
- widthInFrames.resize(nBases);
- basWidthInFramesArray.Read(0, nBases, &widthInFrames[0]);
- }
-
- int GetAllHoleStatus(std::vector<unsigned char> &holeStatus) {
- CheckMemoryAllocation(zmwReader.holeStatusArray.arrayLength, maxAllocNElements, "HoleStatus (base)");
- holeStatus.resize(nReads);
- zmwReader.holeStatusArray.Read(0,nReads, (unsigned char*)&holeStatus[0]);
- return holeStatus.size();
- }
-
- int GetAllReadLengths(std::vector<int> &readLengths) {
- readLengths.resize(nReads);
- zmwReader.numEventArray.ReadDataset(readLengths);
- return readLengths.size();
- }
-
- int Advance(int nSeq) {
- int i;
- // cannot advance past the end of this file
- if (curRead + nSeq >= nReads) { return 0; }
- for (i = curRead; i < curRead + nSeq && i < nReads; i++ ) {
- int seqLength;
- zmwReader.numEventArray.Read(i, i+1, &seqLength);
- curBasePos += seqLength;
- }
- curRead += nSeq;
- zmwReader.Advance(nSeq);
- return curRead;
- }
-
- int GetNextWithoutPosAdvance(FASTASequence &seq) {
- int seqLength;
-
- zmwReader.numEventArray.Read(curRead, curRead+1, &seqLength);
- seq.length = 0;
- seq.seq = NULL;
-
- if (includedFields["Basecall"]) {
- if (seqLength > 0) {
- ResizeSequence(seq, seqLength);
- baseArray.Read(curBasePos, curBasePos + seqLength, (unsigned char*) seq.seq);
- }
- }
-
- std::string readTitle;
- unsigned int holeNumber;
- unsigned char holeStatus;
- zmwReader.holeNumberArray.Read(curRead, curRead+1, &holeNumber);
- seq.StoreHoleNumber(holeNumber);
-
- zmwReader.holeStatusArray.Read(curRead, curRead+1, &holeStatus);
- seq.StoreHoleStatus(holeStatus);
-
- DNALength simIndex=0, simCoordinate=0;
-
- if (includedFields["SimulatedSequenceIndex"] == true) {
- simulatedSequenceIndexArray.Read(curRead,curRead+1,&simIndex);
- }
- if (includedFields["SimulatedCoordinate"] == true) {
- simulatedCoordinateArray.Read(curRead, curRead+1, &simCoordinate);
- }
-
- BuildReadTitle(scanDataReader.GetMovieName(), holeNumber, readTitle, simIndex, simCoordinate);
-
- seq.CopyTitle(readTitle);
- curRead++;
- return seqLength;
- }
-
- int GetNextDeletionQV(FASTQSequence &seq) {
- if (seq.length == 0) return 0;
- seq.AllocateDeletionQVSpace(seq.length);
- deletionQVArray.Read((int)curBasePos, (int) curBasePos + seq.length, (unsigned char*) seq.deletionQV.data);
- return seq.length;
- }
-
- int GetNextMergeQV(FASTQSequence &seq) {
- if (seq.length == 0) return 0;
- seq.AllocateMergeQVSpace(seq.length);
- mergeQVArray.Read((int)curBasePos, (int) curBasePos + seq.length, (unsigned char*) seq.mergeQV.data);
- return seq.length;
- }
-
- int GetNextDeletionTag(FASTQSequence &seq) {
- if (seq.length == 0) return 0;
- seq.AllocateDeletionTagSpace(seq.length);
- deletionTagArray.Read((int)curBasePos, (int) curBasePos + seq.length, (unsigned char*) seq.deletionTag);
- return seq.length;
- }
-
- int GetNextInsertionQV(FASTQSequence &seq) {
- if (seq.length == 0) return 0;
- seq.AllocateInsertionQVSpace(seq.length);
- insertionQVArray.Read((int)curBasePos, (int) curBasePos + seq.length, (unsigned char*) seq.insertionQV.data);
- return seq.length;
- }
-
- int GetNextWidthInFrames(SMRTSequence &seq) {
- if (seq.length == 0) return 0;
- if (seq.widthInFrames) {
- delete [] seq.widthInFrames;
- seq.widthInFrames = NULL;
- }
- seq.widthInFrames = new HalfWord[seq.length];
- basWidthInFramesArray.Read((int)curBasePos, (int) curBasePos + seq.length, (HalfWord*) seq.widthInFrames);
- return seq.length;
- }
-
- int GetNextPreBaseFrames(SMRTSequence &seq) {
- if (seq.length == 0) return 0;
- if (seq.preBaseFrames) {
- delete [] seq.preBaseFrames;
- seq.preBaseFrames = NULL;
- }
- seq.preBaseFrames = new HalfWord[seq.length];
- preBaseFramesArray.Read((int)curBasePos, (int) curBasePos + seq.length, (HalfWord*) seq.preBaseFrames);
- return seq.length;
- }
- int GetNextPulseIndex(SMRTSequence &seq) {
- if (seq.length == 0) return 0;
- if (seq.pulseIndex) {
- delete [] seq.pulseIndex;
- seq.pulseIndex = NULL;
- }
- seq.pulseIndex = new int[seq.length];
- pulseIndexArray.Read((int)curBasePos, (int) curBasePos + seq.length, (int*) seq.pulseIndex);
- return seq.length;
- }
- int GetNextHQRegionSNR(SMRTSequence &seq) {
- hqRegionSNRMatrix.Read(curRead, curRead + 1, seq.hqRegionSnr);
- return 4;
- }
- int GetNextReadScore(SMRTSequence &seq) {
- readScoreArray.Read(curRead, curRead + 1, &seq.readScore);
- return 1;
- }
- int GetNextSubstitutionQV(FASTQSequence &seq) {
- if (seq.length == 0) return 0;
- seq.AllocateSubstitutionQVSpace(seq.length);
- substitutionQVArray.Read((int)curBasePos, (int) curBasePos + seq.length, (unsigned char*) seq.substitutionQV.data);
- return seq.length;
- }
-
- int GetNextSubstitutionTag(FASTQSequence &seq) {
- if (seq.length == 0) return 0;
- seq.AllocateSubstitutionTagSpace(seq.length);
- substitutionTagArray.Read((int)curBasePos, (int) curBasePos + seq.length, (unsigned char*) seq.substitutionTag);
- return seq.length;
- }
-
- void Close() {
-
- baseCallsGroup.Close();
- zmwXCoordArray.Close();
- zmwYCoordArray.Close();
- baseArray.Close();
- qualArray.Close();
- if (useZmwReader) {
- zmwReader.Close();
- }
-
- if (includedFields["DeletionQV"]) {
- deletionQVArray.Close();
- }
- if (includedFields["DeletionTag"]) {
- deletionTagArray.Close();
- }
- if (includedFields["MergeQV"]) {
- mergeQVArray.Close();
- }
- if (includedFields["InsertionQV"]) {
- insertionQVArray.Close();
- }
- if (includedFields["SubstitutionTag"]) {
- substitutionTagArray.Close();
- }
- if (includedFields["SubstitutionQV"]) {
- substitutionQVArray.Close();
- }
- if (includedFields["WidthInFrames"]) {
- basWidthInFramesArray.Close();
- }
- if (includedFields["PreBaseFrames"]) {
- preBaseFramesArray.Close();
- }
- if (includedFields["PulseIndex"]) {
- pulseIndexArray.Close();
- }
-
- // ZMWMetrics fields
- if (includedFields["HQRegionSNR"]) {
- hqRegionSNRMatrix.Close();
- }
- if (includedFields["ReadScore"]) {
- readScoreArray.Close();
- }
-
- HDFPulseDataFile::Close();
- }
-
- void ReadAllHoleXY(BaseFile &baseFile) {
- baseFile.holeXY.resize(nReads);
- int i;
- for (i = 0; i < nReads; i++) {
- zmwReader.xyArray.Read(i,i+1, baseFile.holeXY[i].xy);
- }
- }
-
- //
- // Return size of an entire field.
- //
- UInt GetFieldSize(const std::string & field) {
- if (not includedFields[field]) {
- cout << "ERROR, field [" << field << "] is not included in the base file." << endl;
- exit(1);
- }
- if (field == "Basecall") {
- return baseArray.arrayLength / 1024 * sizeof(unsigned char);
- } else if (field == "QualityValue") {
- return qualArray.arrayLength / 1024 * sizeof(unsigned char);
- } else if (field == "DeletionQV") {
- return deletionQVArray.arrayLength / 1024 * sizeof(unsigned char);
- } else if (field == "DeletionTag") {
- return deletionTagArray.arrayLength / 1024 * sizeof(unsigned char);
- } else if (field == "MergeQV") {
- return mergeQVArray.arrayLength / 1024 * sizeof(unsigned char);
- } else if (field == "InsertionQV") {
- return insertionQVArray.arrayLength / 1024 * sizeof(unsigned char);
- } else if (field == "SubstitutionQV") {
- return substitutionQVArray.arrayLength / 1024 * sizeof(unsigned char);
- } else if (field == "SubstitutionTag") {
- return substitutionTagArray.arrayLength / 1024 * sizeof(unsigned char);
- } else if (field == "WidthInFrames") {
- return basWidthInFramesArray.arrayLength / 1024 * sizeof(uint16_t);
- } else if (field == "PreBaseFrames") {
- return preBaseFramesArray.arrayLength / 1024 * sizeof(uint16_t);
- } else if (field == "PulseIndex") {
- return pulseIndexArray.arrayLength / 1024 * sizeof(int);
- } else {
- cout << "ERROR, field [" << field << "] is not supported. " << endl ;
- exit(1);
- }
- }
-
- //
- // Read an entire field.
- //
- void ReadField(BaseFile & baseFile, const std::string & field) {
- if (not includedFields[field]) {
- cout << "ERROR, field [" << field << "] is not included in the base file." << endl;
- exit(1);
- }
- if (field == "Basecall") {
- assert(nBases == baseArray.arrayLength);
- baseArray.ReadDataset(baseFile.baseCalls);
- } else if (field == "QualityValue") {
- qualArray.ReadDataset(baseFile.qualityValues);
- } else if (field == "DeletionQV") {
- deletionQVArray.ReadDataset(baseFile.deletionQV);
- } else if (field == "DeletionTag") {
- deletionTagArray.ReadDataset(baseFile.deletionTag);
- } else if (field == "MergeQV") {
- mergeQVArray.ReadDataset(baseFile.mergeQV);
- } else if (field == "InsertionQV") {
- insertionQVArray.ReadDataset(baseFile.insertionQV);
- } else if (field == "SubstitutionQV") {
- substitutionQVArray.ReadDataset(baseFile.substitutionQV);
- } else if (field == "SubstitutionTag") {
- substitutionTagArray.ReadDataset(baseFile.substitutionTag);
- } else if (field == "WidthInFrames") {
- basWidthInFramesArray.ReadDataset(baseFile.basWidthInFrames);
- } else if (field == "PreBaseFrames") {
- preBaseFramesArray.ReadDataset(baseFile.preBaseFrames);
- } else if (field == "PulseIndex") {
- pulseIndexArray.ReadDataset(baseFile.pulseIndex);
- } else {
- cout << "ERROR, field [" << field << "] is not supported. " << endl ;
- exit(1);
- }
- }
-
- //
- // Clear memory allocated for a field
- //
- void ClearField(BaseFile & baseFile, const std::string & field) {
- if (not includedFields[field]) {
- cout << "ERROR, field [" << field << "] is not included in the base file." << endl;
- exit(1);
- }
- if (field == "Basecall") {
- ClearMemory(baseFile.baseCalls);
- } else if (field == "QualityValue") {
- ClearMemory(baseFile.qualityValues);
- } else if (field == "DeletionQV") {
- ClearMemory(baseFile.deletionQV);
- } else if (field == "DeletionTag") {
- ClearMemory(baseFile.deletionTag);
- } else if (field == "MergeQV") {
- ClearMemory(baseFile.mergeQV);
- } else if (field == "InsertionQV") {
- ClearMemory(baseFile.insertionQV);
- } else if (field == "SubstitutionQV") {
- ClearMemory(baseFile.substitutionQV);
- } else if (field == "SubstitutionTag") {
- ClearMemory(baseFile.substitutionTag);
- } else if (field == "WidthInFrames") {
- ClearMemory(baseFile.basWidthInFrames);
- } else if (field == "PreBaseFrames") {
- ClearMemory(baseFile.preBaseFrames);
- } else if (field == "PulseIndex") {
- ClearMemory(baseFile.pulseIndex);
- } else {
- cout << "ERROR, field [" << field << "] is supported. " << endl ;
- exit(1);
- }
- }
-
- //
- // Initialization for reading a base file.
- //
- void ReadBaseFileInit(BaseFile & baseFile) {
- if (scanDataReader.fileHasScanData) {
- scanDataReader.Read(baseFile.scanData);
- }
-
- baseFile.nReads = nReads;
-
- if (useBasHoleXY) {
- ReadAllHoleXY(baseFile);
- }
- GetAllHoleNumbers(baseFile.holeNumbers);
- GetAllHoleStatus(baseFile.holeStatus);
- zmwReader.numEventArray.ReadDataset(baseFile.readLengths);
-
- //
- // Cache the start positions of all reads.
- //
- assert(baseFile.nReads == baseFile.readLengths.size());
- baseFile.readStartPositions.resize(baseFile.readLengths.size()+1);
-
- if ( baseFile.readLengths.size() > 0 ) {
- int i;
- baseFile.readStartPositions[0] = 0;
- for (i = 1; i < baseFile.readLengths.size()+1; i++) {
- baseFile.readStartPositions[i] =
- (baseFile.readStartPositions[i-1] +
- baseFile.readLengths[i-1]);
- }
- }
- }
-
- //
- // Read a base file.
- //
- void ReadBaseFile(BaseFile &baseFile) {
- ReadBaseFileInit(baseFile);
-
- if (includedFields["Basecall"]) {
- baseFile.baseCalls.resize(nBases);
- baseArray.Read(0,nBases, &baseFile.baseCalls[0]);
- }
-
- /*
- * This can probably be fixed eventually with an object factory or
- * collection of some sorts.
- */
- if (includedFields["WidthInFrames"]) {
- basWidthInFramesArray.ReadDataset(baseFile.basWidthInFrames);
- }
- if (includedFields["PreBaseFrames"]) {
- preBaseFramesArray.ReadDataset(baseFile.preBaseFrames);
- }
- if (includedFields["PulseIndex"]) {
- pulseIndexArray.ReadDataset(baseFile.pulseIndex);
- }
- if (includedFields["QualityValue"]) {
- qualArray.ReadDataset(baseFile.qualityValues);
- }
- if (includedFields["InsertionQV"]) {
- insertionQVArray.ReadDataset(baseFile.insertionQV);
- }
- if (includedFields["SubstitutionTag"]) {
- substitutionTagArray.ReadDataset(baseFile.substitutionTag);
- }
- if (includedFields["SubstitutionQV"]) {
- substitutionQVArray.ReadDataset(baseFile.substitutionQV);
- }
- if (includedFields["MergeQV"]) {
- mergeQVArray.ReadDataset(baseFile.mergeQV);
- }
- if (includedFields["DeletionQV"]) {
- deletionQVArray.ReadDataset(baseFile.deletionQV);
- }
- if (includedFields["DeletionTag"]) {
- deletionTagArray.ReadDataset(baseFile.deletionTag);
- }
-
- baseFile.nBases = nBases;
- baseFile.scanData.platformId = scanDataReader.platformId;
- }
-
- void GetMinMaxHoleNumber(UInt &minHole, UInt &maxHole) {
- assert(nReads >= 0);
- // Assume that hole numbers are ascendingly sorted in ZMW/HoleNumber.
- if (not zmwReader.GetHoleNumberAt(0, minHole) or
- not zmwReader.GetHoleNumberAt(nReads - 1, maxHole)) {
- cout << "ERROR, could not get the minimum and maximum hole numbers "
- << "from ZMW HoleNumbers." << endl;
- exit(1);
- }
- }
-};
-
-class HDFSmrtReader: public T_HDFBasReader<SMRTSequence> {
-public:
- int Advance(int nSteps);
-};
-
-typedef T_HDFBasReader<FASTASequence> HDFBasReader;
-typedef T_HDFBasReader<FASTQSequence> HDFQualReader;
-
-
-#endif
diff --git a/libcpp/hdf/HDFBasWriter.hpp b/libcpp/hdf/HDFBasWriter.hpp
deleted file mode 100644
index dc4bac9..0000000
--- a/libcpp/hdf/HDFBasWriter.hpp
+++ /dev/null
@@ -1,390 +0,0 @@
-#ifndef _BLASR_HDF_BAS_WRITER_HPP_
-#define _BLASR_HDF_BAS_WRITER_HPP_
-
-#include <sstream>
-#include "Types.h"
-#include "Enumerations.h"
-#include "utils/SMRTReadUtils.hpp"
-#include "SMRTSequence.hpp"
-#include "HDFAtom.hpp"
-#include "HDFFile.hpp"
-#include "DatasetCollection.hpp"
-#include "HDFArray.hpp"
-#include "HDFScanDataWriter.hpp"
-#include "HDF2DArray.hpp"
-
-using namespace H5;
-using namespace std;
-
-class HDFBasWriter : public DatasetCollection {
- HDFFile outFile;
- string hdfFileName;
- static const int bufferSize = 16;
-
- string changeListID;
- HDFAtom<string> changeListIDAtom;
-
- BufferedHDFArray<int> nElemArray;
- BufferedHDFArray<int> zmwXCoordArray;
- BufferedHDFArray<int> zmwYCoordArray;
- BufferedHDFArray<unsigned char> baseArray;
- BufferedHDFArray<unsigned char> qualArray;
- BufferedHDFArray<unsigned int> simulatedCoordinateArray;
- BufferedHDFArray<unsigned int> simulatedSequenceIndexArray;
-
-
- //
- // Astro specific arrays.
- //
- BufferedHDF2DArray<int16_t> holeXY2D;
-
- //
- // Springfield specific arrays.
- //
- BufferedHDFArray<unsigned int> holeNumberArray;
- BufferedHDFArray<unsigned char> holeStatusArray;
-
- //
- // Define arrays for rich quality values.
- //
- BufferedHDFArray<unsigned char> deletionQVArray;
- BufferedHDFArray<unsigned char> deletionTagArray;
- BufferedHDFArray<unsigned char> insertionQVArray;
- BufferedHDFArray<unsigned char> substitutionTagArray;
- BufferedHDFArray<unsigned char> substitutionQVArray;
- BufferedHDFArray<unsigned char> mergeQVArray;
- BufferedHDFArray<HalfWord> preBaseFramesArray;
- BufferedHDFArray<HalfWord> widthInFramesArray;
- BufferedHDFArray<int> pulseIndexArray;
- BufferedHDF2DArray<unsigned char> preBaseDeletionQVArray;
- HDFGroup rootGroup;
-
- HDFGroup baseCallGroup;
- HDFGroup zmwGroup;
- HDFGroup plsZMWGroup;
-
- PlatformId platformId;
- ScanData sd;
-public:
- HDFGroup pulseDataGroup;
- ~HDFBasWriter() {
- //
- // Assume that flushing out and closing the hdf file must be one
- // manually and not in a destructor.
- //
- }
- void InitializeDefaultIncludedFields() {
- IncludeField("Basecall");
- IncludeField("DeletionQV");
- IncludeField("DeletionTag");
- IncludeField("InsertionQV");
- IncludeField("SubstitutionTag");
- IncludeField("SubstitutionQV");
- IncludeField("QualityValue");
- IncludeField("WidthInFrames");
- IncludeField("PulseIndex");
- IncludeField("PreBaseFrames");
- IncludeField("HoleNumber");
- IncludeField("HoleStatus");
- IncludeField("MergeQV");
- }
-
-
- void Flush() {
- nElemArray.Flush();
-
- if (includedFields["zmwXCoord"])
- zmwXCoordArray.Flush();
- if (includedFields["zmwYCoord"])
- zmwYCoordArray.Flush();
- if (includedFields["Basecall"])
- baseArray.Flush();
- if (includedFields["QualityValue"])
- qualArray.Flush();
- if (includedFields["DeletionQV"])
- deletionQVArray.Flush();
- if (includedFields["DeletionTag"])
- deletionTagArray.Flush();
- if (includedFields["InsertionQV"])
- insertionQVArray.Flush();
- if (includedFields["SubstitutionTag"])
- substitutionTagArray.Flush();
- if (includedFields["SubstitutionQV"])
- substitutionQVArray.Flush();
- if (includedFields["HoleNumber"])
- holeNumberArray.Flush();
- if (includedFields["HoleStatus"])
- holeStatusArray.Flush();
- if (includedFields["PreBaseFrames"])
- preBaseFramesArray.Flush();
- if (includedFields["PulseIndex"])
- pulseIndexArray.Flush();
- if (includedFields["WidthInFrames"])
- widthInFramesArray.Flush();
- if (includedFields["HoleXY"])
- holeXY2D.Flush();
- if (includedFields["MergeQV"])
- mergeQVArray.Flush();
- if (includedFields["SimulatedCoordinate"])
- simulatedCoordinateArray.Flush();
- if (includedFields["SimulatedSequenceIndex"])
- simulatedSequenceIndexArray.Flush();
- }
-
- HDFBasWriter() {
- /*
- * Default to astro for now. This may need to change to a NO_ID
- * platform, in which case it must be set with Initialize().
- */
- fieldNames.push_back("zmwXCoord");
- fieldNames.push_back("zmwYCoord");
- fieldNames.push_back("QualityValue");
- fieldNames.push_back("Basecall");
- fieldNames.push_back("DeletionQV");
- fieldNames.push_back("DeletionTag");
- fieldNames.push_back("InsertionQV");
- fieldNames.push_back("SubstitutionQV");
- fieldNames.push_back("SubstitutionTag");
- fieldNames.push_back("MergeQV");
- fieldNames.push_back("WidthInFrames");
- fieldNames.push_back("HoleNumber");
- fieldNames.push_back("HoleStatus");
- fieldNames.push_back("HoleXY");
- fieldNames.push_back("PreBaseFrames");
- fieldNames.push_back("PulseIndex");
- fieldNames.push_back("SimulatedCoordinate");
- fieldNames.push_back("SimulatedSequenceIndex");
- InitializeAllFields(false);
- sd.platformId = Springfield;
- }
-
- void Close() {
- Flush();
- outFile.Close();
- }
-
- void SetPlatform(PlatformId _platform) {
- sd.platformId = platformId = _platform;
- }
- void SetMovieName(string _movieName) {
- sd.movieName = _movieName;
- }
- void SetRunCode(string _runCode) {
- sd.runCode = _runCode;
- }
- void SetChangeListID(string _changeListID) {
- changeListID = _changeListID;
- }
-
-
- /*
- * Initialization without a runCode is implicitly a springfield
- * platform. You can change it if you really want.
- */
- void Initialize(string _hdfFileName, string movieName, string _changeListID) {
- SetChangeListID(_changeListID);
- SetPlatform(Springfield);
- SetMovieName(movieName);
- Initialize(_hdfFileName);
- }
-
- void Initialize(string _hdfFileName, string movieName, PlatformId _platform = Springfield) {
- SetMovieName(movieName);
- SetPlatform(Springfield);
- Initialize(_hdfFileName);
- }
-
- void Initialize(string _hdfFileName, string movieName, string runCode, string _changeListID ) {
- SetChangeListID(_changeListID);
- SetMovieName(movieName);
- SetRunCode(runCode);
- Initialize(_hdfFileName);
- }
-
-
- void WriteSimulatedCoordinate(unsigned int coord) {
- simulatedCoordinateArray.Write(&coord,1);
- }
-
- void WriteSimulatedSequenceIndex(unsigned int index) {
- simulatedSequenceIndexArray.Write(&index,1);
- }
-
- void Initialize(string _hdfFileName, const H5::FileAccPropList &
- fileAccPropList = H5::FileAccPropList::DEFAULT) {
- hdfFileName = _hdfFileName;
- outFile.Open(hdfFileName, H5F_ACC_TRUNC, fileAccPropList);
- outFile.rootGroup.AddGroup("PulseData");
-
- if (pulseDataGroup.Initialize(outFile.rootGroup, "PulseData") == 0) {
- cout << "ERROR, could not create file " << hdfFileName
- << ". Error creating group /PulseData." << endl;
- exit(1);
- }
-
- pulseDataGroup.AddGroup("BaseCalls");
- if (baseCallGroup.Initialize(pulseDataGroup, "BaseCalls") == 0) {
- cout << "ERROR, could not create file " << hdfFileName
- << ". Error creating group /PulseData/BaseCall." << endl;
- exit(1);
- }
-
- baseCallGroup.AddGroup("ZMW");
- if (zmwGroup.Initialize(baseCallGroup, "ZMW") == 0) {
- cout << "ERROR, could not create file " << hdfFileName
- << ". Error creating group /PulseData/BaseCall/ZMW." << endl;
- exit(1);
- }
-
- HDFScanDataWriter sdWriter(outFile);
- //
- // Reset ScanData attributes if neccessary.
- //
- sdWriter.Write(sd);
-
- if (changeListID != "") {
- changeListIDAtom.Create(baseCallGroup.group, "ChangeListID", changeListID);
- }
-
- nElemArray.Initialize(zmwGroup, "NumEvent");
- if (includedFields["Basecall"])
- baseArray.Initialize(baseCallGroup, "Basecall");
- if (includedFields["QualityValue"])
- qualArray.Initialize(baseCallGroup, "QualityValue");
- if (includedFields["DeletionQV"])
- deletionQVArray.Initialize(baseCallGroup, "DeletionQV");
- if (includedFields["DeletionTag"])
- deletionTagArray.Initialize(baseCallGroup, "DeletionTag");
- if (includedFields["InsertionQV"])
- insertionQVArray.Initialize(baseCallGroup, "InsertionQV");
- if (includedFields["MergeQV"])
- mergeQVArray.Initialize(baseCallGroup, "MergeQV");
- if (includedFields["PreBaseDeletionQV"])
- preBaseDeletionQVArray.Initialize(baseCallGroup, "PreBaseDeletionQV", 4);
- if (includedFields["SubstitutionTag"])
- substitutionTagArray.Initialize(baseCallGroup, "SubstitutionTag");
- if (includedFields["SubstitutionQV"])
- substitutionQVArray.Initialize(baseCallGroup, "SubstitutionQV");
- if (includedFields["WidthInFrames"])
- widthInFramesArray.Initialize(baseCallGroup, "WidthInFrames");
- if (includedFields["PreBaseFrames"])
- preBaseFramesArray.Initialize(baseCallGroup, "PreBaseFrames");
-
- if (includedFields["SimulatedCoordinate"]) {
- simulatedCoordinateArray.Initialize(baseCallGroup, "SimulatedCoordinate");
- }
- if (includedFields["SimulatedSequenceIndex"]) {
- simulatedSequenceIndexArray.Initialize(baseCallGroup, "SimulatedSequenceIndex");
- }
- if (includedFields["PulseIndex"]) {
- pulseIndexArray.Initialize(baseCallGroup, "PulseIndex");
- }
-
- if (platformId == Astro or includedFields["HoleXY"]) {
- holeXY2D.Initialize(zmwGroup, "HoleXY", 2);
- }
- includedFields["HoleNumber"] = true;
- holeNumberArray.Initialize(zmwGroup, "HoleNumber");
- includedFields["HoleStatus"] = true;
- holeStatusArray.Initialize(zmwGroup, "HoleStatus");
- }
-
- int WriteHoleXY(int x=0, int y=0) {
- int16_t xy[2] = {static_cast<int16_t>(x), static_cast<int16_t>(y)};
- holeXY2D.WriteRow(xy, 2);
- }
-
- int WriteIdentifiers(UInt holeNumber, unsigned char holeStatus, int x=0, int y=0 ) {
- //
- // Write hole number regardless of platform type.
- //
- holeNumberArray.Write(&holeNumber, 1);
- holeStatusArray.Write(&holeStatus, 1);
- if (platformId == Astro or includedFields["HoleXY"]) {
- WriteHoleXY(x,y);
- }
- return 1;
- }
-
-
- int WriteQualities(FASTQSequence &seq) {
- qualArray.Write(seq.qual.data, seq.length);
-
- if (includedFields["DeletionQV"] and seq.deletionQV.Empty() == false) {
- deletionQVArray.Write(seq.deletionQV.data, seq.length);
- }
- if (includedFields["PreBaseDeletionQV"] and seq.preBaseDeletionQV.Empty() == false) {
- DNALength readPos;
- for (readPos = 0; readPos < seq.length; readPos++) {
- preBaseDeletionQVArray.WriteRow(&seq.preBaseDeletionQV[readPos*4], 4);
- }
- }
- if (includedFields["DeletionTag"] and seq.deletionTag != NULL) {
- deletionTagArray.Write(seq.deletionTag, seq.length);
- }
- if (includedFields["InsertionQV"] and seq.insertionQV.Empty() == false) {
- insertionQVArray.Write(seq.insertionQV.data, seq.length);
- }
- if (includedFields["SubstitutionQV"] and seq.substitutionQV.Empty() == false) {
- substitutionQVArray.Write(seq.substitutionQV.data, seq.length);
- }
- if (includedFields["SubstitutionTag"] and seq.substitutionTag != NULL) {
- substitutionTagArray.Write(seq.substitutionTag, seq.length);
- }
- if (includedFields["MergeQV"] and seq.mergeQV.Empty() == false) {
- mergeQVArray.Write(seq.mergeQV.data, seq.length);
- }
-
- }
-
- int WriteBases(FASTASequence &seq ) {
- int lenArray[1] = {static_cast<int>(seq.length)};
- nElemArray.Write(lenArray, 1);
- baseArray.Write((const unsigned char*) seq.seq, seq.length);
- return 1;
- }
-
- int Write(SMRTSequence &seq) {
- WriteBases(seq);
- WriteQualities(seq);
-
- if (includedFields["PreBaseFrames"] and seq.preBaseFrames != NULL) {
- preBaseFramesArray.Write(seq.preBaseFrames, seq.length);
- }
- if (includedFields["WidthInFrames"] and seq.widthInFrames != NULL) {
- widthInFramesArray.Write(seq.widthInFrames, seq.length);
- }
- if (includedFields["PulseIndex"] and seq.pulseIndex != NULL) {
- pulseIndexArray.Write(seq.pulseIndex, seq.length);
- }
- WriteIdentifiers(seq.zmwData.holeNumber, seq.zmwData.holeStatus, seq.xy[0], seq.xy[1]);
-
- return 1;
- }
-
- int Write(FASTQSequence &seq) {
- int x, y;
- UInt holeNumber;
- unsigned char holeStatus;
-
- WriteBases(seq);
- WriteQualities(seq);
-
- if (platformId == Astro) {
- //
- // now extract the x an y coordinates.
- GetSMRTReadCoordinates(seq, x, y);
- holeStatus = 0;
- seq.GetHoleNumber((int&) holeNumber);
- }
- if (platformId == Springfield){
- GetSpringfieldHoleNumberFromTitle(seq, holeNumber);
- }
-
- WriteIdentifiers(holeNumber,holeStatus,x,y);
-
- return 1;
- }
-};
-
-#endif
diff --git a/libcpp/hdf/HDFCCSReader.hpp b/libcpp/hdf/HDFCCSReader.hpp
deleted file mode 100644
index c93be14..0000000
--- a/libcpp/hdf/HDFCCSReader.hpp
+++ /dev/null
@@ -1,257 +0,0 @@
-#ifndef _BLASR_HDF_CCS_READER_HPP_
-#define _BLASR_HDF_CCS_READER_HPP_
-
-#include "HDFBasReader.hpp"
-
-template<typename T_Sequence>
-class HDFCCSReader : public T_HDFBasReader<T_Sequence> {
- public:
- HDFGroup ccsGroup, passesGroup;
-
- HDFArray<Byte> baseCallArray;
- HDFArray<UInt> passStartPulseArray, passNumPulsesArray, passStartBaseArray,
- passNumBasesArray, numPassesArray;
- HDFArray<Byte> passDirectionArray, adapterHitAfterArray, adapterHitBeforeArray;
-
- HDFZMWReader zmwReader;
- T_HDFBasReader<SMRTSequence> ccsBasReader;
- int curPassPos;
-
- HDFCCSReader() : T_HDFBasReader<T_Sequence>() {
- curPassPos = 0;
- this->fieldNames.push_back("AdapterHitAfter");
- this->fieldNames.push_back("AdapterHitBefore");
- this->fieldNames.push_back("NumPasses");
- this->fieldNames.push_back("PassDirection");
- this->fieldNames.push_back("PassNumPase");
- this->fieldNames.push_back("PassStartBase");
- this->fieldNames.push_back("PassStartPulse");
- this->fieldNames.push_back("PassNumPulses");
- InitializeAllCCSFields(true);
- }
-
- void InitializeAllCCSFields(bool value) {
- this->includedFields["AdapterHitAfter"] = value;
- this->includedFields["AdapterHitBefore"] = value;
- this->includedFields["NumPasses"] = value;
- this->includedFields["PassDirection"] = value;
- this->includedFields["PassNumPase"] = value;
- this->includedFields["PassStartBase"] = value;
- this->includedFields["PassStartPulse"] = value;
- this->includedFields["PassNumPulses"] = value;
- }
-
- bool BasFileHasCCS(string ccsBasFileName) {
- try {
- H5::Exception::dontPrint();
- this->hdfBasFile.openFile(ccsBasFileName.c_str(), H5F_ACC_RDONLY, H5P_DEFAULT);
- }
- catch (H5::Exception &e) {
- cout << "ERROR, could not open hdf file " << ccsBasFileName << " Stopping." << endl;
- exit(1);
- }
-
- HDFGroup ccsBasecallsGroup;
- bool fileContainsCCS = false;
- HDFGroup pulseDataGroup;
- if (pulseDataGroup.Initialize(this->hdfBasFile, "PulseData") == 0) {
- cout << "ERROR, ccs base file " << ccsBasFileName
- << " does not have a PulseData field." << endl;
- exit(1);
- }
- if (pulseDataGroup.ContainsObject("ConsensusBaseCalls")) {
- fileContainsCCS = true;
- }
-
- this->hdfBasFile.close();
- return fileContainsCCS;
- }
-
- int Advance(int nSteps) {
- cout << "ERROR! Advance is not yet implemented for ccs reader" << endl;
- assert(0);
- return 0;
- }
-
- int Initialize(string ccsBasFileName,
- const H5::FileAccPropList & fileAccPropList = H5::FileAccPropList::DEFAULT) {
- //
- // Open the file and initialize for reading reads.
- //
-
- //
- // First, initialize for reading the unrolled bases from this
- // file.
- //
- if (this->T_HDFBasReader<T_Sequence>::Initialize(ccsBasFileName, fileAccPropList) == 0) {
- cout << "ERROR, Could not initialize ccs file " << ccsBasFileName << endl;
- exit(1);
- }
-
- if (this->pulseDataGroup.ContainsObject("ConsensusBaseCalls") and
- ccsGroup.Initialize(this->hdfBasFile, "PulseData/ConsensusBaseCalls") == 0) {
- cout << "ERROR, attempting to read cicular consensus data from '" << ccsBasFileName
- << "', which does not contain a ConsensusBaseCalls field." << endl;
- cout << "Check HDF file structure." << endl;
- exit(1);
- }
- curPassPos = 0;
- int passesSuccess = 1;
- if (ccsGroup.ContainsObject("Passes") == 0) {
- passesSuccess = 0;
- }
- else {
- if (passesGroup.Initialize(ccsGroup.group,"Passes") == 0) {
- passesSuccess = 0;
- }
- }
-
- if (passesSuccess == 0) {
- cout <<"ERROR, attempting to read circular consensus group Passes but it does not exist. " << endl;
- cout <<"Check HDF file structure."<<endl;
- exit(1);
- }
-
- //
- // Initialize the bas reader to read ccs reads as normal bas reads.
- //
-
- // Next, the location of the bases is in a non-standard group.
- ccsBasReader.baseCallsGroupName = "ConsensusBaseCalls";
-
-
- //
- // Read in the CCS fields that are the same as the base fields,
- // but in a different group.
- //
-
- // ccsBasReader.OpenHDFFile(ccsBasFileName);
-
- //
- // Initialize the fields that are read.
- //
- ccsBasReader.IncludeField("Basecall");
- ccsBasReader.IncludeField("InsertionQV");
- ccsBasReader.IncludeField("DeletionQV");
- ccsBasReader.IncludeField("DeletionTag");
- ccsBasReader.IncludeField("SubstitutionQV");
- ccsBasReader.IncludeField("SubstitutionTag");
- ccsBasReader.IncludeField("QualityValue");
- //
- // Initialize this without opening a file.
- //
- ccsBasReader.Initialize(&this->rootGroup);
- //ccsBasReader.InitializeForReadingPulseInformation();
- //ccsBasReader.LoadRunInfo();
- /*
- * Initialize pass information for reading.
- */
- if (this->InitializeField(passesGroup, "AdapterHitAfter", adapterHitAfterArray, this->includedFields["AdapterHitAfter"]) == 0) return 0;
- if (this->InitializeField(passesGroup, "AdapterHitBefore", adapterHitBeforeArray, this->includedFields["AdapterHitBefore"]) == 0) return 0;
- if (this->InitializeField(passesGroup, "NumPasses", numPassesArray, this->includedFields["NumPasses"]) == 0) return 0;
- if (this->InitializeField(passesGroup, "PassDirection", passDirectionArray, this->includedFields["PassDirection"]) == 0) return 0;
- if (this->InitializeField(passesGroup, "PassNumBases", passNumBasesArray, this->includedFields["PassNumBases"]) == 0) return 0;
- if (this->InitializeField(passesGroup, "PassStartBase", passStartBaseArray, this->includedFields["PassStartBase"]) == 0) return 0;
- //
- // The following two fields are not critical.
- //
- this->InitializeField(passesGroup, "PassStartPulse", passStartPulseArray, this->includedFields["PassStartPulse"]);
- this->InitializeField(passesGroup, "PassNumPulses", passNumPulsesArray, this->includedFields["PassNumPulses"]);
-
- //
- // The zmw reader contains the group that hols all pass information
- //
- zmwReader.Initialize(&ccsBasReader.baseCallsGroup);
-
- return 1;
- }
-
- unsigned int GetNumPasses(int readIndex) {
- unsigned int numPasses;
- numPassesArray.Read(readIndex, readIndex+1, &numPasses);
- return numPasses;
- }
-
- int GetNext(T_Sequence &ccsSequence) {
- //
- // Read in all ccs pass data.
- //
-
- ccsSequence.Free();
- int retVal = 0;
- if (this->curRead == ccsBasReader.nReads) {
- return 0;
- }
- if (this->curBasePos == ccsBasReader.nBases) {
- return 0;
- }
- try {
- UInt numPasses;
- numPassesArray.Read(this->curRead, this->curRead+1, &numPasses);
- if (numPasses > 0) {
- // Read in the ccs bases
- if ((retVal = ccsBasReader.GetNext((SMRTSequence&)ccsSequence)) == 0)
- return 0;
-
- ccsSequence.numPasses = numPasses;
-
- if (this->includedFields["AdapterHitAfter"]) {
- ccsSequence.adapterHitAfter.resize(ccsSequence.numPasses);
- adapterHitAfterArray.Read(curPassPos, curPassPos + ccsSequence.numPasses, &ccsSequence.adapterHitAfter[0]);
- }
- if (this->includedFields["AdapterHitBefore"]) {
- ccsSequence.adapterHitBefore.resize(ccsSequence.numPasses);
- adapterHitBeforeArray.Read(curPassPos, curPassPos + ccsSequence.numPasses, &ccsSequence.adapterHitBefore[0]);
- }
- if (this->includedFields["PassDirection"]) {
- ccsSequence.passDirection.resize(ccsSequence.numPasses);
- passDirectionArray.Read(curPassPos, curPassPos + ccsSequence.numPasses, &ccsSequence.passDirection[0]);
- }
- if (this->includedFields["PassNumBases"]) {
- ccsSequence.passNumBases.resize(ccsSequence.numPasses);
- passNumBasesArray.Read(curPassPos, curPassPos + ccsSequence.numPasses, &ccsSequence.passNumBases[0]);
- }
- if (this->includedFields["PassStartBase"]) {
- ccsSequence.passStartBase.resize(ccsSequence.numPasses);
- passStartBaseArray.Read(curPassPos, curPassPos + ccsSequence.numPasses, &ccsSequence.passStartBase[0]);
- }
- if (this->includedFields["PassStartPulse"]) {
- ccsSequence.passStartPulse.resize(ccsSequence.numPasses);
- passStartPulseArray.Read(curPassPos, curPassPos + ccsSequence.numPasses, &ccsSequence.passStartPulse[0]);
- }
- if (this->includedFields["PassNumPulses"]) {
- ccsSequence.passNumPulses.resize(ccsSequence.numPasses);
- passNumPulsesArray.Read(curPassPos, curPassPos + ccsSequence.numPasses, &ccsSequence.passNumPulses[0]);
- }
- curPassPos += ccsSequence.numPasses;
- }
- else {
- // advance a read in the ccs sequence without advancing positions.
- ccsBasReader.curRead++;
- }
- //
- // Regardless whether or not a ccs read was called, read the next
- // unrolled read, since an unrolled read is called for each zmw.
- //
- retVal = ((T_HDFBasReader<SMRTSequence>*)this)->GetNext(ccsSequence.unrolledRead);
- ccsSequence.zmwData = ccsSequence.unrolledRead.zmwData;
- ccsSequence.CopyTitle(ccsSequence.unrolledRead.title);
- string newTitle = string(ccsSequence.title) + string("/ccs");
- ccsSequence.CopyTitle(newTitle.c_str());
- } catch (H5::DataSetIException e) {
- cout << "ERROR, could not read ccs data for CCS Sequence "
- << ccsSequence.unrolledRead.title << endl;
- exit(1);
- }
- // cout << "title: " << ccsSequence.title << endl;
- if (retVal == 0) {
- return 0;
- }
- else {
- return 1;
- }
- }
-};
-
-
-#endif
diff --git a/libcpp/hdf/HDFCmpData.hpp b/libcpp/hdf/HDFCmpData.hpp
deleted file mode 100644
index dd9e54e..0000000
--- a/libcpp/hdf/HDFCmpData.hpp
+++ /dev/null
@@ -1,36 +0,0 @@
-#ifndef _BLASR_HDF_CMP_DATA_HPP_
-#define _BLASR_HDF_CMP_DATA_HPP_
-
-#include "HDFAtom.hpp"
-#include "HDFCmpRefAlignmentGroup.hpp"
-
-class HDFCmpData {
-public:
- HDFAtom<std::string> commandLine;
- H5::H5File hdfCmpFile;
- HDFArray<int> movieNameIdArray;
- HDFStringArray movieNameArray;
-
- HDFStringArray readGroupPathArray;
- HDFArray<int> readGroupPathIdArray;
-
- HDFArray<int> refSeqNameIdArray;
- HDFStringArray refSeqNameArray;
- static const int NCols=22;
- vector<HDFAtom<std::string> > colNameAtoms;
- vector<HDFCmpRefAlignmentGroup*> refAlignGroups;
- map<std::string, int> nameToAlignmentGroupIndex;
- static const char *colNameIds[];
-
- void Close() {
- hdfCmpFile.close();
- }
-};
-
-const char * HDFCmpData::colNameIds[] = {
- "00", "01", "02", "03", "04", "05", "06", "07", "08", "09",
- "10", "11", "12", "13", "14", "15", "16", "17", "18", "19",
- "20", "21"};
-
-
-#endif
diff --git a/libcpp/hdf/HDFCmpExperimentGroup.cpp b/libcpp/hdf/HDFCmpExperimentGroup.cpp
deleted file mode 100644
index 6f6459c..0000000
--- a/libcpp/hdf/HDFCmpExperimentGroup.cpp
+++ /dev/null
@@ -1,193 +0,0 @@
-#include <iostream>
-#include "HDFCmpExperimentGroup.hpp"
-
-using namespace std;
-
-bool HDFCmpExperimentGroup::Create(HDFGroup &parent,
- string experimentGroupName) {
-
- parent.AddGroup(experimentGroupName);
- if (experimentGroup.Initialize(parent.group, experimentGroupName) == 0) { return 0; }
- alignmentArray.Create(experimentGroup, "AlnArray");
- return true;
-}
-
-
-void HDFCmpExperimentGroup::AddAlignment(std::vector<unsigned char> &alignment,
- unsigned int &offsetBegin, unsigned int &offsetEnd) {
-
- offsetBegin = offsetEnd = 0;
- if (alignment.size() == 0 ) {
- //
- // Do not increment anything.
- //
- return;
- }
-
- // Make a copy of alignment.
- vector<unsigned char> paddedAlignment = alignment;
- // Pad '0' to the end of the alignment.
- paddedAlignment.push_back(0);
-
- offsetBegin = alignmentArray.size(); // 0 based, inclusive
- offsetEnd = offsetBegin + alignment.size(); // 0 based, exclusive
- // alignmentArray[offsetEnd] is not a part of the real alignment, it is the padded 0.
- alignmentArray.Write(&paddedAlignment[0], paddedAlignment.size());
-}
-
-//template<typename T>
-//void HDFCmpExperimentGroup::AddQualityValues(const std::vector<T> &qualityValues,
-// const std::string &fieldName,
-// unsigned int *offsetBegin,
-// unsigned int *offsetEnd) {
-//
-// std::vector<T> paddedQualityValues = qualityValues;
-// paddedQualityValues.push_back(0);
-// HDFArray<T> *arrayPtr = NULL;
-//
-// // This seems to be how we do it
-// if (fieldName == "DeletionQV") {
-// arrayPtr = &deletionQV;
-// } else if (fieldName == "InsertionQV") {
-// arrayPtr = &insertionQV;
-// } else if (fieldName == "MergeQV") {
-// arrayPtr = &mergeQV;
-// } else if (fieldName == "SubstitutionQV") {
-// arrayPtr = &substitutionQV;
-// } else if (fieldName == "DeletionTag") {
-// arrayPtr = &deletionTag;
-// } else if (fieldName == "SubstitutionTag") {
-// arrayPtr = &substitutionTag;
-// } else {
-// assert(false);
-// }
-//
-// *offsetBegin = arrayPtr->size();
-// *offsetEnd = arrayPtr->size() + qualityValues.size();
-//
-// arrayPtr->Write(&paddedQualityValues[0], paddedQualityValues.size());
-//}
-//
-//// One for tags, one for QVs
-//template void HDFCmpExperimentGroup::AddQualityValues<char>(
-// const std::vector<char>&, const std::string&,
-// unsigned int*, unsigned int*);
-//
-//template void HDFCmpExperimentGroup::AddQualityValues<UChar>(
-// const std::vector<UChar>&, const std::string&,
-// unsigned int*, unsigned int*);
-//
-int HDFCmpExperimentGroup::Initialize(HDFGroup &refGroup,
- string experimentGroupName, set<string> &fieldNames) {
- //
- // Normal initialization that prepares for reading alignments
- //
- Initialize(refGroup, experimentGroupName);
-
- //
- // Field initialization for reading in pulse/quality information.
- //
- set<string>::iterator fieldNameIt, fieldEnd;
- fieldEnd = fieldNames.end();
- for (fieldNameIt = fieldNames.begin(); fieldNameIt != fieldEnd; ++fieldNameIt) {
- if (supportedFields.find(*fieldNameIt) != supportedFields.end() and
- experimentGroup.ContainsObject(*fieldNameIt)) {
- fields[*fieldNameIt]->Initialize(experimentGroup, *fieldNameIt);
- }
- else {
- cout << "Unable to initialize requested field " << *fieldNameIt << " in experiment group " << experimentGroupName << endl;
- }
- }
- return 1;
-}
-
-int HDFCmpExperimentGroup::Initialize(HDFGroup &refGroup, string experimentGroupName) {
-
- if (experimentGroup.Initialize(refGroup.group, experimentGroupName) == 0) { return 0; }
- if (alignmentArray.Initialize(experimentGroup, "AlnArray") == 0) { return 0; }
- return 1;
-}
-
-
-HDFCmpExperimentGroup::HDFCmpExperimentGroup() {
- fields["StartTimeOffset"] = &this->startTimeOffset;
- fields["QualityValue"] = &this->qualityValue;
- fields["IPD"] = &this->ipd;
- fields["PreBaseFrames"] = &this->preBaseFrames;
- fields["DeletionQV"] = &this->deletionQV;
- fields["InsertionQV"] = &this->insertionQV;
- fields["ClassifierQV"] = &this->classifierQV;
- fields["SubstitutionQV"] = &this->substitutionQV;
- fields["Light"] = &this->light;
- fields["WidthInFrames"] = &this->widthInFrames;
- fields["PulseWidth"] = &this->pulseWidth;
- fields["StartFrame"] = &this->startTime;
- // StartFrame computed from Pulse metrics and Base metrics
- fields["StartFramePulse"] = &this->startTimePulse;
- fields["StartFrameBase"] = &this->startTimeBase;
-
- fields["pkmid"] = &this->pkmid;
- fields["pkmax"] = &this->pkmax;
- fields["pkmean"] = &this->pkmean;
- fields["DeletionTag"] = &this->deletionTag;
- fields["SubstitutionTag"] = &this->substitutionTag;
- fields["PulseIndex"] = &this->pulseIndex;
- fields["MergeQV"] = &this->mergeQV;
-}
-
-// Return reference alignment AlnArray size in KB.
-UInt HDFCmpExperimentGroup::GetAlnArraySize() {
- return alignmentArray.arrayLength / 1024 * sizeof (unsigned char);
-}
-
-void HDFCmpExperimentGroup::AddQVs(const std::vector<UChar> &qualityValues,
- const std::string &fieldName,
- unsigned int *offsetBegin,
- unsigned int *offsetEnd) {
- std::vector<UChar> paddedQualityValues = qualityValues;
- paddedQualityValues.push_back(0);
- HDFArray<UChar> *arrayPtr = NULL;
-
- // This seems to be how we do it
- if (fieldName == "DeletionQV") {
- arrayPtr = &deletionQV;
- } else if (fieldName == "InsertionQV") {
- arrayPtr = &insertionQV;
- } else if (fieldName == "MergeQV") {
- arrayPtr = &mergeQV;
- } else if (fieldName == "SubstitutionQV") {
- arrayPtr = &substitutionQV;
- } else {
- assert(false);
- }
-
- if (!arrayPtr->isInitialized) arrayPtr->Initialize(experimentGroup, fieldName);
- *offsetBegin = arrayPtr->size();
- *offsetEnd = arrayPtr->size() + qualityValues.size();
-
- arrayPtr->Write(&paddedQualityValues[0], paddedQualityValues.size());
-}
-
-void HDFCmpExperimentGroup::AddTags(const std::vector<char> &qualityValues,
- const std::string &fieldName,
- unsigned int *offsetBegin,
- unsigned int *offsetEnd) {
- std::vector<char> paddedQualityValues = qualityValues;
- paddedQualityValues.push_back(0);
- HDFArray<char> *arrayPtr = NULL;
-
- if (fieldName == "DeletionTag") {
- arrayPtr = &deletionTag;
- } else if (fieldName == "SubstitutionTag") {
- arrayPtr = &substitutionTag;
- } else {
- assert(false);
- }
-
- if (!arrayPtr->isInitialized) arrayPtr->Initialize(experimentGroup, fieldName);
- *offsetBegin = arrayPtr->size();
- *offsetEnd = arrayPtr->size() + qualityValues.size();
-
- arrayPtr->Write(&paddedQualityValues[0], paddedQualityValues.size());
-}
-
diff --git a/libcpp/hdf/HDFCmpExperimentGroup.hpp b/libcpp/hdf/HDFCmpExperimentGroup.hpp
deleted file mode 100644
index 05d5cfb..0000000
--- a/libcpp/hdf/HDFCmpExperimentGroup.hpp
+++ /dev/null
@@ -1,70 +0,0 @@
-#ifndef _BLASR_HDF_CMP_EXPERIMENT_GROUP_HPP_
-#define _BLASR_HDF_CMP_EXPERIMENT_GROUP_HPP_
-
-#include <map>
-#include <vector>
-#include <set>
-#include <cstdint>
-#include "Types.h"
-#include "HDFGroup.hpp"
-#include "HDFArray.hpp"
-#include "HDFCmpSupportedFields.hpp"
-
-class HDFCmpExperimentGroup {
-public:
- HDFCmpSupportedFields supportedFields;
- HDFArray<unsigned int> startTimeOffset;
- HDFArray<HalfWord> ipd;
- HDFArray<HalfWord> preBaseFrames;
- HDFArray<char> deletionTag;
- HDFArray<char> substitutionTag;
- HDFArray<UChar> qualityValue;
- HDFArray<UChar> deletionQV;
- HDFArray<UChar> insertionQV;
- HDFArray<float> classifierQV;
- // ClassifierQV date type is float in cmp.h5
- HDFArray<UChar> substitutionQV;
- HDFArray<UChar> mergeQV;
- HDFArray<HalfWord> light;
- HDFArray<HalfWord> widthInFrames;
- HDFArray<HalfWord> pulseWidth;
- HDFArray<unsigned int> startTime;
- // StartFrame computed from Pulse metrics and Base metric
- HDFArray<unsigned int> startTimeBase;
- HDFArray<unsigned int> startTimePulse;
- HDFArray<float> pkmid;
- HDFArray<float> pkmax;
- HDFArray<float> pkmean;
- HDFArray<uint32_t> numPasses;
- HDFArray<uint32_t> pulseIndex;
- std::map<std::string, HDFData*> fields;
- HDFGroup experimentGroup;
- HDFArray<unsigned char> alignmentArray;
-
- bool Create(HDFGroup &parent, string experimentGroupName);
-
- void AddAlignment(std::vector<unsigned char> &alignment,
- unsigned int &offsetBegin, unsigned int &offsetEnd);
-
- // AddQVs and AddTags are like AddAlignment, but for QVs and Tags,
- // respectively. They are responsible for initializing and writing to the
- // correct member HDFArray, given a vector of values to write and the name
- // of the QV or Tag
- void AddQVs(const std::vector<UChar> &qualityValues, const std::string &fieldName,
- unsigned int *offsetBegin, unsigned int *offsetEnd);
- void AddTags(const std::vector<char> &qualityValues, const std::string &fieldName,
- unsigned int *offsetBegin, unsigned int *offsetEnd);
-
- int Initialize(HDFGroup &refGroup, std::string experimentGroupName,
- std::set<string> &fieldNames);
-
- int Initialize(HDFGroup &refGroup, std::string experimentGroupName);
-
- void Read();
-
- HDFCmpExperimentGroup();
-
- // Return reference alignment AlnArray size in KB.
- UInt GetAlnArraySize();
-};
-#endif
diff --git a/libcpp/hdf/HDFCmpFile.hpp b/libcpp/hdf/HDFCmpFile.hpp
deleted file mode 100644
index d4d6984..0000000
--- a/libcpp/hdf/HDFCmpFile.hpp
+++ /dev/null
@@ -1,844 +0,0 @@
-#ifndef _BLASR_HDF_CMP_FILE_HPP_
-#define _BLASR_HDF_CMP_FILE_HPP_
-
-#include <iostream>
-#include <assert.h>
-#include <sstream>
-#include <map>
-
-#include "H5Cpp.h"
-
-#include "HDFAtom.hpp"
-#include "HDFArray.hpp"
-#include "HDF2DArray.hpp"
-#include "HDFCmpData.hpp"
-#include "HDFCmpRefAlignmentGroup.hpp"
-#include "HDFCmpExperimentGroup.hpp"
-#include "HDFAlnGroupGroup.hpp"
-#include "HDFAlnInfoGroup.hpp"
-
-#include "HDFRefGroupGroup.hpp"
-#include "HDFRefInfoGroup.hpp"
-#include "HDFMovieInfoGroup.hpp"
-#include "HDFCmpRootGroup.hpp"
-#include "HDFCmpSupportedFields.hpp"
-#include "HDFFileLogGroup.hpp"
-
-#include "SMRTSequence.hpp"
-
-#include "datastructures/alignment/CmpFile.hpp"
-#include "datastructures/alignment/Alignment.hpp"
-#include "datastructures/alignment/AlignmentCandidate.hpp"
-#include "alignment/CmpAlignment.hpp"
-#include "datastructures/alignment/CmpReadGroupTable.h"
-#include "datastructures/alignment/CmpRefSeqTable.h"
-#include "datastructures/alignment/ByteAlignment.h"
-#include "saf/RefInfo.hpp"
-
-using namespace H5;
-using namespace std;
-
-template<typename T_Alignment>
-class HDFCmpFile : public HDFCmpData {
-public:
- map<int,int> movieNameIdToArrayIndex, readGroupPathIdToArrayIndex, refGroupIdToArrayIndex;
- map<string, int> refNameToArrayIndex;
- // map<string,string> readGroupPathToReadGroup;
- map<int, string> alnGroupIdToReadGroupName;
-
- HDFAlnGroupGroup alnGroupGroup;
- HDFAlnInfoGroup alnInfoGroup;
- HDFMovieInfoGroup movieInfoGroup;
- HDFRefGroupGroup refGroupGroup;
- HDFRefInfoGroup refInfoGroup;
- HDFCmpRootGroup<T_Alignment> rootGroup;
- set<string> includedFields;
- HDFCmpSupportedFields supportedFields;
- HDFAtom<string> readTypeAtom;
- HDFFileLogGroup fileLogGroup;
-
- void AstroInitializeColumnNameMap() {
- CmpAlignmentBase::columnNameToIndex["AlignmentId"] = 0;
- CmpAlignmentBase::columnNameToIndex["ReadGroupId"] = 1;
- CmpAlignmentBase::columnNameToIndex["MovieId"] = 2;
- CmpAlignmentBase::columnNameToIndex["RefSeqId"] = 3;
- CmpAlignmentBase::columnNameToIndex["tStart"] = 4;
- CmpAlignmentBase::columnNameToIndex["tEnd"] = 5;
- CmpAlignmentBase::columnNameToIndex["AlignedStrand"] = 6;
- CmpAlignmentBase::columnNameToIndex["ExpId"] = 7;
- CmpAlignmentBase::columnNameToIndex["RunId"] = 8;
- CmpAlignmentBase::columnNameToIndex["Panel"] = 9;
- CmpAlignmentBase::columnNameToIndex["x"] = 10;
- CmpAlignmentBase::columnNameToIndex["y"] = 11;
- CmpAlignmentBase::columnNameToIndex["SubreadId"] = 12;
- CmpAlignmentBase::columnNameToIndex["rStart"] = 13;
- CmpAlignmentBase::columnNameToIndex["rEnd"] = 14;
- CmpAlignmentBase::columnNameToIndex["Z"] = 15;
- CmpAlignmentBase::columnNameToIndex["nM"] = 16;
- CmpAlignmentBase::columnNameToIndex["nMM"] = 17;
- CmpAlignmentBase::columnNameToIndex["nIns"] = 18;
- CmpAlignmentBase::columnNameToIndex["nDel"] = 19;
- CmpAlignmentBase::columnNameToIndex["offset_begin"] = 20;
- CmpAlignmentBase::columnNameToIndex["offset_end"] = 21;
- }
-
- void SpringfieldInitializeColumnNameMap() {
- CmpAlignmentBase::columnNameToIndex["AlignmentId"] = 0;
- CmpAlignmentBase::columnNameToIndex["ReadGroupId"] = 1;
- CmpAlignmentBase::columnNameToIndex["AlnGroupID"] = 1;
- CmpAlignmentBase::columnNameToIndex["AlnGroupId"] = 1;
- CmpAlignmentBase::columnNameToIndex["MovieId"] = 2;
- CmpAlignmentBase::columnNameToIndex["RefSeqId"] = 3;
- CmpAlignmentBase::columnNameToIndex["tStart"] = 4;
- CmpAlignmentBase::columnNameToIndex["tEnd"] = 5;
- CmpAlignmentBase::columnNameToIndex["RCRefStrand"] = 6;
- CmpAlignmentBase::columnNameToIndex["HoleNumber"] = 7;
- CmpAlignmentBase::columnNameToIndex["SetNumber"] = 8;
- CmpAlignmentBase::columnNameToIndex["StrobeNumber"] = 9;
- CmpAlignmentBase::columnNameToIndex["SubreadId"] = 10;
- CmpAlignmentBase::columnNameToIndex["rStart"] = 11;
- CmpAlignmentBase::columnNameToIndex["rEnd"] = 12;
- CmpAlignmentBase::columnNameToIndex["MapQV"] = 13;
- CmpAlignmentBase::columnNameToIndex["nM"] = 14;
- CmpAlignmentBase::columnNameToIndex["nMM"] = 15;
- CmpAlignmentBase::columnNameToIndex["nIns"] = 16;
- CmpAlignmentBase::columnNameToIndex["nDel"] = 17;
- CmpAlignmentBase::columnNameToIndex["offset_begin"] = 18;
- CmpAlignmentBase::columnNameToIndex["offset_end"] = 19;
- CmpAlignmentBase::columnNameToIndex["nBackRead"] = 20;
- CmpAlignmentBase::columnNameToIndex["nReadOverlap"] = 21;
-
- // All synonyms, the code requiring these should be refactored so
- // that it no synonyms are needed.
- //
- CmpAlignmentBase::columnNameToIndex["AlnID"] = 0;
- CmpAlignmentBase::columnNameToIndex["AlnGroupID"] = 1;
- CmpAlignmentBase::columnNameToIndex["MovieID"] = 2;
- CmpAlignmentBase::columnNameToIndex["RefGroupID"] = 3;
- CmpAlignmentBase::columnNameToIndex["RefGroupId"] = 3;
- CmpAlignmentBase::columnNameToIndex["MoleculeID"] = 10;
- CmpAlignmentBase::columnNameToIndex["Offset_begin"] = 18;
- CmpAlignmentBase::columnNameToIndex["Offset_end"] = 19;
-
- }
-
-
- int Initialize(string &hdfCmpFileName, set<string> includedFieldsP, unsigned int flags=H5F_ACC_RDONLY, const H5::FileAccPropList & fileAccPropList = H5::FileAccPropList::DEFAULT) {
- Initialize(hdfCmpFileName, flags, fileAccPropList);
- includedFields = includedFieldsP;
- }
-
- void Create(string &hdfCmpFileName) {
- H5File newFile(hdfCmpFileName.c_str(), H5F_ACC_TRUNC, FileCreatPropList::DEFAULT, FileAccPropList::DEFAULT);
- hdfCmpFile.openFile(hdfCmpFileName.c_str(), H5F_ACC_RDWR, H5P_DEFAULT);
- rootGroup.Initialize(hdfCmpFile);
- refGroupGroup.Create(rootGroup.rootGroup);
- alnGroupGroup.Create(rootGroup.rootGroup);
- refInfoGroup.Create(rootGroup.rootGroup);
- movieInfoGroup.Create(rootGroup.rootGroup);
- alnInfoGroup.Create(rootGroup.rootGroup);
- fileLogGroup.Create(rootGroup.rootGroup);
-
- //
- // Add atom data
- //
- readTypeAtom.Create(rootGroup.rootGroup.group, "ReadType");
- readTypeAtom.Write("standard");
-
- // Add some proxy data for now.
- HDFAtom<string> primaryVersionAtom, versionAtom;
- primaryVersionAtom.Create(rootGroup.rootGroup.group, "PrimaryVersion");
- primaryVersionAtom.Write("2.0.0.135558");
- versionAtom.Create(rootGroup.rootGroup.group, "Version");
- versionAtom.Write("2.0.0");
- }
-
- void SetReadType(string readType) {
- readTypeAtom.Write(readType.c_str());
- }
-
- void GenerateNextRefGroupName(string &name) {
- stringstream nameStrm;
- nameStrm << "ref";
- nameStrm.width(6);
- nameStrm.fill('0');
- nameStrm << right << refGroupIdToArrayIndex.size() + 1;
- name = nameStrm.str();
- }
-
-
- int AddReference(string refName, unsigned int length, string md5, string &refGroupName) {
- //
- // Adding a reference requires:
- //
- // 1. Creating a new refgroup name.
- // 2. Create the new reference group to add alignments to.
- // 3. Adding this new name to the set of paths of ref groups.
- // 4. Adding information for this ref group.
- //
-
- // 1.
- this->GenerateNextRefGroupName(refGroupName);
-
- // 2.
- HDFCmpRefAlignmentGroup *newGroup = new HDFCmpRefAlignmentGroup;
- newGroup->Create(rootGroup.rootGroup, refGroupName);
- refAlignGroups.push_back(newGroup);
- unsigned int id = refAlignGroups.size();
-
- // 3.
- refGroupGroup.AddPath("/" + refGroupName, id);
- refGroupIdToArrayIndex[id] = id - 1;
- refNameToArrayIndex[refName] = id - 1;
- // 4.
- refInfoGroup.AddRefInfo(refName, id, length, md5);
- return id;
- }
-
- int StoreAlnArray(vector<unsigned char> &alnArray, string refName, string &experimentName,
- unsigned int &offsetBegin,
- unsigned int &offsetEnd) {
- //
- // First find the reference group.
- //
- assert(refNameToArrayIndex.find(refName) != refNameToArrayIndex.end());
- int refIndex = refNameToArrayIndex[refName];
- assert(refIndex < refAlignGroups.size());
- HDFCmpExperimentGroup *expGroup;
- expGroup = refAlignGroups[refIndex]->GetExperimentGroup(experimentName);
- expGroup->AddAlignment(alnArray, offsetBegin, offsetEnd);
- }
-
- // Write a vector of quality values to the appropriate experiment group.
- // This is similar to StoreAlignment, but for QVs
- int StoreQVs(const vector<UChar> &qvArray, const string &refName, const string &fieldName,
- const string &experimentName, unsigned int *offsetBegin,
- unsigned int *offsetEnd) {
- assert(refNameToArrayIndex.find(refName) != refNameToArrayIndex.end());
- int refIndex = refNameToArrayIndex[refName];
- assert(refIndex < refAlignGroups.size());
- HDFCmpExperimentGroup *expGroup;
- expGroup = refAlignGroups[refIndex]->GetExperimentGroup(experimentName);
- expGroup->AddQVs(qvArray, fieldName, offsetBegin, offsetEnd);
- }
-
- // Write a vector of tag to the appropriate experiment group.
- // This is similar to StoreAlignment, but for DeletionTag and
- // SubstitutionTag.
- int StoreTags(const vector<char> &qvArray, const string &refName, const string &fieldName,
- const string &experimentName, unsigned int *offsetBegin,
- unsigned int *offsetEnd) {
- assert(refNameToArrayIndex.find(refName) != refNameToArrayIndex.end());
- int refIndex = refNameToArrayIndex[refName];
- assert(refIndex < refAlignGroups.size());
- HDFCmpExperimentGroup *expGroup;
- expGroup = refAlignGroups[refIndex]->GetExperimentGroup(experimentName);
- expGroup->AddTags(qvArray, fieldName, offsetBegin, offsetEnd);
- }
-
- int Initialize(string &hdfCmpFileName,
- unsigned int flags=H5F_ACC_RDONLY,
- const H5::FileAccPropList fileAccPropList=H5::FileAccPropList::DEFAULT) {
- /*
- * Initialize access to the HDF file.
- */
- try {
- hdfCmpFile.openFile(hdfCmpFileName.c_str(), flags, fileAccPropList);
- }
- catch (Exception &e) {
- cout << e.getDetailMsg() << endl;
- return 0;
- }
-
- rootGroup.Initialize(hdfCmpFile);
- readTypeAtom.Initialize(rootGroup.rootGroup, "ReadType");
-
- if (alnGroupGroup.Initialize(rootGroup.rootGroup) == 0) {
- cout << "ERROR, could not read AlnGroup of the cmp file." << endl;
- exit(1);
- }
- if (refInfoGroup.Initialize(rootGroup.rootGroup) == 0) {
- cout << "ERROR, could not read RefInfo of the cmp file." << endl;
- exit(1);
- }
- if (refGroupGroup.Initialize(rootGroup.rootGroup) == 0) {
- cout << "ERROR, could not read RefGroup of the cmp file." << endl;
- exit(1);
- }
- if (movieInfoGroup.Initialize(rootGroup.rootGroup) == 0) {
- cout << "ERROR, could not read MovieInfo of the cmp file." << endl;
- exit(1);
- }
- if (alnInfoGroup.Initialize(rootGroup.rootGroup) == 0) {
- cout << "ERROR, could not read AlnInfo of the cmp file." << endl;
- exit(1);
- }
- if (fileLogGroup.Initialize(rootGroup.rootGroup) == 0) {
- cout << "ERROR, could not read FileLog of the cmp file." << endl;
- exit(1);
- }
-
- SpringfieldInitializeColumnNameMap();
-
- return 1;
- }
-
- bool HasNoAlignments() {
- // return true if there is no alignment in the cmp file.
- if (alnInfoGroup.alnIndexArray.GetNRows()==0) {
- return true;
- }
- return false;
- }
-
- unsigned int GetAlignmentIndexSize() {
- if (alnInfoGroup.alnInfoGroup.groupIsInitialized == false) {
- cout << "ERROR, getting the size of an index before initializing the cmp.h5 file." << endl;
- exit(1);
- }
- return alnInfoGroup.alnIndexArray.GetNRows();
- }
-
- // Add synonym
- unsigned int GetNAlignments() {
- return GetAlignmentIndexSize();
- }
-
- static void ParseReadGroupPath(string &path, string &refName, string &readGroupName){
- int delimPos;
- delimPos = path.find_last_of('/');
- if (delimPos != path.npos) {
- refName = path.substr(0, delimPos);
- //
- // Check the ref name to see if it has a preceeding '/'
- //
- readGroupName = path.substr(delimPos+1, path.size());
- }
- else {
- refName ="";
- readGroupName = "";
- }
- }
-
- void StorePlatformId(CmpFile &cmpFile) {
- //
- // For now, hard wire as a springfield. Later if the fields
- // change per platform, this may be updated.
- //
- cmpFile.platformId = Springfield;
- }
-
- void ReadAlignmentDescriptions(CmpFile &cmpFile) {
-
- //
- // Gather run information.
- //
- rootGroup.ReadAttributes(cmpFile);
-
- string readTypeString;
- readTypeAtom.Read(readTypeString);
- cmpFile.StoreReadType(readTypeString);
- //
- // Read in the groups that describe what alignments are present.
- //
-
- alnGroupGroup.Read(cmpFile.alnGroup);
- alnInfoGroup.Read(cmpFile.alnInfo);
- refGroupGroup.Read(cmpFile.refGroup);
- movieInfoGroup.Read(cmpFile.movieInfo);
- refInfoGroup.Read(cmpFile.refInfo);
- StorePlatformId(cmpFile);
-
- }
-
- void ReadStructure(CmpFile &cmpFile) {
- //
- // Now for every reference group in the cmp file, create a group.
- //
- map<string,int> refNameToArrayIndex;
-
- unsigned int refSeqIndex;
-
- for (refSeqIndex = 0; refSeqIndex < cmpFile.refGroup.path.size(); refSeqIndex++) {
- HDFCmpRefAlignmentGroup* refAlignGroup;
- refAlignGroup = new HDFCmpRefAlignmentGroup;
- refAlignGroup->Initialize(rootGroup.rootGroup.group, cmpFile.refGroup.path[refSeqIndex]);
- int refAlignGroupIndex = refAlignGroups.size();
- refAlignGroups.push_back(refAlignGroup);
- //
- // Allow one to index directly into this group given a string
- // representing the reference name.
- //
- refNameToArrayIndex[cmpFile.refGroup.path[refSeqIndex]] = refAlignGroupIndex;
- refGroupIdToArrayIndex[cmpFile.refGroup.id[refSeqIndex]] = refAlignGroupIndex;
- }
-
- //
- // Now that all ref groups are created, add read groups that
- // are aligned to the ref groups.
- //
- // Note that groups are not necessarily named by movie, especially in
- // a deep-sorted cmp.h5, read groups may look like:
- // /ref00001/rg8953-0
- // /ref00001/rg2453-1
- //
- unsigned int alnGroupIndex;
- for (alnGroupIndex = 0; alnGroupIndex < cmpFile.alnGroup.path.size(); alnGroupIndex++) {
- string refName, readGroupName;
- ParseReadGroupPath(cmpFile.alnGroup.path[alnGroupIndex], refName, readGroupName);
-
- //
- // Create an index that maps alnGroupId (/AlnGroup/Id) to readGroupName
- //
- alnGroupIdToReadGroupName[cmpFile.alnGroup.id[alnGroupIndex]] = readGroupName;
-
- //
- // Look up the group where this alignment should be found.
- //
- unsigned int refGroupArrayIndex;
- if (refNameToArrayIndex.find(refName) != refNameToArrayIndex.end()) {
- refGroupArrayIndex = refNameToArrayIndex[refName];
- }
- else {
- cout << "ERROR! The reference name '" << refName << "' does not have an entry though it is "
- << " specified in the path for " << cmpFile.readGroupTable.names[alnGroupIndex]
- << endl;
- assert(0);
- }
-
- HDFCmpExperimentGroup *alnGroupPtr;
- alnGroupPtr = refAlignGroups[refGroupArrayIndex]->InitializeExperimentGroup(readGroupName, includedFields);
- // experimentNameToIndex should have been set in InitializeExperimentGroup();
- assert( refAlignGroups[refGroupArrayIndex]->experimentNameToIndex[readGroupName]
- == refAlignGroups[refGroupArrayIndex]->readGroups.size()-1);
- refAlignGroups[refGroupArrayIndex]->experimentNameToIndex[readGroupName] = refAlignGroups[refGroupArrayIndex]->readGroups.size()-1;
- }
- }
-
- void Read(CmpFile &cmpFile, bool readAllAlignments = true) {
-
- ReadAlignmentDescriptions(cmpFile);
- ReadStructure(cmpFile);
-
- if (!readAllAlignments)
- return;
-
- /*
- * Now that the alignment indices are all read in, read the base-by-base alignments.
- */
-
- unsigned int alignmentIndex;
-
- for (alignmentIndex = 0; alignmentIndex < cmpFile.alnInfo.alignments.size(); alignmentIndex++) {
- unsigned int alnGroupId = cmpFile.alnInfo.alignments[alignmentIndex].GetAlnGroupId();
- unsigned int refGroupId = cmpFile.alnInfo.alignments[alignmentIndex].GetRefGroupId();
- string refSeqName;
-
- //
- // Make sure the refGroupId specified in the alignment index exists in the alignment groups.
- //
- int refGroupArrayIndex;
- if (refGroupIdToArrayIndex.find(refGroupId) == refGroupIdToArrayIndex.end()) {
- cout << "ERROR! Alignment " << cmpFile.alnInfo.alignments[alignmentIndex].GetAlignmentId()
- << " has ref seq id " << refGroupId << " that does not exist in the HDF file." << endl;
- assert(0);
- }
- else {
- refGroupArrayIndex = refGroupIdToArrayIndex[refGroupId];
- }
-
- //
- // Point to the refGroup that this alignment is part of.
- //
- HDFCmpRefAlignmentGroup* refAlignGroup = refAlignGroups[refGroupArrayIndex];
-
- //
- // Now locate the read group that is part of this ref align group.
- //
- string readGroupName = alnGroupIdToReadGroupName[alnGroupId];
-
- if (refAlignGroup->experimentNameToIndex.find(readGroupName) ==
- refAlignGroup->experimentNameToIndex.end()) {
- cout << "Internal ERROR! The read group name " << readGroupName << " is specified as part of "
- << " the path in alignment " << cmpFile.alnInfo.alignments[alignmentIndex].GetAlignmentId()
- << " though it does not exist in the ref align group specified for this alignment." << endl;
- assert(0);
- }
-
- int experimentIndex;
- experimentIndex = refAlignGroup->experimentNameToIndex[readGroupName];
-
- unsigned int alignmentLength = cmpFile.alnInfo.alignments[alignmentIndex].GetOffsetEnd() -
- cmpFile.alnInfo.alignments[alignmentIndex].GetOffsetBegin();
-
- vector<unsigned char> alignmentArray;
- vector<UChar> fieldArray;
-
- if (alignmentArray.size() < alignmentLength) {
- alignmentArray.resize(alignmentLength);
- }
-
- /*
- * Read in the base by base alignment.
- */
-
- refAlignGroup->readGroups[experimentIndex]->alignmentArray.Read(cmpFile.alnInfo.alignments[alignmentIndex].GetOffsetBegin(),
- cmpFile.alnInfo.alignments[alignmentIndex].GetOffsetEnd(),
- &alignmentArray[0]);
-
- cmpFile.alnInfo.alignments[alignmentIndex].StoreAlignmentArray(&alignmentArray[0], alignmentLength);
-
- /*
- * Read in all additional fields such as quality values, etc..
- */
- set<string>::iterator fieldIt, fieldEnd;
- fieldEnd = includedFields.end();
-
- for (fieldIt = includedFields.begin(); fieldIt != fieldEnd; ++fieldIt) {
- if (fieldArray.size() < alignmentLength) {
- fieldArray.resize(alignmentLength);
- }
- HDFArray<UChar>* fieldArrayPtr = dynamic_cast<HDFArray<UChar>* >(refAlignGroup->readGroups[experimentIndex]->fields[*fieldIt]);
-
- int ob = cmpFile.alnInfo.alignments[alignmentIndex].GetOffsetBegin();
- int oe = cmpFile.alnInfo.alignments[alignmentIndex].GetOffsetEnd();
- fieldArrayPtr->Read(ob, oe, &fieldArray[0]);
-
- cmpFile.alnInfo.alignments[alignmentIndex].StoreField(*fieldIt, &fieldArray[0], alignmentLength);
- }
- }
- }
-
- void IncludeField(string fieldName) {
- if (supportedFields.find(fieldName) == supportedFields.end()) {
- cout << "ERROR, attempting to include field " << fieldName << " that is not supported." << endl;
- exit(1);
- }
- includedFields.insert(fieldName);
- }
-
- template<typename T_Value, typename T_QV>
- void StoreQualityValueFromAlignment(vector<T_Value> &fieldValues,
- vector<int> &baseToAlignmentMap,
- T_QV *qv) {
- int i;
- for (i = 0; i < baseToAlignmentMap.size();i++) {
- qv[i] = fieldValues[baseToAlignmentMap[i]];
- }
- }
- /*
- void ReadAlignment(int alignmentIndex, CmpAlignment &cmpAlignment) {
- alnInfoGroup.ReadCmpAlignment(alignmentIndex, cmpAlignment);
- ReadAlignmentArray(alignmentIndex, cmpAlignment.alignmentArray);
- }
- */
- void ReadAlignment(int alignmentIndex, T_Alignment &alignment) {
- CmpAlignment cmpAln;
- ReadAlignment(alignmentIndex, cmpAln);
-
- string refSequence;
- string readSequence;
- readSequence.resize(cmpAln.alignmentArray.size());
- refSequence.resize(cmpAln.alignmentArray.size());
-
- ByteAlignmentToQueryString(&cmpAln.alignmentArray[0], cmpAln.alignmentArray.size(), &readSequence[0]);
- ByteAlignmentToRefString(&cmpAln.alignmentArray[0], cmpAln.alignmentArray.size(), &refSequence[0]);
- string ungappedRead, ungappedRef;
- RemoveGaps(readSequence, ungappedRead);
- RemoveGaps(refSequence, ungappedRef);
-
- GappedStringsToAlignment(readSequence, refSequence, alignment);
- FASTASequence qAlignedSeq, rAlignedSeq;
- qAlignedSeq.seq = (Nucleotide*) &ungappedRead[0];
- qAlignedSeq.length = ungappedRead.size();
- rAlignedSeq.seq = (Nucleotide*) &ungappedRef[0];
- rAlignedSeq.length = ungappedRef.size();
-
- alignment.tAlignedSeq.Copy(rAlignedSeq);
- alignment.qAlignedSeq.Copy(qAlignedSeq);
-
- unsigned int qStart = cmpAln.GetQueryStart();
- unsigned int tStart = cmpAln.GetRefStart();
-
- alignment.tPos = cmpAln.GetRefStart();
- alignment.qPos = cmpAln.GetQueryStart();
- alignment.nIns = cmpAln.GetNInsertions();
- alignment.nDel = cmpAln.GetNDeletions();
- alignment.nMatch = cmpAln.GetNMatch();
- alignment.nMismatch=cmpAln.GetNMismatch();
- alignment.qStrand= 0;
- alignment.tStrand = cmpAln.GetTStrand();
- alignment.pctSimilarity = ((float)alignment.nMatch) / (alignment.nMatch + alignment.nMismatch + alignment.nIns + alignment.nDel);
- alignment.mapQV = cmpAln.GetMapQV();
- }
-
- void ReadAlignmentArray(int alignmentIndex, ByteAlignment &alignmentArray) {
- CmpAlignment cmpAlignment;
- alnInfoGroup.ReadCmpAlignment(alignmentIndex, cmpAlignment);
-
- //
- // Cache some stats about the read, and where it was aligned to.
- //
- int queryStart = cmpAlignment.GetQueryStart();
- int queryEnd = cmpAlignment.GetQueryEnd();
- int refGroupId = cmpAlignment.GetRefGroupId();
- int alnGroupId = cmpAlignment.GetAlnGroupId();
-
- int refGroupIndex = refGroupIdToArrayIndex[refGroupId];
- if (alnGroupIdToReadGroupName.find(alnGroupId) ==
- alnGroupIdToReadGroupName.end()) {
- cout << "INTERNAL ERROR! Could not find read group name for alignment "
- << "group with Id " << alnGroupId << "." << endl;
- assert(0);
- }
- string readGroupName = alnGroupIdToReadGroupName[alnGroupId];
- if (refAlignGroups[refGroupIndex]->experimentNameToIndex.find(readGroupName) ==
- refAlignGroups[refGroupIndex]->experimentNameToIndex.end()) {
- cout << "Internal ERROR! The read group name " << readGroupName << " is specified as part of "
- << " the path in alignment " << alignmentIndex
- << " though it does not exist in the ref align group specified for this alignment." << endl;
- assert(0);
- }
- int readGroupIndex = refAlignGroups[refGroupIndex]->experimentNameToIndex[readGroupName];
-
- HDFCmpExperimentGroup* expGroup = refAlignGroups[refGroupIndex]->readGroups[readGroupIndex];
-
- int offsetBegin = cmpAlignment.GetOffsetBegin();
- int offsetEnd = cmpAlignment.GetOffsetEnd();
-
- int alignedSequenceLength = offsetEnd - offsetBegin;
-
- if (alignedSequenceLength >= 0) {
- alignmentArray.resize(alignedSequenceLength);
- }
- else {
- return;
- }
- //
- // Read the alignment string. All alignments
- //
- refAlignGroups[refGroupIndex]->readGroups[readGroupIndex]->alignmentArray.Read(offsetBegin,
- offsetEnd,
- &alignmentArray[0]);
- }
-
- void ImportReadFromCmpH5(int alignmentIndex, CmpAlignment &cmpAlignment, SMRTSequence &read) {
- alnInfoGroup.ReadCmpAlignment(alignmentIndex, cmpAlignment);
-
- //
- // Cache some stats about the read, and where it was aligned to.
- //
- int queryStart = cmpAlignment.GetQueryStart();
- int queryEnd = cmpAlignment.GetQueryEnd();
- read.holeNumber = cmpAlignment.GetHoleNumber();
- int refGroupId = cmpAlignment.GetRefGroupId();
- int alnGroupId = cmpAlignment.GetAlnGroupId();
- int refGroupIndex = refGroupIdToArrayIndex[refGroupId];
- if (alnGroupIdToReadGroupName.find(alnGroupId) == alnGroupIdToReadGroupName.end()) {
- cout << "INTERNAL ERROR! Could not find read group name for alignment "
- << "group with Id " << alnGroupId << "." << endl;
- assert(0);
- }
- string readGroupName = alnGroupIdToReadGroupName[alnGroupId];
-
- if (refAlignGroups[refGroupIndex]->experimentNameToIndex.find(readGroupName) ==
- refAlignGroups[refGroupIndex]->experimentNameToIndex.end()) {
- cout << "Internal ERROR! The read group name " << readGroupName << " is specified as part of "
- << " the path in alignment " << alignmentIndex
- << " though it does not exist in the ref align group specified for this alignment." << endl;
- assert(0);
- }
-
- int readGroupIndex = refAlignGroups[refGroupIndex]->experimentNameToIndex[readGroupName];
- HDFCmpExperimentGroup* expGroup = refAlignGroups[refGroupIndex]->readGroups[readGroupIndex];
-
- int offsetBegin = cmpAlignment.GetOffsetBegin();
- int offsetEnd = cmpAlignment.GetOffsetEnd();
-
- int alignedSequenceLength = offsetEnd - offsetBegin;
- string alignedSequence;
- string readSequence;
- vector<unsigned char> byteAlignment;
-
- if (alignedSequenceLength >= 0) {
- alignedSequence.resize(alignedSequenceLength);
- byteAlignment.resize(alignedSequenceLength);
- }
-
- //
- // Read the alignment string. All alignments
- //
- refAlignGroups[refGroupIndex]->readGroups[readGroupIndex]->alignmentArray.Read(offsetBegin,
- offsetEnd,
- &byteAlignment[0]);
-
- //
- // Convert to something we can compare easily.
- //
- ByteAlignmentToQueryString(&byteAlignment[0], byteAlignment.size(), &alignedSequence[0]);
-
-
- //
- // Initialize the sequence of the read.
- //
- RemoveGaps(alignedSequence, readSequence);
-
- //
- // Make space for the sequence and all fields.
- //
- read.length = readSequence.size();
- read.Allocate(read.length);
- memcpy(read.seq, readSequence.c_str(), readSequence.size() * sizeof(char));
-
- vector<int> baseToAlignmentMap;
- CreateSequenceToAlignmentMap(byteAlignment, baseToAlignmentMap);
-
- //
- // Read in the quality values
- //
-
-
- vector<unsigned char> storedQVArray;
-
- vector<UChar> qvValues;
- vector<HalfWord> frameValues;
- int length = offsetEnd - offsetBegin;
- qvValues.resize(length);
- frameValues.resize(length);
- int i;
-
-
- if (expGroup->experimentGroup.ContainsObject("QualityValue")) {
- expGroup->qualityValue.Read(offsetBegin, offsetEnd, &qvValues[0]);
- StoreQualityValueFromAlignment(qvValues, baseToAlignmentMap, &read.qual.data[0]);
- int i;
- for (i= 0; i < read.length; i++) {
- assert(read.qual[i] < 100);
- }
- }
-
- if (expGroup->experimentGroup.ContainsObject("InsertionQV")) {
- expGroup->insertionQV.Read(offsetBegin, offsetEnd, &qvValues[0]);
- StoreQualityValueFromAlignment(qvValues, baseToAlignmentMap, &read.insertionQV.data[0]);
- }
-
- if (expGroup->experimentGroup.ContainsObject("SubstitutionQV")) {
- expGroup->substitutionQV.Read(offsetBegin, offsetEnd, &qvValues[0]);
- StoreQualityValueFromAlignment(qvValues, baseToAlignmentMap, &read.substitutionQV.data[0]);
- }
-
- if (expGroup->experimentGroup.ContainsObject("DeletionQV")) {
- expGroup->deletionQV.Read(offsetBegin, offsetEnd, &qvValues[0]);
- StoreQualityValueFromAlignment(qvValues, baseToAlignmentMap, &read.deletionQV.data[0]);
- }
-
- if (expGroup->experimentGroup.ContainsObject("DeletionTag")) {
- vector<char> deletionTagValues;
- deletionTagValues.resize(offsetEnd-offsetBegin);
- expGroup->deletionTag.Read(offsetBegin, offsetEnd, &deletionTagValues[0]);
- StoreQualityValueFromAlignment(deletionTagValues, baseToAlignmentMap, read.deletionTag);
- }
-
- if (expGroup->experimentGroup.ContainsObject("SubstitutionTag")) {
- vector<char> substitutionTagValues;
- substitutionTagValues.resize(offsetEnd-offsetBegin);
- expGroup->substitutionTag.Read(offsetBegin, offsetEnd, &substitutionTagValues[0]);
- StoreQualityValueFromAlignment(substitutionTagValues, baseToAlignmentMap, read.substitutionTag);
- }
-
- if (expGroup->experimentGroup.ContainsObject("PulseIndex")) {
- vector<uint32_t> pulseIndexValues;
- pulseIndexValues.resize(offsetEnd-offsetBegin);
- expGroup->pulseIndex.Read(offsetBegin, offsetEnd, &pulseIndexValues[0]);
- StoreQualityValueFromAlignment(pulseIndexValues, baseToAlignmentMap, read.pulseIndex);
- }
-
- if (expGroup->experimentGroup.ContainsObject("PreBaseFrames")) {
- expGroup->preBaseFrames.Read(offsetBegin, offsetEnd, &frameValues[0]);
- StoreQualityValueFromAlignment(frameValues, baseToAlignmentMap, read.preBaseFrames);
- }
-
- if (expGroup->experimentGroup.ContainsObject("WidthInFrames")) {
- expGroup->widthInFrames.Read(offsetBegin, offsetEnd, &frameValues[0]);
- StoreQualityValueFromAlignment(frameValues, baseToAlignmentMap, read.widthInFrames);
- }
-
- }
-
- void ReadReadGroupPathTable(CmpIndexedStringTable &readGroupPathTable) {
- UInt numElem = readGroupPathTable.ids.size();
- readGroupPathTable.resize(numElem); // resizes all tables
- readGroupPathIdArray.Read(0, numElem, &readGroupPathTable.ids[0]);
- readGroupPathArray.Read(0, numElem, &readGroupPathTable.names[0]);
- readGroupPathTable.StoreArrayIndexMap();
- }
-
- void ReadRefSeqTable(CmpIndexedStringTable &refSeqTable) {
- UInt numElem = refSeqTable.ids.size();
- refSeqTable.resize(numElem);
- refSeqNameIdArray.Read(0, numElem, &refSeqTable.ids[0]);
- refSeqNameArray.Read(0, numElem, &refSeqTable.names[0]);
- refSeqTable.StoreArrayIndexMap();
- }
-
- void ReadMovieNameTable(CmpIndexedStringTable &movieTable) {
- UInt numElem = movieTable.ids.size();
- movieTable.resize(numElem);
- movieNameIdArray.Read(0, numElem, &movieTable.ids[0]);
- movieNameArray.Read(0, numElem, &movieTable.names[0]);
- movieTable.StoreArrayIndexMap();
- }
-
- // Store reference FullName, ID, Length and MD5 to /RefInfo
- unsigned int AddRefInfo(string refName, unsigned int length, string md5) {
- return refInfoGroup.AddRefInfo(refName, length, md5);
- }
-
- unsigned int AddRefGroup(string refName, unsigned int refInfoId,
- string & refGroupName) {
- if (refInfoId > 999999) {
- // ref000001 ~ ref999999
- cout << "ERROR. Could not store more than 999999 references in "
- << " a cmp.h5 file." << endl;
- exit(1);
- }
-
- // Adding a new refGroup requires:
- // 1. Creating a new refgroup name, e.g., /ref000001.
- // 2. Create the new reference group to add alignments to.
- // 3. Adding this new name to the set of paths of ref groups.
- // 4. Adding information for this ref group.
-
- // 1.
- GenerateRefGroupName(refInfoId, refGroupName);
-
- // 2.
- HDFCmpRefAlignmentGroup *newGroup = new HDFCmpRefAlignmentGroup;
- newGroup->Create(rootGroup.rootGroup, refGroupName);
- refAlignGroups.push_back(newGroup);
-
- // 3.
- unsigned int refGroupId = refGroupGroup.AddPath("/" + refGroupName, refInfoId);
-
- // 4.
- refGroupIdToArrayIndex[refGroupId] = refGroupId - 1;
- refNameToArrayIndex[refName] = refGroupId - 1;
-
- return refGroupId;
- }
-
- void GenerateRefGroupName(unsigned int refInfoId, string & name) {
- // In order to mimic the behaviour of compareSequences,
- // refGroupName should equal to ref00000x, where x is refInfoId.
- // (x used to be refGroupIdToArrayIndex.size() + 1)
- stringstream nameStrm;
- nameStrm << "ref";
- nameStrm.width(6);
- nameStrm.fill('0');
- nameStrm << right << refInfoId;
- name = nameStrm.str();
- }
-
-};
-
-#endif
diff --git a/libcpp/hdf/HDFCmpReader.hpp b/libcpp/hdf/HDFCmpReader.hpp
deleted file mode 100644
index f12d2e6..0000000
--- a/libcpp/hdf/HDFCmpReader.hpp
+++ /dev/null
@@ -1,663 +0,0 @@
-#ifndef _BLASR_HDF_CMP_READER_HPP_
-#define _BLASR_HDF_CMP_READER_HPP_
-
-#include "H5Cpp.h"
-#include <iostream>
-#include <assert.h>
-#include "datastructures/alignment/CmpFile.h"
-#include "datastructures/alignment/Alignment.h"
-#include "datastructures/alignment/AlignmentCandidate.h"
-#include "datastructures/alignment/CmpAlignment.h"
-#include "datastructures/alignment/CmpReadGroupTable.h"
-#include "datastructures/alignment/CmpRefSeqTable.h"
-#include "datastructures/alignment/ByteAlignment.h"
-#include "data/hdf/HDFAtom.h"
-#include "data/hdf/HDFArray.h"
-#include "data/hdf/HDF2DArray.h"
-#include "data/hdf/HDFCmpData.h"
-#include "data/hdf/HDFCmpRefAlignmentGroup.h"
-#include "data/hdf/HDFCmpExperimentGroup.h"
-#include "HDFAlnGroupGroup.h"
-#include "HDFAlnInfoGroup.h"
-#include "HDFRefGroupGroup.h"
-#include "HDFRefInfoGroup.h"
-#include "HDFMovieInfoGroup.h"
-#include "HDFCmpRootGroup.h"
-#include "HDFCmpSupportedFields.h"
-#include "SMRTSequence.h"
-#include <sstream>
-#include <map>
-
-using namespace H5;
-using namespace std;
-
-template <typename T_Alignment>
-class HDFCmpReader : public HDFCmpData {
-public:
- map<int,int> movieNameIdToArrayIndex, readGroupPathIdToArrayIndex, refGroupIdToArrayIndex;
- map<string,string> readGroupPathToReadGroup;
- HDFAlnGroupGroup alnGroupGroup;
- HDFAlnInfoGroup alnInfoGroup;
- HDFMovieInfoGroup movieInfoGroup;
- HDFRefGroupGroup refGroupGroup;
- HDFRefInfoGroup refInfoGroup;
- HDFCmpRootGroup<T_Alignment> rootGroup;
- set<string> includedFields;
- HDFCmpSupportedFields supportedFields;
- HDFAtom<string> readTypeAtom;
-
- void AstroInitializeColumnNameMap() {
- CmpAlignmentBase::columnNameToIndex["AlignmentId"] = 0;
- CmpAlignmentBase::columnNameToIndex["ReadGroupId"] = 1;
- CmpAlignmentBase::columnNameToIndex["MovieId"] = 2;
- CmpAlignmentBase::columnNameToIndex["RefSeqId"] = 3;
- CmpAlignmentBase::columnNameToIndex["tStart"] = 4;
- CmpAlignmentBase::columnNameToIndex["tEnd"] = 5;
- CmpAlignmentBase::columnNameToIndex["AlignedStrand"] = 6;
- CmpAlignmentBase::columnNameToIndex["ExpId"] = 7;
- CmpAlignmentBase::columnNameToIndex["RunId"] = 8;
- CmpAlignmentBase::columnNameToIndex["Panel"] = 9;
- CmpAlignmentBase::columnNameToIndex["x"] = 10;
- CmpAlignmentBase::columnNameToIndex["y"] = 11;
- CmpAlignmentBase::columnNameToIndex["SubreadId"] = 12;
- CmpAlignmentBase::columnNameToIndex["rStart"] = 13;
- CmpAlignmentBase::columnNameToIndex["rEnd"] = 14;
- CmpAlignmentBase::columnNameToIndex["Z"] = 15;
- CmpAlignmentBase::columnNameToIndex["nM"] = 16;
- CmpAlignmentBase::columnNameToIndex["nMM"] = 17;
- CmpAlignmentBase::columnNameToIndex["nIns"] = 18;
- CmpAlignmentBase::columnNameToIndex["nDel"] = 19;
- CmpAlignmentBase::columnNameToIndex["offset_begin"] = 20;
- CmpAlignmentBase::columnNameToIndex["offset_end"] = 21;
- }
-
- void SpringfieldInitializeColumnNameMap() {
- CmpAlignmentBase::columnNameToIndex["AlignmentId"] = 0;
- CmpAlignmentBase::columnNameToIndex["ReadGroupId"] = 1;
- CmpAlignmentBase::columnNameToIndex["AlnGroupID"] = 1;
- CmpAlignmentBase::columnNameToIndex["AlnGroupId"] = 1;
- CmpAlignmentBase::columnNameToIndex["MovieId"] = 2;
- CmpAlignmentBase::columnNameToIndex["RefSeqId"] = 3;
- CmpAlignmentBase::columnNameToIndex["tStart"] = 4;
- CmpAlignmentBase::columnNameToIndex["tEnd"] = 5;
- CmpAlignmentBase::columnNameToIndex["RCRefStrand"] = 6;
- CmpAlignmentBase::columnNameToIndex["HoleNumber"] = 7;
- CmpAlignmentBase::columnNameToIndex["SetNumber"] = 8;
- CmpAlignmentBase::columnNameToIndex["StrobeNumber"] = 9;
- CmpAlignmentBase::columnNameToIndex["SubreadId"] = 10;
- CmpAlignmentBase::columnNameToIndex["rStart"] = 11;
- CmpAlignmentBase::columnNameToIndex["rEnd"] = 12;
- CmpAlignmentBase::columnNameToIndex["MapQV"] = 13;
- CmpAlignmentBase::columnNameToIndex["nM"] = 14;
- CmpAlignmentBase::columnNameToIndex["nMM"] = 15;
- CmpAlignmentBase::columnNameToIndex["nIns"] = 16;
- CmpAlignmentBase::columnNameToIndex["nDel"] = 17;
- CmpAlignmentBase::columnNameToIndex["offset_begin"] = 18;
- CmpAlignmentBase::columnNameToIndex["offset_end"] = 19;
- CmpAlignmentBase::columnNameToIndex["nBackRead"] = 20;
- CmpAlignmentBase::columnNameToIndex["nReadOverlap"] = 21;
-
- // All synonyms, the code requiring these should be refactored so
- // that it no synonyms are needed.
- //
- CmpAlignmentBase::columnNameToIndex["AlnID"] = 0;
- CmpAlignmentBase::columnNameToIndex["AlnGroupID"] = 1;
- CmpAlignmentBase::columnNameToIndex["MovieID"] = 2;
- CmpAlignmentBase::columnNameToIndex["RefGroupID"] = 3;
- CmpAlignmentBase::columnNameToIndex["RefGroupId"] = 3;
- CmpAlignmentBase::columnNameToIndex["MoleculeID"] = 10;
- CmpAlignmentBase::columnNameToIndex["Offset_begin"] = 18;
- CmpAlignmentBase::columnNameToIndex["Offset_end"] = 19;
-
- }
-
-
- int Initialize(string &hdfCmpFileName, set<string> includedFieldsP, unsigned int flags=H5F_ACC_RDONLY, const H5::FileAccPropList & fileAccPropList=H5::FileAccPropList::DEFAULT) {
- Initialize(hdfCmpFileName, flags, fileAccPropList);
- includedFields = includedFieldsP;
- }
-
- int Initialize(string &hdfCmpFileName, unsigned int flags=H5F_ACC_RDONLY, const H5::FileAccPropList & fileAccPropList=H5::FileAccPropList::DEFAULT) {
- /*
- * Initialize access to the HDF file.
- */
- try {
- hdfCmpFile.openFile(hdfCmpFileName.c_str(), flags, fileAccPropList);
- }
- catch (Exception &e) {
- cout << e.getDetailMsg() << endl;
- return 0;
- }
-
- rootGroup.Initialize(hdfCmpFile);
- readTypeAtom.Initialize(rootGroup.rootGroup, "ReadType");
-
- if (alnGroupGroup.Initialize(rootGroup.rootGroup) == 0) {
- cout << "ERROR, could not read AlnGroup of the cmp file." << endl;
- exit(1);
- }
- if (refInfoGroup.Initialize(rootGroup.rootGroup) == 0) {
- cout << "ERROR, could not read RefInfo of the cmp file." << endl;
- exit(1);
- }
- if (refGroupGroup.Initialize(rootGroup.rootGroup) == 0) {
- cout << "ERROR, could not read RefGroup of the cmp file." << endl;
- exit(1);
- }
- if (movieInfoGroup.Initialize(rootGroup.rootGroup) == 0) {
- cout << "ERROR, could not read MovieInfo of the cmp file." << endl;
- exit(1);
- }
- if (alnInfoGroup.Initialize(rootGroup.rootGroup) == 0) {
- cout << "ERROR, could not read AlnInfo of the cmp file." << endl;
- exit(1);
- }
- if (fileLogGroup.Initialize(rootGroup.rootGroup) == 0) {
- cout << "ERROR, could not read FileLog of the cmp file." << endl;
- exit(1);
- }
-
- SpringfieldInitializeColumnNameMap();
-
- return 1;
- }
-
- unsigned int GetAlignmentIndexSize() {
- if (alnInfoGroup.alnInfoGroup.groupIsInitialized == false) {
- cout << "ERROR, getting the size of an index before initializing the cmp.h5 file." << endl;
- exit(1);
- }
- return alnInfoGroup.alnIndexArray.GetNRows();
- }
-
- // Add synonym
- unsigned int GetNAlignments() {
- return GetAlignmentIndexSize();
- }
-
- static void ParseReadGroupPath(string &path, string &refName, string &readGroupName){
- int delimPos;
- delimPos = path.find_last_of('/');
- if (delimPos != path.npos) {
- refName = path.substr(0, delimPos);
- //
- // Check the ref name to see if it has a preceeding '/'
- //
- readGroupName = path.substr(delimPos+1, path.size());
- }
- else {
- refName ="";
- readGroupName = "";
- }
- }
-
- void StorePlatformId(CmpFile &cmpFile) {
- //
- // For now, hard wire as a springfield. Later if the fields
- // change per platform, this may be updated.
- //
- cmpFile.platformId = Springfield;
- }
-
- void ReadAlignmentDescriptions(CmpFile &cmpFile) {
-
- //
- // Gather run information.
- //
- rootGroup.ReadAttributes(cmpFile);
-
- string readTypeString;
- readTypeAtom.Read(readTypeString);
- cmpFile.StoreReadType(readTypeString);
- //
- // Read in the groups that describe what alignments are present.
- //
-
- alnGroupGroup.Read(cmpFile.alnGroup);
- alnInfoGroup.Read(cmpFile.alnInfo);
- refGroupGroup.Read(cmpFile.refGroup);
- movieInfoGroup.Read(cmpFile.movieInfo);
- refInfoGroup.Read(cmpFile.refInfo);
- StorePlatformId(cmpFile);
-
- }
-
- void ReadStructure(CmpFile &cmpFile) {
- //
- // Now for every reference group in the cmp file, create a group.
- //
- map<string,int> refNameToArrayIndex;
-
- unsigned int refSeqIndex;
-
- for (refSeqIndex = 0; refSeqIndex < cmpFile.refGroup.path.size(); refSeqIndex++) {
- HDFCmpRefAlignmentGroup* refAlignGroup;
- refAlignGroup = new HDFCmpRefAlignmentGroup;
- refAlignGroup->Initialize(rootGroup.rootGroup.group, cmpFile.refGroup.path[refSeqIndex]);
- int refAlignGroupIndex = refAlignGroups.size();
- refAlignGroups.push_back(refAlignGroup);
- //
- // Allow one to index directly into this group given a string
- // representing the reference name.
- //
- refNameToArrayIndex[cmpFile.refGroup.path[refSeqIndex]] = refAlignGroupIndex;
- refGroupIdToArrayIndex[cmpFile.refGroup.id[refSeqIndex]] = refAlignGroupIndex;
- }
-
- //
- // Now that all ref groups are created, add read groups that
- // are aligned to the ref groups.
- //
- // Note that groups are not necessarily named by movie, especially in
- // a deep-sorted cmp.h5, read groups may look like:
- // /ref00001/rg8953-0
- // /ref00001/rg2453-1
- //
- unsigned int alnGroupIndex;
- for (alnGroupIndex = 0; alnGroupIndex < cmpFile.alnGroup.path.size(); alnGroupIndex++) {
- string refName, readGroupName;
- ParseReadGroupPath(cmpFile.alnGroup.path[alnGroupIndex], refName, readGroupName);
-
- //
- // Create an index that maps alnGroupId (/AlnGroup/Id) to readGroupName
- //
- alnGroupIdToReadGroupName[cmpFile.alnGroup.id[alnGroupIndex]] = readGroupName;
-
- //
- // Look up the group where this alignment should be found.
- //
- unsigned int refGroupArrayIndex;
- if (refNameToArrayIndex.find(refName) != refNameToArrayIndex.end()) {
- refGroupArrayIndex = refNameToArrayIndex[refName];
- }
- else {
- cout << "ERROR! The reference name '" << refName << "' does not have an entry though it is "
- << " specified in the path for " << cmpFile.readGroupTable.names[alnGroupIndex]
- << endl;
- assert(0);
- }
-
- HDFCmpExperimentGroup *alnGroupPtr;
- alnGroupPtr = refAlignGroups[refGroupArrayIndex]->InitializeExperimentGroup(readGroupName, includedFields);
- // experimentNameToIndex should have been set in InitializeExperimentGroup();
- assert( refAlignGroups[refGroupArrayIndex]->experimentNameToIndex[readGroupName]
- == refAlignGroups[refGroupArrayIndex]->readGroups.size()-1);
- refAlignGroups[refGroupArrayIndex]->experimentNameToIndex[readGroupName] = refAlignGroups[refGroupArrayIndex]->readGroups.size()-1;
- }
- }
-
- void Read(CmpFile &cmpFile) {
-
- ReadAlignmentDescriptions(cmpFile);
- ReadStructure(cmpFile);
-
- /*
- * Now that the alignment indices are all read in, read the base-by-base alignments.
- */
-
- unsigned int alignmentIndex;
-
- for (alignmentIndex = 0; alignmentIndex < cmpFile.alnInfo.alignments.size(); alignmentIndex++) {
- unsigned int alnGroupId = cmpFile.alnInfo.alignments[alignmentIndex].GetAlnGroupId();
- unsigned int refGroupId = cmpFile.alnInfo.alignments[alignmentIndex].GetRefGroupId();
- string refSeqName;
-
- //
- // Make sure the refGroupId specified in the alignment index exists in the alignment groups.
- //
- int refGroupArrayIndex;
- if (refGroupIdToArrayIndex.find(refGroupId) == refGroupIdToArrayIndex.end()) {
- cout << "ERROR! Alignment " << cmpFile.alnInfo.alignments[alignmentIndex].GetAlignmentId()
- << " has ref seq id " << refGroupId << " that does not exist in the HDF file." << endl;
- assert(0);
- }
- else {
- refGroupArrayIndex = refGroupIdToArrayIndex[refGroupId];
- }
-
- //
- // Point to the refGroup that this alignment is part of.
- //
- HDFCmpRefAlignmentGroup* refAlignGroup = refAlignGroups[refGroupArrayIndex];
-
- //
- // Now locate the read group that is part of this ref align group.
- //
- string readGroupName = alnGroupIdToReadGroupName[alnGroupId];
-
- if (refAlignGroup->experimentNameToIndex.find(readGroupName) ==
- refAlignGroup->experimentNameToIndex.end()) {
- cout << "Internal ERROR! The read group name " << readGroupName << " is specified as part of "
- << " the path in alignment " << cmpFile.alnInfo.alignments[alignmentIndex].GetAlignmentId()
- << " though it does not exist in the ref align group specified for this alignment." << endl;
- assert(0);
- }
-
- int experimentIndex;
- experimentIndex = refAlignGroup->experimentNameToIndex[readGroupName];
-
- unsigned int alignmentLength = cmpFile.alnInfo.alignments[alignmentIndex].GetOffsetEnd() -
- cmpFile.alnInfo.alignments[alignmentIndex].GetOffsetBegin();
-
- vector<unsigned char> alignmentArray;
- vector<float> fieldArray;
-
- if (alignmentArray.size() < alignmentLength) {
- alignmentArray.resize(alignmentLength);
- }
-
- /*
- * Read in the base by base alignment.
- */
-
- refAlignGroup->readGroups[experimentIndex]->alignmentArray.Read(cmpFile.alnInfo.alignments[alignmentIndex].GetOffsetBegin(),
- cmpFile.alnInfo.alignments[alignmentIndex].GetOffsetEnd(),
- &alignmentArray[0]);
-
- cmpFile.alnInfo.alignments[alignmentIndex].StoreAlignmentArray(&alignmentArray[0], alignmentLength);
-
- /*
- * Read in all additional fields such as quality values, etc..
- */
- set<string>::iterator fieldIt, fieldEnd;
- fieldEnd = includedFields.end();
-
- for (fieldIt = includedFields.begin(); fieldIt != fieldEnd; ++fieldIt) {
- if (fieldArray.size() < alignmentLength) {
- fieldArray.resize(alignmentLength);
- }
- HDFArray<float>* fieldArrayPtr = dynamic_cast<HDFArray<float>* >(refAlignGroup->readGroups[experimentIndex]->fields[*fieldIt]);
-
- int ob = cmpFile.alnInfo.alignments[alignmentIndex].GetOffsetBegin();
- int oe = cmpFile.alnInfo.alignments[alignmentIndex].GetOffsetEnd();
- fieldArrayPtr->Read(ob, oe, &fieldArray[0]);
-
- cmpFile.alnInfo.alignments[alignmentIndex].StoreFloatField(*fieldIt, &fieldArray[0], alignmentLength);
- }
- }
- }
-
- void IncludeField(string fieldName) {
- if (supportedFields.find(fieldName) == supportedFields.end()) {
- cout << "ERROR, attempting to include field " << fieldName << " that is not supported." << endl;
- exit(1);
- }
- includedFields.insert(fieldName);
- }
-
- template<typename T_Value, typename T_QV>
- void StoreQualityValueFromAlignment(vector<T_Value> &fieldValues,
- vector<int> &baseToAlignmentMap,
- T_QV *qv) {
- int i;
- for (i = 0; i < baseToAlignmentMap.size();i++) {
- qv[i] = fieldValues[baseToAlignmentMap[i]];
- }
- }
-
- void ReadAlignment(int alignmentIndex, CmpAlignment &cmpAlignment) {
- alnInfoGroup.ReadCmpAlignment(alignmentIndex, cmpAlignment);
- ReadAlignmentArray(alignmentIndex, cmpAlignment.alignmentArray);
- }
-
- void ReadAlignment(int alignmentIndex, AlignmentCandidate<FASTASequence, FASTASequence> &alignment) {
- CmpAlignment cmpAln;
- ReadAlignment(alignmentIndex, cmpAln);
-
- string refSequence;
- string readSequence;
- readSequence.resize(cmpAln.alignmentArray.size());
- refSequence.resize(cmpAln.alignmentArray.size());
-
- ByteAlignmentToQueryString(&cmpAln.alignmentArray[0], cmpAln.alignmentArray.size(), &readSequence[0]);
- ByteAlignmentToRefString(&cmpAln.alignmentArray[0], cmpAln.alignmentArray.size(), &refSequence[0]);
- string ungappedRead, ungappedRef;
- RemoveGaps(readSequence, ungappedRead);
- RemoveGaps(refSequence, ungappedRef);
-
- GappedStringsToAlignment(readSequence, refSequence, alignment);
- FASTASequence qAlignedSeq, rAlignedSeq;
- qAlignedSeq.seq = (Nucleotide*) &ungappedRead[0];
- qAlignedSeq.length = ungappedRead.size();
- rAlignedSeq.seq = (Nucleotide*) &ungappedRef[0];
- rAlignedSeq.length = ungappedRef.size();
-
- alignment.tAlignedSeq.Copy(rAlignedSeq);
- alignment.qAlignedSeq.Copy(qAlignedSeq);
-
- unsigned int qStart = cmpAln.GetQueryStart();
- unsigned int tStart = cmpAln.GetRefStart();
-
- alignment.tPos = cmpAln.GetRefStart();
- alignment.qPos = cmpAln.GetQueryStart();
- alignment.nIns = cmpAln.GetNInsertions();
- alignment.nDel = cmpAln.GetNDeletions();
- alignment.nMatch = cmpAln.GetNMatch();
- alignment.nMismatch=cmpAln.GetNMismatch();
- alignment.qStrand= 0;
- alignment.tStrand = cmpAln.GetTStrand();
- alignment.pctSimilarity = ((float)alignment.nMatch) / (alignment.nMatch + alignment.nMismatch + alignment.nIns + alignment.nDel);
- alignment.mapQV = cmpAln.GetMapQV();
- }
-
- void ReadAlignmentArray(int alignmentIndex, ByteAlignment &alignmentArray) {
- CmpAlignment cmpAlignment;
- alnInfoGroup.ReadCmpAlignment(alignmentIndex, cmpAlignment);
-
- //
- // Cache some stats about the read, and where it was aligned to.
- //
- int queryStart = cmpAlignment.GetQueryStart();
- int queryEnd = cmpAlignment.GetQueryEnd();
- int refGroupId = cmpAlignment.GetRefGroupId();
- int alnGroupId = cmpAlignment.GetAlnGroupId();
-
- int refGroupIndex = refGroupIdToArrayIndex[refGroupId];
- if (alnGroupIdToReadGroupName.find(alnGroupId) ==
- alnGroupIdToReadGroupName.end()) {
- cout << "INTERNAL ERROR! Could not find read group name for alignment "
- << "group with Id " << alnGroupId << "." << endl;
- assert(0);
- }
- string readGroupName = alnGroupIdToReadGroupName[alnGroupId];
- if (refAlignGroups[refGroupIndex]->experimentNameToIndex.find(readGroupName) ==
- refAlignGroups[refGroupIndex]->experimentNameToIndex.end()) {
- cout << "Internal ERROR! The read group name " << readGroupName << " is specified as part of "
- << " the path in alignment " << alignmentIndex
- << " though it does not exist in the ref align group specified for this alignment." << endl;
- assert(0);
- }
- int readGroupIndex = refAlignGroups[refGroupIndex]->experimentNameToIndex[readGroupName];
-
- HDFCmpExperimentGroup* expGroup = refAlignGroups[refGroupIndex]->readGroups[readGroupIndex];
-
- int offsetBegin = cmpAlignment.GetOffsetBegin();
- int offsetEnd = cmpAlignment.GetOffsetEnd();
-
- int alignedSequenceLength = offsetEnd - offsetBegin;
-
- if (alignedSequenceLength >= 0) {
- alignmentArray.resize(alignedSequenceLength);
- }
- else {
- return;
- }
- //
- // Read the alignment string. All alignments
- //
- refAlignGroups[refGroupIndex]->readGroups[readGroupIndex]->alignmentArray.Read(offsetBegin,
- offsetEnd,
- &alignmentArray[0]);
- }
-
- void ImportReadFromCmpH5(int alignmentIndex, SMRTSequence &read) {
- CmpAlignment cmpAlignment;
- alnInfoGroup.ReadCmpAlignment(alignmentIndex, cmpAlignment);
-
- //
- // Cache some stats about the read, and where it was aligned to.
- //
- int queryStart = cmpAlignment.GetQueryStart();
- int queryEnd = cmpAlignment.GetQueryEnd();
- read.holeNumber = cmpAlignment.GetHoleNumber();
- int refGroupId = cmpAlignment.GetRefGroupId();
- int alnGroupId = cmpAlignment.GetAlnGroupId();
- int refGroupIndex = refGroupIdToArrayIndex[refGroupId];
- if (alnGroupIdToReadGroupName.find(alnGroupId) == alnGroupIdToReadGroupName.end()) {
- cout << "INTERNAL ERROR! Could not find read group name for alignment "
- << "group with Id " << alnGroupId << "." << endl;
- assert(0);
- }
- string readGroupName = alnGroupIdToReadGroupName[alnGroupId];
-
- if (refAlignGroups[refGroupIndex]->experimentNameToIndex.find(readGroupName) ==
- refAlignGroups[refGroupIndex]->experimentNameToIndex.end()) {
- cout << "Internal ERROR! The read group name " << readGroupName << " is specified as part of "
- << " the path in alignment " << alignmentIndex
- << " though it does not exist in the ref align group specified for this alignment." << endl;
- assert(0);
- }
-
- int readGroupIndex = refAlignGroups[refGroupIndex]->experimentNameToIndex[readGroupName];
- HDFCmpExperimentGroup* expGroup = refAlignGroups[refGroupIndex]->readGroups[readGroupIndex];
-
- int offsetBegin = cmpAlignment.GetOffsetBegin();
- int offsetEnd = cmpAlignment.GetOffsetEnd();
-
- int alignedSequenceLength = offsetEnd - offsetBegin;
- string alignedSequence;
- string readSequence;
- vector<unsigned char> byteAlignment;
-
- if (alignedSequenceLength >= 0) {
- alignedSequence.resize(alignedSequenceLength);
- byteAlignment.resize(alignedSequenceLength);
- }
-
- //
- // Read the alignment string. All alignments
- //
- refAlignGroups[refGroupIndex]->readGroups[readGroupIndex]->alignmentArray.Read(offsetBegin,
- offsetEnd,
- &byteAlignment[0]);
-
- //
- // Convert to something we can compare easily.
- //
- ByteAlignmentToQueryString(&byteAlignment[0], byteAlignment.size(), &alignedSequence[0]);
-
-
- //
- // Initialize the sequence of the read.
- //
- RemoveGaps(alignedSequence, readSequence);
-
- //
- // Make space for the sequence and all fields.
- //
- read.length = readSequence.size();
- read.Allocate(read.length);
- memcpy(read.seq, readSequence.c_str(), readSequence.size() * sizeof(char));
-
- vector<int> baseToAlignmentMap;
- CreateSequenceToAlignmentMap(byteAlignment, baseToAlignmentMap);
-
- //
- // Read in the quality values
- //
-
-
- vector<unsigned char> storedQVArray;
-
- vector<UChar> qvValues;
- vector<HalfWord> frameValues;
- int length = offsetEnd - offsetBegin;
- qvValues.resize(length);
- frameValues.resize(length);
- int i;
-
-
- if (expGroup->experimentGroup.ContainsObject("QualityValue")) {
- expGroup->qualityValue.Read(offsetBegin, offsetEnd, &qvValues[0]);
- StoreQualityValueFromAlignment(qvValues, baseToAlignmentMap, &read.qual.data[0]);
- int i;
- for (i= 0; i < read.length; i++) {
- assert(read.qual[i] < 100);
- }
- }
-
- if (expGroup->experimentGroup.ContainsObject("InsertionQV")) {
- expGroup->insertionQV.Read(offsetBegin, offsetEnd, &qvValues[0]);
- StoreQualityValueFromAlignment(qvValues, baseToAlignmentMap, &read.insertionQV.data[0]);
- }
-
- if (expGroup->experimentGroup.ContainsObject("SubstitutionQV")) {
- expGroup->substitutionQV.Read(offsetBegin, offsetEnd, &qvValues[0]);
- StoreQualityValueFromAlignment(qvValues, baseToAlignmentMap, &read.substitutionQV.data[0]);
- }
-
- if (expGroup->experimentGroup.ContainsObject("DeletionQV")) {
- expGroup->deletionQV.Read(offsetBegin, offsetEnd, &qvValues[0]);
- StoreQualityValueFromAlignment(qvValues, baseToAlignmentMap, &read.deletionQV.data[0]);
- }
-
- if (expGroup->experimentGroup.ContainsObject("DeletionTag")) {
- vector<char> deletionTagValues;
- deletionTagValues.resize(offsetEnd-offsetBegin);
- expGroup->deletionTag.Read(offsetBegin, offsetEnd, &deletionTagValues[0]);
- StoreQualityValueFromAlignment(deletionTagValues, baseToAlignmentMap, read.deletionTag);
- }
-
- if (expGroup->experimentGroup.ContainsObject("SubstitutionTag")) {
- vector<char> substitutionTagValues;
- substitutionTagValues.resize(offsetEnd-offsetBegin);
- expGroup->substitutionTag.Read(offsetBegin, offsetEnd, &substitutionTagValues[0]);
- StoreQualityValueFromAlignment(substitutionTagValues, baseToAlignmentMap, read.substitutionTag);
- }
-
- if (expGroup->experimentGroup.ContainsObject("PulseIndex")) {
- vector<uint32_t> pulseIndexValues;
- pulseIndexValues.resize(offsetEnd-offsetBegin);
- expGroup->pulseIndex.Read(offsetBegin, offsetEnd, &pulseIndexValues[0]);
- StoreQualityValueFromAlignment(pulseIndexValues, baseToAlignmentMap, read.pulseIndex);
- }
-
- if (expGroup->experimentGroup.ContainsObject("PreBaseFrames")) {
- expGroup->preBaseFrames.Read(offsetBegin, offsetEnd, &frameValues[0]);
- StoreQualityValueFromAlignment(frameValues, baseToAlignmentMap, read.preBaseFrames);
- }
-
- if (expGroup->experimentGroup.ContainsObject("WidthInFrames")) {
- expGroup->widthInFrames.Read(offsetBegin, offsetEnd, &frameValues[0]);
- StoreQualityValueFromAlignment(frameValues, baseToAlignmentMap, read.widthInFrames);
- }
-
- }
-
- void ReadReadGroupPathTable(CmpIndexedStringTable &readGroupPathTable) {
- UInt numElem = readGroupPathTable.ids.size();
- readGroupPathTable.resize(numElem); // resizes all tables
- readGroupPathIdArray.Read(0, numElem, &readGroupPathTable.ids[0]);
- readGroupPathArray.Read(0, numElem, &readGroupPathTable.names[0]);
- readGroupPathTable.StoreArrayIndexMap();
- }
-
- void ReadRefSeqTable(CmpIndexedStringTable &refSeqTable) {
- UInt numElem = refSeqTable.ids.size();
- refSeqTable.resize(numElem);
- refSeqNameIdArray.Read(0, numElem, &refSeqTable.ids[0]);
- refSeqNameArray.Read(0, numElem, &refSeqTable.names[0]);
- refSeqTable.StoreArrayIndexMap();
- }
-
- void ReadMovieNameTable(CmpIndexedStringTable &movieTable) {
- UInt numElem = movieTable.ids.size();
- movieTable.resize(numElem);
- movieNameIdArray.Read(0, numElem, &movieTable.ids[0]);
- movieNameArray.Read(0, numElem, &movieTable.names[0]);
- movieTable.StoreArrayIndexMap();
- }
-
-};
-
-#endif
diff --git a/libcpp/hdf/HDFCmpRefAlignmentGroup.hpp b/libcpp/hdf/HDFCmpRefAlignmentGroup.hpp
deleted file mode 100644
index 69650ec..0000000
--- a/libcpp/hdf/HDFCmpRefAlignmentGroup.hpp
+++ /dev/null
@@ -1,102 +0,0 @@
-#ifndef _BLASR_HDF_CMP_REF_ALIGNMENT_GROUP_HPP_
-#define _BLASR_HDF_CMP_REF_ALIGNMENT_GROUP_HPP_
-
-#include <map>
-#include <string>
-#include "H5Cpp.h"
-#include "HDFData.hpp"
-#include "HDFGroup.hpp"
-#include "HDFCmpExperimentGroup.hpp"
-
-using namespace std;
-
-class HDFCmpRefAlignmentGroup {
- public:
- HDFGroup refGroup;
- string refGroupName;
- vector<HDFCmpExperimentGroup*> readGroups;
- HDFAtom<string> annotationStringAtom;
- map<string,int> experimentNameToIndex;
- // A RefAlignmentGroup may contain one or more
- // ExperimentGroups. The following shows a
- // RefAlignmentGroup containing two ExperimentGroups.
- // /ref00001/m121219_103658_42194_c000447032559900001500000112311426_s1_p0
- // /ref00001/m121219_103658_42194_c000447032559900001500000112311426_s2_p0
- //
- // But these ExperimentGroups are not necessarily
- // grouped by movie. For example, the following groups
- // can be seen in deep-sorted cmp.h5
- // /ref00001/rg8953-0
- // /ref00001/rg2453-1
-
- int Initialize(H5::CommonFG &group, string _refGroupName) {
- refGroupName = _refGroupName;
- refGroup.Initialize(group, _refGroupName);
- // annotationStringAtom.Initialize(refGroup.group, "annotationString");
- }
-
- void Create(HDFGroup parent, string refGroupNameP) {
- refGroupName = refGroupNameP;
- parent.AddGroup(refGroupName);
- refGroup.Initialize(parent, refGroupName);
- }
-
- HDFCmpExperimentGroup *GetExperimentGroup(string readGroupName) {
- //
- // In contrast to initialization, only create one group.
- //
- map<string,int>::iterator it = experimentNameToIndex.find(readGroupName);
- if (it != experimentNameToIndex.end()) {
- assert(it->second < readGroups.size());
- return readGroups[it->second];
- }
-
- //
- // Allocate the new group structure
- //
- int newReadGroupIndex = readGroups.size();
- HDFCmpExperimentGroup* readGroupPtr = new HDFCmpExperimentGroup;
- readGroups.push_back(readGroupPtr);
- experimentNameToIndex[readGroupName] = newReadGroupIndex;
-
- //
- // Now add it to the cmp.h5 file.
- //
- if (readGroupPtr->Create(refGroup, readGroupName) == 0) {
- delete readGroupPtr;
- experimentNameToIndex[readGroupName] = -1;
- return NULL;
- }
- return readGroupPtr;
- }
-
- bool ContainsExperimentGroup(string readGroupName) {
- return experimentNameToIndex.find(readGroupName) != experimentNameToIndex.end();
- }
-
- HDFCmpExperimentGroup* InitializeExperimentGroup(string experimentGroupName, set<string> &includedFields) {
- if (refGroup.ContainsObject(experimentGroupName)) {
- HDFCmpExperimentGroup* newGroup = new HDFCmpExperimentGroup;
-
- if (newGroup->Initialize(refGroup, experimentGroupName, includedFields) == 0) {
- cout << "ERROR, could not initialize the exp group." << endl;
- exit(1);
- }
- experimentNameToIndex[experimentGroupName] = readGroups.size();
- readGroups.push_back(newGroup);
- return newGroup;
- }
- else {
- return NULL;
- }
- }
-
-
- HDFCmpExperimentGroup* InitializeExperimentGroup(string experimentGroupName) {
- set<string> EMPTYIncludedFields;
- return InitializeExperimentGroup(experimentGroupName, EMPTYIncludedFields);
- }
-};
-
-
-#endif
diff --git a/libcpp/hdf/HDFCmpRootGroup.hpp b/libcpp/hdf/HDFCmpRootGroup.hpp
deleted file mode 100644
index d84084f..0000000
--- a/libcpp/hdf/HDFCmpRootGroup.hpp
+++ /dev/null
@@ -1,66 +0,0 @@
-#ifndef _BLASR_HDF_CMP_ROOT_GROUP_HPP_
-#define _BLASR_HDF_CMP_ROOT_GROUP_HPP_
-
-#include "HDFAtom.hpp"
-#include "HDF2DArray.hpp"
-#include "datastructures/alignment/CmpFile.hpp"
-template <typename T_Alignment>
-class HDFCmpRootGroup {
- public:
- HDFGroup rootGroup;
- HDFAtom<string> version;
- HDFAtom<string> index;
- HDFAtom<string> readType;
- HDFAtom<string> commandLine;
- HDF2DArray<string> fileLog;
-
- ~HDFCmpRootGroup() {
- rootGroup.Close();
- }
-
- int Initialize(H5::H5File &cmpFile) {
- if (rootGroup.Initialize(cmpFile, "/") == 0) { return 0; }
- if (rootGroup.ContainsObject("Version")) {
- if (version.Initialize(rootGroup.group, "Version") == 0) { return 0; }
- }
- if (rootGroup.ContainsObject("Index")) {
- if (index.Initialize(rootGroup.group, "Index") == 0) { return 0; }
- }
- if (rootGroup.ContainsObject("ReadType")) {
- if (readType.Initialize(rootGroup.group, "ReadType") == 0) { return 0; }
- }
- if (rootGroup.ContainsObject("CommandLine")) {
- if (commandLine.Initialize(rootGroup.group, "CommandLine") == 0) { return 0; }
- }
-
- //
- // For now, disable file log initialization until
- // hdf2darray<string> is tested more thoroughly
- //
- // if (fileLog.Initialize(rootGroup.group, "FileLog") == 0) {
- // return 0;}
- //
- return 1;
- }
-
- void ReadAttributes(CmpFile &cmpFile) {
- if (rootGroup.ContainsObject("Version")) {
- version.Read(cmpFile.version);
- }
- if (rootGroup.ContainsObject("Index")) {
- index.Read(cmpFile.index);
- }
- if (rootGroup.ContainsObject("ReadType")) {
- string readTypeString;
- readType.Read(readTypeString);
- cmpFile.StoreReadType(readTypeString);
- }
- if (rootGroup.ContainsObject("CommandLine")) {
- commandLine.Read(cmpFile.commandLine);
- }
- }
-};
-
-
-
-#endif
diff --git a/libcpp/hdf/HDFCmpSupportedFields.cpp b/libcpp/hdf/HDFCmpSupportedFields.cpp
deleted file mode 100644
index b240d39..0000000
--- a/libcpp/hdf/HDFCmpSupportedFields.cpp
+++ /dev/null
@@ -1,25 +0,0 @@
-#include "HDFCmpSupportedFields.hpp"
-
-HDFCmpSupportedFields::HDFCmpSupportedFields() {
- this->insert("StartTimeOffset");
- this->insert("QualityValue");
- this->insert("IPD");
- this->insert("PreBaseFrames");
- this->insert("DeletionQV");
- this->insert("InsertionQV");
- this->insert("ClassifierQV");
- this->insert("SubstitutionQV");
- this->insert("MergeQV");
- this->insert("Light");
- this->insert("WidthInFrames");
- this->insert("PulseWidth");
- this->insert("StartTime");
- this->insert("pkmid");
- this->insert("pkmax");
- this->insert("pkmean");
- this->insert("pkmean");
- this->insert("SubstitutionTag");
- this->insert("DeletionTag");
- this->insert("PulseIndex");
-
-}
diff --git a/libcpp/hdf/HDFCmpSupportedFields.hpp b/libcpp/hdf/HDFCmpSupportedFields.hpp
deleted file mode 100644
index 8ac0e87..0000000
--- a/libcpp/hdf/HDFCmpSupportedFields.hpp
+++ /dev/null
@@ -1,13 +0,0 @@
-#ifndef _BLASR_CMP_SUPPORTED_FIELDS_HPP_
-#define _BLASR_CMP_SUPPORTED_FIELDS_HPP_
-
-#include <string>
-#include <set>
-
-class HDFCmpSupportedFields : public std::set<std::string> {
-public:
- HDFCmpSupportedFields();
-};
-
-
-#endif
diff --git a/libcpp/hdf/HDFCommonFG.hpp b/libcpp/hdf/HDFCommonFG.hpp
deleted file mode 100644
index 2b859eb..0000000
--- a/libcpp/hdf/HDFCommonFG.hpp
+++ /dev/null
@@ -1,13 +0,0 @@
-#ifndef _BLASR_HDF_COMMON_FG_HPP_
-#define _BLASR_HDF_COMMON_FG_HPP_
-
-
-
-using namespace std;
-using namespace H5;
-
-class HDFCommonFG {
- public:
-
-};
-#endif
diff --git a/libcpp/hdf/HDFConfig.hpp b/libcpp/hdf/HDFConfig.hpp
deleted file mode 100644
index 6dbd24a..0000000
--- a/libcpp/hdf/HDFConfig.hpp
+++ /dev/null
@@ -1,7 +0,0 @@
-#ifndef _BLASR_HDF_CONFIG_HPP_
-#define _BLASR_HDF_CONFIG_HPP_
-
-#define MAX_DIMS 10
-
-
-#endif
diff --git a/libcpp/hdf/HDFData.cpp b/libcpp/hdf/HDFData.cpp
deleted file mode 100644
index 0283992..0000000
--- a/libcpp/hdf/HDFData.cpp
+++ /dev/null
@@ -1,74 +0,0 @@
-#include "HDFData.hpp"
-
-using namespace std;
-using namespace H5;
-
-H5Location* HDFData::GetObject() {
- return &dataset;
-}
-
-HDFData::HDFData(CommonFG* _container, string _datasetName) {
- container = _container;
- datasetName = _datasetName;
- fileDataSpaceInitialized = false;
- isInitialized = false;
-}
-
-HDFData::HDFData() {
- container = NULL;
- fileDataSpaceInitialized = false;
- isInitialized = false;
-}
-
-bool HDFData::IsInitialized() {
- return isInitialized;
-}
-
-//
-// Allow derived classes to be initialized generically.
-//
-int HDFData::Initialize(HDFGroup &parentGroup, const string &datasetName) {
- cout << "ERROR! Only a subclass should call this." << endl;
- exit(1);
-}
-
-int HDFData::BaseInitializeDataset(CommonFG &hdfFile, string _datasetName) {
- dataset = hdfFile.openDataSet(_datasetName.c_str());
- isInitialized = true;
- fileDataSpaceInitialized = true;
- return 1;
-}
-
-int HDFData::InitializeDataset(HDFGroup &group, string _datasetName) {
- return InitializeDataset(group.group, _datasetName);
-}
-
-int HDFData::InitializeDataset(CommonFG &hdfFile, string _datasetName) {
- try {
- datasetName = _datasetName;
- dataset = hdfFile.openDataSet(_datasetName.c_str());
- isInitialized = true;
- fileDataSpaceInitialized = true;
- }
- catch(FileIException &e) {
- cerr << e.getDetailMsg() <<endl;
- return 0;
- }
- catch(GroupIException &e) {
- cerr << e.getDetailMsg() << endl;
- return 0;
- }
- catch(H5::Exception &e) {
- cerr << e.getDetailMsg() << endl;
- return 0;
- }
- return 1;
-}
-
-void HDFData::Close() {
- if (isInitialized) {
- dataspace.close();
- dataset.close();
- isInitialized = false;
- }
-}
diff --git a/libcpp/hdf/HDFData.hpp b/libcpp/hdf/HDFData.hpp
deleted file mode 100644
index 5ca1455..0000000
--- a/libcpp/hdf/HDFData.hpp
+++ /dev/null
@@ -1,52 +0,0 @@
-#ifndef _BLASR_HDF_DATA_HPP_
-#define _BLASR_HDF_DATA_HPP_
-
-#include <string>
-#include "H5Cpp.h"
-#include "HDFConfig.hpp"
-#include "HDFGroup.hpp"
-#include "HDFAttributable.hpp"
-
-class HDFData : public HDFAttributable {
-public:
- H5::DataSet dataset;
- H5::DataSpace dataspace;
- H5::DataSpace sourceSpace, destSpace;
- H5::DataSpace fullSourceSpace;
- bool fileDataSpaceInitialized;
- H5::CommonFG *container;
- std::string datasetName;
- bool isInitialized;
-
- H5::H5Location* GetObject();
-
- HDFData(H5::CommonFG* _container, std::string _datasetName);
-
- HDFData();
-
- bool IsInitialized();
-
- //
- // Allow derived classes to be initialized generically.
- //
- // FIXME(yli): This method and the Initialize methods in
- // subclasses cause compilation warnings under clang. For
- // example, see the discussion here:
- //
- // http://stackoverflow.com/questions/18515183/c-overloaded-virtual-function-warning-by-clang
- //
- // To fix the problem here may require rethinking the initialize
- // method more carefully.
- //
- virtual int Initialize(HDFGroup &parentGroup, const std::string &datasetName);
-
- int BaseInitializeDataset(H5::CommonFG &hdfFile, std::string _datasetName);
-
- int InitializeDataset(HDFGroup &group, std::string _datasetName);
-
- int InitializeDataset(H5::CommonFG &hdfFile, std::string _datasetName);
-
- void Close();
-};
-
-#endif
diff --git a/libcpp/hdf/HDFFile.cpp b/libcpp/hdf/HDFFile.cpp
deleted file mode 100644
index 285b8f6..0000000
--- a/libcpp/hdf/HDFFile.cpp
+++ /dev/null
@@ -1,53 +0,0 @@
-#include "HDFFile.hpp"
-
-using namespace H5;
-using namespace std;
-
-HDFFile::HDFFile() {
-}
-
-//
-// Open a file. By default, if the file already exists, open it in
-// read/write mode. The only other flag that is allowed is
-// H5F_ACC_TRUNC, which will truncate the file to zero size.
-//
-void HDFFile::Open(string fileName, unsigned int flags,
- const FileAccPropList& fileAccPropList) {
-
- assert (flags == H5F_ACC_RDWR || flags == H5F_ACC_TRUNC || flags == H5F_ACC_RDONLY);
- ifstream testIn(fileName.c_str());
- bool fileExists = static_cast<bool>(testIn);
- bool flagsIsNotTrunc = flags != H5F_ACC_TRUNC;
-
- if (fileExists and H5File::isHdf5(fileName.c_str()) and flagsIsNotTrunc) {
- try {
- hdfFile.openFile(fileName.c_str(), flags, fileAccPropList);
- }
- catch (FileIException e) {
- cout << "Error opening file " << fileName << endl;
- exit(1);
- }
- }
- else {
- try {
- //
- // Open a new file with TRUNC permissions, always read/write.
- //
- FileCreatPropList filePropList;
- filePropList.setUserblock(512);
- hdfFile = H5File(fileName.c_str(), H5F_ACC_TRUNC, filePropList);
- }
- catch (FileIException fileException) {
- cout << "Error creating file " << fileName << endl;
- exit(1);
- }
- }
- if (rootGroup.Initialize(hdfFile, "/") != 1) {
- cout << "Error initializing the root group for file " << fileName << endl;
- exit(1);
- }
-}
-
-void HDFFile::Close() {
- hdfFile.close();
-}
diff --git a/libcpp/hdf/HDFFile.hpp b/libcpp/hdf/HDFFile.hpp
deleted file mode 100644
index ae67c3e..0000000
--- a/libcpp/hdf/HDFFile.hpp
+++ /dev/null
@@ -1,32 +0,0 @@
-#ifndef _BLASR_HDF_FILE_HPP_
-#define _BLASR_HDF_FILE_HPP_
-
-#include <iostream>
-#include <string>
-#include <vector>
-#include "H5Cpp.h"
-#include "HDFConfig.hpp"
-#include "HDFGroup.hpp"
-
-class HDFFile {
-public:
- // Make this public for easy access.
- H5::H5File hdfFile;
- HDFGroup rootGroup;
-
- HDFFile();
-
- //
- // Open a file. By default, if the file already exists, open it in
- // read/write mode. The only other flag that is allowed is
- // H5F_ACC_TRUNC, which will truncate the file to zero size.
- //
- void Open(string fileName, unsigned int flags=H5F_ACC_RDWR,
- const H5::FileAccPropList& fileAccPropList=H5::FileAccPropList::DEFAULT);
-
- void Close();
-
-};
-
-
-#endif
diff --git a/libcpp/hdf/HDFFileLogGroup.hpp b/libcpp/hdf/HDFFileLogGroup.hpp
deleted file mode 100644
index caaca07..0000000
--- a/libcpp/hdf/HDFFileLogGroup.hpp
+++ /dev/null
@@ -1,55 +0,0 @@
-#ifndef HDF_FILE_LOG_GROUP_H_
-#define HDF_FILE_LOG_GROUP_H_
-#include "HDFGroup.hpp"
-#include "HDFArray.hpp"
-
-class HDFFileLogGroup {
- public:
- HDFGroup group;
- HDFStringArray commandLineArray;
- HDFStringArray versionArray;
- HDFStringArray timestampArray;
- HDFArray<unsigned int> idArray;
- HDFStringArray logArray;
- HDFStringArray programArray;
-
- int Initialize(HDFGroup &parentGroup) {
- if (group.Initialize(parentGroup.group, "FileLog") == 0) { return 0; }
- int ret = 1;
- ret *= commandLineArray.Initialize(group, "CommandLine");
- ret *= versionArray.Initialize(group, "Version");
- ret *= timestampArray.Initialize(group, "Timestamp");
- ret *= idArray.Initialize(group, "ID");
- ret *= logArray.Initialize(group, "Log");
- ret *= programArray.Initialize(group, "Program");
- return ret;
- }
-
-
- void AddEntry(string command, string log, string program, string timestamp, string version) {
- commandLineArray.Write(&command, 1);
- versionArray.Write(&version, 1);
- timestampArray.Write(×tamp, 1);
- programArray.Write(&program, 1);
- logArray.Write(&log, 1);
-
- unsigned int id = idArray.size();
- id = id + 1;
- idArray.Write(&id, 1);
-
- }
-
- bool Create(HDFGroup &parent) {
- parent.AddGroup("FileLog");
- if (group.Initialize(parent.group, "FileLog") == 0) { return 0; }
- commandLineArray.Create(group, "CommandLine");
- versionArray.Create(group, "Version");
- timestampArray.Create(group, "Timestamp");
- programArray.Create(group, "Program");
- logArray.Create(group, "Log");
- idArray.Create(group, "ID");
- }
-
-};
-
-#endif
diff --git a/libcpp/hdf/HDFGroup.cpp b/libcpp/hdf/HDFGroup.cpp
deleted file mode 100644
index 396943b..0000000
--- a/libcpp/hdf/HDFGroup.cpp
+++ /dev/null
@@ -1,58 +0,0 @@
-#include "HDFGroup.hpp"
-
-using namespace H5;
-using namespace std;
-
-HDFGroup::HDFGroup() : HDFAttributable() {
- groupIsInitialized = false;
-}
-
-void HDFGroup::AddGroup(string groupName) {
- group.createGroup(groupName);
- return;
-}
-
-H5Location* HDFGroup::GetObject() {
- return &group;
-}
-
-int HDFGroup::Initialize(CommonFG &fg, string groupName){
- try {
- group = fg.openGroup(groupName.c_str());
- groupIsInitialized = true;
- return 1;
- }
- catch(FileIException &e) {
- return 0;
- }
- catch(GroupIException &e) {
- return 0;
- }
- catch(Exception &e ) {
- return 0;
- }
- return 1;
-}
-
-int HDFGroup::Initialize(HDFGroup & parentGroup, string groupName) {
- return Initialize(parentGroup.group, groupName);
-}
-
-bool HDFGroup::ContainsObject(string queryObjectName) {
- hsize_t objIdx;
- hsize_t numGroupObjs = group.getNumObjs();
- for (objIdx = 0; objIdx < numGroupObjs; objIdx++) {
- H5std_string groupObjectName;
- groupObjectName = group.getObjnameByIdx(objIdx);
- if (groupObjectName == queryObjectName) {
- return true;
- }
- }
- return false;
-}
-
-void HDFGroup::Close() {
- if (groupIsInitialized) {
- group.close();
- }
-}
diff --git a/libcpp/hdf/HDFGroup.hpp b/libcpp/hdf/HDFGroup.hpp
deleted file mode 100644
index e9f806c..0000000
--- a/libcpp/hdf/HDFGroup.hpp
+++ /dev/null
@@ -1,36 +0,0 @@
-#ifndef _BLASR_HDF_GROUP_HPP_
-#define _BLASR_HDF_GROUP_HPP_
-
-#include <vector>
-#include <iostream>
-#include <string>
-#include <stdlib.h>
-#include "H5Cpp.h"
-#include "HDFAttributable.hpp"
-#include "StringUtils.hpp"
-
-
-class HDFGroup : public HDFAttributable {
-public:
- std::vector<std::string> objectNames;
- std::string objectName;
- H5::Group group;
- bool groupIsInitialized;
-
- HDFGroup();
-
- void AddGroup(std::string groupName);
-
- H5::H5Location* GetObject();
-
- int Initialize(H5::CommonFG& fg, std::string groupName);
-
- int Initialize(HDFGroup& parentGroup, std::string groupName);
-
- bool ContainsObject(std::string queryObjectName);
-
- void Close();
-};
-
-
-#endif
diff --git a/libcpp/hdf/HDFMovieInfoGroup.hpp b/libcpp/hdf/HDFMovieInfoGroup.hpp
deleted file mode 100644
index 988bc95..0000000
--- a/libcpp/hdf/HDFMovieInfoGroup.hpp
+++ /dev/null
@@ -1,79 +0,0 @@
-#ifndef HDF_MOVIE_INFO_GROUP_H_
-#define HDF_MOVIE_INFO_GROUP_H_
-
-#include "HDFGroup.hpp"
-#include "HDFArray.hpp"
-#include "saf/MovieInfo.hpp"
-
-class HDFMovieInfoGroup {
- public:
-
- HDFGroup movieInfoGroup;
- HDFArray<UInt> idArray;
- HDFStringArray nameArray;
-
- HDFStringArray whenStartedArray;
- HDFArray<float> frameRateArray;
-
- ~HDFMovieInfoGroup() {
- movieInfoGroup.Close();
- }
-
- bool Create(HDFGroup &parentGroup) {
- parentGroup.AddGroup("MovieInfo");
- if (movieInfoGroup.Initialize(parentGroup.group, "MovieInfo") == 0) { return 0; }
- idArray.Create(movieInfoGroup, "ID");
- nameArray.Create(movieInfoGroup, "Name");
- return true;
- }
-
- int Initialize(HDFGroup &parentGroup) {
- if (movieInfoGroup.Initialize(parentGroup.group, "MovieInfo") == 0) { return 0; }
- if (idArray.Initialize(movieInfoGroup, "ID") == 0) { return 0; }
- if (nameArray.Initialize(movieInfoGroup, "Name") == 0) { return 0; }
- return 1;
- }
-
- void Read(MovieInfo &movieInfo) {
- int nId = idArray.arrayLength;
- movieInfo.id.resize(nId);
- idArray.Read(0, nId, &movieInfo.id[0]);
-
- int nName = nameArray.arrayLength;
- movieInfo.name.resize(nName);
- int i;
- for (i = 0; i < nName; i++ ){
- nameArray.Read(i,i+1,&movieInfo.name[i]);
- }
- }
-
- int AddMovie(string &movieName) {
- nameArray.Write(&movieName, 1);
- unsigned int id = nameArray.size();
- idArray.Write(&id, 1);
- return id;
- }
-
- void StoreFrameRate(int movieIndex, float frameRate) {
- if (movieIndex < 0) {
- cout << "ERROR. Invalid movie index " << movieIndex << endl;
- exit(1);
- }
-
- if (!frameRateArray.IsInitialized()) {
- if (!movieInfoGroup.ContainsObject("FrameRate")) {
- frameRateArray.Create(movieInfoGroup, "FrameRate");
- }
- else {
- frameRateArray.Initialize(movieInfoGroup, "FrameRate");
- }
- }
- frameRateArray.WriteToPos(&frameRate, 1, movieIndex);
- }
-
-};
-
-
-
-
-#endif
diff --git a/libcpp/hdf/HDFNewBasReader.cpp b/libcpp/hdf/HDFNewBasReader.cpp
deleted file mode 100644
index 14ddc3a..0000000
--- a/libcpp/hdf/HDFNewBasReader.cpp
+++ /dev/null
@@ -1,72 +0,0 @@
-#include "HDFNewBasReader.hpp"
-
-int
-HDFNewBasReader::Initialize (const std::string & hdfBasFileName) {
- //
- // Initialize access to the HDF file. For reading bas files, this
- // involves:
- // - Opening the h5 file, and initializing the rootGroup.
- //
- try {
- H5::Exception::dontPrint();
- hdfBasFile.openFile(hdfBasFileName.c_str(),
- H5F_ACC_RDONLY);
- } catch (H5::Exception &e) {
- std::cout << "ERROR, could not open bas.h5 file" << hdfBasFileName
- << ", exiting." << std::endl;
- return 0;
- }
-
- if (rootGroup.Initialize(hdfBasFile, "/") == 0) {
- return 0;
- }
- // If /MultiPart/Parts exists, initialize and return 1;
- // otherwise, return 0
- if (rootGroup.ContainsObject("MultiPart") and
- multiPartGroup.Initialize(rootGroup.group, "MultiPart") != 0) {
- if (multiPartGroup.ContainsObject("Parts") and
- partsArray.InitializeForReading(multiPartGroup, "Parts") != 0) {
- basFileName = hdfBasFileName;
- return 1; // Success
- }
- }
- return 0; // Fail
-}
-
-std::vector<std::string>
-HDFNewBasReader::GetBaxMovieNames() {
- // Read bax.h5 names from /MultiPart/Parts, not including path prefix.
- // e.g., m...._s1_p0.1.bax.h5
- std::vector<std::string> baxNames;
- baxNames.resize(BAXPERBAS); // 3 bax files per bas file.
- for (int i = 0; i < BAXPERBAS; i++) {
- partsArray.Read(i, i+1, &baxNames[i]);
- }
- return baxNames;
-}
-
-std::vector<std::string>
-HDFNewBasReader::GetBaxFileNames() {
- // Get full paths to bax.h5 files,
- // e.g., /mnt/data3/vol53/2450598/0001/Analysis_Results/m..._s1_p0.1.bax.h5
- // Assumption: bax.h5 files are in the same directory as bas.h5.
- std::string prefix = "";
- size_t slashPos = basFileName.rfind("/");
- if (slashPos != std::string::npos) {
- prefix = basFileName.substr(0, slashPos + 1);
- }
- std::vector<std::string> baxNames = GetBaxMovieNames();
- for (int i = 0; i < int(baxNames.size()); i++) {
- baxNames[i] = prefix + baxNames[i];
- }
- return baxNames;
-}
-
-void
-HDFNewBasReader::Close() {
- partsArray.Close();
- multiPartGroup.Close();
- rootGroup.Close();
- hdfBasFile.close();
- basFileName = "";
-}
diff --git a/libcpp/hdf/HDFNewBasReader.hpp b/libcpp/hdf/HDFNewBasReader.hpp
deleted file mode 100644
index 4992cff..0000000
--- a/libcpp/hdf/HDFNewBasReader.hpp
+++ /dev/null
@@ -1,39 +0,0 @@
-#ifndef _BLASR_HDF_NEW_BAS_READER_HPP_
-#define _BLASR_HDF_NEW_BAS_READER_HPP_
-
-#include <stdlib.h>
-#include <sstream>
-#include <vector>
-
-#include "HDFArray.hpp"
-#include "HDFGroup.hpp"
-
-const int BAXPERBAS = 3; // Number of bax files per base file.
-
-class HDFNewBasReader {
-// The new bas.h5 file contains:
-// /MultiPart group,
-// /MultiPart/HoleLookup Dataset (which is ignored), and
-// /MultiPart/Parts Dataset.
-public:
- H5::H5File hdfBasFile;
- HDFGroup rootGroup;
- HDFGroup multiPartGroup;
- //HDFArray<std::string> partsArray;
- HDFStringArray partsArray;
- std::string basFileName;
-
- HDFNewBasReader() {
- basFileName = "";
- }
-
- int Initialize (const std::string & hdfBasFileName);
-
- std::vector<std::string> GetBaxMovieNames();
-
- std::vector<std::string> GetBaxFileNames();
-
- void Close();
-};
-
-#endif
diff --git a/libcpp/hdf/HDFPlsReader.hpp b/libcpp/hdf/HDFPlsReader.hpp
deleted file mode 100644
index 750be08..0000000
--- a/libcpp/hdf/HDFPlsReader.hpp
+++ /dev/null
@@ -1,542 +0,0 @@
-#ifndef _BLASR_HDF_PLS_READER_HPP_
-#define _BLASR_HDF_PLS_READER_HPP_
-
-#include "HDFArray.hpp"
-#include "HDF2DArray.hpp"
-#include "HDFAtom.hpp"
-#include "HDFGroup.hpp"
-#include "HDFBasReader.hpp"
-#include "HDFPulseDataFile.hpp"
-#include "DatasetCollection.hpp"
-#include "HDFZMWReader.hpp"
-#include "reads/PulseFile.hpp"
-#include "HDFScanDataReader.hpp"
-#include "FASTQSequence.hpp"
-#include "VectorUtils.hpp"
-#include <sstream>
-#include <vector>
-#include <set>
-using namespace H5;
-using namespace std;
-/*
- * Interface for reading pulse information from a .pls.h5 file.
- * To read both pls and bas information, use the HDFBasReader.
- */
-
-class HDFPlsReader : public DatasetCollection, public HDFPulseDataFile {
- DNALength curPos;
- int curRead;
-
- HDFGroup pulseCallsGroup;
-
- int meanSignalNDims, midSignalNDims, maxSignalNDims;
-
- HDF2DArray<uint16_t> meanSignalMatrix;
- HDF2DArray<uint16_t> midSignalMatrix;
- HDF2DArray<uint16_t> maxSignalMatrix;
- HDFArray<uint16_t> meanSignalArray;
- HDFArray<uint16_t> midSignalArray;
- HDFArray<uint16_t> maxSignalArray;
- HDFArray<uint16_t> plsWidthInFramesArray;
- HDFArray<unsigned int> startFrameArray;
- HDFArray<float> classifierQVArray;
-
-
- public:
- HDFPlsReader() : HDFPulseDataFile(), DatasetCollection() {
- fieldNames.push_back("MeanSignal");
- fieldNames.push_back("MidSignal");
- fieldNames.push_back("MaxSignal");
- fieldNames.push_back("StartFrame");
- fieldNames.push_back("ClassifierQV");
- fieldNames.push_back("WidthInFrames");
- fieldNames.push_back("FrameRate");
- fieldNames.push_back("WhenStarted");
- fieldNames.push_back("NumEvent"); // this is read from the zmw, but control it here.
- InitializeAllFields(false);
- }
-
- int InitializeCommon() {
- return 1;
- }
-
- int Initialize(string hdfPlsFileName, const H5::FileAccPropList & fileAccPropList=H5::FileAccPropList::DEFAULT) {
- /*
- * Initialize access to the HDF file.
- */
-
- if (HDFPulseDataFile::Initialize(hdfPlsFileName, fileAccPropList) == 0) {
- return 0;
- }
-
- if (pulseDataGroup.ContainsObject("PulseCalls") == 0 or
- pulseCallsGroup.Initialize(pulseDataGroup.group, "PulseCalls") == 0) {
- return 0;
- }
- zmwReader.Initialize(&pulseCallsGroup);
-
-
- //
- // Initialize arrays for reading. This has been preconfigured to
- //
- if (!InitializePulseGroup()) return 0;
-
- if ( (meanSignalNDims = GetDatasetNDim(pulseCallsGroup.group, "MeanSignal")) == 1) {
- if (!meanSignalArray.Initialize(pulseCallsGroup, "MeanSignal")) return 0;
- }
- else if (meanSignalNDims == 2) {
- if (!meanSignalMatrix.Initialize(pulseCallsGroup, "MeanSignal")) return 0;
- }
-
- if ((midSignalNDims = GetDatasetNDim(pulseCallsGroup.group, "MidSignal")) == 1) {
- if (!midSignalArray.Initialize(pulseCallsGroup, "MidSignal")) return 0;
- }
- else if (midSignalNDims == 2) {
- if (!midSignalMatrix.Initialize(pulseCallsGroup, "MidSignal")) return 0;
- }
-
- if ((maxSignalNDims = GetDatasetNDim(pulseCallsGroup.group, "MaxSignal")) == 1) {
- if (!maxSignalArray.Initialize(pulseCallsGroup, "MaxSignal")) return 0;
- }
- else if (maxSignalNDims == 2) {
- if (!maxSignalMatrix.Initialize(pulseCallsGroup, "MaxSignal")) return 0;
- }
-
- //
- // Astro pulse files may not have the ClassifierQV dataset, check
- // to see if it exists, and then try and initialize it.
- //
- if (pulseCallsGroup.ContainsObject("ClassifierQV")) {
- if (!classifierQVArray.Initialize(pulseCallsGroup, "ClassifierQV")) return 0;
- } else {
- includedFields["ClassifierQV"] = false;
- }
-
- //
- // These are all required fields.
- //
- if (!startFrameArray.Initialize(pulseCallsGroup, "StartFrame")) return 0;
- if (!plsWidthInFramesArray.Initialize(pulseCallsGroup, "WidthInFrames")) return 0;
-
- curRead = 0;
- nReads = zmwReader.numEventArray.arrayLength;
- return 1;
- }
-
- UInt GetStartFrameSize() {
- return startFrameArray.arrayLength;
- }
-
- void GetAllMeanSignal(vector<uint16_t> &meanSignal) {
- if (meanSignalNDims == 1) {
- CheckMemoryAllocation(meanSignalArray.arrayLength, maxAllocNElements, "MeanSignal");
- meanSignal.resize(meanSignalArray.arrayLength);
- meanSignalArray.Read(0, meanSignalArray.arrayLength, &meanSignal[0]);
- }
- else if (meanSignalNDims == 2) {
- CheckMemoryAllocation(meanSignalMatrix.GetNCols() * meanSignalMatrix.GetNRows(), maxAllocNElements, "MeanSignal");
- meanSignal.resize(meanSignalMatrix.GetNCols() * meanSignalMatrix.GetNRows());
- meanSignalMatrix.Read(0, meanSignalMatrix.GetNRows(), &meanSignal[0]);
- }
- }
-
- void GetAllMidSignal(vector<uint16_t> &midSignal) {
- if (midSignalNDims == 1) {
- CheckMemoryAllocation(midSignalArray.arrayLength, maxAllocNElements, "MidSignal");
- midSignal.resize(midSignalArray.arrayLength);
- midSignalArray.Read(0, midSignalArray.arrayLength, &midSignal[0]);
- }
- else if (midSignalNDims == 2) {
- CheckMemoryAllocation(midSignalMatrix.GetNCols() * midSignalMatrix.GetNRows(), maxAllocNElements, "MidSignal");
- midSignal.resize(midSignalMatrix.GetNCols() * midSignalMatrix.GetNRows());
- midSignalMatrix.Read(0, midSignalMatrix.GetNRows(), &midSignal[0]);
- }
- }
-
- void GetAllMaxSignal(vector<uint16_t> &maxSignal) {
- if (maxSignalNDims == 1) {
- CheckMemoryAllocation(maxSignalArray.arrayLength, maxAllocNElements, "MaxSignal");
- maxSignal.resize(maxSignalArray.arrayLength);
- maxSignalArray.Read(0, maxSignalArray.arrayLength, &maxSignal[0]);
- }
- else if (maxSignalNDims == 2) {
- CheckMemoryAllocation(maxSignalMatrix.GetNCols() * maxSignalMatrix.GetNRows(), maxAllocNElements, "MaxSignal");
- maxSignal.resize(maxSignalMatrix.GetNCols() * maxSignalMatrix.GetNRows());
- maxSignalMatrix.Read(0, maxSignalMatrix.GetNRows(), &maxSignal[0]);
- }
- }
-
- void GetAllStartFrames(vector<UInt> &startFrame) {
- CheckMemoryAllocation(startFrameArray.arrayLength, maxAllocNElements, "StartFrame");
- startFrame.resize(startFrameArray.arrayLength);
- startFrameArray.Read(0,startFrameArray.arrayLength, &startFrame[0]);
- }
-
- void GetAllPlsWidthInFrames(vector<uint16_t> &widthInFrames) {
- CheckMemoryAllocation(plsWidthInFramesArray.arrayLength, maxAllocNElements, "WidthInFrames (pulse)");
- widthInFrames.resize(plsWidthInFramesArray.arrayLength);
- plsWidthInFramesArray.Read(0,plsWidthInFramesArray.arrayLength, &widthInFrames[0]);
- }
-
- void GetAllClassifierQV(vector<float> &classifierQV) {
- CheckMemoryAllocation(classifierQVArray.arrayLength, maxAllocNElements, "ClassifierQV (pulse)");
- classifierQV.resize(classifierQVArray.arrayLength);
- classifierQVArray.Read(0, classifierQVArray.arrayLength, &classifierQV[0]);
- }
-
- void GetAllNumEvent(vector<int> &numEvent) {
- CheckMemoryAllocation(zmwReader.numEventArray.arrayLength, maxAllocNElements, "NumEvent (pulse)");
- numEvent.resize(zmwReader.numEventArray.arrayLength);
- zmwReader.numEventArray.Read(0, zmwReader.numEventArray.arrayLength, &numEvent[0]);
- }
-
- // Always call ReadPulseFileInit before calling ReadPulseFile()
- // or ReadField()
- void ReadPulseFileInit(PulseFile & pulseFile) {
- if (scanDataReader.fileHasScanData) {
- scanDataReader.Read(pulseFile.scanData);
- }
- // Get hole numbers in PulseCalls/ZMW/HoleNumber. Note that
- // PulseCalls/ZMW/HoleNumber and BaseCalls/ZMW/HoleNumber are
- // not always identical.
- GetAllHoleNumbers(pulseFile.holeNumbers);
-
- // By default, always get the num event. This is used
- // later to copy reads from the pls file.
- GetAllNumEvent(pulseFile.numEvent);
- assert(pulseFile.holeNumbers.size() == pulseFile.numEvent.size());
- if (pulseFile.numEvent.size() > 0) {
- pulseFile.pulseStartPositions.resize(pulseFile.numEvent.size());
- pulseFile.pulseStartPositions[0] = 0;
- for (int i = 1; i < pulseFile.numEvent.size(); i++) {
- pulseFile.pulseStartPositions[i] = pulseFile.pulseStartPositions[i-1] +
- pulseFile.numEvent[i-1];
- }
- }
- }
-
- void ReadPulseFile(PulseFile &pulseFile) {
- ReadPulseFileInit(pulseFile);
-
- if (includedFields["StartFrame"]) {
- GetAllStartFrames(pulseFile.startFrame);
- }
- if (includedFields["WidthInFrames"]) {
- GetAllPlsWidthInFrames(pulseFile.plsWidthInFrames);
- }
- if (includedFields["MeanSignal"]) {
- GetAllMeanSignal(pulseFile.meanSignal);
- pulseFile.meanSignalNDims = meanSignalNDims;
- }
- if (includedFields["MidSignal"]) {
- GetAllMidSignal(pulseFile.midSignal);
- pulseFile.midSignalNDims = midSignalNDims;
- }
- if (includedFields["MaxSignal"]) {
- GetAllMaxSignal(pulseFile.maxSignal);
- pulseFile.maxSignalNDims = maxSignalNDims;
- }
-
- if (includedFields["ClassifierQV"]) {
- GetAllClassifierQV(pulseFile.classifierQV);
- }
- }
-
- //
- // Return size of the entire field in KB.
- //
- UInt GetFieldSize(const string & field) {
- if (not includedFields[field]) {
- cout << "ERROR, field " << field << " is not included in the pulse file. " << endl;
- exit(1);
- }
- if (field == "StartFrame") {
- return startFrameArray.arrayLength / 1024 * sizeof(unsigned int);
- } else if (field == "WidthInFrames") {
- return plsWidthInFramesArray.arrayLength / 1024 * sizeof (uint16_t);
- } else if (field == "MeanSignal") {
- return meanSignalArray.arrayLength / 1024 * sizeof(uint16_t);
- } else if (field == "MidSignal") {
- return midSignalArray.arrayLength / 1024 * sizeof(uint16_t);
- } else if (field == "MaxSignal") {
- return maxSignalArray.arrayLength / 1024 * sizeof(uint16_t);
- } else if (field == "NumEvent") {
- return zmwReader.numEventArray.arrayLength / 1024 * sizeof (int);
- } else if (field == "ClassifierQV") {
- return classifierQVArray.arrayLength /1024 * sizeof(float);
- } else {
- cout << "ERROR, field [" << field << "] is not supported. " << endl ;
- exit(1);
- }
- }
-
- //
- // Read the entire field to memory
- //
- void ReadField(PulseFile & pulseFile, const string & field) {
- if (not includedFields[field]) {
- cout << "ERROR, field " << field << " is not included in the pulse file. " << endl;
- exit(1);
- }
- if (field == "StartFrame") {
- GetAllStartFrames(pulseFile.startFrame);
- } else if (field == "WidthInFrames") {
- GetAllPlsWidthInFrames(pulseFile.plsWidthInFrames);
- } else if (field == "MeanSignal") {
- GetAllMeanSignal(pulseFile.meanSignal);
- pulseFile.meanSignalNDims = meanSignalNDims;
- } else if (field == "MidSignal") {
- GetAllMidSignal(pulseFile.midSignal);
- pulseFile.midSignalNDims = midSignalNDims;
- } else if (field == "MaxSignal") {
- GetAllMaxSignal(pulseFile.maxSignal);
- pulseFile.maxSignalNDims = maxSignalNDims;
- } else if (field == "NumEvent") {
- GetAllNumEvent(pulseFile.numEvent);
- } else if (field == "ClassifierQV") {
- // GetAllClassifierQV(pulseFile.classifierQV) is equivalent to
- // classifierQVArray.ReadDataset(pulseFile.classifierQV) with
- // memory check
- GetAllClassifierQV(pulseFile.classifierQV);
- } else {
- cout << "ERROR, field [" << field << "] is not supported. " << endl ;
- exit(1);
- }
- }
-
- // Copy a field for a hole
- void CopyFieldAt(PulseFile & pulseFile, const string & field,
- int holeIndex, int * basToPlsIndex,
- void * dest, int destLength, const string & destSequence="") {
-
- Nucleotide * destSeqCopy = NULL;
- if (destSequence != "") {
- destSeqCopy = new Nucleotide[destSequence.size()];
- for(int i = 0 ; i < destSequence.size(); i++) {
- destSeqCopy[i] = (Nucleotide)destSequence[i];
- }
- }
-
- if (not includedFields[field]) {
- cout << "ERROR, field " << field << " is not included in the pulse file. " << endl;
- exit(1);
- }
- UInt pulseStartPos= pulseFile.pulseStartPositions[holeIndex];
-
- if (field == "StartFrame") {
- assert(pulseFile.startFrame.size() > 0 and
- pulseFile.startFrame.size() > pulseStartPos);
- StoreField(pulseFile.startFrame, basToPlsIndex, ((UInt*)dest), destLength);
- } else if (field == "WidthInFrames") {
- assert(pulseFile.plsWidthInFrames.size() > 0 and
- pulseFile.plsWidthInFrames.size() > pulseStartPos);
- StoreField(pulseFile.plsWidthInFrames, basToPlsIndex, (uint16_t*)dest, destLength);
-
- } else if (field == "MeanSignal") {
- assert(pulseFile.meanSignal.size() > 0 and
- pulseFile.meanSignal.size() > pulseStartPos);
- assert(destLength == destSequence.size());
-
- pulseFile.CopySignal((HalfWord*)(&pulseFile.meanSignal[0]),
- meanSignalNDims,
- 0, //basToPlsIndex maps bases to abs pulse positions
- basToPlsIndex,
- destSeqCopy, destLength,
- (HalfWord*)dest);
-
- } else if (field == "MidSignal") {
- assert(pulseFile.midSignal.size() > 0 and
- pulseFile.midSignal.size() > pulseStartPos);
- assert(destLength == destSequence.size());
-
- pulseFile.CopySignal((HalfWord*)(&pulseFile.midSignal[0]),
- midSignalNDims,
- 0, //basToPlsIndex maps bases to abs pulse positions
- basToPlsIndex,
- destSeqCopy, destLength,
- (HalfWord*)dest);
-
- } else if (field == "MaxSignal") {
- assert(pulseFile.maxSignal.size() > 0 and
- pulseFile.maxSignal.size() > pulseStartPos);
- assert(destLength == destSequence.size());
- pulseFile.CopySignal((HalfWord*)(&pulseFile.maxSignal[0]),
- maxSignalNDims,
- 0, //basToPlsIndex maps bases to abs pulse positions
- basToPlsIndex,
- destSeqCopy, destLength,
- (HalfWord*)dest);
-
- } else if (field == "ClassifierQV") {
- assert(pulseFile.classifierQV.size() > 0 and
- pulseFile.classifierQV.size() > pulseStartPos);
- StoreField(pulseFile.classifierQV, basToPlsIndex, (float*)dest, destLength);
-
- } else if (field == "NumEvent") {
- cout << "ERROR, control of copying numEvent should not go here." << endl;
- exit(1);
- } else {
- cout << "ERROR, field [" << field << "] is not supported. " << endl ;
- exit(1);
- }
-
- if (destSeqCopy != NULL) {
- delete [] destSeqCopy;
- }
- }
-
- // Clear memory allocated for the specified field
- void ClearField(PulseFile & pulseFile, const string & field) {
- if (not includedFields[field]) {
- cout << "ERROR, field " << field << " is not included in the pulse file. " << endl;
- exit(1);
- }
- if (field == "StartFrame") {
- ClearMemory(pulseFile.startFrame);
- } else if (field == "WidthInFrames") {
- ClearMemory(pulseFile.plsWidthInFrames);
- } else if (field == "MeanSignal") {
- ClearMemory(pulseFile.meanSignal);
- pulseFile.meanSignalNDims = -1;
- } else if (field == "MidSignal") {
- ClearMemory(pulseFile.midSignal);
- pulseFile.midSignalNDims = -1;
- } else if (field == "MaxSignal") {
- ClearMemory(pulseFile.maxSignal);
- pulseFile.maxSignalNDims = -1;
- } else if (field == "NumEvent") {
- ClearMemory(pulseFile.numEvent);
- } else if (field == "ClassifierQV") {
- ClearMemory(pulseFile.classifierQV);
- } else {
- cout << "ERROR, field [" << field << "] is not supported. " << endl ;
- exit(1);
- }
- }
-
-
- int GetReadAt(int holeNumber, int* &basToPlsIndex, SMRTSequence &read) {
- if (preparedForRandomAccess == false) {
- PrepareForRandomAccess();
- }
- curRead = holeNumber;
- curPos = eventOffset[holeNumber];
- zmwReader.curZMW = holeNumber;
- return GetNextFlattenedToBase(read, basToPlsIndex);
- }
-
- template<typename T_FieldType>
- void StoreField(vector<T_FieldType> &source, int *basToPlsIndex, T_FieldType *dest, int destLength) {
- int i;
- for (i = 0 ; i < destLength; i++) {
- dest[i] = source[basToPlsIndex[i]];
- }
- }
-
- void ReadSignal(string fieldName,
- HDFArray<HalfWord> &signalArray, HDF2DArray<HalfWord> &signalMatrix,
- int plsSeqLength, int nDims,
- Nucleotide *basSeq, int basSeqLength,
- int *basToPlsIndex, HalfWord* dest) {
-
- if (includedFields[fieldName]) {
- vector<HalfWord> signal;
- if (nDims == 2) {
- signal.resize(plsSeqLength * 4);
- signalMatrix.Read(curPos, curPos + plsSeqLength, &signal[0]); // read off one row.
- int i;
- for (i = 0; i < basSeqLength; i++) {
- dest[i] = signal[basToPlsIndex[i]*4 + scanDataReader.baseMap[basSeq[i]]];
- }
- }
- else {
- signal.resize(plsSeqLength);
- signalArray.Read(curPos, curPos + plsSeqLength, &signal[0]);
- int i;
- for (i = 0; i < basSeqLength; i++) {
- dest[i] = signal[basToPlsIndex[i]];
- }
- }
- }
- }
-
- int GetNextFlattenedToBase(SMRTSequence &read, int* basToPlsIndex) {
-
- /*
- * Get the pulse values, but only store values that correspond to called bases.
- * This requires that the read has the read.seq field assigned.
- */
- assert(read.seq != NULL);
- int seqLength;
-
- try{
- //
- // Find out how many pulses are called for this read.
- zmwReader.numEventArray.Read(curRead, curRead+1, &seqLength);
-
- if (includedFields["StartFrame"]) {
- vector<unsigned int> pulseStartFrame;
- pulseStartFrame.resize(seqLength);
- startFrameArray.Read(curPos, curPos + seqLength, &pulseStartFrame[0]);
- if (read.startFrame) {delete [] read.startFrame; read.startFrame = NULL;}
- read.startFrame = new unsigned int[read.length];
- StoreField(pulseStartFrame, basToPlsIndex, read.startFrame, read.length);
- }
-
- if (includedFields["WidthInFrames"]) {
- vector<HalfWord> pulseWidthInFrames;
- pulseWidthInFrames.resize(seqLength);
- plsWidthInFramesArray.Read(curPos, curPos + seqLength, &pulseWidthInFrames[0]);
- if (read.widthInFrames) {delete [] read.widthInFrames; read.widthInFrames = NULL;}
- read.widthInFrames = new HalfWord[read.length];
- StoreField(pulseWidthInFrames, basToPlsIndex, read.widthInFrames, read.length);
- }
-
- if (includedFields["MidSignal"]) {
- if (read.midSignal) {delete [] read.midSignal; read.midSignal = NULL;}
- read.midSignal = new HalfWord[read.length];
- ReadSignal("MidSignal", midSignalArray, midSignalMatrix, seqLength, midSignalNDims,
- read.seq, read.length, basToPlsIndex, read.midSignal);
- }
-
- if (includedFields["MaxSignal"]) {
- if (read.maxSignal) {delete [] read.maxSignal; read.maxSignal = NULL;}
- read.maxSignal = new HalfWord[read.length];
- ReadSignal("MaxSignal", maxSignalArray, maxSignalMatrix, seqLength, maxSignalNDims,
- read.seq, read.length, basToPlsIndex, read.maxSignal);
- }
-
- if (includedFields["MeanSignal"]) {
- if (read.meanSignal) {delete [] read.meanSignal; read.meanSignal = NULL;}
- read.meanSignal = new HalfWord[read.length];
- ReadSignal("MeanSignal", meanSignalArray, meanSignalMatrix, seqLength, meanSignalNDims,
- read.seq, read.length, basToPlsIndex, read.meanSignal);
- }
-
- if (includedFields["ClassifierQV"]) {
- vector<float> pulseClassifierQV;
- pulseClassifierQV.resize(seqLength);
- classifierQVArray.Read(curPos, curPos + seqLength, &pulseClassifierQV[0]);
- if (read.classifierQV) {delete [] read.classifierQV; read.classifierQV = NULL;}
- read.classifierQV = new float[read.length];
- StoreField(pulseClassifierQV, basToPlsIndex, read.classifierQV, read.length);
- }
-
- curRead++;
- curPos += seqLength;
- } catch (DataSetIException e) {
- cout << "ERROR, could not read pulse metrics for SMRTSequence "
- << read.GetName() << endl;
- exit(1);
- }
- return 1;
- }
-
-
- void Close() {
-
- }
-};
-
-
-#endif
diff --git a/libcpp/hdf/HDFPlsWriter.hpp b/libcpp/hdf/HDFPlsWriter.hpp
deleted file mode 100644
index 9efc92b..0000000
--- a/libcpp/hdf/HDFPlsWriter.hpp
+++ /dev/null
@@ -1,195 +0,0 @@
-#ifndef _BLASR_HDF_PLS_WRITER_HPP_
-#define _BLASR_HDF_PLS_WRITER_HPP_
-
-#include "data/hdf/HDFArray.h"
-#include "data/hdf/BufferedHDFArray.h"
-#include "data/hdf/HDF2DArray.h"
-#include "data/hdf/BufferedHDF2DArray.h"
-#include "data/hdf/HDFAtom.h"
-#include "data/hdf/HDFFile.h"
-#include "data/hdf/PlatformId.h"
-#include "utils/SMRTReadUtils.h"
-#include "FASTQSequence.h"
-#include <sstream>
-
-using namespace H5;
-using namespace std;
-
-class HDFPlsWriter {
- HDFFile outFile;
- string hdfFileName;
- string movieName, runCode;
- PlatformId platformId;
- static const int bufferSize = 16;
-
- BufferedHDFArray<int> nElemArray;
- BufferedHDFArray<int> zmwXCoordArray;
- BufferedHDFArray<int> zmwYCoordArray;
- BufferedHDFArray<char> baseArray;
- BufferedHDFArray<unsigned char> qualArray;
-
- /*
- HDFArray<int> nElemArray;
- HDFArray<int> zmwXCoordArray;
- HDFArray<int> zmwYCoordArray;
- HDFArray<char> baseArray;
- HDFArray<unsigned char> qualArray;
- */
- HDFAtom<string> movieNameAtom, runCodeAtom;
-
- //
- // Astro specific arrays.
- //
- BufferedHDF2DArray<uint16_t> holeXY2D;
-
- //
- // Springfield specific arrays.
- //
- BufferedHDFArray<unsigned int> holeNumberArray;
-
- //
- // Define arrays for rich quality values.
- //
-
- BufferedHDFArray<unsigned char> deletionQVArray;
- BufferedHDFArray<unsigned char> deletionTagArray;
- BufferedHDFArray<unsigned char> insertionQVArray;
- BufferedHDFArray<unsigned char> substitutionTagArray;
- BufferedHDFArray<unsigned char> substitutionQVArray;
-
-
- BufferedHDF2DArray<unsigned char> preBaseDeletionQVArray;
- HDFGroup rootGroup;
- Group runInfoGroup;
- Group baseCallGroup;
- Group zmwGroup;
- public:
- ~HDFPlsWriter() {
- nElemArray.Flush();
- zmwXCoordArray.Flush();
- zmwYCoordArray.Flush();
- baseArray.Flush();
- qualArray.Flush();
- deletionQVArray.Flush();
- deletionTagArray.Flush();
- insertionQVArray.Flush();
- substitutionTagArray.Flush();
- substitutionQVArray.Flush();
- holeNumberArray.Flush();
- }
-
- HDFPlsWriter() {
- /*
- * Default to astro for now. This may need to change to a NO_ID
- * platform, in which case it must be set with Initialize().
- */
- platformId = Astro;
- }
- void AddMovieName(string movieName) {
- movieNameAtom.Create(runInfoGroup, "MovieName",movieName);
- }
- /*
- * Initialization without a runCode is implicitly a springfield
- * platform. You can change it if you really want.
- */
- void Initialize(string _hdfFileName, string movieName, PlatformId _platformId = SpringfieldPlatform) {
- Initialize(_hdfFileName, _platformId);
- AddMovieName(movieName);
- }
- void Initialize(string _hdfFileName, string movieName, string runCode, PlatformId _platformId = Astro) {
- Initialize(_hdfFileName, _platformId);
- if (movieName != "" and runCode != "")
- AddRunInfo(movieName, runCode);
- }
-
- void AddRunInfo(string movieName, string runCode) {
- AddMovieName(movieName);
- runCodeAtom.Create(runInfoGroup, "RunCode", runCode);
- }
-
- void Initialize(string _hdfFileName, PlatformId _platformId) {
- hdfFileName = _hdfFileName;
- platformId = _platformId;
- outFile.Create(hdfFileName);
- rootGroup.Initialize(*outFile.hdfFile, "/");
- rootGroup.AddGruop("PulseData");
- rootGroup.AddGroup("PulseData/BaesCalls");
- rootGroup.AddGroup("PulseData/BaseCalls/ZMW");
- rootGroup.AddGroup("ScanData/RunInfo");
- outFile.OpenGroup("ScanData/RunInfo", runInfoGroup);
- outFile.OpenGroup("PulseData/BaseCalls", baseCallGroup);
- outFile.OpenGroup("PulseData/BaseCalls/ZMW", zmwGroup);
-
- nElemArray.Initialize(&zmwGroup, "NumEvent", bufferSize);
- baseArray.Initialize(&baseCallGroup, "Basecall", bufferSize);
- qualArray.Initialize(&baseCallGroup, "QualityValue", bufferSize);
-
- deletionQVArray.Initialize(&baseCallGroup, "DeletionQV", bufferSize);
- deletionTagArray.Initialize(&baseCallGroup, "DeletionTag", bufferSize);
- insertionQVArray.Initialize(&baseCallGroup, "InsertionQV", bufferSize);
- preBaseDeletionQVArray.Initialize(&baseCallGroup, "PreBaseDeletionQV", 4, bufferSize);
- substitutionTagArray.Initialize(&baseCallGroup, "SubstitutionTag", bufferSize);
- substitutionQVArray.Initialize(&baseCallGroup, "SubstitutionQV", bufferSize);
-
- if (platformId == Astro) {
- holeXY2D.Initialize(&zmwGroup, "HoleXY", 2, bufferSize);
- }
- else if (platformId == SpringfieldPlatform) {
- holeNumberArray.Initialize(&zmwGroup, "HoleNumber", bufferSize);
- }
- }
-
- int Write(FASTQSequence &seq) {
- int lenArray[1] = {seq.length};
- nElemArray.Write(lenArray, 1);
- qualArray.Write(seq.qual, seq.length);
- baseArray.Write((const char*) seq.seq, seq.length);
-
- if (seq.deletionQV != NULL) {
- deletionQVArray.Write(seq.deletionQV, seq.length);
- }
- if (seq.preBaseDeletionQV != NULL) {
- DNALength readPos;
- for (readPos = 0; readPos < seq.length; readPos++) {
- preBaseDeletionQVArray.WriteRow(&seq.preBaseDeletionQV[readPos*4], 4);
- }
- }
- if (seq.deletionTag != NULL) {
- deletionTagArray.Write(seq.deletionTag, seq.length);
- }
- if (seq.insertionQV != NULL) {
- insertionQVArray.Write(seq.insertionQV, seq.length);
- }
- if (seq.substitutionQV != NULL) {
- substitutionQVArray.Write(seq.substitutionQV, seq.length);
- }
- if (seq.substitutionTag != NULL) {
- substitutionTagArray.Write(seq.substitutionTag, seq.length);
- }
-
- if (platformId == Astro) {
- // now extract the x an y coordinates.
- int x, y;
- GetSMRTReadCoordinates(seq, x, y);
- uint16_t xy[2] = {(uint16_t) x, (uint16_t) y};
- holeXY2D.WriteRow(xy, 2);
- int holeNumber = 0;
- seq.GetHoleNumber(holeNumber);
- holeNumberArray.Write(&holeNumber, 1);
- }
- else if( platformId == SpringfieldPlatform){
- unsigned int holeNumber;
- GetSpringfieldHoleNumberFromTitle(seq, holeNumber);
- holeNumberArray.Write(&holeNumber, 1);
- }
- // For now say this always works. HDF will choke if a problem
- // happens.
- return 1;
- }
-};
-
-
-
-
-
-#endif
diff --git a/libcpp/hdf/HDFPulseDataFile.cpp b/libcpp/hdf/HDFPulseDataFile.cpp
deleted file mode 100644
index cd88874..0000000
--- a/libcpp/hdf/HDFPulseDataFile.cpp
+++ /dev/null
@@ -1,151 +0,0 @@
-#include "HDFPulseDataFile.hpp"
-
-using namespace std;
-
-int HDFPulseDataFile::GetAllReadLengths(vector<DNALength> &readLengths) {
- nReads = zmwReader.numEventArray.arrayLength;
- readLengths.resize(nReads);
- zmwReader.numEventArray.Read(0,nReads, (int*) &readLengths[0]);
- return readLengths.size();
-}
-
-void HDFPulseDataFile::CheckMemoryAllocation(long allocSize, long allocLimit, const char *fieldName) {
- if (allocSize > allocLimit) {
- if (fieldName == NULL) {
- cout << "Allocating too large of memory" << endl;
- }
- else {
- cout << "Allocate size " << allocSize << " > allocate limit " << allocLimit << endl;
- cout << "ERROR! Reading the dataset " << fieldName << " will use too much memory." << endl;
- cout << "The pls/bas file is too large, exiting." << endl;
- }
- exit(1);
- }
-}
-
-HDFPulseDataFile::HDFPulseDataFile() {
- pulseDataGroupName = "PulseData";
- nReads = 0;
- useScanData = false;
- closeFileOnExit = false;
- maxAllocNElements = INT_MAX;
- preparedForRandomAccess = false;
- rootGroupPtr = NULL;
-}
-
-void HDFPulseDataFile::PrepareForRandomAccess() {
- GetAllReadLengths(eventOffset);
- size_t i;
- int curOffset = 0;
- for (i = 0; i < eventOffset.size(); i++) {
- int curLength = eventOffset[i];
- eventOffset[i] = curOffset;
- curOffset = curOffset + curLength;
- }
- nReads = eventOffset.size();
- preparedForRandomAccess = true;
-}
-
-
-int HDFPulseDataFile::OpenHDFFile(string fileName,
- const H5::FileAccPropList & fileAccPropList) {
-
- try {
- H5::FileAccPropList propList = fileAccPropList;
- H5::Exception::dontPrint();
- hdfBasFile.openFile(fileName.c_str(), H5F_ACC_RDONLY, propList);
- }
- catch (H5::Exception &e) {
- cout << "ERROR, could not open hdf file" << fileName << ", exiting." << endl;
- exit(1);
- }
- closeFileOnExit = true;
- return 1;
-}
-
-//
-// All pulse data files contain the "PulseData" group name.
-//
-//
-int HDFPulseDataFile::InitializePulseDataFile(string fileName,
- const H5::FileAccPropList & fileAccPropList) {
-
- if (OpenHDFFile(fileName, fileAccPropList) == 0) return 0;
- return 1;
-}
-
-int HDFPulseDataFile::Initialize(string fileName,
- const H5::FileAccPropList & fileAccPropList) {
-
- if (InitializePulseDataFile(fileName, fileAccPropList) == 0) {
- return 0;
- }
- //
- // The pulse group is contained directly below the root group.
- //
- if (rootGroup.Initialize(hdfBasFile, "/") == 0) {
- return 0;
- }
- rootGroupPtr = &rootGroup;
- return Initialize();
-}
-
-//
-// Initialize inside another open group.
-//
-int HDFPulseDataFile::Initialize(HDFGroup *rootGroupP) {
- rootGroupPtr = rootGroupP;
- return Initialize();
-}
-
-//
-// Initialize all fields
-//
-int HDFPulseDataFile::Initialize() {
- preparedForRandomAccess = false;
- if (InitializePulseGroup() == 0) return 0;
- if (rootGroupPtr->ContainsObject("ScanData")) {
- if (scanDataReader.Initialize(rootGroupPtr) == 0) {
- return 0;
- }
- else {
- useScanData = true;
- }
- }
- return 1;
-}
-
-int HDFPulseDataFile::InitializePulseGroup() {
- if (pulseDataGroup.Initialize(rootGroupPtr->group, pulseDataGroupName) == 0) return 0;
- return 1;
-}
-
-int HDFPulseDataFile::GetAllHoleNumbers(vector<unsigned int> &holeNumbers) {
- CheckMemoryAllocation(zmwReader.holeNumberArray.arrayLength, maxAllocNElements, "HoleNumbers (base)");
- holeNumbers.resize(nReads);
- zmwReader.holeNumberArray.Read(0,nReads, (unsigned int*)&holeNumbers[0]);
- return holeNumbers.size();
-}
-
-void HDFPulseDataFile::Close() {
- if (useScanData) {
- scanDataReader.Close();
- }
-
- pulseDataGroup.Close();
- if (rootGroupPtr == &rootGroup) {
- rootGroup.Close();
- }
- /*
- cout << "there are " << hdfBasFile.getObjCount(H5F_OBJ_FILE) << " open files upon closing." <<endl;
- cout << "there are " << hdfBasFile.getObjCount(H5F_OBJ_DATASET) << " open datasets upon closing." <<endl;
- cout << "there are " << hdfBasFile.getObjCount(H5F_OBJ_GROUP) << " open groups upon closing." <<endl;
- cout << "there are " << hdfBasFile.getObjCount(H5F_OBJ_DATATYPE) << " open datatypes upon closing." <<endl;
- cout << "there are " << hdfBasFile.getObjCount(H5F_OBJ_ATTR) << " open attributes upon closing." <<endl;
- */
- if (closeFileOnExit) {
- hdfBasFile.close();
- }
-
-
-}
diff --git a/libcpp/hdf/HDFPulseDataFile.hpp b/libcpp/hdf/HDFPulseDataFile.hpp
deleted file mode 100644
index 0cec337..0000000
--- a/libcpp/hdf/HDFPulseDataFile.hpp
+++ /dev/null
@@ -1,67 +0,0 @@
-#ifndef _BLASR_HDF_PULSE_DATA_FILE_HPP_
-#define _BLASR_HDF_PULSE_DATA_FILE_HPP_
-
-#include <string>
-#include <vector>
-#include "H5Cpp.h"
-#include "HDFGroup.hpp"
-#include "HDFZMWReader.hpp"
-#include "HDFScanDataReader.hpp"
-
-class HDFPulseDataFile {
-public:
- H5::H5File hdfBasFile;
- HDFGroup pulseDataGroup;
- HDFGroup rootGroup;
- HDFGroup *rootGroupPtr;
- string pulseDataGroupName;
- HDFScanDataReader scanDataReader;
- bool useScanData;
- bool closeFileOnExit;
- int maxAllocNElements;
- HDFZMWReader zmwReader;
- std::vector<unsigned int> eventOffset;
- int nReads;
- bool preparedForRandomAccess;
-
- int GetAllReadLengths(std::vector<DNALength> &readLengths);
-
- void CheckMemoryAllocation(long allocSize, long allocLimit,
- const char *fieldName = NULL);
-
- HDFPulseDataFile();
-
- void PrepareForRandomAccess();
-
- int OpenHDFFile(std::string fileName,
- const H5::FileAccPropList & fileAccPropList=H5::FileAccPropList::DEFAULT);
-
- //
- // All pulse data files contain the "PulseData" group name.
- //
- //
- int InitializePulseDataFile(std::string fileName,
- const H5::FileAccPropList & fileAccPropList=H5::FileAccPropList::DEFAULT);
-
- int Initialize(std::string fileName,
- const H5::FileAccPropList & fileAccPropList=H5::FileAccPropList::DEFAULT);
-
- //
- // Initialize inside another open group.
- //
- int Initialize(HDFGroup *rootGroupP);
-
- //
- // Initialize all fields
- //
- int Initialize();
-
- int InitializePulseGroup();
-
- int GetAllHoleNumbers(std::vector<unsigned int> &holeNumbers);
-
- void Close();
-
-};
-
-#endif
diff --git a/libcpp/hdf/HDFRefGroupGroup.hpp b/libcpp/hdf/HDFRefGroupGroup.hpp
deleted file mode 100644
index 727b311..0000000
--- a/libcpp/hdf/HDFRefGroupGroup.hpp
+++ /dev/null
@@ -1,65 +0,0 @@
-#ifndef HDF_REF_GROUP_H_
-#define HDF_REF_GROUP_H_
-
-#include "HDFAtom.hpp"
-#include "HDFArray.hpp"
-#include "HDFGroup.hpp"
-#include "saf/RefGroup.hpp"
-
-class HDFRefGroupGroup {
- public:
- HDFGroup refGroup;
- HDFArray<uint32_t> idArray;
- HDFStringArray pathArray;
-
- HDFArray<uint32_t> refInfoIdArray;
-
- ~HDFRefGroupGroup() {
- refGroup.Close();
- }
-
- bool Create(HDFGroup &parent) {
- parent.AddGroup("RefGroup");
- if (refGroup.Initialize(parent.group, "RefGroup") == 0) {
- return 0;
- }
- idArray.Create(refGroup, "ID");
- pathArray.Create(refGroup, "Path");
- refInfoIdArray.Create(refGroup, "RefInfoID");
- return true;
- }
-
- int AddPath(string path, unsigned int refInfoId) {
- pathArray.Write(&path, 1);
- unsigned int numPath = pathArray.size();
- idArray.Write(&numPath, 1);
- refInfoIdArray.Write(&refInfoId, 1);
- return numPath;
- }
-
- int Initialize(HDFGroup &rootGroup) {
- refGroup.Initialize(rootGroup.group, "RefGroup");
-
- if (idArray.Initialize(refGroup, "ID") == 0) { return 0; }
- if (pathArray.Initialize(refGroup, "Path") == 0) { return 0; }
- if (refInfoIdArray.Initialize(refGroup, "RefInfoID") == 0) { return 0; }
-
- return 1;
- }
-
- void Read(RefGroup &refGroup) {
- int pathArrayNElem = pathArray.arrayLength;
- refGroup.path.resize(pathArrayNElem);
- pathArray.Read(0, pathArrayNElem, &refGroup.path[0]);
-
- int idArrayNElem = idArray.arrayLength;
- refGroup.id.resize(idArrayNElem);
- idArray.Read(0, idArrayNElem, &refGroup.id[0]);
-
- int refIDNElem = refInfoIdArray.arrayLength;
- refGroup.refInfoId.resize(refIDNElem);
- refInfoIdArray.Read(0, refIDNElem, &refGroup.refInfoId[0]);
- }
-};
-
-#endif
diff --git a/libcpp/hdf/HDFRefInfoGroup.hpp b/libcpp/hdf/HDFRefInfoGroup.hpp
deleted file mode 100644
index 72a85fe..0000000
--- a/libcpp/hdf/HDFRefInfoGroup.hpp
+++ /dev/null
@@ -1,84 +0,0 @@
-#ifndef _BLASR_HDF_REF_INFO_HPP_
-#define _BLASR_HDF_REF_INFO_HPP_
-
-#include "saf/RefInfo.hpp"
-
-class HDFRefInfoGroup {
- public:
- HDFGroup refInfoGroup;
- HDFStringArray fullNameArray;
- HDFArray<uint32_t> idArray;
- HDFArray<uint32_t> lengthArray;
- HDFStringArray md5Array;
-
- bool Create(HDFGroup &parent) {
- parent.AddGroup("RefInfo");
- if (refInfoGroup.Initialize(parent.group, "RefInfo") == 0) { return 0; }
-
- fullNameArray.Create(refInfoGroup, "FullName");
- idArray.Create(refInfoGroup, "ID");
- lengthArray.Create(refInfoGroup, "Length");
- md5Array.Create(refInfoGroup, "MD5");
- return true;
- }
-
- void AddRefInfo(string &fullName, unsigned int id, unsigned int length, string md5) {
- fullNameArray.Write(&fullName, 1);
- idArray.Write(&id, 1);
- lengthArray.Write(&length, 1);
- md5Array.Write(&md5, 1);
- }
-
-
- unsigned int AddRefInfo(string &fullName, unsigned int length, string md5) {
- unsigned int numRefs = fullNameArray.size();
- unsigned int id = numRefs + 1; // refInfo Id is 1 based
- assert(numRefs == idArray.size() &&
- numRefs == lengthArray.size() &&
- numRefs == md5Array.size());
- AddRefInfo(fullName, id, length, md5);
- return id;
- }
-
- int Initialize(HDFGroup &parentGroup) {
- if (refInfoGroup.Initialize(parentGroup.group, "RefInfo") == 0) { return 0; }
- if (fullNameArray.Initialize(refInfoGroup, "FullName") == 0) { return 0;}
- if (idArray.Initialize(refInfoGroup,"ID") == 0) { return 0;}
- if (lengthArray.Initialize(refInfoGroup, "Length") == 0) { return 0;}
- if (md5Array.Initialize(refInfoGroup, "MD5") == 0) { return 0;}
- return 1;
- }
-
- ~HDFRefInfoGroup() {
- refInfoGroup.Close();
- }
-
- void Read(RefInfo &refInfo) {
- UInt nRow = fullNameArray.size();
- refInfo.fullName.resize(nRow);
- refInfo.id.resize(nRow);
- refInfo.length.resize(nRow);
- refInfo.md5.resize(nRow);
- /*
- if (refInfo.fullName.size() != refInfo.id.size() or
- refInfo.id.size() != refInfo.length.size() or
- refInfo.length.size() != refInfo.md5.size()) {
- cout << "Error with the RefInfo group in a cmp.h5 file. The datasets " << endl
- << "are of different lengths but should be the same." << endl;
- exit(1);
- }
- */
- int i;
- for (i = 0; i < refInfo.fullName.size();i++) {
- fullNameArray.Read(i,i+1,&refInfo.fullName[i]);
- }
- for (i = 0; i < refInfo.md5.size(); i++) {
- md5Array.Read(i, i+1, &refInfo.md5[i]);
- }
- lengthArray.Read(0, refInfo.length.size(), &refInfo.length[0]);
- idArray.Read(0, refInfo.id.size(), &refInfo.id[0]);
- }
-};
-
-
-#endif
diff --git a/libcpp/hdf/HDFRegionTableReader.cpp b/libcpp/hdf/HDFRegionTableReader.cpp
deleted file mode 100644
index 80bc2db..0000000
--- a/libcpp/hdf/HDFRegionTableReader.cpp
+++ /dev/null
@@ -1,149 +0,0 @@
-#include "HDFRegionTableReader.hpp"
-
-using namespace std;
-
-int HDFRegionTableReader::Initialize(string ®ionTableFileName,
- const H5::FileAccPropList & fileAccPropList) {
- /*
- * Initialize access to the HDF file.
- */
- try {
- regionTableFile.Open(regionTableFileName.c_str(), H5F_ACC_RDONLY, fileAccPropList);
- }
- catch (H5::Exception &e) {
- cout << e.getDetailMsg() << endl;
- return 0;
- }
- if (pulseDataGroup.Initialize(regionTableFile.rootGroup, "PulseData") == 0) {
- return 0;
- }
- if (pulseDataGroup.ContainsObject("Regions") == 0) {
- fileContainsRegionTable = false;
- return 0;
- }
- else {
- fileContainsRegionTable = true;
- }
-
- if (regions.Initialize(pulseDataGroup, "Regions") == 0) {
- return 0;
- }
-
- nRows = regions.GetNRows();
-
- if (columnNames.Initialize(regions.dataset, "ColumnNames") == 0) {
- return 0;
- }
- if (regionTypes.Initialize(regions.dataset, "RegionTypes") == 0) {
- return 0;
- }
- if (regionDescriptions.Initialize(regions.dataset, "RegionDescriptions") == 0) {
- return 0;
- }
- if (regionSources.Initialize(regions.dataset, "RegionSources") == 0) {
- return 0;
- }
-
- curRow = 0;
- return 1;
-}
-
-int HDFRegionTableReader::GetNext(RegionAnnotation &annotation) {
- //
- // Bail with no-op if this is the last row.
- //
-
- if (fileContainsRegionTable == false) {
- return 0;
- }
-
- if (curRow == nRows) {
- return 0;
- }
-
- regions.Read(curRow, curRow+1, annotation.row);
- ++curRow;
- return 1;
-}
-
-void HDFRegionTableReader::RegionTypesToMap(RegionTable &table) {
- size_t i;
- table.regionTypeEnums.resize(table.regionTypes.size());
- for (i = 0;i < table.regionTypes.size(); i++) {
- if (table.regionTypes[i] == "GlobalAccuracy") {
- table.regionTypeEnums[i] = GlobalAccuracy;
- }
- else if (table.regionTypes[i] == "HQRegion") {
- table.regionTypeEnums[i] = HQRegion;
- }
- else if (table.regionTypes[i] == "Adapter") {
- table.regionTypeEnums[i] = Adapter;
- }
- else if (table.regionTypes[i] == "Insert") {
- table.regionTypeEnums[i] = Insert;
- }
- else if (table.regionTypes[i] == "Accuracy") {
- table.regionTypeEnums[i] = Insert;
- }
- else if (table.regionTypes[i] == "ArtifactRegion") {
- table.regionTypeEnums[i] = ArtifactRegion;
- }
- else {
- cout << "ERROR! Region Type " << table.regionTypes[i] << " is not supported. Check Enumerations.h" << endl;
- assert(0);
- }
- }
-}
-
-int HDFRegionTableReader::ReadTableAttributes(RegionTable &table) {
- if (fileContainsRegionTable == false) {
- return 0;
- }
- columnNames.Read(table.columnNames);
- regionTypes.Read(table.regionTypes);
- RegionTypesToMap(table);
- regionDescriptions.Read(table.regionDescriptions);
- regionSources.Read(table.regionSources);
- // All ok.
- return 1;
-}
-
-void HDFRegionTableReader::Close() {
- pulseDataGroup.Close();
- regions.Close();
- regionTableFile.Close();
-}
-
-void HDFRegionTableReader::ReadTable(RegionTable &table) {
- if (fileContainsRegionTable == false) {
- return;
- }
- ReadTableAttributes(table);
- table.table.resize(nRows);
- int i = 0;
- while(GetNext(table.table[curRow])) {
- i++;
- }
-}
-
-
-void HDFRegionTableReader::GetMinMaxHoleNumber(UInt &minHole,
- UInt &maxHole) {
- // Hole numbers may not be sorted ascendingly, so do not
- // return the first and last hole numbers as the min and max.
- UInt saveCurRow = curRow;
- curRow = 0;
- bool init = false;
- RegionAnnotation annotation;
- while (GetNext(annotation) == 1) {
- UInt curHole = annotation.GetHoleNumber();
- if (not init) {
- minHole = maxHole = curHole;
- init = true;
- } else {
- minHole = (minHole > curHole)?(curHole):(minHole);
- maxHole = (maxHole < curHole)?(curHole):(maxHole);
- }
- }
- curRow = saveCurRow;
-}
diff --git a/libcpp/hdf/HDFRegionTableReader.hpp b/libcpp/hdf/HDFRegionTableReader.hpp
deleted file mode 100644
index 470cddf..0000000
--- a/libcpp/hdf/HDFRegionTableReader.hpp
+++ /dev/null
@@ -1,47 +0,0 @@
-#ifndef _BLASR_HDF_REGION_TABLE_READER_HPP_
-#define _BLASR_HDF_REGION_TABLE_READER_HPP_
-
-#include <string>
-#include <vector>
-
-#include "H5Cpp.h"
-
-#include "reads/RegionTable.hpp"
-#include "HDFFile.hpp"
-#include "HDFArray.hpp"
-#include "HDF2DArray.hpp"
-#include "HDFAtom.hpp"
-
-
-class HDFRegionTableReader {
-public:
- HDFFile regionTableFile;
- HDFGroup pulseDataGroup;
- HDF2DArray<int> regions;
-
- HDFAtom<std::vector<std::string> > regionTypes;
- HDFAtom<std::vector<std::string> > regionDescriptions;
- HDFAtom<std::vector<std::string> > regionSources;
- HDFAtom<std::vector<std::string> > columnNames;
- int curRow;
- int nRows;
- bool fileContainsRegionTable;
-
- int Initialize(std::string ®ionTableFileName,
- const H5::FileAccPropList & fileAccPropList = H5::FileAccPropList::DEFAULT);
-
- int GetNext(RegionAnnotation &annotation);
-
- void RegionTypesToMap(RegionTable &table);
-
- int ReadTableAttributes(RegionTable &table);
-
- void Close();
-
- void ReadTable(RegionTable &table);
-
- void GetMinMaxHoleNumber(UInt &minHole, UInt &maxHole);
-};
-
-
-#endif
diff --git a/libcpp/hdf/HDFRegionTableWriter.hpp b/libcpp/hdf/HDFRegionTableWriter.hpp
deleted file mode 100644
index f1c38b9..0000000
--- a/libcpp/hdf/HDFRegionTableWriter.hpp
+++ /dev/null
@@ -1,140 +0,0 @@
-#ifndef _BLASR_HDF_REGION_TABLE_WRITER_HPP_
-#define _BLASR_HDF_REGION_TABLE_WRITER_HPP_
-
-#include <string>
-
-#include "Enumerations.h"
-#include "reads/RegionTable.hpp"
-#include "HDFFile.hpp"
-#include "HDFArray.hpp"
-#include "HDF2DArray.hpp"
-#include "HDFAtom.hpp"
-
-
-using namespace H5;
-using namespace std;
-
-
-class HDFRegionTableWriter {
-public:
- HDFFile regionTableFile;
-
- HDF2DArray<int> regions;
- HDFAtom<vector<string> > regionTypes;
- HDFAtom<vector<string> > regionDescriptions;
- HDFAtom<vector<string> > regionSources;
- HDFAtom<vector<string> > columnNames;
- int curRow;
- int nRows;
- HDFGroup *parentGroupPtr, pulseDataGroup;
-
- void CreateGroupStructure() {
-
- regionTableFile.rootGroup.AddGroup("PulseData");
- if (pulseDataGroup.Initialize(regionTableFile.rootGroup, "PulseData") == 0) {
- cout << "Could not create group PulseData. This is a bug." << endl;
- exit(1);
- }
- parentGroupPtr = &pulseDataGroup;
- regions.Initialize(pulseDataGroup, "Regions", RegionAnnotation::NCOLS);
-
- }
-
- int Create(string fileName) {
- H5File newFile(fileName.c_str(), H5F_ACC_TRUNC, FileCreatPropList::DEFAULT, FileAccPropList::DEFAULT);
- regionTableFile.hdfFile.openFile(fileName.c_str(), H5F_ACC_RDWR, H5P_DEFAULT);
- regionTableFile.rootGroup.Initialize(regionTableFile.hdfFile, "/");
- CreateGroupStructure();
- }
-
- HDFRegionTableWriter() {
- curRow = 0;
- nRows = 0;
- parentGroupPtr = NULL;
- }
-
- int Initialize(HDFGroup &parentGroupP) {
- /*
- * Initialize in an existing file.
- */
- parentGroupPtr = &parentGroupP;
- return Initialize();
- }
-
- int Initialize(string ®ionTableFileName,
- const H5::FileAccPropList & fileAccPropList = H5::FileAccPropList::DEFAULT) {
- /*
- * Initialize access to the HDF file.
- */
- try {
- regionTableFile.Open(regionTableFileName, H5F_ACC_TRUNC, fileAccPropList);
- }
- catch (Exception &e) {
- cout << e.getDetailMsg() << endl;
- return 0;
- }
- CreateGroupStructure();
- return 1;
- }
-
- int Initialize() {
-
- if (regions.Initialize(*parentGroupPtr, "Regions", RegionAnnotation::NCOLS) == 0) {
- return 0;
- }
- nRows = regions.GetNRows();
-
-
- curRow = 0;
- return 1;
- }
-
- void Finalize(vector<string> &columnNamesVect,
- vector<string> ®ionTypesVect,
- vector<string> ®ionDescriptionsVect,
- vector<string> ®ionSourcesVect) {
- //
- // Make sure data has been written to the dataset. If not, the
- // dataset will not exist and creating the attributes will fail.
- //
- if (curRow > 0) {
- regionTypes.Create(regions.dataset, "RegionTypes", regionTypesVect);
- columnNames.Create(regions.dataset, "ColumnNames", columnNamesVect);
- regionDescriptions.Create(regions.dataset, "RegionDescriptions", regionDescriptionsVect);
- regionSources.Create(regions.dataset, "RegionSources", regionSourcesVect);
- }
- }
-
- void WriteRows(vector<RegionAnnotation> &annotations) {
- int i;
- for (i = 0; i < annotations.size(); i++) {
- Write(annotations[i]);
- }
- }
-
- int Write(RegionAnnotation &annotation, int at=-1) {
- if (at == -1) {
- regions.WriteRow(annotation.row, annotation.NCOLS);
- ++curRow;
- }
- else {
-
- }
- return 1;
- }
-
- void Close() {
- regions.Close();
- //
- // Check to see if this is external
- //
- if (parentGroupPtr == &pulseDataGroup) {
- pulseDataGroup.Close();
- }
- regionTableFile.rootGroup.Close();
- }
-
-};
-
-
-#endif
diff --git a/libcpp/hdf/HDFSMRTSequenceReader.hpp b/libcpp/hdf/HDFSMRTSequenceReader.hpp
deleted file mode 100644
index 737f19e..0000000
--- a/libcpp/hdf/HDFSMRTSequenceReader.hpp
+++ /dev/null
@@ -1,71 +0,0 @@
-#ifndef _BLASR_HDF_SMRT_SEQUENCE_READER_HPP_
-#define _BLASR_HDF_SMRT_SEQUENCE_READER_HPP_
-
-#include "data/hdf/HDFBasReader.h"
-#include "data/hdf/HDFZMWReader.h"
-#include "SMRTSequence.h"
-
-template<typename T_SMRT_Sequence>
-class HDFSMRTSequenceReader : public HDFBasReader {
- public:
- HDFZMWReader zmwReader;
- bool readQuality;
- int Initialize(string hdfBasFileName, bool _readQuality=true, const H5::FileAccPropList & fileAccProplist=H5::FileAccPropList::DEFAULT) {
- HDFBasReader::Initialize(hdfBasFileName, fileAccPropList);
- zmwReader.Initialize(hdfBasFile);
- readQuality = _readQuality;
- if (baseCallsGroup.ContainsObject("WidthInFrames")) {
- useWidthInFrames = InitializeField(baseCallsGroup, "WidthInFrames");
- }
- if (baseCallsGroup.ContainsObject("PreBaseFrames")) {
- usePreBaseFrames = InitializeField(baseCallsGroup, "PreBaseFrames");
- }
- if (baseCallsGroup.ContainsObject("PulseIndex")) {
- usePulseIndex = InitializeField(baseCallsGroup, "PulseIndex");
- }
-
- }
-
-
- int GetNext(T_SMRT_Sequence &seq) {
- int retVal;
- //
- // Copy the curBasePos from the bas reader since it gets advanced
- // in the GetNext function.
- //
- DNALength curBasePosCopy = curBasePos;
- retVal = HDFBasReader::GetNext(seq);
- //
- // Bail now if the file is already done
- if (retVal == 0) {
- return retVal;
- }
- zmwReader.GetNext(seq.zmwData);
- return retVal;
- }
- int Advance(int nSteps) {
- int retVal;
- retVal = HDFBasReader::Advance(nSteps);
- zmwReader.Advance(nSteps);
- return retVal;
- }
-
-
-};
-
-template<>
-int HDFSMRTSequenceReader<FASTASequence>::GetNext(FASTASequence &seq) {
- int retVal;
- if (readQuality) {
- retVal = HDFBasReader::GetNext(seq);
- }
- //
- // Bail now if the file is already done
- if (retVal == 0) {
- return retVal;
- }
- zmwReader.GetNext(seq.zmwData);
- return retVal;
- }
-
-#endif
diff --git a/libcpp/hdf/HDFScanDataReader.cpp b/libcpp/hdf/HDFScanDataReader.cpp
deleted file mode 100644
index daed4b2..0000000
--- a/libcpp/hdf/HDFScanDataReader.cpp
+++ /dev/null
@@ -1,262 +0,0 @@
-#include "HDFScanDataReader.hpp"
-
-using namespace std;
-
-HDFScanDataReader::HDFScanDataReader() {
- //
- // Assume the file is written without a movie name. This is
- // flipped when a movie name is found.
- //
- Reset();
-}
-
-void HDFScanDataReader::Reset() {
- useMovieName = false;
- useRunCode = false;
- useWhenStarted = false;
- fileHasScanData = false;
- movieName = "";
- runCode = "";
- platformId = NoPlatform;
- initializedAcqParamsGroup = initializedRunInfoGroup = false;
-}
-
-int HDFScanDataReader::InitializeAcqParamsAtoms() {
- if (frameRateAtom.Initialize(acqParamsGroup.group, "FrameRate") == 0) { return 0; }
- if (numFramesAtom.Initialize(acqParamsGroup.group, "NumFrames") == 0) { return 0; }
- if (acqParamsGroup.ContainsAttribute("WhenStarted")) {
- if (whenStartedAtom.Initialize(acqParamsGroup.group, "WhenStarted") == 0) { return 0; }
- useWhenStarted = true;
- }
- return 1;
-}
-
-//
-// This is created on top of a file that is already opened, so
-// instead of initializing by opening a file, it is initialized by
-// passing the root group that should contain the ScanData group.
-// When shutting down, no file handle needs to be closed.
-//
-int HDFScanDataReader::Initialize(HDFGroup *pulseDataGroup) {
-
- //
- // Initiailze groups for reading data.
- //
-
- initializedAcqParamsGroup = false;
- initializedRunInfoGroup = false;
- if (pulseDataGroup->ContainsObject("ScanData") == 0 or
- scanDataGroup.Initialize(pulseDataGroup->group, "ScanData") == 0) {
- return 0;
- }
- fileHasScanData = true;
-
- if (scanDataGroup.ContainsObject("DyeSet") == 0 or
- dyeSetGroup.Initialize(scanDataGroup.group, "DyeSet") == 0) {
- return 0;
- }
-
- if (scanDataGroup.ContainsObject("AcqParams") == 0 or
- acqParamsGroup.Initialize(scanDataGroup.group, "AcqParams") == 0) {
- return 0;
- }
- initializedAcqParamsGroup = true;
-
- if (scanDataGroup.ContainsObject("RunInfo") == 0 or
- runInfoGroup.Initialize(scanDataGroup.group, "RunInfo") == 0) {
- return 0;
- }
- initializedRunInfoGroup = true;
- if (InitializeAcqParamsAtoms() == 0) {
- return 0;
- }
-
- //
- // Read in the data that will be used later on either per read or
- // when the entire bas/pls file is read.
- //
-
- if (ReadPlatformId(platformId) == 0) {
- return 0;
- }
-
- if (runInfoGroup.ContainsAttribute("RunCode") and
- runCodeAtom.Initialize(runInfoGroup, "RunCode")) {
- useRunCode = true;
- }
-
- //
- // Load baseMap which maps bases (ATGC) to channel orders.
- // This should always be present.
- //
- if (LoadBaseMap(baseMap) == 0)
- return 0;
-
- //
- // Attempt to load the movie name. This is not always present.
- //
- LoadMovieName(movieName);
-
- return 1;
-}
-
-string HDFScanDataReader::GetMovieName() {
- // If this object is correctly initialized, movieName
- // is guaranteed to be loaded if it exists, no need to reload.
- return movieName;
-}
-
-string HDFScanDataReader::GetRunCode() {
- return runCode;
-}
-
-int HDFScanDataReader::Read(ScanData &scanData) {
- // All parameters below are required.
- if (ReadPlatformId(scanData.platformId) == 0) return 0;
- LoadMovieName(scanData.movieName);
- LoadBaseMap(scanData.baseMap);
-
- if (useRunCode) {
- runCodeAtom.Read(scanData.runCode);
- }
- frameRateAtom.Read(scanData.frameRate);
- numFramesAtom.Read(scanData.numFrames);
-
- if (useWhenStarted) {
- whenStartedAtom.Read(scanData.whenStarted);
- }
-
- return 1;
-}
-
-void HDFScanDataReader::ReadWhenStarted(string &whenStarted) {
- whenStartedAtom.Read(whenStarted);
-}
-
-PlatformId HDFScanDataReader::GetPlatformId() {
- return platformId;
-}
-
-int HDFScanDataReader::ReadPlatformId(PlatformId &pid) {
- if (runInfoGroup.ContainsAttribute("PlatformId")) {
- if (platformIdAtom.Initialize(runInfoGroup, "PlatformId") == 0) {
- return 0;
- }
- platformIdAtom.Read((unsigned int&)pid);
- }
- else {
- pid = Astro;
- }
- return 1;
-}
-
-int HDFScanDataReader::ReadStringAttribute(std::string & attributeValue,
- const std::string & attributeName, HDFGroup & group,
- HDFAtom<std::string> & atom) {
-
- if (group.ContainsAttribute(attributeName) and
- (atom.isInitialized or atom.Initialize(group, attributeName))) {
- atom.Read(attributeValue);
- return 1;
- } else {
- return 0;
- }
-}
-
-int HDFScanDataReader::ReadBindingKit(std::string &bindingKit)
-{
- return ReadStringAttribute(bindingKit, "BindingKit", runInfoGroup, bindingKitAtom);
-}
-
-int HDFScanDataReader::ReadSequencingKit(std::string &sequencingKit)
-{
- return ReadStringAttribute(sequencingKit, "SequencingKit", runInfoGroup, sequencingKitAtom);
-}
-
-int HDFScanDataReader::LoadMovieName(string &movieNameP) {
- // Groups for building read names
- if (ReadStringAttribute(movieNameP, "MovieName", runInfoGroup, movieNameAtom) == 0) {
- // Internal analysis may manually edit the movie name and set STRSIZE to a value
- // which != movie name length. Handle this case.
- movieNameP = string(movieNameP.c_str());
- return 0;
- } else {
- useMovieName = true;
- int e = movieNameP.size() - 1;
- while (e > 0 and movieNameP[e] == ' ') e--;
- movieNameP = movieNameP.substr(0, e+1);
- movieNameP = string(movieNameP.c_str());
- return 1;
- }
-}
-
-int HDFScanDataReader::LoadBaseMap(map<char, int> & baseMap) {
- // Map bases to channel order in hdf pls file.
- if (dyeSetGroup.ContainsAttribute("BaseMap") and
- baseMapAtom.Initialize(dyeSetGroup, "BaseMap")) {
- string baseMapStr;
- baseMapAtom.Read(baseMapStr);
- if (baseMapStr.size() != 4) {
- cout << "ERROR, there are more than four types of bases "
- << "according to /ScanData/DyeSet/BaseMap." << endl;
- exit(1);
- }
- baseMap.clear();
- for(size_t i = 0; i < baseMapStr.size(); i++) {
- baseMap[toupper(baseMapStr[i])] = i;
- baseMap[tolower(baseMapStr[i])] = i;
- }
- return 1;
- }
- return 0;
-}
-
-void HDFScanDataReader::Close() {
- if (useMovieName) {
- movieNameAtom.dataspace.close();
- }
- if (useRunCode) {
- runCodeAtom.dataspace.close();
- }
- if (useWhenStarted) {
- whenStartedAtom.dataspace.close();
- }
- baseMapAtom.dataspace.close();
- platformIdAtom.dataspace.close();
- frameRateAtom.dataspace.close();
- numFramesAtom.dataspace.close();
- sequencingKitAtom.dataspace.close();
- bindingKitAtom.dataspace.close();
-
- scanDataGroup.Close();
- dyeSetGroup.Close();
- acqParamsGroup.Close();
- runInfoGroup.Close();
- Reset();
-}
-
-
-std::string HDFScanDataReader::GetMovieName_and_Close(std::string & fileName) {
- HDFFile file;
- file.Open(fileName, H5F_ACC_RDONLY);
-
- fileHasScanData = false;
- if (file.rootGroup.ContainsObject("ScanData") == 0 or
- scanDataGroup.Initialize(file.rootGroup, "ScanData") == 0) {
- return "";
- }
- fileHasScanData = true;
-
- initializedRunInfoGroup = false;
- if (scanDataGroup.ContainsObject("RunInfo") == 0 or
- runInfoGroup.Initialize(scanDataGroup.group, "RunInfo") == 0) {
- return "";
- }
- initializedRunInfoGroup = true;
-
- string movieName;
- LoadMovieName(movieName);
- Close();
- file.Close();
- return movieName;
-}
diff --git a/libcpp/hdf/HDFScanDataReader.hpp b/libcpp/hdf/HDFScanDataReader.hpp
deleted file mode 100644
index 7da6649..0000000
--- a/libcpp/hdf/HDFScanDataReader.hpp
+++ /dev/null
@@ -1,101 +0,0 @@
-#ifndef _BLASR_HDF_SCAN_DATA_READER_HPP_
-#define _BLASR_HDF_SCAN_DATA_READER_HPP_
-
-#include <map>
-#include <string>
-#include "Enumerations.h"
-#include "reads/ScanData.hpp"
-#include "HDFGroup.hpp"
-#include "HDFFile.hpp"
-#include "HDFAtom.hpp"
-
-//
-// The SanDataReader cannot live outside
-
-class HDFScanDataReader {
-public:
- bool fileHasScanData, useRunCode;
- HDFGroup scanDataGroup;
- HDFGroup dyeSetGroup;
- HDFGroup acqParamsGroup;
- HDFGroup runInfoGroup;
- bool initializedAcqParamsGroup, initializedRunInfoGroup;
- bool useWhenStarted;
- HDFAtom<std::string> whenStartedAtom;
- HDFAtom<unsigned int> platformIdAtom;
- HDFAtom<float> frameRateAtom;
- HDFAtom<unsigned int> numFramesAtom;
- HDFAtom<std::string> movieNameAtom;
- HDFAtom<std::string> runCodeAtom;
- HDFAtom<std::string> baseMapAtom;
- HDFAtom<std::string> bindingKitAtom;
- HDFAtom<std::string> sequencingKitAtom;
-
- //
- // It is useful to cache the movie name in the reader since this is
- // loaded once upon initialization, and may be fetched when loading
- // reads one at a time.
- //
- bool useMovieName;
- std::string movieName, runCode;
- std::map<char, int> baseMap;
- PlatformId platformId;
-
- HDFScanDataReader();
-
- void Reset();
-
- int InitializeAcqParamsAtoms();
-
- //
- // This is created on top of a file that is already opened, so
- // instead of initializing by opening a file, it is initialized by
- // passing the root group that should contain the ScanData group.
- // When shutting down, no file handle needs to be closed.
- //
- int Initialize(HDFGroup *pulseDataGroup);
-
- std::string GetMovieName();
-
- // Given a PacBio (pls/plx/bas/bax/ccs/rgn).h5 file, which contains its movie
- // name in group /ScanData/RunInfo attribute MovieName, open the file, return
- // its movie name and finally close the file. Return "" if the movie name
- // does not exist. This is a short path to get movie name.
- std::string GetMovieName_and_Close(std::string & fileName);
-
- std::string GetRunCode();
-
- int Read(ScanData &scanData);
-
- void ReadWhenStarted(std::string &whenStarted);
-
- PlatformId GetPlatformId();
-
- int ReadPlatformId(PlatformId &pid);
-
- /// Reads value of Attribute /ScanData/RunInfo/BindingKit
- int ReadBindingKit(std::string &bindingKit);
-
- /// Reads value of Attribute /ScanData/RunInfo/SequencingKit
- int ReadSequencingKit(std::string &sequencingKit);
-
- int LoadMovieName(std::string &movieName);
-
- int LoadBaseMap(map<char, int> & baseMap);
-
- void Close();
-
-private:
- /// Reads value of a string attribute within a HDFGroup.
- /// \returns 1 if succesfully read value of the string attribute, 0 otherwise.
- /// \param[out] attributeValue, value of a string attribute.
- /// \param[in] attributeName, name of the string attribute.
- /// \param[in] group, HDFGroup of the string attribute .
- /// \param[in] atom, initialized HDFAtom obj for reading attribute .
- int ReadStringAttribute(std::string & attributeValue,
- const std::string & attributeName,
- HDFGroup & group, HDFAtom<std::string> & atom);
-
-};
-
-#endif
diff --git a/libcpp/hdf/HDFScanDataWriter.cpp b/libcpp/hdf/HDFScanDataWriter.cpp
deleted file mode 100644
index 874aba0..0000000
--- a/libcpp/hdf/HDFScanDataWriter.cpp
+++ /dev/null
@@ -1,164 +0,0 @@
-#include "HDFScanDataWriter.hpp"
-
-void HDFScanDataWriter::CreateAcqParamsGroup() {
- if (acqParamsGroup.Initialize(scanDataGroup, "AcqParams") == 0) {
- std::cout << "ERROR could not create /ScanData/AcqParams." << std::endl;
- exit(1);
- }
- frameRateAtom.Create(acqParamsGroup.group, "FrameRate");
- numFramesAtom.Create(acqParamsGroup.group, "NumFrames");
- whenStartedAtom.Create(acqParamsGroup.group, "WhenStarted");
-}
-
-void HDFScanDataWriter::CreateDyeSetGroup(){
- if (dyeSetGroup.Initialize(scanDataGroup, "DyeSet") == 0) {
- std::cout << "ERROR could not create /ScanData/DyeSet." << std::endl;
- exit(1);
- }
- baseMapAtom.Create(dyeSetGroup.group, "BaseMap");
- numAnalogAtom.Create(dyeSetGroup.group, "NumAnalog");
-}
-
-void HDFScanDataWriter::CreateRunInfoGroup(){
- if (runInfoGroup.Initialize(scanDataGroup, "RunInfo") == 0) {
- std::cout << "ERROR, could not create /ScanDta/RunInfo." << std::endl;
- exit(1);
- }
- movieNameAtom.Create(runInfoGroup.group, "MovieName");
- platformIdAtom.Create(runInfoGroup.group, "PlatformId");
- platformNameAtom.Create(runInfoGroup.group, "PlatformName");
- runCodeAtom.Create(runInfoGroup.group, "RunCode");
-}
-
-HDFScanDataWriter::HDFScanDataWriter(HDFFile & _outFile) {
- Initialize(_outFile.rootGroup);
-}
-
-HDFScanDataWriter::HDFScanDataWriter(HDFGroup & _rootGroup) {
- Initialize(_rootGroup);
-}
-
-HDFScanDataWriter::~HDFScanDataWriter() {
- // Assume that closing the hdf file must be done
- // manually and not in a destructor.
-}
-
-int HDFScanDataWriter::Initialize(HDFGroup & _rootGroup) {
- rootGroupPtr = &(_rootGroup);
- rootGroupPtr->AddGroup("ScanData");
- if (scanDataGroup.Initialize(*(rootGroupPtr), "ScanData") == 0) {
- std::cout << "ERROR, could not create /ScanData group." << std::endl;
- exit(1);
- }
- scanDataGroup.AddGroup("AcqParams");
- scanDataGroup.AddGroup("DyeSet");
- scanDataGroup.AddGroup("RunInfo");
-
- CreateAcqParamsGroup();
- CreateDyeSetGroup();
- CreateRunInfoGroup();
-
- return 1;
-}
-
-void HDFScanDataWriter::Write(ScanData & scanData) {
- WriteFrameRate((scanData.frameRate==0)?
- (75):(scanData.frameRate));
- WriteNumFrames((scanData.numFrames==0)?
- (1000000):(scanData.numFrames));
- WriteWhenStarted((scanData.whenStarted.empty())?
- ("2013-01-01T01:01:01"):(scanData.whenStarted));
- std::string baseMapStr = BaseMapToStr(scanData.baseMap);
- WriteBaseMap((baseMapStr == "")?("TGAC"):baseMapStr);
- WriteNumAnalog(4);
-
- WriteMovieName((scanData.movieName.empty()?
- ("simulated_movie"):scanData.movieName));
- WriteRunCode((scanData.runCode.empty())?
- "simulated_runcode":(scanData.runCode));
- WritePlatformId((scanData.platformId==NoPlatform)?
- (Springfield):(scanData.platformId));
-}
-
-void HDFScanDataWriter::WriteFrameRate(float frameRate) {
- // Write /ScanData/AcqParams/FrameRate attribute.
- frameRateAtom.Write(frameRate);
-}
-
-void HDFScanDataWriter::WriteNumFrames(unsigned int numFrames) {
- // Write /ScanData/AcqParams/NumFrames attribute.
- numFramesAtom.Write(numFrames);
-}
-
-void HDFScanDataWriter::WriteWhenStarted(const std::string whenStarted) {
- // Write /ScanData/AcqParams/WhenStarted attribute.
- whenStartedAtom.Write(whenStarted);
-}
-
-std::string HDFScanDataWriter::BaseMapToStr(std::map<char, int> & baseMap) {
- std::string baseMapStr = ""; //4 dye channels.
- if (not baseMap.empty()) {
- baseMapStr = " ";
- map<char, int>::iterator it;
- for (it = baseMap.begin(); it != baseMap.end(); ++it){
- if (it->second > 4 or it->second < 0) {
- std::cout << "ERROR, there are more than four dye channels."
- << std::endl;
- exit(1);
- }
- baseMapStr[it->second]= it->first;
- }
- }
- return baseMapStr;
-}
-
-void HDFScanDataWriter::WriteBaseMap(const std::string baseMapStr) {
- //Write /ScanData/DyeSet/BaseMap attribute.
- baseMapAtom.Write(baseMapStr);
-}
-
-void HDFScanDataWriter::WriteNumAnalog(const unsigned int numAnalog) {
- //Write /ScanData/DyeSet/NumAnalog attribute.
- numAnalogAtom.Write(numAnalog);
-}
-
-void HDFScanDataWriter::WritePlatformId(const PlatformId id) {
- //Write /ScanData/RunInfo/Flatform attribute.
- platformIdAtom.Write(id);
- std::string name = (id == Springfield)?"Springfield":"Astro";
- platformNameAtom.Write(name);
-}
-
-void HDFScanDataWriter::WriteMovieName(const std::string movieName) {
- //Write /ScanData/RunInfo/MovieName attribute.
- movieNameAtom.Write(movieName);
-}
-
-void HDFScanDataWriter::WriteRunCode(const std::string runCode) {
- //Write /ScanData/RunInfo/MovieName attribute.
- runCodeAtom.Write(runCode);
-}
-
-void HDFScanDataWriter::Close() {
- // Close /ScanData/AcqParams attributes.
- whenStartedAtom.dataspace.close();
- frameRateAtom.dataspace.close();
- numFramesAtom.dataspace.close();
-
- // Close /ScanData/DyeSet attributes.
- baseMapAtom.dataspace.close();
-
- // Close /ScanData/RunInfo attributes.
- movieNameAtom.dataspace.close();
- runCodeAtom.dataspace.close();
- platformIdAtom.dataspace.close();
- platformNameAtom.dataspace.close();
-
- // Close /ScanData/AcqParams|DyeSet|RunInfo.
- acqParamsGroup.Close();
- dyeSetGroup.Close();
- runInfoGroup.Close();
-
- // Close /ScanData
- scanDataGroup.Close();
-}
diff --git a/libcpp/hdf/HDFScanDataWriter.hpp b/libcpp/hdf/HDFScanDataWriter.hpp
deleted file mode 100644
index f92d8e6..0000000
--- a/libcpp/hdf/HDFScanDataWriter.hpp
+++ /dev/null
@@ -1,71 +0,0 @@
-#ifndef DATA_HDF_HDF_SCAN_DATA_WRITER_H_
-#define DATA_HDF_HDF_SCAN_DATA_WRITER_H_
-
-#include <string>
-#include <iostream>
-#include "HDFFile.hpp"
-#include "HDFGroup.hpp"
-#include "HDFAtom.hpp"
-#include "Enumerations.h"
-#include "reads/ScanData.hpp"
-
-class HDFScanDataWriter {
-private:
- HDFGroup * rootGroupPtr;
- HDFGroup scanDataGroup;
- HDFGroup acqParamsGroup;
- HDFGroup dyeSetGroup;
- HDFGroup runInfoGroup;
-
- HDFAtom<std::string> whenStartedAtom;
- HDFAtom<float> frameRateAtom;
- HDFAtom<unsigned int> numFramesAtom;
-
- HDFAtom<std::string> baseMapAtom;
- HDFAtom<unsigned int> numAnalogAtom;
-
- HDFAtom<std::string> movieNameAtom;
- HDFAtom<std::string> runCodeAtom;
-
- HDFAtom<unsigned int> platformIdAtom;
- HDFAtom<std::string> platformNameAtom;
-
- void CreateAcqParamsGroup();
-
- void CreateDyeSetGroup();
-
- void CreateRunInfoGroup();
-
-public:
- HDFScanDataWriter(HDFFile & _outFile);
-
- HDFScanDataWriter(HDFGroup & _rootGroup);
-
- ~HDFScanDataWriter();
-
- int Initialize(HDFGroup & _rootGroup);
-
- void Write(ScanData & scanData);
-
- void WriteFrameRate(float frameRate);
-
- void WriteNumFrames(unsigned int numFrames);
-
- void WriteWhenStarted(const std::string whenStarted);
-
- std::string BaseMapToStr(std::map<char, int> & baseMap);
-
- void WriteBaseMap(const std::string baseMapStr);
-
- void WriteNumAnalog(const unsigned int numAnalog);
-
- void WritePlatformId(const PlatformId id);
-
- void WriteMovieName(const std::string movieName);
-
- void WriteRunCode(const std::string runCode);
-
- void Close();
-};
-
-#endif
diff --git a/libcpp/hdf/HDFSentinalFile.hpp b/libcpp/hdf/HDFSentinalFile.hpp
deleted file mode 100644
index 71f7de8..0000000
--- a/libcpp/hdf/HDFSentinalFile.hpp
+++ /dev/null
@@ -1,21 +0,0 @@
-#ifndef _BLASR_SENTINAL_FILE_HPP_
-#define _BLASR_SENTINAL_FILE_HPP_
-
-#include "HDFArray.h"
-#include "HDF2DArray.h"
-
-class HDFSentinal {
- public:
- HDFStringArray parts;
- HDF2DArray<unsigned int> holeLookup;
- HDFGroup multiPartGroup;
-
- void Initialize(HDFGroup &rootGroup) {
- multiPartGroup.Initialize(rootGroup, "MultiPart");
- parts.Initialize(multiPartGroup, "Parts");
- holeLookup.Initialize(multiPartGroup, "HoleLookup");
- }
-};
-
-
-#endif
diff --git a/libcpp/hdf/HDFUtils.cpp b/libcpp/hdf/HDFUtils.cpp
deleted file mode 100644
index ad0739b..0000000
--- a/libcpp/hdf/HDFUtils.cpp
+++ /dev/null
@@ -1,82 +0,0 @@
-#include "HDFUtils.hpp"
-
-std::string GetH5MovieName(std::string fileName) {
- HDFScanDataReader reader;
- return reader.GetMovieName_and_Close(fileName);
-}
-
-std::vector<std::string> GetH5MovieNames(const std::vector<std::string> & fileNames) {
- std::vector<std::string> ret;
- for (size_t i = 0 ; i < fileNames.size(); i++) {
- ret.push_back(GetH5MovieName(fileNames[i]));
- }
- return ret;
-}
-
-std::vector< std::pair<UInt, UInt> > GetMinMaxHoleNumbers(
- const std::vector<std::string> & fileNames, bool isRGN) {
- std::vector< std::pair<UInt, UInt> > ret;
- for (size_t i = 0 ; i < fileNames.size(); i++) {
- ret.push_back(GetMinMaxHoleNumber(fileNames[i], isRGN));
- }
- return ret;
-}
-
-std::pair<UInt, UInt> GetMinMaxHoleNumber(
- std::string fileName, bool isRGN) {
- UInt minHole, maxHole;
-
- if (isRGN) { // is region table
- HDFRegionTableReader rgnReader;
- rgnReader.Initialize(fileName);
- rgnReader.GetMinMaxHoleNumber(minHole, maxHole);
- rgnReader.Close();
- } else { // is bas/bax/pls/plx/ccs.h5
- HDFBasReader basReader;
- basReader.Initialize(fileName);
- vector<UInt> holes;
- basReader.GetMinMaxHoleNumber(minHole, maxHole);
- basReader.Close();
- }
- return std::make_pair(minHole, maxHole);
-}
-
-std::vector<int> MapPls2Rgn(const std::vector<std::string> & plsFNs,
- const std::vector<std::string> & rgnFNs) {
- if (plsFNs.size() != rgnFNs.size() && rgnFNs.size() != 0) {
- std::cout << "ERROR, the number of plx/bax.h5 files and the number of "
- << "region tables are not the same." << std::endl;
- exit(1);
- }
-
- // Movie names of pulse files in P.
- std::vector<std::string> plsMovies = GetH5MovieNames(plsFNs);
- // Movie names of region tables in R.
- std::vector<std::string> rgnMovies = GetH5MovieNames(rgnFNs);
-
- // The first and last hole numbers of pulse files in P.
- std::vector< std::pair<UInt, UInt> > plsHoles = GetMinMaxHoleNumbers(plsFNs, false);
- // The first and last hole numbers of region tables in R.
- std::vector< std::pair<UInt, UInt> > rgnHoles = GetMinMaxHoleNumbers(rgnFNs, true);
-
- std::vector<int> ret;
- for (size_t i = 0; i < plsFNs.size(); i++) {
- size_t j = 0;
- for (; j < rgnFNs.size(); j++) {
- if (plsMovies[i] == rgnMovies[j] and
- plsHoles[i].first <= rgnHoles[j].first and
- plsHoles[i].second >= rgnHoles[j].second) {
- break;
- }
- }
- if (j >= rgnFNs.size()) {
- std::cout << "ERROR, could not find any region table for file "
- << plsFNs[i] << " [" << plsHoles[i].first << ", " << plsHoles[i].second
- <<"." << std::endl;
- exit(1);
- }
- ret.push_back(j);
- }
- return ret;
-}
-
diff --git a/libcpp/hdf/HDFUtils.hpp b/libcpp/hdf/HDFUtils.hpp
deleted file mode 100644
index ee9409e..0000000
--- a/libcpp/hdf/HDFUtils.hpp
+++ /dev/null
@@ -1,44 +0,0 @@
-#ifndef _BLASR_HDF_UTILS_HPP_
-#define _BLASR_HDF_UTILS_HPP_
-
-#include <vector>
-#include <string>
-
-#include "HDFFile.hpp"
-#include "HDFScanDataReader.hpp"
-#include "HDFBasReader.hpp"
-#include "HDFRegionTableReader.hpp"
-#include "reads/RegionTable.hpp"
-
-
-// Given a PacBio (pls/plx/bas/bax/ccs/rgn).h5 file, which contains its movie
-// name in group /ScanData/RunInfo attribute MovieName, return its' movie name
-std::string GetH5MovieName(std::string fileName);
-
-// Given a vector of h5 files, return their movie names.
-std::vector<std::string> GetH5MovieNames(const std::vector<std::string> & fileNames);
-
-// Given a PacBio rgn.h5 file, return the smallest and largest holeNumber in
-// group /PulseData/Regions.
-std::pair<UInt, UInt> GetMinMaxHoleNumber(std::string fileName,
- bool isRGN=false);
-
-std::vector<std::pair<UInt, UInt> > GetMinMaxHoleNumbers(
- std::string fileName, bool isRGN=false);
-
-// Pulse files in input.fofn and regions tables in rgn.fofn may not
-// match, return mapping from plsFNs indices to rgnFNs indices.
-//
-// Input : plsFNs - pulse file names in input.fofn, e.g.,
-// P=(p_0, ..., p_{n-1})
-// rgnFNs - region table file names in rgn.fofn, e.g.,
-// R=(r_0, ..., p_{n-1})
-// Output: mapping from plsFNs indices to rgnFNs indices, e.g.,
-// M=(m_0, ..., m_{n-1})
-// so that for all i from 0 to n-1,
-// r_{m_{i}} matches p_i
-//
-std::vector<int> MapPls2Rgn(const std::vector<std::string> & plsFNs,
- const std::vector<std::string> & rgnFNs);
-
-#endif
diff --git a/libcpp/hdf/HDFWriteBuffer.hpp b/libcpp/hdf/HDFWriteBuffer.hpp
deleted file mode 100644
index 3600c5a..0000000
--- a/libcpp/hdf/HDFWriteBuffer.hpp
+++ /dev/null
@@ -1,52 +0,0 @@
-#ifndef _BLASR_HDF_WRITE_BUFFER_HPP_
-#define _BLASR_HDF_WRITE_BUFFER_HPP_
-
-#include <cstddef>
-
-template<typename T>
-class HDFWriteBuffer {
-public:
- T *writeBuffer;
- int bufferIndex;
- int bufferSize;
-
- HDFWriteBuffer() {
- writeBuffer = NULL;
- bufferIndex = 0;
- bufferSize = 0;
- }
-
- void InitializeBuffer(int pBufferSize) {
- Free(); // Free before reusing the buffer.
- bufferSize = pBufferSize;
- if (bufferSize > 0) {
- writeBuffer = new T[bufferSize];
- }
- else {
- writeBuffer = NULL;
- }
- }
-
- void Free() {
- if (writeBuffer) {
- delete[] writeBuffer;
- writeBuffer = NULL;
- }
- }
-
- ~HDFWriteBuffer() {
- Free();
- }
-
- void ResetWriteBuffer() {
- bufferIndex = 0;
- }
-
- bool WriteBufferEmpty() {
- return (bufferIndex == 0);
- }
-
-};
-
-
-#endif
diff --git a/libcpp/hdf/HDFZMWReader.cpp b/libcpp/hdf/HDFZMWReader.cpp
deleted file mode 100644
index a79107e..0000000
--- a/libcpp/hdf/HDFZMWReader.cpp
+++ /dev/null
@@ -1,136 +0,0 @@
-#include "Types.h"
-#include "HDFZMWReader.hpp"
-
-HDFZMWReader::HDFZMWReader() {
- closeFileOnExit = false;
- readHoleNumber = false;
- readHoleXY = false;
- readNumEvent = false;
- readHoleStatus = false;
- nZMWEntries = curZMW = 0;
- parentGroupPtr = NULL;
-}
-
-int HDFZMWReader::Initialize(HDFGroup *parentGroupP) {
- parentGroupPtr = parentGroupP;
- closeFileOnExit = false;
- return Initialize();
-}
-
-int HDFZMWReader::Initialize() {
-
- //
- // Make sure we can open the component containing the zmw information.
- //
- if (parentGroupPtr->ContainsObject("ZMW") == 0 or
- zmwGroup.Initialize(parentGroupPtr->group, "ZMW") == 0) {
- return 0;
- }
-
- //
- // Now open all the important datasets in the zmw group. Some of
- // these are optional, so flags must be set if they do not exist.
- //
- if (zmwGroup.ContainsObject("HoleNumber")) {
- if (holeNumberArray.Initialize(zmwGroup, "HoleNumber") == 0) {
- return 0;
- }
- readHoleNumber = true;
- }
- else {
- readHoleNumber = false;
- }
-
- if (zmwGroup.ContainsObject("HoleStatus")) {
- if (holeStatusArray.Initialize(zmwGroup, "HoleStatus") == 0) {
- return 0;
- }
- readHoleStatus = true;
- }
- else {
- readHoleStatus = false;
- }
-
-
- if (zmwGroup.ContainsObject("HoleXY")) {
- if (xyArray.Initialize(zmwGroup, "HoleXY") == 0) {
- return 0;
- }
- readHoleXY = true;
- }
- else {
- readHoleXY = false;
- }
- if (numEventArray.Initialize(zmwGroup, "NumEvent") == 0) {
- return 0;
- }
- nZMWEntries = numEventArray.arrayLength;
- readNumEvent = true;
- curZMW = 0;
- return 1;
-}
-
-int HDFZMWReader::Advance(int nSteps) {
- if (curZMW >= nZMWEntries) {
- return 0;
- }
- else {
- curZMW += nSteps;
- return 1;
- }
-}
-
-bool HDFZMWReader::GetNext(ZMWGroupEntry &groupEntry) {
- if (curZMW == nZMWEntries) {
- return false;
- }
- if (readHoleNumber) {
- holeNumberArray.Read(curZMW, curZMW+1, &groupEntry.holeNumber);
- }
- if (readHoleStatus) {
- holeStatusArray.Read(curZMW, curZMW+1, &groupEntry.holeStatus);
- }
- if (readHoleXY){
- int16_t holeXY[2];
- xyArray.Read(curZMW, curZMW+1, holeXY);
- groupEntry.x = holeXY[0];
- groupEntry.y = holeXY[1];
- }
- numEventArray.Read(curZMW, curZMW+1, &groupEntry.numEvents);
- curZMW++;
- return true;
-}
-
-void HDFZMWReader::Close() {
- if (readHoleNumber) {
- holeNumberArray.Close();
- }
- if (readHoleStatus) {
- holeStatusArray.Close();
- }
- if (readHoleXY) {
- xyArray.Close();
- }
- if (readNumEvent) {
- numEventArray.Close();
- }
-
- if (closeFileOnExit == true) {
- //
- // This instance is owner of it's reader. Close the reader file.
- //
- hdfPlsFile.close();
- }
- zmwGroup.Close();
-
-}
-
-bool HDFZMWReader::GetHoleNumberAt(UInt index, UInt &holeNumber) {
- if (index >= nZMWEntries) { return false; }
- holeNumberArray.Read(index, index + 1, (UInt *)&holeNumber);
- return true;
-}
-
-HDFZMWReader::~HDFZMWReader() {
- Close();
-}
diff --git a/libcpp/hdf/HDFZMWReader.hpp b/libcpp/hdf/HDFZMWReader.hpp
deleted file mode 100644
index 8cd7d2d..0000000
--- a/libcpp/hdf/HDFZMWReader.hpp
+++ /dev/null
@@ -1,45 +0,0 @@
-#ifndef _BLASR_HDF_ZMW_READER_HPP_
-#define _BLASR_HDF_ZMW_READER_HPP_
-
-#include <cstdint>
-#include "H5Cpp.h"
-#include "reads/ZMWGroupEntry.hpp"
-#include "HDFArray.hpp"
-#include "HDF2DArray.hpp"
-#include "HDFGroup.hpp"
-
-class HDFZMWReader {
-public:
- HDFGroup *parentGroupPtr;
- HDFGroup zmwGroup;
- HDFArray<unsigned int> holeNumberArray;
- HDFArray<unsigned char> holeStatusArray;
- HDF2DArray<int16_t> xyArray;
- HDFArray<int> numEventArray;
- bool readHoleNumber, readHoleStatus;
- bool readHoleXY;
- bool readNumEvent;
- UInt curZMW;
- UInt nZMWEntries;
- bool closeFileOnExit;
- H5::H5File hdfPlsFile;
-
- HDFZMWReader();
-
- int Initialize(HDFGroup *parentGroupP);
-
- int Initialize();
-
- int Advance(int nSteps);
-
- bool GetNext(ZMWGroupEntry &groupEntry);
-
- void Close();
-
- // Return true if get hole number at ZMW/HoleNumber[index].
- bool GetHoleNumberAt(UInt index, UInt & holeNumber);
-
- ~HDFZMWReader();
-};
-
-#endif
diff --git a/libcpp/hdf/build.mk b/libcpp/hdf/build.mk
deleted file mode 120000
index 2247f36..0000000
--- a/libcpp/hdf/build.mk
+++ /dev/null
@@ -1 +0,0 @@
-makefile
\ No newline at end of file
diff --git a/libcpp/hdf/makefile b/libcpp/hdf/makefile
deleted file mode 100644
index c92a229..0000000
--- a/libcpp/hdf/makefile
+++ /dev/null
@@ -1,28 +0,0 @@
-all:
-
-include ../rules.mk
-include ../defines.mk
-
-CXXOPTS += -std=c++11 -pedantic -MMD -MP
-INCLUDES += ${LIBPBDATA_INCLUDE} ${HDF5_INCLUDE} ${PBBAM_INCLUDE} ${HTSLIB_INCLUDE} ${BOOST_INCLUDE}
-DEP_LIBS += ${LIBPBDATA_LIB} ${HDF5_LIB} ${PBBAM_LIB} ${HTSLIB_LIB} ${ZLIB_LIB}
-LDFLAGS += $(patsubst %,$(dirname %),${DEP_LIBS})
-
-all: libpbihdf.a libpbihdf.so
-
-sources := $(wildcard *.cpp)
-objects := $(sources:.cpp=.o)
-shared_objects := $(sources:.cpp=.shared.o)
-dependencies := $(objects:.o=.d) $(shared_objects:.o=.d)
-
-libpbihdf.a: $(objects)
- $(AR) $(ARFLAGS) $@ $^
-
-libpbihdf.so: $(shared_objects) $(DEP_LIBS)
- $(CXX) $(LD_SHAREDFLAGS) -o $@ -Wl,-soname,$@ $^
-
-clean:
- @rm -f libpbihdf.a libpbihdf.so
- @rm -f $(objects) $(shared_objects) $(dependencies)
-
--include $(dependencies)
diff --git a/libcpp/hdf/old.Makefile b/libcpp/hdf/old.Makefile
deleted file mode 100644
index 1998195..0000000
--- a/libcpp/hdf/old.Makefile
+++ /dev/null
@@ -1,94 +0,0 @@
-
-include ../common.mk
-
-# To enable building a shared library, invoke as "make SHARED_LIB=true ..."
-ifneq ($(SHARED_LIB),)
- # Generating shared library
- CXX_SHAREDFLAGS := -fPIC
- LD_SHAREDFLAGS := -shared -fPIC
- TARGET_LIB := libpbihdf.so
- # Developers should set these to appropriate defaults (other systems
- # will override these on the command line):
- HDF5_LIB := ../../../../prebuilt.out/prebuilt.out/hdf5/hdf5-1.8.12/centos-5/lib/libhdf5.so
- ZLIB_LIB := ../../../../prebuilt.tmpsrc/zlib/zlib_1.2.8/_output/install/lib/libz.so
- HTSLIB_LIB := ../../../staging/PostPrimary/pbbam/_output/install-build/lib/libpbbam.so
- PBBAM_LIB := ../../../staging/PostPrimary/pbbam/third-party/htslib/_output/install-build/lib/libhts.so
- LIBPBDATA_LIB := ../../../staging/PostPrimary/pbbam/third-party/htslib/_output/install-build/lib/libhts.so
-else
- # Generating shared library
- CXX_SHAREDFLAGS :=
- LD_SHAREDFLAGS :=
- TARGET_LIB := libpbihdf.a
- HDF5_LIB :=
- ZLIB_LIB :=
- HTSLIB_LIB :=
- PBBAM_LIB :=
- LIBPBDATA_LIB :=
-endif
-
-DEP_LIBS := $(HDF5_LIB) $(ZLIB_LIB) $(HTSLIB_LIB) $(PBBAM_LIB) $(PBDATA_LIB)
-
-# FIXME: remove PBDATA_INCLUDE and assign directly to LIBPBDATA_INCLUDE.
-# Use only LIBPBDATA_INCLUDE to be consistent with the libblasr Makefile
-PBDATA_INCLUDE := ../pbdata
-LIBPBDATA_INCLUDE := $(PBDATA_INCLUDE)
-PBBAM_INCLUDE := $(PBBAM)/include
-HTSLIB_INCLUDE ?= $(HTSLIB)
-
-INCLUDES = -I$(LIBPBDATA_INCLUDE)
-
-
-ifeq ($(origin nopbbam), undefined)
- INCLUDES += -I$(PBBAM_INCLUDE) -I$(HTSLIB_INCLUDE) -I$(BOOST_INCLUDE)
-endif
-
-ifneq ($(ZLIB_ROOT), notfound)
- INCLUDES += -I$(ZLIB_ROOT)/include
-endif
-
-CXXOPTS := -std=c++11 -pedantic -MMD -MP
-sources := $(wildcard *.cpp)
-objects := $(sources:.cpp=.o)
-shared_objects := $(sources:.cpp=.shared.o)
-dependencies := $(objects:.o=.d) $(shared_objects:.o=.d)
-
-ifneq ($(HDF5_INC),)
-HDF_HEADERS :=
-INCLUDES += -I$(HDF5_INC)
-else
-HDF_HEADERS := hdf5-1.8.12-headers
-INCLUDES += -I./$(HDF_HEADERS)/src -I./$(HDF_HEADERS)/c++/src
-endif
-
-all : CXXFLAGS ?= -O3
-
-debug : CXXFLAGS ?= -g -ggdb -fno-inline
-
-profile : CXXFLAGS ?= -Os -pg
-
-g : CXXFLAGS ?= -g -ggdb -fno-inline -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer
-
-all debug profile g: $(HDF_HEADERS) $(TARGET_LIB)
-
-libpbihdf.a: $(objects)
- $(AR_pp) $(ARFLAGS) $@ $^
-
-libpbihdf.so: $(shared_objects) $(DEP_LIBS)
- $(CXX) $(LD_SHAREDFLAGS) -o $@ $^
-
-%.o: %.cpp
- $(CXX) $(CXXOPTS) $(CXXFLAGS) $(INCLUDES) -MF"$(@:%.o=%.d)" -MT"$(@:%.o=%.o) $(@:%.o=%.d)" -c $< -o $@
-
-%.shared.o: %.cpp
- $(CXX) $(CXX_SHAREDFLAGS) $(CXXOPTS) $(CXXFLAGS) $(INCLUDES) -MF"$(@:%.o=%.d)" -MT"$(@:%.o=%.o) $(@:%.o=%.d)" -c $< -o $@
-
-$(HDF_HEADERS):
- curl -k -L https://www.dropbox.com/s/8971bcyy5o42rxb/hdf5-1.8.12-headers.tar.bz2\?dl\=0 | tar xjf -
-
-# .INTERMEDIATE: $(objects)
-
-clean:
- @rm -f libpbihdf.a libpbihdf.so
- @rm -f $(objects) $(shared_objects) $(dependencies)
-
--include $(dependencies)
diff --git a/libcpp/makefile b/libcpp/makefile
deleted file mode 100644
index 64a113b..0000000
--- a/libcpp/makefile
+++ /dev/null
@@ -1,32 +0,0 @@
-SHELL=/bin/bash
-
-.PHONY: all debug profile gtest clean cleanall
-
-# $Change: 140182 $
-
-all:
- ${MAKE} -C pbdata all
- ${MAKE} -C hdf all
- ${MAKE} -C alignment all
-
-debug:
- ${MAKE} subs
-
-profile:
- ${MAKE} subs
-
-g:
- ${MAKE} subs
-
-gtest:
- ${MAKE} -C unittest -f normal.Makefile gtest
-
-clean:
- ${MAKE} -C pbdata clean
- ${MAKE} -C hdf clean
- ${MAKE} -C alignment clean
- #@${MAKE} -C unittest clean
-
-cleanall: clean
-
-# Note: hdf/ will not build if nohdf=1 is configured.
diff --git a/libcpp/old.Makefile b/libcpp/old.Makefile
deleted file mode 100644
index 1e52e1d..0000000
--- a/libcpp/old.Makefile
+++ /dev/null
@@ -1,28 +0,0 @@
-SHELL=/bin/bash
-
-.PHONY: all debug profile gtest clean cleanall
-
-subs:
- ${MAKE} -C pbdata all
- ${MAKE} -C hdf all
- ${MAKE} -C alignment all
-
-debug:
- ${MAKE} subs
-
-profile:
- ${MAKE} subs
-
-g:
- ${MAKE} subs
-
-gtest:
- ${MAKE} -C unittest gtest
-
-clean:
- @${MAKE} -C pbdata clean
- @${MAKE} -C hdf clean
- @${MAKE} -C alignment clean
- @${MAKE} -C unittest clean
-
-cleanall: clean
diff --git a/libcpp/pbdata/.gitignore b/libcpp/pbdata/.gitignore
deleted file mode 100644
index 4c3cf0b..0000000
--- a/libcpp/pbdata/.gitignore
+++ /dev/null
@@ -1,2 +0,0 @@
-/libconfig.h
-/defines.mk
diff --git a/libcpp/pbdata/CCSSequence.cpp b/libcpp/pbdata/CCSSequence.cpp
deleted file mode 100644
index 1f8e5b9..0000000
--- a/libcpp/pbdata/CCSSequence.cpp
+++ /dev/null
@@ -1,35 +0,0 @@
-#include "CCSSequence.hpp"
-
-void CCSSequence::Free() {
- numPasses = 0;
- numConsensusBases = 0;
- SMRTSequence::Free();
- unrolledRead.Free();
- /*
- ClearMemory(passStartPulse);
- ClearMemory(passNumPulses);
- ClearMemory(passStartBase);
- ClearMemory(passNumBases);
- ClearMemory(passDirection);
- ClearMemory(adapterHitBefore);
- ClearMemory(adapterHitAfter);
- ClearMemory(adapterHitConfidence);
- */
-}
-
-int CCSSequence::GetStorageSize() {
- return SMRTSequence::GetStorageSize() + unrolledRead.GetStorageSize();
-}
-
-//
-// In the first iteration, Explode simply pulls the subreads out
-// that are used in the ccs. Eventually, it will pull out all
-// high-quality subreads.
-//
-void CCSSequence::Explode(std::vector<SMRTSequence> &subreads) {
- subreads.resize(numPasses);
- int subreadIndex;
- for (subreadIndex = 0; subreadIndex < numPasses; subreadIndex++) {
- subreads[subreadIndex].ReferenceSubstring(this->unrolledRead, passStartBase[subreadIndex], passNumBases[subreadIndex]);
- }
-}
diff --git a/libcpp/pbdata/CCSSequence.hpp b/libcpp/pbdata/CCSSequence.hpp
deleted file mode 100644
index 15e89d6..0000000
--- a/libcpp/pbdata/CCSSequence.hpp
+++ /dev/null
@@ -1,43 +0,0 @@
-#ifndef _BLASR_CCS_SEQUENCE_HPP_
-#define _BLASR_CCS_SEQUENCE_HPP_
-
-#include "Enumerations.h"
-#include "SMRTSequence.hpp"
-#include "VectorUtils.hpp"
-
-//
-// A CCS Sequence is both a SMRTSequence itself, and contains a list of SMRTSequences.
-//
-class CCSSequence : public SMRTSequence {
- public:
- UInt numPasses;
- UInt numConsensusBases;
- std::vector<DNALength> passStartPulse, passNumPulses, passStartBase, passNumBases;
- std::vector<Byte> passDirection;
- std::vector<Byte> adapterHitBefore, adapterHitAfter, adapterHitConfidence;
- //
- // The CCS Sequence originates from a full length read. That read
- // is stored here for reference later on. The ccs read is stored in
- // the inherited fields from SMRTSequence so that it may be worked
- // with as if it were a normal non-ccs sequence.
- //
- SMRTSequence unrolledRead;
-
- inline ~CCSSequence();
- void Free();
-
- int GetStorageSize();
- //
- //
- // In the first iteration, Explode simply pulls the subreads out
- // that are used in the ccs. Eventually, it will pull out all
- // high-quality subreads.
- //
- void Explode(std::vector<SMRTSequence> &subreads);
-};
-
-inline CCSSequence::~CCSSequence() {
- CCSSequence::Free();
-}
-
-#endif // _BLASR_CCS_SEQUENCE_HPP_
diff --git a/libcpp/pbdata/ChangeListID.cpp b/libcpp/pbdata/ChangeListID.cpp
deleted file mode 100644
index 2b99c42..0000000
--- a/libcpp/pbdata/ChangeListID.cpp
+++ /dev/null
@@ -1,64 +0,0 @@
-#include <sstream>
-#include "ChangeListID.hpp"
-
-using namespace std;
-
-ChangeListID::ChangeListID() {}
-ChangeListID::ChangeListID(string &idStringP) {
- StoreString(idStringP);
-}
-
-void ChangeListID::StoreString(string &idStringP) {
- idString = idStringP;
- stringstream ss(idString);
- string part;
- intVer.clear();
- while(getline(ss, part, '.')) {
- intVer.push_back(atoi(part.c_str()));
- }
-}
-
-int ChangeListID::LessThan(ChangeListID &rhs, int depth) {
- if (depth == 0) {
- depth = min(intVer.size(), rhs.intVer.size());
- }
- int i;
- for (i = 0; i < depth; i++) {
- if (intVer[i] != rhs.intVer[i]) {
- return intVer[i] < rhs.intVer[i];
- }
- }
- return 0; // making it here they are equal
-}
-
-
-QVScale ChangeListID::DetermineQVScaleFromChangeListID() {
- ChangeListID phredCL;
- phredCL.intVer.resize(3);
- phredCL.intVer[0] = 1; phredCL.intVer[1] = 2; phredCL.intVer[2] = 2;
- if (LessThan(phredCL)) {
- return POverOneMinusP;
- }
- else {
- return PHRED;
- }
-}
-
-// utility method
-void AppendPerforceChangelist(string perforceVersionString, string &version) {
- if (perforceVersionString.size() > 12) {
- version.insert(version.size(), ".");
- version.insert(version.size(), perforceVersionString, 9, perforceVersionString.size() - 11);
- }
-}
-
-std::string ChangeListID::GetVersion() {
- stringstream ss;
- if (intVer.size() == 1) {
- ss << intVer[0];
- } else if(intVer.size() >= 2) {
- ss << intVer[0] << "." << intVer[1];
- }
- return ss.str();
-}
-
diff --git a/libcpp/pbdata/ChangeListID.hpp b/libcpp/pbdata/ChangeListID.hpp
deleted file mode 100644
index eda525e..0000000
--- a/libcpp/pbdata/ChangeListID.hpp
+++ /dev/null
@@ -1,38 +0,0 @@
-#ifndef UTILS_CHANGELIST_ID_H_
-#define UTILS_CHANGELIST_ID_H_
-
-#include <string>
-#include <vector>
-#include <stdlib.h>
-#include <sstream>
-
-#ifndef _QVScale_
-#define _QVScale_
-enum QVScale {POverOneMinusP, // popularized by Illumina
- PHRED};
-#endif
-
-class ChangeListID {
-public:
- std::string idString;
- std::vector<std::string> strVer;
- std::vector<int> intVer;
- ChangeListID();
- ChangeListID(std::string &idStringP);
-
- void StoreString(std::string &idStringP);
-
- int LessThan(ChangeListID &rhs, int depth = 0);
-
- QVScale DetermineQVScaleFromChangeListID();
-
- /// Get version string from ChangeListID.
- /// changeListID "2.3.0.144058" --> Version "2.3".
- /// \returns version string
- std::string GetVersion();
-
-};
-
-void AppendPerforceChangelist(std::string perforceVersionString, std::string &version);
-
-#endif
diff --git a/libcpp/pbdata/CommandLineParser.cpp b/libcpp/pbdata/CommandLineParser.cpp
deleted file mode 100644
index 2f1c92e..0000000
--- a/libcpp/pbdata/CommandLineParser.cpp
+++ /dev/null
@@ -1,846 +0,0 @@
-#include "CommandLineParser.hpp"
-
-CommandLineParser::
-CommandLineParser() {
- lineLength = 80;
- numUnnamedOptions = 0;
- specialVersionFlag = false;
-}
-
-void CommandLineParser::
-SetProgramSummary(std::string summaryp) {
- programSummary = summaryp;
-}
-
-void CommandLineParser::
-SetHelp(std::string _help) {
- helpString = _help;
-}
-
-void CommandLineParser::
-SetConciseHelp(std::string _conciseHelp) {
- conciseHelp = _conciseHelp;
-}
-
-void CommandLineParser::
-SetProgramName(std::string namep) {
- programName = namep;
-}
-
-void CommandLineParser::
-SetVersion(std::string versionp) {
- specialVersionFlag = true;
- version = versionp;
-}
-
-void CommandLineParser::
-SetVerboseHelp(std::string helpp) {
- verboseHelp = helpp;
-}
-
-void CommandLineParser::
-SetExamples(std::string examplesp) {
- examples = examplesp;
-}
-
-void CommandLineParser::
-RegisterPreviousFlagsAsHidden() {
- VectorIndex i;
- for (i = 0; i < named.size(); i++ ){
- named[i] = false;
- }
- numUnnamedOptions = named.size();
-}
-
-void CommandLineParser::
-RegisterVersionFlag(bool *value) {
- specialVersionFlag = true;
- RegisterFlagOption("version", value, "Print version number.");
-}
-
-
-void CommandLineParser::
-RegisterFlagOption(std::string option, bool *value,
- std::string description, bool required) {
-
- named.push_back(true);
- optionList.push_back(option);
- optionTypeList.push_back(Flag);
- optionValueIndexList.push_back(boolValues.size());
- boolValues.push_back(value);
- descriptions.push_back(description);
- optionRequired.push_back(required);
- optionUsed.push_back(false);
-}
-
-void CommandLineParser::
-RegisterIntOption(std::string option, int *value,
- std::string description, OptionType type, bool required, bool hidden) {
-
- named.push_back(true);
- optionList.push_back(option);
- optionTypeList.push_back(type);
- optionValueIndexList.push_back(intValues.size());
- intValues.push_back(value);
- descriptions.push_back(description);
- optionRequired.push_back(required);
- optionUsed.push_back(false);
-}
-
-void CommandLineParser::
-RegisterFloatOption(std::string option, float *value,
- std::string description, OptionType type, bool required) {
-
- named.push_back(true);
- optionList.push_back(option);
- optionTypeList.push_back(type);
- optionValueIndexList.push_back(floatValues.size());
- floatValues.push_back(value);
- descriptions.push_back(description);
- optionRequired.push_back(required);
- optionUsed.push_back(false);
-}
-
-void CommandLineParser::
-RegisterStringOption(std::string option, std::string *value,
- std::string description, bool required) {
-
- named.push_back(true);
- optionList.push_back(option);
- optionTypeList.push_back(String);
- optionValueIndexList.push_back(stringValues.size());
- stringValues.push_back(value);
- descriptions.push_back(description);
- optionRequired.push_back(required);
- optionUsed.push_back(false);
-}
-
-void CommandLineParser::
-RegisterStringListOption(std::string option,
- std::vector<std::string> *value, std::string description,
- bool required) {
-
- named.push_back(true);
- optionList.push_back(option);
- optionTypeList.push_back(StringList);
- optionValueIndexList.push_back(stringListValues.size());
- stringListValues.push_back(value);
- descriptions.push_back(description);
- optionRequired.push_back(required);
- optionUsed.push_back(false);
-}
-
-
-void CommandLineParser::
-RegisterIntListOption(std::string option, std::vector<int> *value,
- std::string description, bool required) {
-
- named.push_back(true);
- optionList.push_back(option);
- optionTypeList.push_back(IntegerList);
- optionValueIndexList.push_back(intListValues.size());
- intListValues.push_back(value);
- descriptions.push_back(description);
- optionRequired.push_back(required);
- optionUsed.push_back(false);
-}
-
-
-int CommandLineParser::
-IsOption(char *str) {
- int len = strlen(str);
- if (len == 0) {
- return 0;
- }
- else {
- return str[0] == '-';
- }
-}
-
-int CommandLineParser::
-IsInteger(char *str) {
- int len = strlen(str);
- int i;
- if (len == 0)
- return 0;
- if (!(str[0] == '-' or (str[0] >= '0' and str[0] <= '9')))
- return 0;
- for (i = 1; i < len; i++) {
- if (!isdigit(str[i]))
- return 0;
- }
- return 1;
-}
-
-int CommandLineParser::
-IsFloat(char *str) {
- int len = strlen(str);
- int i;
- if (len == 0) {
- return 0;
- }
- int nDot = 0;
- int nDigit = 0;
- for (i = 0; i < len; i++) {
- if (isdigit(str[i])) nDigit++;
- if (str[i] == '.') nDot++;
- }
- if (nDot > 1)
- return 0;
- if (nDigit == 0)
- return 0;
- if (!isdigit(str[0]) and str[0] != '-' and str[0] != '.')
- return 0;
- //
- // passed all checks, ok!
- //
- return 1;
-}
-
-int CommandLineParser::
-FindOption(char *option) {
- VectorIndex i;
- for (i = 0; i < optionList.size(); i++ ){
- if (optionList[i].compare(option) == 0) {
- return i;
- }
- }
- return -1;
-}
-
-void CommandLineParser::
-CommandLineToString(int argc, char* argv[],
- std::string& commandLine) {
-
- std::stringstream outstrm;
- int i;
- for (i = 0; i< argc; i++) {
- outstrm << argv[i] << " ";
- }
- commandLine = outstrm.str();
-}
-
-
-int CommandLineParser::
-ParseCommandLine(int argc, char* argv[], bool isProgramNameOnlyAllowed) {
- std::vector<std::string> ufv;
- return ParseCommandLine(argc, argv, ufv, isProgramNameOnlyAllowed);
-}
-
-int CommandLineParser::
-ParseCommandLine(int argc, char* argv[],
- std::vector<std::string> &unflaggedValues, bool isProgramNameOnlyAllowed) {
-
- VectorIndex argi = 1;
- int curUnnamedOption = 0;
- ErrorValue ev;
- //
- // Check for a help flag.
- //
- int i;
- for (i = 1; i < argc; i++) {
- if (strcmp(argv[i], "-h") == 0 or
- (strcmp(argv[i], "--help") == 0 and
- // Check to see if there is non default argument for help
- IsOption(argv[i]) and !FindOption(&argv[i][1]))) {
- PrintUsage();
- exit(0);
- }
- else if (strcmp(argv[i], "-version") == 0 and specialVersionFlag) {
- //
- // Using -version is an early exit since programs will print the
- // version and then return.
- //
- assert(IsOption(argv[i]) and FindOption(&argv[argi][1]));
- PrintVersion();
- exit(0);
- }
- }
-
- if ( !isProgramNameOnlyAllowed ) {
- if ( argc == 1 || argc < numUnnamedOptions) {
- if (conciseHelp != "") {
- std::cout << conciseHelp;
- }
- else {
- PrintUsage();
- }
- exit(0);
- }
- }
-
- //
- // Now parse the (probably optional) options.
- //
- while (argi < (VectorIndex) argc){
- if (IsOption(argv[argi])) {
- //
- // Find which option is specified.
- //
- int optionIndex = FindOption(&argv[argi][1]);
- if (optionIndex == -1) {
- ev = CLBadOption;
- }
- else {
- argi++;
-
- //
- // Record that this option has been specified.
- //
- optionUsed[optionIndex] = true;
- ev = ParseOption(optionIndex, argi, argc, argv);
- }
- if (ev != CLGood) {
- PrintUsage();
- PrintErrorMessage(ev, &argv[argi][1]);
- exit(1);
- }
- }
- else {
- unflaggedValues.push_back(argv[argi]);
- if (curUnnamedOption < numUnnamedOptions) {
- ev = ParseOption(curUnnamedOption, argi, argc, argv);
- optionUsed[curUnnamedOption] = true;
- curUnnamedOption++;
- }
- else {
- ++argi;
- }
- }
- }
-
- ev = PrintErrorOnMissingOptions();
- if (ev != CLGood) {
- PrintUsage();
- PrintErrorMessage(ev, &argv[argi][1]);
- exit(1);
- }
- return 1;
-}
-
-CommandLineParser::ErrorValue CommandLineParser::
-ParseOption(VectorIndex optionIndex, VectorIndex &argi,
- int argc, char *argv[]) {
-
- ErrorValue ev;
- //
- // Extract the value type of this option.
- //
- int optionValueIndex = optionValueIndexList[optionIndex];
- OptionType optionType = optionTypeList[optionIndex];
-
- switch(optionType) {
- case(Flag):
- ev = ParseFlag(optionValueIndex, argi, argc, argv);
- break;
- case(Integer):
- ev = ParseInteger(optionValueIndex, argi, argc, argv);
- break;
- case(PositiveInteger):
- ev = ParsePositiveInteger(optionValueIndex, argi, argc, argv);
- break;
- case(NonNegativeInteger):
- ev = ParseNonNegativeInteger(optionValueIndex, argi, argc, argv);
- break;
- case(Float):
- ev = ParseFloat(optionValueIndex, argi, argc, argv);
- break;
- case( PositiveFloat):
- ev = ParsePositiveFloat(optionValueIndex, argi, argc, argv);
- break;
- case(NonNegativeFloat):
- ev = ParseNonNegativeFloat(optionValueIndex, argi, argc, argv);
- break;
- case(String):
- ev = ParseString(optionValueIndex, argi, argc, argv);
- break;
- case(StringList):
- ev = ParseStringList(optionValueIndex, argi, argc, argv);
- break;
- case(IntegerList):
- ev = ParseIntList(optionValueIndex, argi, argc, argv);
- break;
- };
- if (ev == CLGood) {
- optionUsed[optionValueIndex] = true;
- }
- return ev;
-}
-
-void CommandLineParser::
-PrintErrorMessage(ErrorValue ev, char *option) {
- switch(ev) {
- case(CLBadOption):
- std::cout << "ERROR: " << option
- << " is not a valid option." << std::endl;
- break;
- case(CLMissingValue):
- std::cout << "ERROR: " << option
- << " requires a value." << std::endl;
- break;
- case(CLInvalidInteger):
- std::cout << "ERROR: " << option << " requires an "
- << "integer value (...,-2,-1,0,1,2,...)"
- << std::endl;
- break;
- case(CLInvalidPositiveInteger):
- std::cout << "ERROR: " << option
- << " requires an integer greater than 0."
- << std::endl;
- break;
- case(CLInvalidNonNegativeInteger):
- std::cout << "ERROR: " << option
- << " requires an interger greater "
- << "than or equal to 0." << std::endl;
- break;
- case(CLInvalidFloat):
- std::cout << "ERROR: " << option
- << " requires a number as input." << std::endl;
- break;
- case(CLInvalidPositiveFloat):
- std::cout << "ERROR: " << option
- << " must be greater than 0 (eg. .0001)."
- << std::endl;
- break;
- case (CLInvalidNonNegativeFloat):
- std::cout << "ERROR: " << option
- << " must be greater than or equal to 0."
- << std::endl;
- break;
- default:
- break;
- };
-}
-
-
-CommandLineParser::ErrorValue CommandLineParser::
-ParseFlag(VectorIndex optionValueIndex, VectorIndex &argi,
- int argc, char *argv[]) {
-
- *boolValues[optionValueIndex] = !(*boolValues[optionValueIndex]);
- return CLGood;
-}
-
-
-CommandLineParser::ErrorValue CommandLineParser::
-ParseInteger(VectorIndex optionValueIndex, VectorIndex &argi,
- int argc, char *argv[]) {
-
- if (argi >= argc) {
- --argi;
- return CLMissingValue;
- }
- if (IsInteger(argv[argi])) {
- *intValues[optionValueIndex] = atoi(argv[argi]);
- ++argi;
- return CLGood;
- }
- else {
- // reset argi to the flag that was broken.
- --argi;
- return CLInvalidInteger;
- }
-}
-
-
-CommandLineParser::ErrorValue CommandLineParser::
-ParsePositiveInteger(VectorIndex optionValueIndex,
- VectorIndex &argi, int argc, char *argv[]) {
-
- int value;
- if (argi >= argc) {
- --argi;
- return CLMissingValue;
- }
- if (IsInteger(argv[argi])) {
- value = atoi(argv[argi]);
- if (value > 0) {
- *intValues[optionValueIndex] = value;
- ++argi;
- return CLGood;
- }
- }
- // reset argi to the flag that was broken.
- --argi;
- return CLInvalidPositiveInteger;
-}
-
-CommandLineParser::ErrorValue CommandLineParser::
-ParseNonNegativeInteger(VectorIndex optionValueIndex,
- VectorIndex &argi, int argc, char *argv[]) {
-
- int value;
- if (argi >= argc) {
- --argi;
- return CLMissingValue;
- }
- if (IsInteger(argv[argi])) {
- value = atoi(argv[argi]);
- if (value >= 0) {
- *intValues[optionValueIndex] = value;
- ++argi;
- return CLGood;
- }
- }
- // reset argi to the flag that was broken.
- --argi;
- return CLInvalidNonNegativeInteger;
-}
-
-
-CommandLineParser::ErrorValue CommandLineParser::
-ParseFloat(VectorIndex optionValueIndex,
- VectorIndex &argi, int argc, char *argv[]) {
-
- if (argi >= argc) {
- --argi;
- return CLMissingValue;
- }
- if (IsFloat(argv[argi])) {
- *floatValues[optionValueIndex] = atof(argv[argi]);
- ++argi;
- return CLGood;
- }
- else {
- // reset argi to the flag that was broken.
- --argi;
- return CLInvalidFloat;
- }
-}
-
-
-CommandLineParser::ErrorValue CommandLineParser::
-ParsePositiveFloat(VectorIndex optionValueIndex,
- VectorIndex &argi, int argc, char *argv[]) {
-
- float value;
- if (argi >= argc) {
- --argi;
- return CLMissingValue;
- }
- if (IsFloat(argv[argi])) {
- value = atof(argv[argi]);
- if (value > 0) {
- *floatValues[optionValueIndex] = value;
- ++argi;
- return CLGood;
- }
- }
- // reset argi pointer to bad flag
- --argi;
- return CLInvalidPositiveFloat;
-}
-
-
-CommandLineParser::ErrorValue CommandLineParser::
-ParseNonNegativeFloat(VectorIndex optionValueIndex,
- VectorIndex &argi, int argc, char *argv[]) {
-
- float value;
- if (argi >= argc) {
- --argi;
- return CLMissingValue;
- }
- if (IsFloat(argv[argi])) {
- value = atof(argv[argi]);
- if (value >= 0) {
- *floatValues[optionValueIndex] = value;
- ++argi;
- return CLGood;
- }
- }
- // reset argi to the flag that was broken.
- --argi;
- return CLInvalidNonNegativeFloat;
-}
-
-
-CommandLineParser::ErrorValue CommandLineParser::
-ParseString(VectorIndex optionValueIndex,
- VectorIndex &argi, int argc, char *argv[]) {
-
- if (argi >= argc) {
- --argi;
- return CLMissingValue;
- }
- if (argi < (unsigned int) argc) {
- *stringValues[optionValueIndex] = argv[argi];
- ++argi;
- return CLGood;
- }
- else {
- // reset argi to the flag that was broken.
- --argi;
- return CLMissingValue;
- }
-}
-
-bool CommandLineParser::
-IsValuedOption(OptionType optType) {
- if (optType == Integer or
- optType == PositiveInteger or
- optType == NonNegativeInteger or
- optType == Float or
- optType == PositiveFloat or
- optType == NonNegativeFloat or
- optType == String or
- optType == StringList) {
- return true;
- }
- else {
- return false;
- }
-}
-
-
-CommandLineParser::ErrorValue CommandLineParser::
-ParseIntList(VectorIndex optionValueIndex,
- VectorIndex &argi, int argc, char *argv[]) {
-
- if (argi >= argc) {
- --argi;
- return CLMissingValue;
- }
- ErrorValue ev;
- ev = CLMissingValue;
- while (argi < (unsigned int) argc and !IsOption(argv[argi])) {
- if (IsInteger(argv[argi])) {
- intListValues[optionValueIndex]->push_back(atoi(argv[argi]));
- ++argi;
- ev = CLGood;
- }
- else {
- ev = CLInvalidInteger;
- --argi;
- break;
- }
- }
- if (ev == CLMissingValue) {
- // reset argi to the flag that was broken.
- --argi;
- }
- return ev;
-}
-
-CommandLineParser::ErrorValue CommandLineParser::
-ParseStringList(VectorIndex optionValueIndex,
- VectorIndex &argi, int argc, char *argv[]) {
-
- if (argi >= argc) {
- --argi;
- return CLMissingValue;
- }
- ErrorValue ev;
- ev = CLMissingValue;
- while (argi < (unsigned int) argc and !IsOption(argv[argi])) {
- stringListValues[optionValueIndex]->push_back(argv[argi]);
- ++argi;
- ev = CLGood;
- }
- if (ev == CLMissingValue) {
- // reset argi to the flag that was broken.
- --argi;
- }
- return ev;
-}
-
-
-void CommandLineParser::
-PrintVersion() {
- std::cout << programName << "\t" << version << std::endl;
-}
-
-
-void CommandLineParser::
-PrintUsage() {
- std::ios::fmtflags f = std::cout.flags();
- if (helpString != "") {
- std::cout << helpString << std::endl;
- return;
- }
- else {
- if (programSummary.size() > 0) {
- std::cout << programName << " ";
-
- PrintIndentedText(std::cout, programSummary,
- programName.size(), lineLength);
-
- std::cout << std::endl;
- }
- std::cout << std::endl << "usage: " << programName;
- VectorIndex i = 0;
- int maxOptionLength = GetMaxOptionLength();
- while (i < optionList.size() and named[i] == false) {
- std::cout << " ";
- if (optionRequired[i] == false) {
- std::cout << "[";
- }
- std::cout << optionList[i];
- if (optionRequired[i] == false) {
- std::cout << "]";
- }
- i++;
- }
- if (i < optionList.size()) {
- std::cout << " [options] ";
- }
- std::cout << std::endl << std::endl;
- i = 0;
- while (i < optionList.size() and named[i] == false) {
- if (!named[i]) {
- std::cout << " " << std::setw(maxOptionLength)
- << std::left << optionList[i] << std::endl;
-
- PrintIndentedText(cout, descriptions[i], 15,
- (int)lineLength, 15);
-
- std::cout << std::endl;
- }
- i++;
- }
- for (; i < optionList.size(); i++) {
- std::string wholeName = "-";
- wholeName += optionList[i];
- if (IsValuedOption(optionTypeList[i])) {
- wholeName += " value ";
- }
- std::cout << " " << std::setw(maxOptionLength)
- << std::left << wholeName << std::endl;
-
- PrintIndentedText(cout, descriptions[i], 15,
- (int)lineLength, 15);
-
- std::cout << std::endl;
- }
- }
- if (examples.size() > 0) {
- std::cout << std::endl << std::endl;
- PrintIndentedText(cout, examples, 5, (int) lineLength, 5);
- std::cout << std::endl;
- }
- std::cout.flags(f);
-}
-
-int CommandLineParser::
-GetNextWordLength(std::string &text, int pos) {
- int startPos = pos;
- int textLength = text.size();
- while (pos < textLength and (!IsWhitespace(text[pos]))) {
- pos++;
- }
- return pos - startPos;
-}
-
-void CommandLineParser::
-PrintIndentedText(std::ostream &out, std::string &text,
- int allLineIndent, int lineLength, int firstLineIndent) {
-
- int textPos = 0;
- std::vector<std::string> words;
- ToWords(text, words);
- int w = 0;
- int wordsOnLine;
- int curLineLength;
- int curLineIndent = 0;
- int i;
- if (firstLineIndent == 0) {
- curLineIndent = 0;
- curLineLength = allLineIndent;
- }
- else {
- for (i = 0; i < firstLineIndent; i++) {
- out << " ";
- }
- curLineIndent = allLineIndent;
- curLineLength = allLineIndent;
- }
- std::string indentation;
- indentation.insert(0, allLineIndent, ' ');
- int textLength = text.size();
- while (textPos < textLength) {
- // Print some whitespace
- while (textPos < textLength and
- curLineLength < lineLength and
- IsWhitespace(text[textPos])) {
- out << text[textPos];
- // Some extra logic in case
- if (text[textPos] == '\n') {
- // an extra line was printed, so skip to the next line.
- curLineLength = lineLength + 1;
- // done printing this line.
- curLineLength = 0;
- if (textPos < textLength) {
- out << indentation;
- curLineLength = allLineIndent;
- }
- }
- else {
- curLineLength++;
- if (curLineLength == lineLength) {
- std::cout << std::endl;
- curLineLength = 0;
- if (textPos < textLength) {
- out << indentation;
- curLineLength = allLineIndent;
- }
- }
- }
- textPos++;
- }
- // Possibly print a word.
- if (!IsWhitespace(text[textPos])) {
- int nextWordLength = GetNextWordLength(text, textPos);
- if (nextWordLength + curLineLength >= lineLength) {
- //
- // The next word runs past the end of this line,
- // print it on a newline, or print part of it on
- // this line if the whole word wraps.
- //
- if (nextWordLength > lineLength) {
- // This word will never fit on a line, print part of it.
- int substringLength = lineLength - curLineLength;
- for (; curLineLength < lineLength;
- curLineLength++, textPos++) {
- out << text[textPos];
- }
- }
- out << std::endl;
- out << indentation;
- curLineLength = allLineIndent;
- }
- else {
- int i;
- for (i = 0; i < nextWordLength;
- i++, textPos++, curLineLength++) {
- out << text[textPos];
- }
- }
- }
- }
-}
-
-unsigned int CommandLineParser::
-GetMaxOptionLength() {
- VectorIndex i;
- VectorIndex maxLength = 0;
- for (i = 0; i < optionList.size(); i++ ){
- if (optionList[i].size() > maxLength)
- maxLength = optionList[i].size();
- }
- return maxLength;
-}
-
-
-CommandLineParser::ErrorValue CommandLineParser::
-PrintErrorOnMissingOptions() {
- VectorIndex i;
- ErrorValue ev = CLGood;
- for (i = 0; i < optionList.size(); i++ ){
- if (optionRequired[i] and !optionUsed[i]) {
- std::cout << "ERROR, the option " << optionList[i]
- << " must be specified." << std::endl;
- ev = CLMissingOption;
- }
- }
- return ev;
-}
diff --git a/libcpp/pbdata/CommandLineParser.hpp b/libcpp/pbdata/CommandLineParser.hpp
deleted file mode 100644
index 8cc7a8e..0000000
--- a/libcpp/pbdata/CommandLineParser.hpp
+++ /dev/null
@@ -1,175 +0,0 @@
-#ifndef _BLASR_COMMAND_LINE_PARSER_HPP_
-#define _BLASR_COMMAND_LINE_PARSER_HPP_
-
-#include <vector>
-#include <cstring>
-#include <iostream>
-#include <iomanip>
-#include <stdlib.h>
-#include <assert.h>
-#include "Types.h"
-#include <sstream>
-#include "StringUtils.hpp"
-
-class CommandLineParser {
-public:
- enum ErrorValue {
- CLGood,
- CLBadOption,
- CLMissingOption,
- CLMissingValue,
- CLInvalidInteger,
- CLInvalidPositiveInteger,
- CLInvalidNonNegativeInteger,
- CLInvalidFloat,
- CLInvalidPositiveFloat,
- CLInvalidNonNegativeFloat };
-
-
- enum OptionType {
- Flag,
- Integer,
- PositiveInteger, // > 0
- NonNegativeInteger, // >= 0
- IntegerList,
- Float,
- PositiveFloat, // > 0
- NonNegativeFloat, // >= 0
- String,
- StringList };
-
- std::vector<bool*> boolValues;
- std::vector<int*> intValues;
- std::vector<float*> floatValues;
- std::vector<std::string*> stringValues;
- std::vector<std::vector<std::string> *>stringListValues;
- std::vector<std::vector<int> *> intListValues;
- std::vector<int*> flagList;
- std::vector<std::string> optionList;
- std::vector<OptionType> optionTypeList;
- std::vector<int> optionValueIndexList;
- std::vector<std::string> descriptions;
- std::vector<char> optionRequired;
- std::vector<char> optionUsed;
- std::vector<char> named;
-
- std::string programName;
- std::string programSummary;
- std::string conciseHelp;
- std::string verboseHelp;
- std::string helpString;
- std::string examples;
- std::string version;
-
- int lineLength;
- int numUnnamedOptions;
- bool specialVersionFlag;
-
- CommandLineParser();
-
- void SetProgramSummary(std::string summaryp);
-
- void SetHelp(std::string _help);
-
- void SetConciseHelp(std::string _conciseHelp) ;
-
- void SetProgramName(std::string namep);
-
- void SetVersion(std::string versionp);
-
- void SetVerboseHelp(std::string helpp);
-
- void SetExamples(std::string examplesp);
-
- void RegisterPreviousFlagsAsHidden();
-
- void RegisterVersionFlag(bool *value);
-
- void RegisterFlagOption(std::string option, bool *value,
- std::string description, bool required=false);
-
- void RegisterIntOption(std::string option, int *value,
- std::string description, OptionType type,
- bool required=false, bool hidden=false);
-
- void RegisterFloatOption(std::string option, float *value,
- std::string description, OptionType type, bool required=false);
-
- void RegisterStringOption(std::string option, std::string *value,
- std::string description, bool required=false);
-
- void RegisterStringListOption(std::string option,
- std::vector<std::string> *value, std::string description,
- bool required=false);
-
- void RegisterIntListOption(std::string option, std::vector<int> *value,
- std::string description, bool required=false);
-
- int IsOption(char *str);
-
- int IsInteger(char *str);
-
- int IsFloat(char *str);
-
- int FindOption(char *option);
-
- static void CommandLineToString(int argc, char* argv[],
- std::string& commandLine);
-
- int ParseCommandLine(int argc, char* argv[], bool isProgramNameOnlyAllowed=false);
-
- int ParseCommandLine(int argc, char* argv[],
- std::vector<std::string> &unflaggedValues, bool isProgramNameOnlyAllowed=false);
-
- ErrorValue ParseOption(VectorIndex optionIndex,
- VectorIndex &argi, int argc, char *argv[]);
-
- void PrintErrorMessage(ErrorValue ev, char *option);
-
- ErrorValue ParseFlag(VectorIndex optionValueIndex,
- VectorIndex &argi, int argc, char *argv[]);
-
- ErrorValue ParseInteger(VectorIndex optionValueIndex,
- VectorIndex &argi, int argc, char *argv[]);
-
- ErrorValue ParsePositiveInteger(VectorIndex optionValueIndex,
- VectorIndex &argi, int argc, char *argv[]);
-
- ErrorValue ParseNonNegativeInteger(VectorIndex optionValueIndex,
- VectorIndex &argi, int argc, char *argv[]);
-
- ErrorValue ParseFloat(VectorIndex optionValueIndex,
- VectorIndex &argi, int argc, char *argv[]);
-
- ErrorValue ParsePositiveFloat(VectorIndex optionValueIndex,
- VectorIndex &argi, int argc, char *argv[]);
-
- ErrorValue ParseNonNegativeFloat(VectorIndex optionValueIndex,
- VectorIndex &argi, int argc, char *argv[]);
-
- ErrorValue ParseString(VectorIndex optionValueIndex, VectorIndex &argi,
- int argc, char *argv[]);
-
- bool IsValuedOption(OptionType optType);
-
- ErrorValue ParseIntList(VectorIndex optionValueIndex, VectorIndex &argi,
- int argc, char *argv[]);
-
- ErrorValue ParseStringList(VectorIndex optionValueIndex, VectorIndex &argi,
- int argc, char *argv[]);
-
- void PrintVersion();
-
- void PrintUsage();
-
- int GetNextWordLength(std::string &text, int pos);
-
- void PrintIndentedText(std::ostream &out, std::string &text,
- int allLineIndent, int lineLength = 80, int firstLineIndent=0);
-
- unsigned int GetMaxOptionLength();
-
- ErrorValue PrintErrorOnMissingOptions();
-};
-
-#endif
diff --git a/libcpp/pbdata/Compare4BitCompressed.hpp b/libcpp/pbdata/Compare4BitCompressed.hpp
deleted file mode 100644
index f94f37f..0000000
--- a/libcpp/pbdata/Compare4BitCompressed.hpp
+++ /dev/null
@@ -1,98 +0,0 @@
-/*
- * ============================================================================
- *
- * Filename: Compare4BitCompressed.h
- *
- * Description: Imported from BLASR algorithm/compare
- *
- * Version: 1.0
- * Created: 12/19/2013 05:22:46 PM
- * Revision: none
- * Compiler: gcc
- *
- * Author: Yuan Li (yli), yli at pacificbiosciences.com
- * Company: Pacific Biosciences
- *
- * ============================================================================
- */
-#ifndef _BLASR_COMPARE_4BIT_COMPRESSED_HPP_
-#define _BLASR_COMPARE_4BIT_COMPRESSED_HPP_
-
-#include "defs.h"
-
-template<typename TNuc>
-class Compare4BitCompressed {
- public:
- const static unsigned char MaskCount = 0xf;
-
- static int Compare(TNuc *lhs, TNuc *rhs) {
- return ThreeBit[*lhs & MaskCount] - ThreeBit[*rhs & MaskCount];
- }
-
- static int Compare(TNuc *lhs, TNuc *rhs, int length) {
- int i;
- int res;
- i = 0;
- TNuc *lhsptr;
- TNuc *rhsptr;
- lhsptr = lhs;
- rhsptr = rhs;
- char *lhsend = lhs + length;
- res = 0;
- while (lhsptr != lhsend and res == 0) {
- res = ThreeBit[*lhsptr & MaskCount] - ThreeBit[*rhsptr & MaskCount];
- ++lhsptr;
- ++rhsptr;
- }
- return res;
- }
-
- static int Equal(TNuc a, TNuc b) {
- return (a & MaskCount) == (b & MaskCount);
- }
-
- static int LessThan(TNuc *a, int aLen, TNuc *b, int bLen) {
- int minabLen = MIN(aLen, bLen);
- if (minabLen <= 0)
- return 0;
- // int cmpRes;
-
- int cmpRes = Compare(a, b, minabLen);
- if (cmpRes < 0) {
- return 1;
- }
- else {
- return 0;
- }
- }
-
- static int LessThanEqual(TNuc *a, int aLen, TNuc *b, int bLen) {
- int minabLen = MIN(aLen, bLen);
- if (minabLen <= 0)
- return 1;
- int cmpRes = Compare(a, b, minabLen);
- if (cmpRes <= 0) {
- return 1;
- }
- else {
- return 0;
- }
- }
-
- static int Equals(TNuc *a, int aLen, TNuc *b, int bLen) {
- int minabLen = MIN(aLen, bLen);
- if (minabLen < 0)
- return 0;
- if (minabLen == 0)
- return 1;
-
- int cmpRes = Compare(a, b, minabLen);
- if (cmpRes == 0 and aLen <= bLen) {
- return 1;
- }
- else {
- return 0;
- }
- }
-};
-#endif
diff --git a/libcpp/pbdata/CompressedDNASequence.hpp b/libcpp/pbdata/CompressedDNASequence.hpp
deleted file mode 100644
index a3fa6d1..0000000
--- a/libcpp/pbdata/CompressedDNASequence.hpp
+++ /dev/null
@@ -1,89 +0,0 @@
-#ifndef _BLASR_COMPRESSED_DNA_SEQUENCE_HPP_
-#define _BLASR_COMPRESSED_DNA_SEQUENCE_HPP_
-
-#include "DNASequence.hpp"
-#include "FASTASequence.hpp"
-#include "defs.h"
-#include <string.h>
-#include "qvs/QualityValue.hpp"
-#include "Compare4BitCompressed.hpp"
-
-typedef unsigned char CompressedNucleotide;
-
-class CompressedDNASequence: public DNASequence {
- static const unsigned char MaskCount = 0xf;
- static const unsigned char MaskNuc = 0xf0;
- static const unsigned char ShiftCount = 4;
-
- public:
- char *title;
- int titleLength;
- //
- // This is just a placeholder for now.
- // No extra data here, just the ability to decompress. Right now
- // the utilities for the compressed dna sequences
- // are in CompressedSeqUtils.h, which could move here later.
- //
- QualityValue *qual;
-
- CompressedDNASequence() {
- const char t[] = "Compressed sequence\0";
- titleLength = strlen(t);
- title = new char[titleLength+1];
- strcpy(title, t);
- title[titleLength] = '\0';
- }
-
- void MakeRC(CompressedDNASequence &rc) {
- rc.Allocate(length);
- DNALength i;
- for (i = 0; i < length; i++) {
- rc.seq[length - i - 1] = ReverseComplementNuc[ThreeBit[seq[i] & MaskCount]];
- rc.seq[length - i - 1] += (seq[i] & MaskNuc);
- }
- memcpy(rc.title, title, titleLength);
- rc.titleLength = titleLength;
- }
-
- Nucleotide operator[](DNALength i) {
- return GetNuc(i);
- }
-
- Nucleotide GetNuc(DNALength i) {
- return (seq[i] & MaskCount);
- }
-
- unsigned char GetCount(DNALength i) {
- return seq[i] >> ShiftCount;
- }
-
- char *GetName() {
- return (char*) title;
- }
-
- void Copy(FASTASequence &rhs) {
- seq = new CompressedNucleotide[rhs.length];
- memcpy(seq, rhs.seq, rhs.length);
- length = rhs.length;
- if (title != NULL) {
- delete[] title;
- }
- title = new char[rhs.titleLength+1];
- memcpy(title, rhs.title, rhs.titleLength);
- titleLength = rhs.titleLength;
- title[titleLength] = '\0';
- }
- float GetAverageQuality() {
- return 0.0;
- }
-
- void SortHomopolymerQualities() {
- cout << "qualities are not implemented for compressed sequences." << endl;
- assert(0);
- }
-};
-
-
-
-
-#endif
diff --git a/libcpp/pbdata/CompressedSequence.hpp b/libcpp/pbdata/CompressedSequence.hpp
deleted file mode 100644
index 45b3aaa..0000000
--- a/libcpp/pbdata/CompressedSequence.hpp
+++ /dev/null
@@ -1,100 +0,0 @@
-#ifndef _BLASR_COMPRESSED_SEQUENCE_HPP_
-#define _BLASR_COMPRESSED_SEQUENCE_HPP_
-#include <cassert>
-#include <stdint.h>
-#include <iostream>
-#include <fstream>
-#include <ostream>
-#include <cstring>
-#include "utils.hpp"
-#include "Types.h"
-#include "Enumerations.h"
-#include "NucConversion.hpp"
-#include "DNASequence.hpp"
-#include "qvs/QualityValue.hpp"
-#include "reads/ZMWGroupEntry.hpp"
-#include "FASTASequence.hpp"
-#include "ReverseCompressIndex.hpp"
-
-typedef unsigned char CompressedNucleotide;
-
-template<typename T_Sequence>
-class CompressedSequence : public FASTASequence {
-private:
- int hasIndex;
- int hasTitle;
- ReverseCompressIndex index;
-
- static const unsigned char MaskCount = 0xf;
- static const unsigned char MaskNuc = 0xf0;
- static const unsigned char ShiftCount = 4;
-
-public:
- //
- // This is just a placeholder for now.
- // No extra data here, just the ability to decompress. Right now
- // the utilities for the compressed dna sequences
- // are in CompressedSeqUtils.h, which could move here later.
- //
- QualityValue *qual;
-
- void CopyConfiguration(CompressedSequence<T_Sequence> &rhs);
-
- void ShallowCopy(CompressedSequence<T_Sequence> &rhs);
-
- void MakeRC(CompressedSequence &rc);
-
- Nucleotide operator[](DNALength i);
-
- Nucleotide GetNuc(DNALength i);
-
- unsigned char GetCount(DNALength i);
-
- char *GetName();
-
- void Copy(FASTASequence &rhs);
-
- float GetAverageQuality();
-
- void SortHomopolymerQualities();
-
- CompressedSequence();
- ~CompressedSequence();
-
- void Free();
-
- void SetHasTitle();
-
- void SetHasIndex();
-
- void Write(std::string outFileName);
-
- void Read(std::string inFileName);
-
- int BuildFourBitReverseIndex(int binSize);
-
- int BuildReverseIndex(int maxRun, int binSize);
-
- long Lookup4BitCompressedSequencePos(int cpPos);
-
- int LookupSequencePos(int cpPos);
-
- char GetCount(unsigned char ch);
-
- DNALength FourBitCompressHomopolymers();
-
- static int Only4BitACTG(CompressedNucleotide *seq, int seqLength);
-
- int Only4BitACTG();
-
- void RemoveCompressionCounts();
-
- DNALength FourBitDecompressHomopolymers(int start, int end,
- T_Sequence &decompSeq);
-
- DNALength CondenseHomopolymers();
-};
-
-#include "CompressedSequenceImpl.hpp"
-
-#endif // _BLASR_COMPRESSED_SEQUENCE_HPP_
diff --git a/libcpp/pbdata/CompressedSequenceImpl.hpp b/libcpp/pbdata/CompressedSequenceImpl.hpp
deleted file mode 100644
index 7759541..0000000
--- a/libcpp/pbdata/CompressedSequenceImpl.hpp
+++ /dev/null
@@ -1,343 +0,0 @@
-#ifndef _BLASR_COMPRESSED_SEQUENCES_IMPL_HPP_
-#define _BLASR_COMPRESSED_SEQUENCES_IMPL_HPP_
-
-template<typename T_Sequence>
-void CompressedSequence<T_Sequence>::CopyConfiguration(CompressedSequence<T_Sequence> &rhs) {
- hasIndex = rhs.hasIndex;
- hasTitle = rhs.hasTitle;
-}
-
-template<typename T_Sequence>
-void CompressedSequence<T_Sequence>::ShallowCopy(CompressedSequence<T_Sequence> &rhs) {
- //
- // Copy over non sequence information
- index.ShallowCopy(rhs.index);
- CopyConfiguration(rhs);
-
- // Copy sequence information
- ((FASTASequence*)this)->ShallowCopy((FASTASequence&)rhs);
-}
-
-template<typename T_Sequence>
-void CompressedSequence<T_Sequence>::MakeRC(CompressedSequence &rc) {
- rc.Free(); //Free rc.seq and rc.title before allocate.
-
- rc.Allocate(length);
- DNALength i;
- for (i = 0; i < length; i++) {
- rc.seq[length - i - 1] = ReverseComplementNuc[ThreeBit[seq[i] & MaskCount]];
- rc.seq[length - i - 1] += (seq[i] & MaskNuc);
- }
-
- rc.CopyTitle(title, titleLength);
-}
-
-template<typename T_Sequence>
-Nucleotide CompressedSequence<T_Sequence>::operator[](DNALength i) {
- return GetNuc(i);
-}
-
-template<typename T_Sequence>
-Nucleotide CompressedSequence<T_Sequence>::GetNuc(DNALength i) {
- return (seq[i] & MaskCount);
-}
-
-template<typename T_Sequence>
-unsigned char CompressedSequence<T_Sequence>::GetCount(DNALength i) {
- return seq[i] >> ShiftCount;
-}
-
-template<typename T_Sequence>
-char* CompressedSequence<T_Sequence>::GetName() {
- return (char*) title;
-}
-
-template<typename T_Sequence>
-void CompressedSequence<T_Sequence>::Copy(FASTASequence &rhs) {
- seq = new CompressedNucleotide[rhs.length];
- memcpy(seq, rhs.seq, rhs.length);
- length = rhs.length;
- if (title != NULL) {
- delete[] title;
- }
- title = new char[rhs.titleLength+1];
- memcpy(title, rhs.title, rhs.titleLength);
- titleLength = rhs.titleLength;
- title[titleLength] = '\0';
-}
-
-template<typename T_Sequence>
-float CompressedSequence<T_Sequence>::GetAverageQuality() {
- return 0.0;
-}
-
-template<typename T_Sequence>
-void CompressedSequence<T_Sequence>::SortHomopolymerQualities() {
- std::cout << "qualities are not implemented for compressed sequences."
- << std::endl;
-}
-
-template<typename T_Sequence>
-CompressedSequence<T_Sequence>::CompressedSequence() {
- hasIndex = 0;
- hasTitle = 0;
- qual = NULL;
- FASTASequence();
-}
-
-template<typename T_Sequence>
-CompressedSequence<T_Sequence>::~CompressedSequence() {
- CompressedSequence::Free();
-}
-
-template<typename T_Sequence>
-void CompressedSequence<T_Sequence>::Free() {
- if (hasIndex) {
- index.Free();
- }
- if(qual) {delete [] qual; qual = NULL;}
- FASTASequence::Free();
- hasIndex = 0;
- hasTitle = 0;
-}
-
-template<typename T_Sequence>
-void CompressedSequence<T_Sequence>::SetHasTitle() {
- hasTitle = 1;
-}
-template<typename T_Sequence>
-
-void CompressedSequence<T_Sequence>::SetHasIndex() {
- hasIndex = 1;
-}
-
-template<typename T_Sequence>
-void CompressedSequence<T_Sequence>::Write(std::string outFileName) {
- std::ofstream out;
- CrucialOpen(outFileName,out, std::ios::binary | std::ios::in);
- out.write((char*) &hasTitle, sizeof(int));
- out.write((char*) &hasIndex, sizeof(int));
- if (hasTitle) {
- out.write((char*)&titleLength, sizeof(int));
- out.write((char*)title, titleLength);
- }
- out.write((char*) &length, sizeof(int));
- out.write((char*) seq, sizeof(char) * length);
- if (hasIndex) {
- index.Write(out);
- }
- out.close();
-}
-
-template<typename T_Sequence>
-void CompressedSequence<T_Sequence>::Read(std::string inFileName) {
- Free(); //Free before reusing this object.
- std::ifstream in;
- CrucialOpen(inFileName, in, std::ios::binary | std::ios::in);
- // step 1, read in the options.
- in.read((char*) &hasTitle, sizeof(int));
- in.read((char*) &hasIndex, sizeof(int));
- if (hasTitle) {
- int inTitleLength;
- in.read((char*) &inTitleLength, sizeof(int));
- char * inTitle = new char[inTitleLength+1];
- in.read((char*) inTitle, inTitleLength);
- inTitle[titleLength] = '\0';
- CopyTitle(inTitle, inTitleLength);
- delete [] inTitle;
- }
- in.read((char*) &length, sizeof(DNALength));
- seq = new Nucleotide[length];
- in.read((char*) seq, length * sizeof(Nucleotide));
- if (hasIndex) {
- index.Read(in);
- }
- deleteOnExit = true;
-}
-
-template<typename T_Sequence>
-int CompressedSequence<T_Sequence>::BuildFourBitReverseIndex(int binSize) {
- BuildReverseIndex(15, binSize);
-}
-
-template<typename T_Sequence>
-int CompressedSequence<T_Sequence>::BuildReverseIndex(int maxRun, int binSize) {
- hasIndex = 1;
-
- DNALength i;
- DNALength hpi;
-
- //
- // Phase 1. Count the number of nucleotide transitions-1
- //
-
- hpi = 0;
- for (i = 0; i < length; i++) {
- // if (hpi % binSize == 0 ){
- // index.push_back(i);
- // }
- int run = 1;
- while (i < length - 1
- and ThreeBit[seq[i]] == ThreeBit[seq[i+1]] and
- (run == 0 or
- run < maxRun)) {i++, run++;};
- hpi++;
- }
-
-
- //
- // Phase 2. Store the index.
- //
- index.Free();
- index.indexLength = hpi/index.binSize + 1;
- index.index = new int[index.indexLength];
- hpi = 0;
- int ii = 0;
- for (i = 0; i < length; i++) {
- if (hpi % index.binSize == 0 ) {
- assert(ii < index.indexLength);
- index.index[ii] = i;
- ++ii;
- }
- int run = 1;
- while (i < length - 1
- and ThreeBit[seq[i]] == ThreeBit[seq[i+1]] and
- (run == 0 or
- run < maxRun)) {i++, run++;};
- hpi++;
- }
-
- return index.size();
-}
-
-template<typename T_Sequence>
-long CompressedSequence<T_Sequence>::Lookup4BitCompressedSequencePos(int cpPos) {
- int bin = cpPos / index.binSize;
- int origPos = index.index[bin];
- int cpBinPos = bin * index.binSize;
- int cp;
- for (cp = cpBinPos; cp < cpPos; cp++ ){
- origPos += GetCount(seq[cp]);
- }
- return origPos;
-}
-
-
-template<typename T_Sequence>
-int CompressedSequence<T_Sequence>::LookupSequencePos(int hpPos) {
- int origPos = index.index[hpPos % index.binSize];
- int hpi;
- for (hpi = (hpPos / index.binSize) * index.binSize; hpi < hpPos; hpi++, origPos++ ) {
- //
- // advance orig across all homopolymer stretches.
- //
- while (origPos < length - 1 and
- seq[origPos] == seq[origPos+1])
- ++origPos;
- }
- return origPos;
-}
-
-template<typename T_Sequence>
-char CompressedSequence<T_Sequence>::GetCount(unsigned char ch) {
- return (ch >> 4);
-}
-
-template<typename T_Sequence>
-DNALength CompressedSequence<T_Sequence>::FourBitCompressHomopolymers() {
- VectorIndex i, c;
- unsigned char count = 0;
- for (i =0, c = 0; i < length; c++, i++) {
- count = 1;
- while (count < 15 and
- i < length - 1
- and ThreeBit[seq[i]] == ThreeBit[seq[i+1]]) {
- i++; count++;
- }
- // store nuc into the lower 4 bits
- seq[c] = ThreeBit[seq[i]];
-
- // store count into the upper 4 bits.
- count = count << 4;
- seq[c] = seq[c] | count;
-
- }
- length = c;
- return length;
-}
-
-template<typename T_Sequence>
-int CompressedSequence<T_Sequence>::Only4BitACTG(CompressedNucleotide *seq, int seqLength) {
- int i;
- for (i = 0; i < seqLength; i++ ){
- if (ThreeBit[seq[i] & MaskCount] > 3) {
- return 0;
- }
- }
- return 1;
-}
-
-template<typename T_Sequence>
-int CompressedSequence<T_Sequence>::Only4BitACTG() {
- return Only4BitACTG(seq, length);
-}
-
-template<typename T_Sequence>
-void CompressedSequence<T_Sequence>::RemoveCompressionCounts() {
- DNALength i;
- unsigned char mask =0xf;
- for (i = 0; i< length; i++) {
- seq[i] = seq[i] & mask;
- }
-}
-
-template<typename T_Sequence>
-DNALength CompressedSequence<T_Sequence>::FourBitDecompressHomopolymers(int start, int end,
- T_Sequence &decompSeq) {
- decompSeq.Free(); // Free before decomp;
-
- //
- // first compute the length of the decoded
- //
- DNALength i;
- decompSeq.length = 0;
- for (i = start; i < end; i++ ){
- unsigned char count;
- count = (unsigned char) seq[i];
- count >>= 4;
- decompSeq.length += count;
- }
- decompSeq.seq = new Nucleotide[decompSeq.length];
-
- //
- // Now store the actual decompressed seq.
- //
- int d = 0;
- unsigned char mask = 0xf;
- for (i = start; i < end; i++ ){
- unsigned char count;
- count = (unsigned char) seq[i];
- count >>= 4;
- int j;
- for (j = 0; j < count; j++ ){
- decompSeq.seq[d] = FourBitToAscii[(seq[i] & mask)];
- d++;
- }
- }
- decompSeq.bitsPerNuc = 4;
- decompSeq.deleteOnExit = true;
- return decompSeq.length;
-}
-
-template<typename T_Sequence>
-DNALength CompressedSequence<T_Sequence>::CondenseHomopolymers() {
- VectorIndex i, c;
- for (i =0, c = 0; i < length; c++, i++) {
- while (i < length - 1 and ThreeBit[seq[i]] == ThreeBit[seq[i+1]]) i++;
- seq[c] = seq[i];
- }
- length = c;
- return length;
-}
-
-#endif
diff --git a/libcpp/pbdata/DNASequence.cpp b/libcpp/pbdata/DNASequence.cpp
deleted file mode 100644
index cec3fab..0000000
--- a/libcpp/pbdata/DNASequence.cpp
+++ /dev/null
@@ -1,402 +0,0 @@
-#include <cassert>
-#include <cstring>
-#include "Types.h"
-#include "DNASequence.hpp"
-
-DNALength DNASequence::size() {
- return length;
-}
-
-void DNASequence::TakeOwnership(DNASequence &rhs) {
- CheckBeforeCopyOrReference(rhs);
- // Free this DNASequence before take owner ship from rhs.
- DNASequence::Free();
-
- seq = rhs.seq;
- length = rhs.length;
- deleteOnExit = rhs.deleteOnExit;
-
- rhs.deleteOnExit = false;
-}
-
-void DNASequence::Append(const DNASequence &rhs, DNALength appendPos) {
- assert(deleteOnExit); // must have control over seq.
- //
- // Simply append rhs to this seuqence, unless appendPos is nonzero
- // in which case rhs is inserted at attendPos, overwriting this
- // sequence from appendPos to the end.
- //
- Nucleotide *newSeq;
- //
- // Handle the two cases (appendPos == 0 and appendPos > 0)
- // separately in order to handle memory deallocation correctly.
- //
- if (appendPos == 0) {
- DNALength newSeqLength = length + rhs.length;
- newSeq = new Nucleotide[newSeqLength];
- memcpy(newSeq, seq, length);
- memcpy(&newSeq[length], rhs.seq, rhs.length);
-
- if (length != 0) {
- delete[] seq;
- }
- seq = newSeq;
- length = newSeqLength;
- }
- else {
- if (appendPos + rhs.length < length) {
- memcpy(&seq[appendPos], rhs.seq, rhs.length);
- length = appendPos + rhs.length;
- }
- else {
- DNALength lengthCopy = length;
- length = appendPos;
- DNALength newSeqLength;
- newSeqLength = length + rhs.length;
- newSeq = new Nucleotide[newSeqLength];
- memcpy(newSeq, seq, length);
- memcpy(&newSeq[length], rhs.seq, rhs.length);
- if (deleteOnExit and lengthCopy != 0) {
- delete[] seq;
- }
- seq = newSeq;
- length = newSeqLength;
- }
- }
- deleteOnExit = true;
-}
-
-// Copy FROM rhs to this DNASequence.
-DNASequence& DNASequence::Copy(const DNASequence &rhs, DNALength rhsPos, DNALength rhsLength) {
- CheckBeforeCopyOrReference(rhs);
- // Free this DNASequence before copying from rhs
- DNASequence::Free();
-
- //
- // When initializing a vector of DNASequence's, the copy
- // constructor will initialze a list and call this
- // function with a zero-length DNASequence as the rhs to
- // initialize every element in the vector The check
- // below will fail on zero-length sequences, so add a boundary
- // condition check before that to allow the copy-constructor to
- // work.
- //
- if (rhs.length == 0) {
- seq = NULL;
- length = 0;
- deleteOnExit = true;
- return *this;
- }
-
- //
- // Silently ignoring this case could lead to problems later on,
- // catastrophically assert here if the input is not valid.
- // In case rhsLength + rhsPos > ULONG_MAX (4294967295), check
- // both rhsLength and rhsPos, fix bug 21794
- //
- if (not (rhsLength <= rhs.length &&
- rhsPos <= rhs.length + 1 &&
- rhsLength + rhsPos <= rhs.length + 2 )) {
- std::cout << "ERROR. The subsequence to copy is out of bounds."
- << std::endl
- << " Failed to copy a subsequence starting at " << rhsPos
- << std::endl
- << " with length "<< rhsLength
- << " from a sequence of length " << rhs.length << "."
- << std::endl;
- exit(1);
- }
-
- if (rhsLength == 0) {
- rhsLength = rhs.length - rhsPos;
- }
- if (rhsLength == 0) {
- seq = NULL;
- }
- else {
- seq = new Nucleotide [rhsLength];
- memcpy(seq, &rhs.seq[rhsPos], rhsLength);
- }
- length = rhsLength;
- deleteOnExit = true;
- return *this;
-}
-
-DNASequence& DNASequence::Copy(const std::string &rhsSeq) {
- // Free this DNASequence before copying from rhs
- DNASequence::Allocate(static_cast<DNALength>(rhsSeq.size()));
- memcpy(seq, rhsSeq.c_str(), length);
- return *this;
-}
-
-DNASequence & DNASequence::operator=(const std::string & rhsSeq) {
- return DNASequence::Copy(rhsSeq);
-}
-
-void DNASequence::ShallowCopy(const DNASequence &rhs) {
- seq = rhs.seq;
- length = rhs.length;
- deleteOnExit = false;
-}
-
-int DNASequence::GetStorageSize() {
- return (length * sizeof(Nucleotide));
-}
-
-DNASequence &DNASequence::operator=(const DNASequence &rhs){
- DNASequence::Copy(rhs);
- return *this;
-}
-
-//
-// synonym for printseq
-//
-void DNASequence::Print(std::ostream &out, int lineLength) {
- PrintSeq(out, lineLength);
-}
-
-void DNASequence::PrintSeq(std::ostream &out, int lineLength) {
- if (lineLength == 0) {
- std::string line;
- line.assign((char*)seq, length);
- out << line;
- }
- else {
- //
- // Make sure this isn't
- assert(lineLength > 0);
- DNALength curPos = 0;
- int curLineLength = lineLength;
- while (curPos < length) {
- if (curPos + curLineLength > length) {
- curLineLength = length - curPos;
- }
- std::string line;
- line.assign((char*) &seq[curPos], curLineLength);
- out << line << std::endl;
- curPos += curLineLength;
- }
- }
-}
-
-void DNASequence::Allocate(DNALength plength) {
- DNASequence::Free();
-
- seq = new Nucleotide [plength];
- length = plength;
- deleteOnExit = true;
-}
-
-void DNASequence::ReferenceSubstring(const DNASequence &rhs, DNALength pos, DNALength substrLength) {
- CheckBeforeCopyOrReference(rhs);
-
- // Free this DNASequence before referencing rhs.
- DNASequence::Free();
-
- //
- // This makes a reference therefore it should not be deleted.
- //
- assert(pos >= 0 && pos <= rhs.length &&
- substrLength >= 0 && substrLength <= rhs.length);
- if (substrLength == 0) {
- substrLength = rhs.length - pos;
- }
- assert(pos + substrLength <= rhs.length);
- seq = &rhs.seq[pos];
- length = substrLength;
- deleteOnExit = false;
-}
-
-DNALength DNASequence::MakeRCCoordinate(DNALength forPos ) {
- return length - forPos - 1;
-}
-
-// Create a reverse complement DNAsequence of this DNASequence and assign to rc.
-void DNASequence::MakeRC(DNASequence &rc, DNALength pos, DNALength rcLength) {
- if (rcLength == 0) {
- rcLength = length - pos;
- }
-
- ((DNASequence&)rc).Allocate(rcLength);
- DNALength i;
- for (i = 0; i < rcLength; i++) {
- rc.seq[rcLength - i - 1] = ReverseComplementNuc[seq[i+pos]];
- }
- rc.length = rcLength;
- rc.deleteOnExit = true;
-}
-
-void DNASequence::ToTwoBit() {
- DNALength i;
- for (i = 0; i < length; i++) {
- seq[i] = TwoBit[seq[i]];
- }
- bitsPerNuc = 2;
-}
-
-void DNASequence::ToFourBit() {
- DNALength i;
- if (bitsPerNuc != 4)
- for (i = 0; i < length; i++) { seq[i] = FourBit[seq[i]]; }
- bitsPerNuc = 4;
-}
-
-void DNASequence::ConvertThreeBitToAscii() {
- DNALength i;
- for (i = 0; i < length; i++ ){
- seq[i] = ThreeBitToAscii[seq[i]];
- }
-}
-
-void DNASequence::ToAscii() {
- DNALength i;
- if (bitsPerNuc != 8) {
- for (i = 0; i < length; i++ ){
- seq[i] = FourBitToAscii[seq[i]];
- }
- bitsPerNuc = 8;
- }
-}
-
-// Copy rhs[start:start+plength] to this DNASequence.
-void DNASequence::Assign(DNASequence &ref, DNALength start, DNALength plength) {
- CheckBeforeCopyOrReference(ref);
- // Free this DNASequence before assigning anything
- DNASequence::Free();
-
- if (plength) {
- length = plength;
- seq = new Nucleotide[length];
- memcpy(seq, &ref.seq[start], length);
- }
- else if (start) {
- length = ref.length - start;
- seq = new Nucleotide[length];
- memcpy(seq, &ref.seq[start], length);
- }
- else {
- ((DNASequence*)this)->Copy(ref);
- }
- deleteOnExit = true;
-}
-
-void DNASequence::ToLower() {
- DNALength i;
- for (i = 0; i < length; i++) {
- seq[i] = AllToLower[seq[i]];
- }
-}
-
-void DNASequence::ToUpper() {
- DNALength i;
- for (i = 0; i < length; i++) {
- seq[i] = AllToUpper[seq[i]];
- }
-}
-
-void DNASequence::Concatenate(const Nucleotide *moreSeq, DNALength moreSeqLength) {
- DNALength prevLength = length;
- length += moreSeqLength;
- Nucleotide *prev = seq;
- seq = new Nucleotide[length];
- if (prev != NULL) {
- memcpy(seq, prev, prevLength);
- delete[] prev;
- }
- memcpy((Nucleotide*) &seq[prevLength], moreSeq, moreSeqLength);
- deleteOnExit = true;
-}
-
-std::string DNASequence::GetTitle() const {
- return std::string("");
-}
-
-void DNASequence::Concatenate(const Nucleotide* moreSeq) {
- DNALength moreSeqLength = strlen((char*) moreSeq);
- Concatenate(moreSeq, moreSeqLength);
-}
-
-void DNASequence::Concatenate(DNASequence &seq) {
- Concatenate(seq.seq, seq.length);
-}
-
-int DNASequence::Compare(DNALength pos, DNASequence &rhs, DNALength rhsPos, DNALength length) {
- return memcmp(&seq[pos], &rhs.seq[rhsPos], length);
-}
-
-int DNASequence::LessThanEqual(DNALength pos, DNASequence &rhs, DNALength rhsPos, DNALength length) {
- int res = Compare(pos, rhs, rhsPos, length);
- if (res <= 0)
- return 1;
- else
- return 0;
-}
-
-int DNASequence::Equals(DNASequence &rhs, DNALength rhsPos, DNALength length, DNALength pos) {
- int res = Compare(pos, rhs, rhsPos, length);
- return res == 0;
-}
-
-int DNASequence::LessThan(DNALength pos, DNASequence &rhs, DNALength rhsPos, DNALength length) {
- int res= Compare(pos, rhs, rhsPos, length);
- return (res < 0);
-}
-
-void DNASequence::CleanupASCII() {
- DNALength i;
- for (i = 0; i < length; i++ ){
- if (ThreeBit[seq[i]] == 255) {
- seq[i] = 'N';
- }
- }
-}
-
-Nucleotide DNASequence::GetNuc(DNALength i) {
- return seq[i];
-}
-
-DNALength DNASequence::GetRepeatContent() {
- DNALength i;
- DNALength nRepeat = 0;
- for (i =0 ; i < length;i++) {
- if (tolower(seq[i]) == seq[i]) { nRepeat++;}
- }
- return nRepeat;
-}
-
-void DNASequence::CleanupOnFree() {
- deleteOnExit = true;
-}
-
-void DNASequence::Free() {
- if (deleteOnExit == true) {
- // if has control, delete seq
- // Otherwise, seq in memory is controlled by another object,
- // and will be deleted later.
- if (seq != NULL) {
- delete[] seq;
- }
- }
- // Reset seq, length and deleteOnExit
- seq = NULL;
- length = 0;
- deleteOnExit = false;
-}
-
-void DNASequence::Resize(DNALength newLength) {
- DNASequence::Free();
- seq = new Nucleotide[newLength];
- length = newLength;
- deleteOnExit = true;
-}
-
-DNALength DNASequence::GetSeqStorage() {
- return length;
-}
-
-#ifdef USE_PBBAM
-DNASequence & DNASequence::Copy(const PacBio::BAM::BamRecord & record) {
- return DNASequence::Copy(record.Sequence());
-}
-#endif
-
diff --git a/libcpp/pbdata/DNASequence.hpp b/libcpp/pbdata/DNASequence.hpp
deleted file mode 100644
index 286e7d8..0000000
--- a/libcpp/pbdata/DNASequence.hpp
+++ /dev/null
@@ -1,183 +0,0 @@
-#ifndef _BLASR_DNA_SEQUENCE_HPP_
-#define _BLASR_DNA_SEQUENCE_HPP_
-
-#include <stdint.h>
-#include <stdlib.h>
-#include <iostream>
-#include <string>
-#include <cassert>
-#include "Types.h"
-#include "NucConversion.hpp"
-#include "libconfig.h"
-
-#ifdef USE_PBBAM
-#include "pbbam/BamRecord.h"
-#endif
-
-
-class DNASequence {
-public:
- DNALength length;
- Nucleotide *seq;
- int bitsPerNuc;
- bool deleteOnExit;
-
- inline DNASequence();
- inline ~DNASequence();
-
- //--- functions ---//
-
- DNALength size();
-
- inline void CheckBeforeCopyOrReference(const DNASequence & rhs, std::string seqType = "DNASequence");
-
- void TakeOwnership(DNASequence &rhs);
-
- void Append(const DNASequence &rhs, DNALength appendPos=0);
-
- DNASequence &Copy(const DNASequence &rhs, DNALength rhsPos=0, DNALength rhsLength=0);
-
- void ShallowCopy(const DNASequence &rhs);
-
- DNASequence & Copy(const std::string & rhs);
-
- int GetStorageSize();
-
- DNASequence &operator=(const DNASequence &rhs);
-
- DNASequence &operator=(const std::string &rhs);
-
- void Print(std::ostream &out, int lineLength = 50);
-
- void PrintSeq(std::ostream &out, int lineLength = 50);
-
- void Allocate(DNALength plength);
-
- void ReferenceSubstring(const DNASequence &rhs, DNALength pos=0, DNALength substrLength=0);
-
- DNALength MakeRCCoordinate(DNALength forPos );
-
- inline void CopyAsRC(DNASequence &rc, DNALength pos=0, DNALength rcLength =0);
-
- void MakeRC(DNASequence &rc, DNALength pos=0, DNALength rcLength=0);
-
- void ToTwoBit();
-
- inline void ToThreeBit();
-
- void ToFourBit();
-
- void ConvertThreeBitToAscii();
-
- void ToAscii();
-
- void Assign(DNASequence &ref, DNALength start=0, DNALength plength=0);
-
- void ToLower();
-
- void ToUpper();
-
- void Concatenate(const Nucleotide *moreSeq, DNALength moreSeqLength);
-
- std::string GetTitle() const;
-
- void Concatenate(const Nucleotide* moreSeq);
-
- void Concatenate(DNASequence &seq);
-
- int Compare(DNALength pos, DNASequence &rhs, DNALength rhsPos, DNALength length);
-
- int LessThanEqual(DNALength pos, DNASequence &rhs, DNALength rhsPos, DNALength length);
-
- int Equals(DNASequence &rhs, DNALength rhsPos, DNALength length, DNALength pos=0 );
-
- int LessThan(DNALength pos, DNASequence &rhs, DNALength rhsPos, DNALength length);
-
- void CleanupASCII();
-
- Nucleotide operator[](int i) {
- return seq[i];
- }
-
- Nucleotide GetNuc(DNALength i);
-
- DNALength GetRepeatContent();
-
- void CleanupOnFree();
-
- virtual void Free();
-
- void Resize(DNALength newLength);
-
- DNALength GetSeqStorage();
-
-#ifdef USE_PBBAM
- /// Copies a BamRecord as a DNASequence.
- DNASequence & Copy(const PacBio::BAM::BamRecord & record);
-#endif
-};
-
-inline DNASequence::DNASequence() {
- seq = NULL;
- length = 0;
- bitsPerNuc = 8;
- deleteOnExit = false;
-}
-
-inline DNASequence::~DNASequence() {
- DNASequence::Free();
-}
-
-
-// Sanity check:
-// If this DNASequence and rhs are pointing to the same seq
-// in memory, make sure this DNASequence's deleteOnExit is false.
-// (otherwise, seq in memory will be deleted before being copied)
-inline void DNASequence::CheckBeforeCopyOrReference(const DNASequence & rhs, std::string seqType) {
-
- if (seq == rhs.seq and seq != NULL and deleteOnExit) {
- std::cout << "ERROR, trying to copying a " << seqType << " to itself." << std::endl;
- exit(1);
- }
-}
-
-inline void DNASequence::ToThreeBit() {
- DNALength i;
- if (bitsPerNuc != 3)
- for (i = 0; i < length; i++) { seq[i] = ThreeBit[seq[i]]; }
- bitsPerNuc = 3;
-}
-
-inline void DNASequence::CopyAsRC(DNASequence &rc, DNALength pos, DNALength rcLength) {
- // Free rc before copying any data to rc.
- ((DNASequence&)rc).Free();
- //
- // Different way of accounting for position. The position is on
- // the rc strand, not the forward strand.
- //
- if (rcLength == 0) {
- rcLength = length - pos;
- }
- DNALength rcStart = length - (pos + rcLength);
- ((DNASequence&)rc).Resize(rcLength);
- DNALength i;
- for (i = 0; i < rcLength; i++) {
- rc.seq[i] = ReverseComplementNuc[seq[rcStart - 1 + (rcLength - i)]];
- }
-
- // The reverse complement controls its own memory now.
- rc.deleteOnExit = true;
-}
-
-
-template<typename T>
-DNALength ResizeSequence(T &dnaseq, DNALength newLength) {
- assert(newLength > 0);
- ((T&)dnaseq).Free();
- dnaseq.seq = new Nucleotide[newLength];
- dnaseq.length = newLength;
- dnaseq.deleteOnExit = true;
- return newLength;
-}
-
-#endif // _BLASR_DNA_SEQUENCE_HPP_
diff --git a/libcpp/pbdata/Enumerations.h b/libcpp/pbdata/Enumerations.h
deleted file mode 100644
index b51575b..0000000
--- a/libcpp/pbdata/Enumerations.h
+++ /dev/null
@@ -1,39 +0,0 @@
-#ifndef _BLASR_ENUMERATIONS_HPP_
-#define _BLASR_ENUMERATIONS_HPP_
-
-typedef enum T_FileType {Fasta,
- Fastq,
- HDFPulse,
- Fourbit,
- HDFBase,
- HDFCCS,
- HDFCCSONLY,
- PBBAM,
- None
-} FileType;
-
-typedef enum T_Strand {Forward, Reverse} Strand;
-
-typedef enum T_PlatformType {
- Springfield,
- Astro,
- NoPlatform
-} PlatformId;
-
-typedef enum T_RegionType {
- GlobalAccuracy,
- HQRegion,
- Adapter,
- Insert,
- ArtifactRegion
-} RegionType;
-
-typedef enum T_PulseMetricType {
- QualityValueMetric,ClassifierQVMetric,StartTimeMetric,PulseWidthMetric,WidthInFramesMetric,
- pkmidMetric,IPDMetric,LightMetric, PreBaseFramesMetric
-} PulseMetricType;
-
-
-typedef enum T_AlignMode { NoAlignMode, Fullread, Subread, CCSDeNovo, CCSFullPass, CCSAllPass, ZmwSubreads } AlignMode;
-
-#endif
diff --git a/libcpp/pbdata/FASTAReader.cpp b/libcpp/pbdata/FASTAReader.cpp
deleted file mode 100644
index 6477fc0..0000000
--- a/libcpp/pbdata/FASTAReader.cpp
+++ /dev/null
@@ -1,420 +0,0 @@
-#include <stdlib.h>
-#include <string>
-#include <iostream>
-#include <vector>
-#include <limits.h>
-#include <sys/types.h>
-#include <unistd.h>
-#include "sys/mman.h"
-#include "sys/fcntl.h"
-
-#include "Enumerations.h"
-#include "NucConversion.hpp"
-#include "FASTASequence.hpp"
-#include "FASTAReader.hpp"
-
-using namespace std;
-
-void FASTAReader::SetFileSize() {
- //
- // Seek operation returns the amount seeked forwared in bytes.
- // This is the size used to map (which is rounded up by the
- // system).
- //
- fileSize = lseek(fileDes, 0, SEEK_END);
- lseek(fileDes, 0, SEEK_SET);
-}
-
-void FASTAReader::Init() {
- padding = 0;
- fileDes = -1;
- fileSize = 0;
- endOfReadDelim = '>';
- readStartDelim = '>';
- doToUpper = false;
- convMat = PreserveCase;
- computeMD5 = false;
- filePtr = NULL;
- curPos = 0;
-}
-
-FASTAReader::FASTAReader() {
- Init();
-}
-
-FASTAReader::FASTAReader(string &fileName) {
- Init(); // initialze defaults.
- Init(fileName); // open file.
- padding = 0;
- endOfReadDelim = '>';
- readStartDelim = '>';
-}
-
-void FASTAReader::SetSpacePadding(int _padding) {
- assert(_padding >= 0);
- padding = _padding;
-}
-
-void FASTAReader::SetToUpper() {
- doToUpper = true;
- convMat = AllToUpper;
-}
-
-//
-// Synonym for Init() for consistency.
-//
-int FASTAReader::Initialize(string &seqInName) {
- return Init(seqInName);
-}
-
-int FASTAReader::Init(string &seqInName, int passive) {
- fileDes = open(seqInName.c_str(), O_RDONLY);
- padding = 0;
- if (fileDes == -1) {
- if (passive) {
- return 0;
- }
- else {
- cout << "Could not open FASTA file " << seqInName << endl;
- exit(1);
- }
- }
- SetFileSize();
- filePtr = (char*) mmap(0, fileSize, PROT_READ, MAP_PRIVATE, fileDes, 0);
- if (filePtr == NULL) {
- cout << "ERROR, Fail to load FASTA file " << seqInName
- << " to virtual memory." << endl;
- exit(1);
- }
- curPos = 0;
- return 1;
-}
-
-void FASTAReader::AdvanceToTitleStart(long &p, char delim) {
- while (p < fileSize and
- filePtr[p] != delim) {
- p++;
- }
-}
-
-
-void FASTAReader::CheckValidTitleStart(long &p, char delim) {
- if (p >= fileSize or filePtr[p] != delim) {
- cout << "ERROR, FASTA entry must begin with \"" << delim << "\"" << endl;
- exit(1);
- }
-}
-
-long FASTAReader::ReadAllSequencesIntoOne(FASTASequence &seq, SequenceIndexDatabase<FASTASequence> *seqDBPtr) {
- seq.Free();
- long p = curPos;
- AdvanceToTitleStart(p);
- CheckValidTitleStart(p);
- ReadTitle(p, seq);
-
- if (seq.title == NULL) {
- cout << "ERROR, sequence must have a nonempty title." << endl;
- exit(1);
- }
- if (seqDBPtr != NULL) {
- seqDBPtr->growableName.push_back(seq.title);
- }
- long seqLength;
- seqLength = fileSize - p;
- long memorySize = seqLength+padding+1;
-
- long a = memorySize;
- if (memorySize > UINT_MAX) {
- cout << "ERROR! Reading fasta files greater than 4Gbytes is not supported." << endl;
- exit(1);
- }
- seq.Resize(memorySize);
- long i;
- i = 0L;
- for (; p < fileSize; p++, i++ ) {
- seq.seq[i] = filePtr[p];
- }
- i = p = 0;
- while (p < seqLength) {
- //
- // If this is the beginning of another read, add an 'N'
- // to delineate spaces between reads.
- //
-
- while (p < seqLength and
- (seq.seq[p] == ' ' or
- seq.seq[p] == '\n' or
- seq.seq[p] == '\t' or
- seq.seq[p] == '\r')) {
- p++;
- }
- if (p < seqLength and seq.seq[p] == '>') {
- seq.seq[i] = 'N';
-
- long titleStartPos = p+1;
- i++;
- while (p < seqLength and seq.seq[p] != '\n') p++;
- if (seqDBPtr != NULL and p < seqLength) {
- string title;
- long tp;
- for (tp = titleStartPos; tp < p; tp++) {
- title.push_back(seq.seq[tp]);
- }
-
- seqDBPtr->growableName.push_back(title);
- seqDBPtr->growableSeqStartPos.push_back(i);
- int nSeq = seqDBPtr->growableSeqStartPos.size();
- if (nSeq > 1 and computeMD5) {
- string md5Str;
- MakeMD5((const char*) &seq.seq[seqDBPtr->growableSeqStartPos[nSeq-2]],
- seqDBPtr->growableSeqStartPos[nSeq-1] - seqDBPtr->growableSeqStartPos[nSeq-2] - 1,
- md5Str);
- seqDBPtr->md5.push_back(md5Str);
- }
- }
- }
- else if (p < seqLength) {
- // Otherwise, p may be at whitespace
- // advance past that as well.
- seq.seq[i] = convMat[seq.seq[p]];
- i++;
- p++;
- }
- }
- if (i > UINT_MAX) {
- cout << "ERROR! Sequences greater than 4Gbase are not supported." << endl;
- exit(1);
- }
- //
- // Append an 'N' at the end of the last sequence for consistency
- // between different orderings of reference input.
- //
- seq.seq[i] = 'N';
- i++;
- seq.length = i;
- // fill padding.
- for (; i < memorySize; i++ ){
- seq.seq[i] = 0;
- }
- seq.deleteOnExit = true;
- if (seqDBPtr != NULL) {
- seqDBPtr->growableSeqStartPos.push_back(seq.length);
- int nSeq = seqDBPtr->growableSeqStartPos.size();
- if (nSeq > 1 and computeMD5) {
- string md5Str;
- MakeMD5((const char*) &seq.seq[seqDBPtr->growableSeqStartPos[nSeq-2]],
- seqDBPtr->growableSeqStartPos[nSeq-1] - seqDBPtr->growableSeqStartPos[nSeq-2] - 1,
- md5Str);
- seqDBPtr->md5.push_back(md5Str);
- }
- seqDBPtr->Finalize();
- }
- return seq.length;
-}
-
-void FASTAReader::ReadTitle(long &p, FASTASequence & seq) {
- char * seqTitle = NULL;
- int seqTitleLen;
- ReadTitle(p, seqTitle, seqTitleLen);
- seq.CopyTitle(seqTitle, seqTitleLen);
- if (seqTitle) {delete seqTitle;}
-}
-
-void FASTAReader::ReadTitle(long &p, char *&title, int &titleLength) {
- //
- // Extract the title. The length of the title does not include the newline.
- //
- p++; // Move past '>'
- curPos = p;
- while (p < fileSize and
- filePtr[p] != '\n') {
- p++;
- }
- titleLength = p - curPos;
- if (titleLength > 0) {
- if (title) {delete [] title; title = NULL;}
- title = new char[titleLength+1];
- int t = 0;
- for (p = curPos; p < curPos + titleLength; p++, t++) {
- title[t] = filePtr[p];
- }
- title[titleLength] = '\0';
- }
- else {
- title = NULL;
- titleLength = 0;
- }
-}
-
-int FASTAReader::GetNext(FASTASequence &seq) {
- if (curPos == fileSize) {
- return 0;
- }
-
- seq.Free(); //Free seq before read
-
- //
- // Extract the title of the current record.
- //
- long p = curPos;
-
- AdvanceToTitleStart(p);
-
- //
- // Make sure there is a '>'
- //
- CheckValidTitleStart(p);
-
- ReadTitle(p, seq);
-
- //
- // Read in the next sequence.
- //
-
- // Count the length of the sequence.
-
- long seqLength = 0;
- curPos = p;
- char c;
- while (p < fileSize and
- (c = filePtr[p]) != endOfReadDelim) {
- if (c != ' ' and
- c != '\t' and
- c != '\n' and
- c != '\r') {
- seqLength++;
- }
- p++;
- }
- if (seqLength > UINT_MAX) {
- cout << "ERROR! Reading sequences stored in more than 4Gbytes of space is not supported." << endl;
- exit(1);
- }
-
- seq.length = 0;
- if (seqLength > 0) {
- seq.length = seqLength;
- seq.seq = new Nucleotide[seqLength+padding+1];
- p = curPos;
- seq.deleteOnExit = true;
- long s = 0;
- while (p < fileSize and
- (c = filePtr[p]) != endOfReadDelim) {
- if (c != ' ' and
- c != '\t' and
- c != '\n' and
- c != '\r') {
- seq.seq[s] = convMat[filePtr[p]];
- s++;
- }
- p++;
- }
- seq.seq[seqLength] = 0;
- }
- curPos = p;
-
- if (computeMD5) {
- MakeMD5((const char*) &seq.seq, seq.length, curReadMD5);
- }
- return 1;
-}
-/*
- Advance to the read nSeq forward.
-
-input: nSeq, the number of sequences to skip.
-output:
-returns 1 if after advancing nSeq sequences, the file pointer is pointing to
-a new sequence.
-0 otherwise.
-A return value of 0 will signal that the file is done being processed if it is
-iterting over reads.
-*/
-int FASTAReader::Advance(int nSeq) {
-
- int nAdvanced = 0;
- long p = curPos;
- // base case -- it's always ok to advance 0
- if (nSeq == 0) { return 1; }
-
- // Make sure the advance starts at
- // the beginning of a sequence.
- while(p < fileSize and filePtr[p] != endOfReadDelim) p++;
- // No sequence was found, coudln't advance.
- if (p >= fileSize) { return 0; }
-
- p++;
- nAdvanced = 1;
- while (nAdvanced <= nSeq and p < fileSize) {
- if (filePtr[p] == endOfReadDelim) {
- if (nAdvanced == nSeq) {
- //
- // Want to end with the reader on a '>', so return before
- // hitting the rest of the loop.
- //
- curPos = p;
- return 1;
- }
- else {
- nAdvanced++;
- }
- }
- p++;
- }
- curPos = p;
- return 0;
-}
-
-int FASTAReader::CriticalGetNext(FASTASequence &seq) {
- if (!GetNext(seq)) {
- cout << "Could not read a sequence." << endl;
- exit(1);
- }
- return 1;
-}
-
-int FASTAReader::ConcatenateNext(FASTASequence &cur) {
- FASTASequence next;
- int retVal;
- if ((retVal = GetNext(next))) {
- next.CleanupASCII();
- cur.Concatenate((Nucleotide*) "N");
- cur.Concatenate(next);
- }
- next.Free();
- return retVal;
-}
-
-void FASTAReader::Close() {
- if (fileDes == -1) {
- cout << "ERROR, calling close on an uninitialized fasta reader" << endl;
- exit(1);
- }
- else {
- munmap(filePtr, fileSize);
- close(fileDes);
- fileDes = -1;
- }
-}
-
-void FASTAReader::ReadAllSequences(vector<FASTASequence> &sequences) {
- //
- // Step 1, compute the number of reads in the file.
- //
-
- long p;
- p = 0;
- int nSeq = 0;
- while (p < fileSize) {
- if (filePtr[p] == '>') {
- ++nSeq;
- }
- p++;
- }
-
- p = 0;
- sequences.resize(nSeq);
- int curSeq = 0;
- while(GetNext(sequences[curSeq])) {
- ++curSeq;
- }
-}
diff --git a/libcpp/pbdata/FASTAReader.hpp b/libcpp/pbdata/FASTAReader.hpp
deleted file mode 100644
index 6cc5ca9..0000000
--- a/libcpp/pbdata/FASTAReader.hpp
+++ /dev/null
@@ -1,80 +0,0 @@
-#ifndef _BLASR_FASTA_READER_HPP_
-#define _BLASR_FASTA_READER_HPP_
-#include <stdint.h>
-#include <string>
-#include "FASTASequence.hpp"
-#include "metagenome/SequenceIndexDatabase.hpp"
-
-class FASTAReader {
-protected:
- long fileSize;
- int fileDes;
- char* filePtr;
- long curPos;
- int padding;
- char endOfReadDelim;
- char readStartDelim;
- bool doToUpper;
- unsigned char *convMat;
- //
- // Quick check to see how much to read.
- //
- void SetFileSize();
-
- void ReadTitle(long &p, char *&title, int &titleLength);
-
-public:
- bool computeMD5;
- std::string curReadMD5;
-
- void Init();
-
- FASTAReader();
-
- FASTAReader(std::string &fileName);
-
- void SetSpacePadding(int _padding);
-
- void SetToUpper();
-
- //
- // Synonym for Init() for consistency.
- //
- int Initialize(std::string &seqInName);
-
- int Init(std::string &seqInName, int passive=0);
-
- void AdvanceToTitleStart(long &p, char delim='>');
-
- void CheckValidTitleStart(long &p, char delim='>');
-
- long ReadAllSequencesIntoOne(FASTASequence &seq, SequenceIndexDatabase<FASTASequence> *seqDBPtr=NULL);
-
- void ReadTitle(long &p, FASTASequence & seq);
-
- int GetNext(FASTASequence &seq);
- /*
- Advance to the read nSeq forward.
-
-input: nSeq, the number of sequences to skip.
-output:
-returns 1 if after advancing nSeq sequences, the file pointer is pointing to
-a new sequence.
-0 otherwise.
-A return value of 0 will signal that the file is done being processed if it is
-iterting over reads.
-*/
- int Advance(int nSeq);
-
- int CriticalGetNext(FASTASequence &seq);
-
- int ConcatenateNext(FASTASequence &cur);
-
- void Close();
-
- void ReadAllSequences(vector<FASTASequence> &sequences);
-
-};
-
-
-#endif // _BLASR_FASTA_READER_HPP_
diff --git a/libcpp/pbdata/FASTASequence.cpp b/libcpp/pbdata/FASTASequence.cpp
deleted file mode 100644
index 4b579cc..0000000
--- a/libcpp/pbdata/FASTASequence.cpp
+++ /dev/null
@@ -1,246 +0,0 @@
-#include <stdlib.h>
-#include "FASTASequence.hpp"
-
-using namespace std;
-
-FASTASequence::FASTASequence() : DNASequence() {
- title = NULL;
- titleLength = 0;
- deleteTitleOnExit = false;
- // If deleteTitleOnExist is false, whether to delete title
- // or not should depend on deleteOnExit; otherwise, delete title
- // regardless of deleteOnExit.
-}
-
-void FASTASequence::PrintSeq(ostream &out, int lineLength, char delim) {
- out << delim;
- if (title) out << title;
- out << endl;
- static_cast<DNASequence*>(this)->PrintSeq(out, lineLength);
-}
-
-int FASTASequence::GetStorageSize() {
- if (!title)
- return DNASequence::GetStorageSize();
- return strlen(title) + DNASequence::GetStorageSize();
-}
-
-string FASTASequence::GetName() const {
- string name;
- int i;
- for (i = 0; i < titleLength; i++) {
- if (title[i] != ' ' and
- title[i] != '\t' and
- title[i] != '\n' and
- title[i] != '\r') {
- name.push_back(title[i]);
- }
- else {
- break;
- }
- }
- return name;
-}
-
-//
-// Define some no-ops to satisfy instantiating templates that
-// expect these to exist.
-//
-bool FASTASequence::StoreHoleNumber(int holeNumber) {return false;}
-bool FASTASequence::StoreHoleStatus(unsigned char holeStatus) {return false;}
-bool FASTASequence::StorePlatformId(PlatformId platformId) { return false;}
-bool FASTASequence::StoreZMWData(ZMWGroupEntry &data) { return false;}
-bool GetHoleNumber (int &holeNumberP) {
- //
- // There is no notion of a hole number for a fasta sequence.
- //
- return false;
-}
-
-bool FASTASequence::StoreXY(int16_t xy[]) {return false;}
-
-bool FASTASequence::GetXY(int xyP[]) {
- //
- // Although the xyP is stored in the fasta title for astro reads
- // this class is more general than an astro read, so do not assume
- // that it may be found in the title.
- //
- // So, this function is effectively a noop.
- //
- xyP[0] = xyP[1] = 0;
- return false;
-}
-
-
-void FASTASequence::ShallowCopy(const FASTASequence &rhs) {
- CheckBeforeCopyOrReference(rhs, "FASTASequence");
- FASTASequence::Free();
-
- static_cast<DNASequence*>(this)->ShallowCopy(rhs);
-
- title = rhs.title;
- titleLength = rhs.titleLength;
- deleteTitleOnExit = false;
-}
-
-string FASTASequence::GetTitle() const {
- return string(title);
-}
-
-// Delete title if this FASTASequence is under control or
-// only title is under control.
-void FASTASequence::DeleteTitle() {
- if (deleteOnExit or deleteTitleOnExit) {
- if (title != NULL) {
- delete[] title;
- }
- } // otherwise, title is controlled by another obj
- title = NULL;
- titleLength = 0;
- deleteTitleOnExit = false;
-}
-
-void FASTASequence::CopyTitle(const char* str, int strlen) {
- FASTASequence::DeleteTitle();
-
- // No segfault when str is NULL;
- if (str == NULL) {
- title = NULL;
- titleLength = 0;
- } else {
- title = new char[strlen+1];
- memcpy(title, str, strlen);
- titleLength = strlen;
- title[titleLength] = '\0';
- }
-
- // In some cases, (e.g., when ReferenceSubstring and CopyTitle
- // are called together), this Sequence may only have control over
- // title but not seq.
- deleteTitleOnExit = true;
-}
-
-void FASTASequence::CopyTitle(string str) {
- FASTASequence::CopyTitle(str.c_str(), str.size());
-}
-
-void FASTASequence::GetFASTATitle(string& fastaTitle) {
- // look for the first space, and return the string until there.
- int i;
- for (i = 0; i < titleLength; i++ ){
- if (title[i] == ' ' or
- title[i] == '\t') {
- break;
- }
- }
- fastaTitle.assign(title, i);
-}
-
-// Copy rhs.seq[readStart:readEnd] to this Sequence.
-void FASTASequence::CopySubsequence(FASTASequence &rhs, int readStart, int readEnd) {
- CheckBeforeCopyOrReference(rhs, "FASTASequence");
-
- // Free before copying anything
- FASTASequence::Free();
-
- if (readEnd == -1) {
- readEnd = rhs.length;
- }
-
- if (readEnd > readStart) {
- length = readEnd - readStart;
- DNASequence::Copy(rhs, readStart, length);
- }
- else {
- seq = NULL;
- length = 0;
- deleteOnExit = true;
- }
- FASTASequence::CopyTitle(rhs.title);
-}
-
-void FASTASequence::AppendToTitle(string str) {
- int newLength = titleLength + str.size() + 1;
- if (newLength == 0) {
- DeleteTitle();
- return;
- }
-
- char *tmpTitle = new char[newLength];
- memcpy(tmpTitle, title, titleLength);
- memcpy(&tmpTitle[titleLength], str.c_str(), str.size());
- tmpTitle[newLength-1] = '\0';
- delete[] title;
- title = tmpTitle;
- titleLength = newLength;
- deleteTitleOnExit = true;
-}
-
-void FASTASequence::Assign(FASTASequence &rhs) {
- *this = (FASTASequence&)rhs;
-}
-
-// Create a reverse complement FASTASequence of *this and assign to rhs.
-void FASTASequence::MakeRC(FASTASequence &rhs, DNALength rhsPos, DNALength rhsLength) {
- rhs.Free();
- DNASequence::MakeRC((DNASequence&) rhs, rhsPos, rhsLength);
- if (title != NULL) {
- (static_cast<FASTASequence*>(&rhs))->CopyTitle(title);
- }
-}
-
-void FASTASequence::ReverseComplementSelf() {
- DNALength i;
- for (i = 0; i < length/2 + length % 2; i++) {
- char c = seq[i];
- seq[i] = ReverseComplementNuc[seq[length - i - 1]];
- seq[length - i - 1] = ReverseComplementNuc[static_cast<int>(c)];
- }
-}
-
-void FASTASequence::operator=(const FASTASequence &rhs) {
- CheckBeforeCopyOrReference(rhs, "FASTASequence");
-
- // Free before copying anything
- FASTASequence::Free();
-
- // Copy seq from rhs
- ((DNASequence*)this)->Copy((DNASequence&)rhs);
-
- assert(deleteOnExit);
-
- // Copy title from rhs
- FASTASequence::CopyTitle(rhs.title, rhs.titleLength);
-
- assert(deleteOnExit);
-}
-
-void FASTASequence::Copy(const std::string & rhsTitle, const std::string & rhsSeq) {
- this->Copy(rhsSeq);
- this->CopyTitle(rhsTitle);
-}
-
-void FASTASequence::Copy(const std::string & rhsSeq) {
- (static_cast<DNASequence*>(this))->Copy(rhsSeq);
-}
-
-void FASTASequence::Copy(const FASTASequence &rhs) {
- *this = (FASTASequence&)rhs;
-}
-
-#ifdef USE_PBBAM
-void FASTASequence::Copy(const PacBio::BAM::BamRecord & record) {
- FASTASequence::Copy(record.Impl().Name(), record.Sequence());
-}
-#endif
-
-void FASTASequence::Free() {
- // Delete title if title is under control, reset deleteTitleOnExit.
- FASTASequence::DeleteTitle();
-
- // Delete seq if under control, reset deleteOnExit.
- // Don't call Free() before calling DeleteTitle().
- DNASequence::Free();
-}
-
-template DNALength ResizeSequence<FASTASequence>(FASTASequence &, DNALength);
diff --git a/libcpp/pbdata/FASTASequence.hpp b/libcpp/pbdata/FASTASequence.hpp
deleted file mode 100644
index bfadb58..0000000
--- a/libcpp/pbdata/FASTASequence.hpp
+++ /dev/null
@@ -1,91 +0,0 @@
-#ifndef _BLASR_FASTA_SEQUENCE_HPP_
-#define _BLASR_FASTA_SEQUENCE_HPP_
-
-#include <string>
-#include <iostream>
-#include <stdint.h>
-#include <string>
-#include <cstring>
-#include <ostream>
-#include "Types.h"
-#include "NucConversion.hpp"
-#include "Enumerations.h"
-#include "DNASequence.hpp"
-#include "reads/ZMWGroupEntry.hpp"
-
-//
-// NO proteins for now.
-class FASTASequence : public DNASequence {
-private:
- // Whether or not to delete title in Free()
- // regardless of deleteOnExit (to prevent memory leak
- // when ReferenceSubstring and CopyTitle are called together).
- bool deleteTitleOnExit;
-
-public:
- char *title;
- int titleLength;
-
- FASTASequence();
- inline ~FASTASequence();
-
- void PrintSeq(std::ostream &out, int lineLength = 50, char delim='>');
-
- int GetStorageSize();
-
- std::string GetName() const;
-
- virtual bool StoreHoleNumber(int holeNumber);
- virtual bool StoreHoleStatus(unsigned char holeStatus);
- virtual bool StorePlatformId(PlatformId platformId);
- virtual bool StoreZMWData(ZMWGroupEntry &data);
- virtual bool StoreXY(int16_t xy[]);
-
- bool GetHoleNumber (int &holeNumberP);
-
- bool GetXY(int xyP[]);
-
- void ShallowCopy(const FASTASequence &rhs);
-
- std::string GetTitle() const;
-
- void DeleteTitle();
-
- void CopyTitle(const char* str, int strlen);
-
- void CopyTitle(std::string str);
-
- void GetFASTATitle(std::string& fastaTitle);
-
- void CopySubsequence(FASTASequence &rhs, int readStart, int readEnd=-1);
-
- void AppendToTitle(std::string str);
-
- void Assign(FASTASequence &rhs);
-
- void MakeRC(FASTASequence &rhs, DNALength rhsPos=0, DNALength rhsLength=0);
-
- void ReverseComplementSelf();
-
- void operator=(const FASTASequence &rhs);
-
- void Copy(const FASTASequence &rhs);
-
- void Copy(const std::string & rhsTitle, const std::string & rhsSeq);
-
- void Copy(const std::string & rhsSeq);
-
-#ifdef USE_PBBAM
- /// Copies a BamRecord as a FASTASequence.
- void Copy(const PacBio::BAM::BamRecord & record);
-#endif
-
- void Free();
-};
-
-
-inline FASTASequence::~FASTASequence(){
- FASTASequence::Free();
-}
-
-#endif
diff --git a/libcpp/pbdata/FASTQReader.cpp b/libcpp/pbdata/FASTQReader.cpp
deleted file mode 100644
index 324d57a..0000000
--- a/libcpp/pbdata/FASTQReader.cpp
+++ /dev/null
@@ -1,89 +0,0 @@
-#include <cstdio>
-#include <climits>
-#include <cmath>
-#include "FASTQReader.hpp"
-
-FASTQReader::FASTQReader() : FASTAReader() {
- endOfReadDelim = '\n';
-}
-
-long FASTQReader::GetNext(FASTASequence &seq) {
- return ((FASTAReader*)this)->GetNext(seq);
-}
-
-unsigned char FASTQReader::phredQVtoPacbioQV(unsigned char phredQV){
- int qual = floor(100.0 * log10(pow(10.0, phredQV/10.0) - 1.0) + 0.5);
- qual = qual > 250 ? 250 : qual;
- qual = qual < 1 ? 1 : qual;
- return (unsigned char) qual;
-}
-
-int FASTQReader::GetNext(FASTQSequence &seq) {
- seq.Free(); // Free seq before being reused.
- char c;
- while( curPos < fileSize and ( (c = filePtr[curPos]) == ' ' or c == '\t' or c == '\n' or c == '\r') ) {
- curPos++;
- }
-
- if (curPos >= fileSize) {
- return false;
- }
- long p = curPos;
- AdvanceToTitleStart(p, '@');
- CheckValidTitleStart(p,'@');
- ReadTitle(p, seq);
- // Title ends on '\n', consume that;
- p++;
- long p2;
- p2 = p;
- while(p2 < fileSize and filePtr[p2] != '\n') { p2++;}
- if (p2 - p > UINT_MAX) {
- cout << "ERROR! Reading sequences stored in more than 4Gbytes of space is not supported." << endl;
- exit(1);
- }
-
- seq.length = p2 - p;
- long seqPos;
- if (seq.length > 0) {
- seq.seq = new Nucleotide[seq.length];
- p2 = p;
- seqPos = 0;
- while(p2 < fileSize and filePtr[p2] != '\n') { seq.seq[seqPos] = filePtr[p2]; p2++; seqPos++;}
- }
- else {
- seq.seq = 0;
- }
- p = p2;
-
- AdvanceToTitleStart(p,'+');
- CheckValidTitleStart(p,'+');
- while(p < fileSize and filePtr[p] != '\n') { p++;}
- p++; // skip '\n'
- p2 = p;
- while(p2 < fileSize and filePtr[p2] != '\n') { p2++;}
- seq.length = p2 - p;
- if (seq.length > 0) {
- seq.qual.Allocate(seq.length);
- p2 = p;
- long seqPos = 0;
- while(p2 < fileSize and filePtr[p2] != '\n') {
- seq.qual[seqPos] = filePtr[p2] - FASTQSequence::charToQuality;
- p2++; seqPos++;
- }
- }
- else {
- seq.qual.data = NULL;
- }
- curPos = p2;
- seq.deleteOnExit = true;
- return true;
-}
-
-
-
-int FASTQReader::Advance(int nSteps) {
- // An advance of a FASTQ file is simply twice the number of
- // advances of FASTA, since each nucleotide sequence has a quality
- // sequence.
- return ((FASTAReader*)this)->Advance(nSteps*2);
-}
diff --git a/libcpp/pbdata/FASTQReader.hpp b/libcpp/pbdata/FASTQReader.hpp
deleted file mode 100644
index 4caeab3..0000000
--- a/libcpp/pbdata/FASTQReader.hpp
+++ /dev/null
@@ -1,24 +0,0 @@
-#ifndef _BLASR_FASTQ_READER_HPP_
-#define _BLASR_FASTQ_READER_HPP_
-
-#include "FASTASequence.hpp"
-#include "FASTAReader.hpp"
-#include "FASTQSequence.hpp"
-#include "qvs/QualityValue.hpp"
-
-class FASTQReader : public FASTAReader {
-public:
-
- FASTQReader();
-
- long GetNext(FASTASequence &seq);
-
- unsigned char phredQVtoPacbioQV(unsigned char phredQV);
-
- int GetNext(FASTQSequence &seq);
-
- int Advance(int nSteps);
-};
-
-
-#endif // _BLASR_FASTQ_READER_HPP_
diff --git a/libcpp/pbdata/FASTQSequence.cpp b/libcpp/pbdata/FASTQSequence.cpp
deleted file mode 100644
index 26789ac..0000000
--- a/libcpp/pbdata/FASTQSequence.cpp
+++ /dev/null
@@ -1,651 +0,0 @@
-#include <cassert>
-#include <vector>
-#include <cstring>
-#include <iostream>
-#include <iomanip>
-#include <algorithm>
-#include <stdint.h>
-#include "Types.h"
-#include "NucConversion.hpp"
-#include "DNASequence.hpp"
-#include "Enumerations.h"
-#include "FASTQSequence.hpp"
-
-using namespace std;
-
-//
-// Initialize a read with quality probabilities from one with quality values.
-//
-int FASTQSequence::charToQuality = FASTQ_CHAR_TO_QUALITY;
-
-QVScale FASTQSequence::GetQVScale() {
- return qvScale;
-}
-
-void FASTQSequence::SetQVScale(QVScale qvScaleP) {
- qvScale = qvScaleP;
- qual.qvScale = qvScale;
- deletionQV.qvScale = qvScale;
- preBaseDeletionQV.qvScale = qvScale;
- insertionQV.qvScale = qvScale;
- substitutionQV.qvScale = qvScale;
- mergeQV.qvScale = qvScale;
-}
-
-QualityValueVector<QualityValue>*
-FASTQSequence::GetQVPointerByIndex(int index) {
- if (index == 0) { return &qual; }
- if (index == 1) { return &insertionQV; }
- if (index == 2) { return &deletionQV; }
- if (index == 3) { return &substitutionQV; }
- if (index == 4) { return &mergeQV; }
- return NULL;
-}
-
-int FASTQSequence::GetStorageSize() {
- int total = 0;
- int nQV = 0;
- int nTag =0;
- if (!qual.Empty()) {
- nQV++;
- }
- if (!deletionQV.Empty()) {
- nQV++;
- }
- if (!preBaseDeletionQV.Empty()) {
- nQV+=4;
- }
- if (!insertionQV.Empty()) {
- nQV++;
- }
- if (!substitutionQV.Empty()) {
- nQV++;
- }
- if (!mergeQV.Empty()) {
- nQV++;
- }
- if (deletionTag != NULL) {
- nTag++;
- }
- if (substitutionTag !=NULL) {
- nTag++;
- }
- total = nQV*sizeof(QualityValue)*length + nTag*sizeof(Nucleotide)*length;
- return total + FASTASequence::GetStorageSize();
-}
-
-FASTQSequence::FASTQSequence() : FASTASequence() {
- deletionTag = NULL;
- substitutionTag = NULL;
-
- //
- // For now assume a prior distribution to be the variation of the human genome.
- // FIXME: these were set to 0.001, which ends up being 0 because these priors are integer types
- // I'm setting these explicitly to 0 to silence the warning and maintain behavior,
- // but mkinsella recommends revisiting these for potential removal
- //
- deletionQVPrior = 0;
- insertionQVPrior = 0;
- substitutionQVPrior = 0;
- preBaseDeletionQVPrior = 0;
-
- subreadStart = subreadEnd = 0;
- qvScale = PHRED;
-}
-
-QualityValue FASTQSequence::GetDeletionQV(DNALength pos) {
- assert(pos < ((unsigned int)-1));
- assert(pos < length);
- if (deletionQV.Empty()) {
- return deletionQVPrior;
- }
- else {
- return deletionQV[pos];
- }
-}
-
-QualityValue FASTQSequence::GetMergeQV(DNALength pos) {
- assert(pos < ((unsigned int)-1));
- assert(pos < length);
- if (mergeQV.Empty()) {
- return 0;
- }
- else {
- return mergeQV[pos];
- }
-}
-
-Nucleotide FASTQSequence::GetSubstitutionTag(DNALength pos) {
- if (substitutionTag == NULL) {
- return 'N';
- }
- assert(pos < ((unsigned int)-1));
- assert(pos < length);
- return substitutionTag[pos];
-}
-
-Nucleotide FASTQSequence::GetDeletionTag(DNALength pos) {
- if (deletionTag == NULL) {
- return 'N';
- }
- assert(pos < ((unsigned int)-1));
- assert(pos < length);
- return deletionTag[pos];
-}
-
-QualityValue FASTQSequence::GetInsertionQV(DNALength pos) {
- if (insertionQV.Empty()) {
- return insertionQVPrior;
- }
- assert(pos < ((unsigned int)-1));
- assert(pos < length);
- return insertionQV[pos];
-}
-
-QualityValue FASTQSequence::GetSubstitutionQV(DNALength pos) {
- if (substitutionQV.Empty()) {
- return substitutionQVPrior;
- }
- assert(pos < ((unsigned int)-1));
- assert(pos < length);
- return substitutionQV[pos];
-}
-
-QualityValue FASTQSequence::GetPreBaseDeletionQV(DNALength pos, Nucleotide nuc) {
- if (preBaseDeletionQV.Empty()) {
- return preBaseDeletionQVPrior;
- }
- assert(pos < ((unsigned int)-1));
- assert(pos < length);
- return preBaseDeletionQV[pos*4 + TwoBit[nuc]];
-}
-
-void FASTQSequence::ShallowCopy(const FASTQSequence &rhs) {
- CheckBeforeCopyOrReference(rhs, "FASTQSequence");
- FASTQSequence::Free();
-
- qual.ShallowCopy(rhs.qual, 0, length);
- FASTASequence::ShallowCopy(rhs);
-}
-
-void FASTQSequence::ReferenceSubstring(const FASTQSequence &rhs) {
- FASTQSequence::ReferenceSubstring(rhs, 0, rhs.length);
-}
-
-void FASTQSequence::ReferenceSubstring(const FASTQSequence &rhs, DNALength pos) {
- FASTQSequence::ReferenceSubstring(rhs, pos, rhs.length - pos);
-}
-
-void FASTQSequence::ReferenceSubstring(const FASTQSequence &rhs, DNALength pos, DNALength substrLength) {
- // Sanity check.
- CheckBeforeCopyOrReference(rhs, "FASTQSequence");
-
- // Free this FASTQSequence before referencing rhs.
- FASTQSequence::Free();
-
- SetQVScale(rhs.qvScale);
- if (substrLength == 0) {
- substrLength = rhs.length - pos;
- }
- FASTASequence::ReferenceSubstring(rhs,pos,substrLength);
- if (rhs.qual.Empty() == false) {
- qual.ShallowCopy(rhs.qual, pos, substrLength);
- }
- if (rhs.deletionQV.Empty() == false) {
- deletionQV.ShallowCopy(rhs.deletionQV, pos, substrLength);
- }
- if (rhs.mergeQV.Empty() == false) {
- mergeQV.ShallowCopy(rhs.mergeQV, pos, substrLength);
- }
- if (rhs.insertionQV.Empty() == false) {
- insertionQV.ShallowCopy(rhs.insertionQV, pos, substrLength);
- }
- if (rhs.preBaseDeletionQV.Empty() == false ){
- preBaseDeletionQV.ShallowCopy(rhs.preBaseDeletionQV, pos, substrLength);
- }
- if (rhs.deletionTag != NULL) {
- deletionTag = &rhs.deletionTag[pos];
- }
- if (rhs.substitutionTag != NULL) {
- substitutionTag = &rhs.substitutionTag[pos];
- }
- if (rhs.substitutionQV.Empty() == false) {
- substitutionQV.ShallowCopy(rhs.substitutionQV, pos, substrLength);
- }
- deletionQVPrior = rhs.deletionQVPrior;
- insertionQVPrior = rhs.insertionQVPrior;
- substitutionQVPrior = rhs.substitutionQVPrior;
- preBaseDeletionQVPrior = rhs.preBaseDeletionQVPrior;
-}
-
-void FASTQSequence::ClearAndNull(QualityValue *value) {
- if (value != NULL) {
- delete[] value;
- }
- value = NULL;
-}
-
-void FASTQSequence::CopyQualityValues(const FASTQSequence &rhs) {
- // Make sure QVs and seq are all under control, if seq is referenced
- // while QVs are copied, memory leak can happen.
- assert(deleteOnExit);
-
- SetQVScale(rhs.qvScale);
- qual.Copy(rhs.qual, rhs.length);
- deletionQV.Copy(rhs.deletionQV, rhs.length);
- insertionQV.Copy(rhs.insertionQV, rhs.length);
- substitutionQV.Copy(rhs.substitutionQV, rhs.length);
- mergeQV.Copy(rhs.mergeQV, rhs.length);
- //
- // Handle the tags separtely (and verbosely)
- //
- if (rhs.deletionTag) {
- AllocateDeletionTagSpace(rhs.length);
- memcpy(deletionTag, rhs.deletionTag, sizeof(Nucleotide)*rhs.length);
- }
- else {
- ClearAndNull(deletionTag);
- }
-
- if (rhs.substitutionTag) {
- AllocateSubstitutionTagSpace(rhs.length);
- memcpy(substitutionTag, rhs.substitutionTag, sizeof(Nucleotide)*rhs.length);
- }
- else {
- ClearAndNull(substitutionTag);
- }
-}
-
-void FASTQSequence::AllocateQualitySpace(DNALength qualLength) {
- qual.Allocate(qualLength);
-}
-
-void FASTQSequence::AllocateDeletionQVSpace(DNALength qualLength) {
- deletionQV.Allocate(qualLength);
-}
-
-void FASTQSequence::AllocateMergeQVSpace(DNALength len) {
- mergeQV.Allocate(len);
-}
-
-void FASTQSequence::AllocateDeletionTagSpace(DNALength qualLength) {
- if (deletionTag != NULL) delete[] deletionTag;
- deletionTag = new Nucleotide[qualLength];
-}
-
-void FASTQSequence::AllocatePreBaseDeletionQVSpace(DNALength qualLength) {
- preBaseDeletionQV.Allocate(qualLength);
-}
-
-void FASTQSequence::AllocateInsertionQVSpace(DNALength qualLength) {
- insertionQV.Allocate(qualLength);
-}
-
-void FASTQSequence::AllocateSubstitutionQVSpace(DNALength qualLength ){
- substitutionQV.Allocate(qualLength);
-}
-
-void FASTQSequence::AllocateSubstitutionTagSpace(DNALength qualLength ){
- if (substitutionTag != NULL) delete[] substitutionTag;
- substitutionTag = new Nucleotide[qualLength];
-}
-
-void FASTQSequence::AllocateRichQualityValues(DNALength qualLength) {
- AllocateDeletionQVSpace(qualLength);
- AllocateDeletionTagSpace(qualLength);
- AllocatePreBaseDeletionQVSpace(qualLength);
- AllocateInsertionQVSpace(qualLength);
- AllocateSubstitutionQVSpace(qualLength);
- AllocateSubstitutionTagSpace(qualLength);
- AllocateMergeQVSpace(qualLength);
-}
-
-void FASTQSequence::Copy(const FASTQSequence &rhs) {
- CheckBeforeCopyOrReference(rhs, "FASTQSequence");
-
- // Free *this before copying anything.
- FASTQSequence::Free();
-
- // Copy FASTASequence from rhs, including seq and title
- FASTASequence::Copy(rhs);
-
- assert(deleteOnExit);
-
- // Copy Quality values from rhs.
- FASTQSequence::CopyQualityValues(rhs);
-}
-
-FASTQSequence& FASTQSequence::operator=(const FASTQSequence &rhs) {
- ((FASTQSequence*)this)->Copy(rhs);
- return *this;
-}
-
-FASTQSequence::FASTQSequence(const FASTQSequence &rhs) {
- ((FASTQSequence*)this)->Copy(rhs);
-}
-
-// Copy rhs to this, including seq, title and QVs.
-void FASTQSequence::Assign(FASTQSequence &rhs) {
- CheckBeforeCopyOrReference(rhs);
- FASTQSequence::Free();
-
- // copy the nucleotide part
- FASTASequence::Assign(rhs);
- // copy the qual part, qual scal is set in CopyQualityValues
- FASTQSequence::CopyQualityValues(rhs);
-}
-
-void FASTQSequence::PrintFastq(ostream &out, int lineLength) {
- PrintSeq(out, lineLength, '@');
- if (lineLength == 0) {
- out << endl;
- }
- PrintFastqQuality(out, lineLength);
- if (lineLength == 0) {
- out << endl;
- }
-}
-
-void FASTQSequence::PrintFastqQuality(ostream &out, int lineLength) {
- out << "+" << endl;
- PrintAsciiQual(out, lineLength);
-}
-
-bool FASTQSequence::GetQVs(const QVIndex & qvIndex, std::vector<uint8_t> & qvs, bool reverse) {
- qvs.clear();
- uint8_t * qualPtr;
- int charOffset = charToQuality;
- if (qvIndex == I_QualityValue) {
- qualPtr = qual.data;
- } else if (qvIndex == I_InsertionQV) {
- qualPtr = insertionQV.data;
- } else if (qvIndex == I_DeletionQV) {
- qualPtr = deletionQV.data;
- } else if (qvIndex == I_SubstitutionQV) {
- qualPtr = substitutionQV.data;
- } else if (qvIndex == I_MergeQV) {
- qualPtr = mergeQV.data;
- } else if (qvIndex == I_SubstitutionTag) {
- qualPtr = (uint8_t*)(substitutionTag);
- charOffset = 0;
- } else if (qvIndex == I_DeletionTag) {
- qualPtr = (uint8_t*)(deletionTag);
- charOffset = 0;
- }
- if (qualPtr == NULL) {
- return false;
- }
-
- qvs.resize(length);
- for (DNALength i = 0; i < length; i++) {
- if (not reverse) { // The same orientation
- qvs[i] = static_cast<uint8_t>(qualPtr[i] + charOffset);
- } else if (qvIndex != I_SubstitutionTag and qvIndex != I_DeletionTag) {
- // Reverse orientation, reverse QVs, except SubstitutionTag and DeletionTag
- qvs[i] = static_cast<uint8_t>(qualPtr[length - i - 1] + charOffset);
- } else { // Reverse and complement SubstitutionTag and DeletionTag
- qvs[i] = static_cast<uint8_t>(ReverseComplementNuc[qualPtr[length - i - 1] + charOffset]);
- }
- //assert(qvs[i] > 32 and qvs[i] < 127);
- }
- return true;
-}
-
-QVIndex FASTQSequence::GetQVIndex(const std::string & qvName) {
- if (qvName == "QualityValue") {
- return I_QualityValue;
- } else if (qvName == "InsertionQV") {
- return I_InsertionQV;
- } else if (qvName == "DeletionQV") {
- return I_DeletionQV;
- } else if (qvName == "SubstitutionQV") {
- return I_SubstitutionQV;
- } else if (qvName == "MergeQV") {
- return I_MergeQV;
- } else if (qvName == "SubstitutionTag") {
- return I_SubstitutionTag;
- } else if (qvName == "DeletionTag"){
- return I_DeletionTag;
- } else {
- std::cout << "ERROR: unknown Quality Value " << qvName << std::endl;
- assert(false);
- }
-}
-
-bool FASTQSequence::GetQVs(const std::string & qvName, std::vector<uint8_t> & qvs, bool reverse){
- return GetQVs(GetQVIndex(qvName), qvs, reverse);
-}
-
-bool FASTQSequence::GetQVs(const std::string & qvName, std::string & qvsStr, bool reverse) {
- std::vector<uint8_t> qvs;
- bool OK = GetQVs(qvName, qvs, reverse);
- qvsStr = string(qvs.begin(), qvs.end());
- return OK;
-}
-
-void FASTQSequence::PrintAsciiRichQuality(ostream &out,
- int whichQuality, int lineLength) {
- vector<uint8_t> qvs;
- bool OK = GetQVs(static_cast<QVIndex>(whichQuality), qvs);
-
- DNALength i;
- if (lineLength == 0) {
- for (i = 0; i < length; i++) {
- if (OK) {
- out << static_cast<char>(qvs[i]);
- }
- else {
- // Fake bad quality
- out << "5";
- }
- }
- }
- else {
- for (i = 0; i < length; i++) {
- if (OK) {
- out << static_cast<char>(qvs[i]);
- }
- else {
- // Fake pretty bad quality.
- out << "5";
- }
- assert(lineLength != 0);
- if (i > 0 and (i+1) % lineLength==0) {
- out << endl;
- }
- }
- if (i == 0 or i % lineLength != 0) {
- out << endl;
- }
- }
-}
-
-void FASTQSequence::PrintAsciiQual(ostream &out, int lineLength) {
- PrintAsciiRichQuality(out, 0, lineLength);
-}
-
-void FASTQSequence::PrintQual(ostream &out, int lineLength) {
- out << ">" << this->title << endl;
- DNALength i;
- for (i = 0; i < length; i++ ){
- out << (int) qual[i];
- if (i > 0 and (i+1) % lineLength == 0)
- out << endl;
- else
- out << " ";
- }
- if (i == 0 or i % lineLength != 0) {
- out << endl;
- }
-}
-
-void FASTQSequence::PrintQualSeq(ostream &out, int lineLength) {
- FASTASequence::PrintSeq(out, lineLength);
- lineLength /= 4;
- PrintQual(out, lineLength);
-}
-
-// Create a reverse complement FASTQSequence of *this and assign to rhs.
-void FASTQSequence::MakeRC(FASTQSequence &rc) {
- rc.Free();
- FASTASequence::MakeRC(rc);
- rc.SetQVScale(qvScale);
-
- if (not qual.Empty()) {
- // QVs are independent of one another. A FASTQSequence can have
- // insertionQV without having QualityValue.
- (static_cast<FASTQSequence*>(&rc))->AllocateQualitySpace(length);
- for (DNALength pos = 0; pos < length; pos++ ){
- rc.qual.data[length - pos - 1] = qual[pos];
- }
- }
-
- //
- // The read contains rich quality values. Reverse them here.
- //
- if (deletionQV.Empty() == false) {
- (static_cast<FASTQSequence*>(&rc))->AllocateDeletionQVSpace(length);
- for (DNALength pos = 0; pos < length; pos++) {
- rc.deletionQV[length - pos - 1] = deletionQV[pos];
- }
- }
-
- if (insertionQV.Empty() == false) {
- (static_cast<FASTQSequence*>(&rc))->AllocateInsertionQVSpace(length);
- for (DNALength pos = 0; pos < length; pos++) {
- rc.insertionQV[length - pos - 1] = insertionQV[pos];
- }
- }
-
- if (substitutionQV.Empty() == false) {
- (static_cast<FASTQSequence*>(&rc))->AllocateSubstitutionQVSpace(length);
- for (DNALength pos = 0; pos < length; pos++) {
- rc.substitutionQV[length - pos - 1] = substitutionQV[pos];
- }
- }
-
- if (mergeQV.Empty() == false) {
- (static_cast<FASTQSequence*>(&rc))->AllocateMergeQVSpace(length);
- for (DNALength pos = 0; pos < length; pos++) {
- rc.mergeQV[length - pos - 1] = mergeQV[pos];
- }
- }
-
- if (substitutionTag != NULL) {
- (static_cast<FASTQSequence*>(&rc))->AllocateSubstitutionTagSpace(length);
- for (DNALength pos = 0; pos < length; pos++) {
- rc.substitutionTag[length - pos - 1] = ReverseComplementNuc[substitutionTag[pos]];
- }
- }
-
- if (deletionTag != NULL) {
- (static_cast<FASTQSequence*>(&rc))->AllocateDeletionTagSpace(length);
- for (DNALength pos = 0; pos < length; pos++) {
- rc.deletionTag[length - pos - 1] = ReverseComplementNuc[deletionTag[pos]];
- }
- }
-
- if (preBaseDeletionQV.Empty() == false) {
- (static_cast<FASTQSequence*>(&rc))->AllocatePreBaseDeletionQVSpace(length);
- for (DNALength pos = 0; pos < length; pos++) {
- rc.preBaseDeletionQV[length - pos - 1] = preBaseDeletionQV[pos];
- }
- }
-
- deletionQVPrior = rc.deletionQVPrior;
- insertionQVPrior = rc.insertionQVPrior;
- substitutionQVPrior = rc.substitutionQVPrior;
- preBaseDeletionQVPrior = rc.preBaseDeletionQVPrior;
-}
-
-void FASTQSequence::Free() {
- if (deleteOnExit == true) { // Free Quality Values if under control
- qual.Free();
- deletionQV.Free();
- preBaseDeletionQV.Free();
- insertionQV.Free();
- substitutionQV.Free();
- mergeQV.Free();
- if (deletionTag != NULL) {
- delete[] deletionTag;
- }
- if (substitutionTag != NULL) {
- delete[] substitutionTag;
- }
- }
- //Reset deletionTag and substitionTag anyway
- deletionTag = NULL;
- substitutionTag = NULL;
-
- // Free seq and title, reset deleteOnExit.
- // Don't call FASTASequence::Free before freeing QVs.
- FASTASequence::Free();
-}
-
-void FASTQSequence::LowerCaseMask(int qThreshold) {
- int i;
- if (qual.Empty() == true) return;
-
- for (i = 0; i < length; i++ ){
- if (qual[i] < qThreshold) {
- seq[i] = tolower(seq[i]);
- }
- }
-}
-
-float FASTQSequence::GetAverageQuality() {
- DNALength p;
- float totalQ;
- if (qual.Empty() == true) { return 0.0; }
- assert(qual.Empty() == false);
- assert(length > 0);
- for (p = 0, totalQ = 0.0; p < length; p++) {
- totalQ += qual[p];
- }
- return totalQ / length;
-}
-
-#ifdef USE_PBBAM
-void FASTQSequence::Copy(const PacBio::BAM::BamRecord & record) {
- FASTQSequence::Free();
-
- // Copy title and sequence.
- static_cast<FASTASequence*>(this)->Copy(record);
-
- // Copy QVs.
- qual.Copy(record.Qualities().Fastq());
-
- // iq
- if (record.HasInsertionQV()) {
- insertionQV.Copy(record.InsertionQV().Fastq());
- }
- // dq
- if (record.HasDeletionQV()) {
- deletionQV.Copy(record.DeletionQV().Fastq());
- }
- // sq
- if (record.HasSubstitutionQV()) {
- substitutionQV.Copy(record.SubstitutionQV().Fastq());
- }
- // mq
- if (record.HasMergeQV()) {
- mergeQV.Copy(record.MergeQV().Fastq());
- }
- // st
- if (record.HasSubstitutionTag()) {
- std::string qvs = record.SubstitutionTag();
- AllocateSubstitutionTagSpace(static_cast<DNALength>(qvs.size()));
- std::memcpy(substitutionTag, qvs.c_str(), qvs.size() * sizeof(char));
- }
- // dt
- if (record.HasDeletionTag()) {
- std::string qvs = record.DeletionTag();
- AllocateDeletionTagSpace(static_cast<DNALength>(qvs.size()));
- std::memcpy(deletionTag, qvs.c_str(), qvs.size() * sizeof(char));
- }
- // preBaseQVs are not included in BamRecord, and will not be copied.
-
- subreadStart = static_cast<int>(record.QueryStart());
- subreadEnd = static_cast<int>(record.QueryEnd());
-}
-#endif
diff --git a/libcpp/pbdata/FASTQSequence.hpp b/libcpp/pbdata/FASTQSequence.hpp
deleted file mode 100644
index f94b2b0..0000000
--- a/libcpp/pbdata/FASTQSequence.hpp
+++ /dev/null
@@ -1,146 +0,0 @@
-#ifndef _BLASR_FASTQ_SEQUENCE_HPP_
-#define _BLASR_FASTQ_SEQUENCE_HPP_
-
-#include "DNASequence.hpp"
-#include "FASTASequence.hpp"
-#include "qvs/QualityValue.hpp"
-#include "qvs/QualityValueVector.hpp"
-#include "matrix/Matrix.hpp"
-#include "reads/ZMWGroupEntry.hpp"
-
-enum QVList {InsertionQV=0x1, DeletionQV=0x2, SubstitutionQV=0x4, MergeQV=0x8, SubstitutionTag=0x10, DeletionTag=0x20};
-enum QVIndex {I_QualityValue=0, I_InsertionQV=1,I_DeletionQV=2,I_SubstitutionQV=3,I_MergeQV=4, I_SubstitutionTag=5,I_DeletionTag=6};
-
-class FASTQSequence : public FASTASequence {
-public:
- static int charToQuality;
- QualityValueVector<QualityValue> qual;
- QualityValueVector<QualityValue> deletionQV;
- QualityValueVector<QualityValue> preBaseDeletionQV;
- QualityValueVector<QualityValue> insertionQV;
- QualityValueVector<QualityValue> substitutionQV;
- QualityValueVector<QualityValue> mergeQV;
- Nucleotide *deletionTag;
- Nucleotide *substitutionTag;
- int subreadStart, subreadEnd;
- QualityValue deletionQVPrior, insertionQVPrior, substitutionQVPrior, preBaseDeletionQVPrior;
-
- QVScale qvScale;
-
- QVScale GetQVScale();
-
- void SetQVScale(QVScale qvScaleP);
-
- QualityValueVector<QualityValue>* GetQVPointerByIndex(int index);
-
- int GetStorageSize();
-
- FASTQSequence();
- inline ~FASTQSequence();
-
- QualityValue GetDeletionQV(DNALength pos);
-
- QualityValue GetMergeQV(DNALength pos);
-
- Nucleotide GetSubstitutionTag(DNALength pos);
-
- Nucleotide GetDeletionTag(DNALength pos);
-
- QualityValue GetInsertionQV(DNALength pos);
-
- QualityValue GetSubstitutionQV(DNALength pos);
-
- QualityValue GetPreBaseDeletionQV(DNALength pos, Nucleotide nuc);
-
- void ShallowCopy(const FASTQSequence &rhs);
-
- void ReferenceSubstring(const FASTQSequence &rhs);
-
- void ReferenceSubstring(const FASTQSequence &rhs, DNALength pos);
-
- void ReferenceSubstring(const FASTQSequence &rhs, DNALength pos, DNALength substrLength);
-
- void ClearAndNull(QualityValue *value);
-
- void CopyQualityValues(const FASTQSequence &rhs);
-
- void AllocateQualitySpace(DNALength qualLength);
-
- void AllocateDeletionQVSpace(DNALength qualLength);
-
- void AllocateMergeQVSpace(DNALength len);
-
- void AllocateDeletionTagSpace(DNALength qualLength);
-
- void AllocatePreBaseDeletionQVSpace(DNALength qualLength);
-
- void AllocateInsertionQVSpace(DNALength qualLength);
-
- void AllocateSubstitutionQVSpace(DNALength qualLength );
-
- void AllocateSubstitutionTagSpace(DNALength qualLength );
-
- void AllocateRichQualityValues(DNALength qualLength);
-
- void Copy(const FASTQSequence &rhs);
-
- FASTQSequence& operator=(const FASTQSequence &rhs);
-
- FASTQSequence(const FASTQSequence &rhs);
-
- void Assign(FASTQSequence &rhs);
-
- void PrintFastq(std::ostream &out, int lineLength=50);
-
- void PrintFastqQuality(std::ostream &out, int lineLength=50);
-
- QVIndex GetQVIndex(const std::string & qvName);
-
- /// Get QVs in vector<uint8_t> associated with the given QVIndex.
- /// \returns true if qvs are available, false otherwise
- /// \param [in] qvIndex - enum QVIndex
- /// \param [out] qvs - obtained QVs.
- /// \param [in] reverse - reverse orders of QVs or not
- bool GetQVs(const QVIndex & qvIndex, std::vector<uint8_t> & qvs, bool reverse=false);
-
- /// Get QVs in vector<uint8_t>, given with QV Name.
- /// \returns true if qvs are available, false, otherwise
- /// \param [in] qvName - InsertionQV, DeletionQV, SubstitionQV, MergeQV, SubstitutionTag, DeletionTag
- /// \param [out] qvs - obtians QVs.
- /// \param [in] reverse - reverse orders of QVs or not.
- bool GetQVs(const std::string & qvName, std::vector<uint8_t> & qvs, bool reverse=false);
-
- /// Get QVs in string, given with QV Name.
- /// \returns true if qvs are available, false, otherwise
- /// \param [in] qvName - InsertionQV, DeletionQV, SubstitionQV, MergeQV, SubstitutionTag, DeletionTag
- /// \param [out] qvs - obtians QVs.
- /// \param [in] reverse - reverse order of QVs or not
- bool GetQVs(const std::string & qvName, std::string & qvs, bool reverse=false);
-
- void PrintAsciiRichQuality(std::ostream &out, int whichQuality, int lineLength=50);
-
- void PrintAsciiQual(std::ostream &out, int lineLength=50) ;
-
- void PrintQual(std::ostream &out, int lineLength = 50);
-
- void PrintQualSeq(std::ostream &out, int lineLength = 50);
-
- void MakeRC(FASTQSequence &rc);
-
- void Free();
-
- void LowerCaseMask(int qThreshold);
-
- float GetAverageQuality();
-
-#ifdef USE_PBBAM
- /// Copy name, sequence, and QVs from BamRecord.
- void Copy(const PacBio::BAM::BamRecord & record);
-#endif
-};
-
-inline FASTQSequence::~FASTQSequence() {
- FASTQSequence::Free();
-}
-
-#endif // _BLASR_FASTQ_SEQUENCE_HPP_
diff --git a/libcpp/pbdata/GFFFile.cpp b/libcpp/pbdata/GFFFile.cpp
deleted file mode 100644
index d9f36e1..0000000
--- a/libcpp/pbdata/GFFFile.cpp
+++ /dev/null
@@ -1,39 +0,0 @@
-#include "GFFFile.hpp"
-
-GFFEntry::GFFEntry(std::string & _name, std::string & _source,
- std::string & _type, UInt & _start, UInt & _end,
- float & _score, char & _strand,
- std::string & _frame, std::string _attributes) {
- name = _name;
- source = _source;
- type = _type;
- start = _start;
- end = _end;
- score = _score;
- strand = _strand;
- frame = _frame;
-}
-
-void GFFFile::ReadAll(std::string & gffFileName) {
- std::fstream gffIn;
- CrucialOpen(gffFileName, gffIn, std::ios::in);
- while(gffIn) {
- std::string line;
- getline(gffIn, line);
- std::stringstream linestrm(line);
- std::string name, source, type;
- UInt start, end;
- char strand;
- float score;
- std::string frame, attributes;
- // A sample record in adapterGffFile:
- // ref000001 . adapter 10955 10999 0.00 + . xxxx
- linestrm >> name >> source >> type
- >> start >> end >> score
- >> strand >> frame >> attributes;
- entries.push_back(GFFEntry(
- name, source, type, start, end,
- score, strand, frame, attributes));
- }
- gffIn.close();
-}
diff --git a/libcpp/pbdata/GFFFile.hpp b/libcpp/pbdata/GFFFile.hpp
deleted file mode 100644
index 2e410ec..0000000
--- a/libcpp/pbdata/GFFFile.hpp
+++ /dev/null
@@ -1,33 +0,0 @@
-#ifndef _BLASR_GFF_FILE_HPP_
-#define _BLASR_GFF_FILE_HPP_
-
-#include <iostream>
-#include <fstream>
-#include <sstream>
-#include <string>
-#include <vector>
-
-#include "utils.hpp"
-#include "Types.h"
-
-class GFFEntry {
-public:
- std::string name, type, source;
- UInt start, end;
- char strand;
- float score;
- std::string frame;
- std::string attributes;
- GFFEntry(std::string & _name, std::string & _source,
- std::string & _type, UInt & _start, UInt & _end,
- float & _score, char & _strand,
- std::string & _frame, std::string _attributes);
-};
-
-class GFFFile {
-public:
- std::vector<GFFEntry> entries;
- void ReadAll(std::string & gffFileName);
-};
-
-#endif
diff --git a/libcpp/pbdata/MD5Utils.cpp b/libcpp/pbdata/MD5Utils.cpp
deleted file mode 100644
index dd1f45a..0000000
--- a/libcpp/pbdata/MD5Utils.cpp
+++ /dev/null
@@ -1,464 +0,0 @@
-
-// MD5.CC - source code for the C++/object oriented translation and
-// modification of MD5.
-
-// Translation and modification (c) 1995 by Mordechai T. Abzug
-
-// This translation/ modification is provided "as is," without express or
-// implied warranty of any kind.
-
-// The translator/ modifier does not claim (1) that MD5 will do what you think
-// it does; (2) that this translation/ modification is accurate; or (3) that
-// this software is "merchantible." (Language for this disclaimer partially
-// copied from the disclaimer below).
-
-/* based on:
-
- MD5C.C - RSA Data Security, Inc., MD5 message-digest algorithm
- MDDRIVER.C - test driver for MD2, MD4 and MD5
-
-
- Copyright (C) 1991-2, RSA Data Security, Inc. Created 1991. All
-rights reserved.
-
-License to copy and use this software is granted provided that it
-is identified as the "RSA Data Security, Inc. MD5 Message-Digest
-Algorithm" in all material mentioning or referencing this software
-or this function.
-
-License is also granted to make and use derivative works provided
-that such works are identified as "derived from the RSA Data
-Security, Inc. MD5 Message-Digest Algorithm" in all material
-mentioning or referencing the derived work.
-
-RSA Data Security, Inc. makes no representations concerning either
-the merchantability of this software or the suitability of this
-software for any particular purpose. It is provided "as is"
-without express or implied warranty of any kind.
-
-These notices must be retained in any copies of any part of this
-documentation and/or software.
-
- */
-
-#include <assert.h>
-#include <strings.h>
-#include <iostream>
-#include "MD5Utils.hpp"
-
-using namespace std;
-
-// MD5 simple initialization method
-
-MD5::MD5(){
-
- init();
-
-}
-
-// MD5 block update operation. Continues an MD5 message-digest
-// operation, processing another message block, and updating the
-// context.
-
-void MD5::update (uint1 *input, uint4 input_length) {
-
- uint4 input_index, buffer_index;
- uint4 buffer_space; // how much space is left in buffer
-
- if (finalized){ // so we can't update!
- cerr << "MD5::update: Can't update a finalized digest!" << endl;
- return;
- }
-
- // Compute number of bytes mod 64
- buffer_index = (unsigned int)((count[0] >> 3) & 0x3F);
-
- // Update number of bits
- if ( (count[0] += ((uint4) input_length << 3))<((uint4) input_length << 3) )
- count[1]++;
-
- count[1] += ((uint4)input_length >> 29);
-
-
- buffer_space = 64 - buffer_index; // how much space is left in buffer
-
- // Transform as many times as possible.
- if (input_length >= buffer_space) { // ie. we have enough to fill the buffer
- // fill the rest of the buffer and transform
- memcpy (buffer + buffer_index, input, buffer_space);
- transform (buffer);
-
- // now, transform each 64-byte piece of the input, bypassing the buffer
- for (input_index = buffer_space; input_index + 63 < input_length;
- input_index += 64)
- transform (input+input_index);
-
- buffer_index = 0; // so we can buffer remaining
- }
- else
- input_index=0; // so we can buffer the whole input
-
-
- // and here we do the buffering:
- memcpy(buffer+buffer_index, input+input_index, input_length-input_index);
-}
-
-
-// MD5 update for files.
-// Like above, except that it works on files (and uses above as a primitive.)
-
-void MD5::update(FILE *file){
-
- unsigned char buffer[1024];
- int len = 0;
-
- while ( (len=fread(buffer, 1, 1024, file) and len != 0))
- update(buffer, len);
-
- fclose (file);
-}
-
-
-// MD5 update for istreams.
-// Like update for files; see above.
-
-void MD5::update(istream& stream){
-
- unsigned char buffer[1024];
- int len;
-
- while (stream.good()){
- stream.read((char*) buffer, 1024); // note that return value of read is unusable.
- len=stream.gcount();
- update(buffer, len);
- }
-
-}
-
-
-
-
-
-
-// MD5 update for ifstreams.
-// Like update for files; see above.
-
-void MD5::update(ifstream& stream){
-
- unsigned char buffer[1024];
- int len;
-
- while (stream.good()){
- stream.read((char*)buffer, 1024); // note that return value of read is unusable.
- len=stream.gcount();
- update(buffer, len);
- }
-
-}
-
-
-
-
-
-
-// MD5 finalization. Ends an MD5 message-digest operation, writing the
-// the message digest and zeroizing the context.
-
-
-void MD5::finalize (){
-
- unsigned char bits[8];
- unsigned int index, padLen;
- static uint1 PADDING[64]={
- 0x80, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
- 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
- 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0
- };
-
- if (finalized){
- cerr << "MD5::finalize: Already finalized this digest!" << endl;
- return;
- }
-
- // Save number of bits
- encode (bits, count, 8);
-
- // Pad out to 56 mod 64.
- index = (uint4) ((count[0] >> 3) & 0x3f);
- padLen = (index < 56) ? (56 - index) : (120 - index);
- update (PADDING, padLen);
-
- // Append length (before padding)
- update (bits, 8);
-
- // Store state in digest
- encode (digest, state, 16);
-
- // Zeroize sensitive information
- memset (buffer, 0, sizeof(*buffer));
-
- finalized=1;
-
-}
-
-
-
-
-MD5::MD5(FILE *file){
-
- init(); // must be called be all constructors
- update(file);
- finalize ();
-}
-
-
-
-
-MD5::MD5(istream& stream){
-
- init(); // must called by all constructors
- update (stream);
- finalize();
-}
-
-
-
-MD5::MD5(ifstream& stream){
-
- init(); // must called by all constructors
- update (stream);
- finalize();
-}
-
-
-
-unsigned char *MD5::raw_digest(){
-
- uint1 *s = new uint1[16];
-
- if (!finalized){
- cerr << "MD5::raw_digest: Can't get digest if you haven't "<<
- "finalized the digest!" <<endl;
- //return ( (unsigned char*) "");
- delete [] s;
- return NULL;
- }
-
- memcpy(s, digest, 16);
- return s;
-}
-
-
-
-char *MD5::hex_digest(){
-
- int i;
- char *s= new char[33];
-
- if (!finalized){
- cerr << "MD5::hex_digest: Can't get digest if you haven't "<<
- "finalized the digest!" <<endl;
- delete [] s;
- return NULL;
- }
-
- for (i=0; i<16; i++)
- sprintf(s+i*2, "%02x", digest[i]);
-
- s[32]='\0';
-
- return s;
-}
-
-
-
-
-
-
-
-// PRIVATE METHODS:
-
-
-
-void MD5::init(){
- finalized=0; // we just started!
-
- // Nothing counted, so count=0
- count[0] = 0;
- count[1] = 0;
-
- // Load magic initialization constants.
- state[0] = 0x67452301;
- state[1] = 0xefcdab89;
- state[2] = 0x98badcfe;
- state[3] = 0x10325476;
-}
-
-
-
-// Constants for MD5Transform routine.
-// Although we could use C++ style constants, defines are actually better,
-// since they let us easily evade scope clashes.
-
-#define S11 7
-#define S12 12
-#define S13 17
-#define S14 22
-#define S21 5
-#define S22 9
-#define S23 14
-#define S24 20
-#define S31 4
-#define S32 11
-#define S33 16
-#define S34 23
-#define S41 6
-#define S42 10
-#define S43 15
-#define S44 21
-
-
-
-
-// MD5 basic transformation. Transforms state based on block.
-void MD5::transform (uint1 block[64]){
-
- uint4 a = state[0], b = state[1], c = state[2], d = state[3], x[16];
-
- decode (x, block, 64);
-
- assert(!finalized); // not just a user error, since the method is private
-
- /* Round 1 */
- FF (a, b, c, d, x[ 0], S11, 0xd76aa478); /* 1 */
- FF (d, a, b, c, x[ 1], S12, 0xe8c7b756); /* 2 */
- FF (c, d, a, b, x[ 2], S13, 0x242070db); /* 3 */
- FF (b, c, d, a, x[ 3], S14, 0xc1bdceee); /* 4 */
- FF (a, b, c, d, x[ 4], S11, 0xf57c0faf); /* 5 */
- FF (d, a, b, c, x[ 5], S12, 0x4787c62a); /* 6 */
- FF (c, d, a, b, x[ 6], S13, 0xa8304613); /* 7 */
- FF (b, c, d, a, x[ 7], S14, 0xfd469501); /* 8 */
- FF (a, b, c, d, x[ 8], S11, 0x698098d8); /* 9 */
- FF (d, a, b, c, x[ 9], S12, 0x8b44f7af); /* 10 */
- FF (c, d, a, b, x[10], S13, 0xffff5bb1); /* 11 */
- FF (b, c, d, a, x[11], S14, 0x895cd7be); /* 12 */
- FF (a, b, c, d, x[12], S11, 0x6b901122); /* 13 */
- FF (d, a, b, c, x[13], S12, 0xfd987193); /* 14 */
- FF (c, d, a, b, x[14], S13, 0xa679438e); /* 15 */
- FF (b, c, d, a, x[15], S14, 0x49b40821); /* 16 */
-
- /* Round 2 */
- GG (a, b, c, d, x[ 1], S21, 0xf61e2562); /* 17 */
- GG (d, a, b, c, x[ 6], S22, 0xc040b340); /* 18 */
- GG (c, d, a, b, x[11], S23, 0x265e5a51); /* 19 */
- GG (b, c, d, a, x[ 0], S24, 0xe9b6c7aa); /* 20 */
- GG (a, b, c, d, x[ 5], S21, 0xd62f105d); /* 21 */
- GG (d, a, b, c, x[10], S22, 0x2441453); /* 22 */
- GG (c, d, a, b, x[15], S23, 0xd8a1e681); /* 23 */
- GG (b, c, d, a, x[ 4], S24, 0xe7d3fbc8); /* 24 */
- GG (a, b, c, d, x[ 9], S21, 0x21e1cde6); /* 25 */
- GG (d, a, b, c, x[14], S22, 0xc33707d6); /* 26 */
- GG (c, d, a, b, x[ 3], S23, 0xf4d50d87); /* 27 */
- GG (b, c, d, a, x[ 8], S24, 0x455a14ed); /* 28 */
- GG (a, b, c, d, x[13], S21, 0xa9e3e905); /* 29 */
- GG (d, a, b, c, x[ 2], S22, 0xfcefa3f8); /* 30 */
- GG (c, d, a, b, x[ 7], S23, 0x676f02d9); /* 31 */
- GG (b, c, d, a, x[12], S24, 0x8d2a4c8a); /* 32 */
-
- /* Round 3 */
- HH (a, b, c, d, x[ 5], S31, 0xfffa3942); /* 33 */
- HH (d, a, b, c, x[ 8], S32, 0x8771f681); /* 34 */
- HH (c, d, a, b, x[11], S33, 0x6d9d6122); /* 35 */
- HH (b, c, d, a, x[14], S34, 0xfde5380c); /* 36 */
- HH (a, b, c, d, x[ 1], S31, 0xa4beea44); /* 37 */
- HH (d, a, b, c, x[ 4], S32, 0x4bdecfa9); /* 38 */
- HH (c, d, a, b, x[ 7], S33, 0xf6bb4b60); /* 39 */
- HH (b, c, d, a, x[10], S34, 0xbebfbc70); /* 40 */
- HH (a, b, c, d, x[13], S31, 0x289b7ec6); /* 41 */
- HH (d, a, b, c, x[ 0], S32, 0xeaa127fa); /* 42 */
- HH (c, d, a, b, x[ 3], S33, 0xd4ef3085); /* 43 */
- HH (b, c, d, a, x[ 6], S34, 0x4881d05); /* 44 */
- HH (a, b, c, d, x[ 9], S31, 0xd9d4d039); /* 45 */
- HH (d, a, b, c, x[12], S32, 0xe6db99e5); /* 46 */
- HH (c, d, a, b, x[15], S33, 0x1fa27cf8); /* 47 */
- HH (b, c, d, a, x[ 2], S34, 0xc4ac5665); /* 48 */
-
- /* Round 4 */
- II (a, b, c, d, x[ 0], S41, 0xf4292244); /* 49 */
- II (d, a, b, c, x[ 7], S42, 0x432aff97); /* 50 */
- II (c, d, a, b, x[14], S43, 0xab9423a7); /* 51 */
- II (b, c, d, a, x[ 5], S44, 0xfc93a039); /* 52 */
- II (a, b, c, d, x[12], S41, 0x655b59c3); /* 53 */
- II (d, a, b, c, x[ 3], S42, 0x8f0ccc92); /* 54 */
- II (c, d, a, b, x[10], S43, 0xffeff47d); /* 55 */
- II (b, c, d, a, x[ 1], S44, 0x85845dd1); /* 56 */
- II (a, b, c, d, x[ 8], S41, 0x6fa87e4f); /* 57 */
- II (d, a, b, c, x[15], S42, 0xfe2ce6e0); /* 58 */
- II (c, d, a, b, x[ 6], S43, 0xa3014314); /* 59 */
- II (b, c, d, a, x[13], S44, 0x4e0811a1); /* 60 */
- II (a, b, c, d, x[ 4], S41, 0xf7537e82); /* 61 */
- II (d, a, b, c, x[11], S42, 0xbd3af235); /* 62 */
- II (c, d, a, b, x[ 2], S43, 0x2ad7d2bb); /* 63 */
- II (b, c, d, a, x[ 9], S44, 0xeb86d391); /* 64 */
-
- state[0] += a;
- state[1] += b;
- state[2] += c;
- state[3] += d;
-
- // Zeroize sensitive information.
- memset ( (uint1 *) x, 0, sizeof(x));
-
-}
-
-// Encodes input (UINT4) into output (unsigned char). Assumes len is
-// a multiple of 4.
-void MD5::encode (uint1 *output, uint4 *input, uint4 len) {
-
- unsigned int i, j;
-
- for (i = 0, j = 0; j < len; i++, j += 4) {
- output[j] = (uint1) (input[i] & 0xff);
- output[j+1] = (uint1) ((input[i] >> 8) & 0xff);
- output[j+2] = (uint1) ((input[i] >> 16) & 0xff);
- output[j+3] = (uint1) ((input[i] >> 24) & 0xff);
- }
-}
-
-
-
-
-// Decodes input (unsigned char) into output (UINT4). Assumes len is
-// a multiple of 4.
-void MD5::decode (uint4 *output, uint1 *input, uint4 len){
-
- unsigned int i, j;
-
- for (i = 0, j = 0; j < len; i++, j += 4)
- output[i] = ((uint4)input[j]) | (((uint4)input[j+1]) << 8) |
- (((uint4)input[j+2]) << 16) | (((uint4)input[j+3]) << 24);
-}
-
-
-
-
-
-// Note: Replace "for loop" with standard memcpy if possible.
-void MD5::memcpy (uint1 *output, uint1 *input, uint4 len){
-
- unsigned int i;
-
- for (i = 0; i < len; i++)
- output[i] = input[i];
-}
-
-
-
-// Note: Replace "for loop" with standard memset if possible.
-void MD5::memset (uint1 *output, uint1 value, uint4 len){
-
- unsigned int i;
-
- for (i = 0; i < len; i++)
- output[i] = value;
-}
diff --git a/libcpp/pbdata/MD5Utils.hpp b/libcpp/pbdata/MD5Utils.hpp
deleted file mode 100644
index 8957933..0000000
--- a/libcpp/pbdata/MD5Utils.hpp
+++ /dev/null
@@ -1,113 +0,0 @@
-#ifndef _BLASR_UTILS_M5UTILS_HPP_
-#define _BLASR_UTILS_M5UTILS_HPP_
-
-// MD5.CC - source code for the C++/object oriented translation and
-// modification of MD5.
-
-// Translation and modification (c) 1995 by Mordechai T. Abzug
-
-// This translation/ modification is provided "as is," without express or
-// implied warranty of any kind.
-
-// The translator/ modifier does not claim (1) that MD5 will do what you think
-// it does; (2) that this translation/ modification is accurate; or (3) that
-// this software is "merchantible." (Language for this disclaimer partially
-// copied from the disclaimer below).
-
-/* based on:
-
- MD5.H - header file for MD5C.C
- MDDRIVER.C - test driver for MD2, MD4 and MD5
-
- Copyright (C) 1991-2, RSA Data Security, Inc. Created 1991. All
- rights reserved.
-
- License to copy and use this software is granted provided that it
- is identified as the "RSA Data Security, Inc. MD5 Message-Digest
- Algorithm" in all material mentioning or referencing this software
- or this function.
-
- License is also granted to make and use derivative works provided
- that such works are identified as "derived from the RSA Data
- Security, Inc. MD5 Message-Digest Algorithm" in all material
- mentioning or referencing the derived work.
-
- RSA Data Security, Inc. makes no representations concerning either
- the merchantability of this software or the suitability of this
- software for any particular purpose. It is provided "as is"
- without express or implied warranty of any kind.
-
- These notices must be retained in any copies of any part of this
- documentation and/or software.
-
-*/
-
-#include <stdio.h>
-#include <fstream>
-#include <iostream>
-
-class MD5 {
-
-public:
- // methods for controlled operation:
- MD5 (); // simple initializer
- void update (unsigned char *input, unsigned int input_length);
- void update (std::istream& stream);
- void update (FILE *file);
- void update (std::ifstream& stream);
- void finalize ();
-
- // constructors for special circumstances. All these constructors finalize
- // the MD5 context.
- MD5 (unsigned char *string); // digest string, finalize
- MD5 (std::istream& stream); // digest stream, finalize
- MD5 (FILE *file); // digest file, close, finalize
- MD5 (std::ifstream& stream); // digest stream, close, finalize
-
- // methods to acquire finalized result
- unsigned char *raw_digest (); // digest as a 16-byte binary array
- char * hex_digest (); // digest as a 33-byte ascii-hex string
- friend std::ostream& operator<< (std::ostream&, MD5 context);
-
-private:
-
- // first, some types:
- typedef unsigned int uint4; // assumes integer is 4 words long
- typedef unsigned short int uint2; // assumes short integer is 2 words long
- typedef unsigned char uint1; // assumes char is 1 word long
-
- // next, the private data:
- uint4 state[4];
- uint4 count[2]; // number of *bits*, mod 2^64
- uint1 buffer[64]; // input buffer
- uint1 digest[16];
- uint1 finalized;
-
- // last, the private methods, mostly static:
- void init (); // called by all constructors
- void transform (uint1 *buffer); // does the real update work. Note
- // that length is implied to be 64.
-
- static void encode (uint1 *dest, uint4 *src, uint4 length);
- static void decode (uint4 *dest, uint1 *src, uint4 length);
- static void memcpy (uint1 *dest, uint1 *src, uint4 length);
- static void memset (uint1 *start, uint1 val, uint4 length);
-
- static inline uint4 rotate_left (uint4 x, uint4 n);
- static inline uint4 F (uint4 x, uint4 y, uint4 z);
- static inline uint4 G (uint4 x, uint4 y, uint4 z);
- static inline uint4 H (uint4 x, uint4 y, uint4 z);
- static inline uint4 I (uint4 x, uint4 y, uint4 z);
- static inline void FF (uint4& a, uint4 b, uint4 c, uint4 d, uint4 x,
- uint4 s, uint4 ac);
- static inline void GG (uint4& a, uint4 b, uint4 c, uint4 d, uint4 x,
- uint4 s, uint4 ac);
- static inline void HH (uint4& a, uint4 b, uint4 c, uint4 d, uint4 x,
- uint4 s, uint4 ac);
- static inline void II (uint4& a, uint4 b, uint4 c, uint4 d, uint4 x,
- uint4 s, uint4 ac);
-};
-
-#include "MD5UtilsImpl.hpp"
-
-#endif // _BLASR_UTILS_M5UTILS_HPP_
diff --git a/libcpp/pbdata/MD5UtilsImpl.hpp b/libcpp/pbdata/MD5UtilsImpl.hpp
deleted file mode 100644
index 3e8f78e..0000000
--- a/libcpp/pbdata/MD5UtilsImpl.hpp
+++ /dev/null
@@ -1,57 +0,0 @@
-#ifndef _BLASR_MD5_UTILS_IMPL_HPP_
-#define _BLASR_MD5_UTILS_IMPL_HPP_
-// ROTATE_LEFT rotates x left n bits.
-
-inline unsigned int MD5::rotate_left (uint4 x, uint4 n){
- return (x << n) | (x >> (32-n)) ;
-}
-
-// F, G, H and I are basic MD5 functions.
-
-inline unsigned int MD5::F (uint4 x, uint4 y, uint4 z){
- return (x & y) | (~x & z);
-}
-
-inline unsigned int MD5::G (uint4 x, uint4 y, uint4 z){
- return (x & z) | (y & ~z);
-}
-
-inline unsigned int MD5::H (uint4 x, uint4 y, uint4 z){
- return x ^ y ^ z;
-}
-
-inline unsigned int MD5::I (uint4 x, uint4 y, uint4 z){
- return y ^ (x | ~z);
-}
-
-
-
-// FF, GG, HH, and II transformations for rounds 1, 2, 3, and 4.
-// Rotation is separate from addition to prevent recomputation.
-
-
-inline void MD5::FF(uint4& a, uint4 b, uint4 c, uint4 d, uint4 x,
- uint4 s, uint4 ac){
- a += F(b, c, d) + x + ac;
- a = rotate_left (a, s) +b;
-}
-
-inline void MD5::GG(uint4& a, uint4 b, uint4 c, uint4 d, uint4 x,
- uint4 s, uint4 ac){
- a += G(b, c, d) + x + ac;
- a = rotate_left (a, s) +b;
-}
-
-inline void MD5::HH(uint4& a, uint4 b, uint4 c, uint4 d, uint4 x,
- uint4 s, uint4 ac){
- a += H(b, c, d) + x + ac;
- a = rotate_left (a, s) +b;
-}
-
-inline void MD5::II(uint4& a, uint4 b, uint4 c, uint4 d, uint4 x,
- uint4 s, uint4 ac){
- a += I(b, c, d) + x + ac;
- a = rotate_left (a, s) +b;
-}
-
-#endif
diff --git a/libcpp/pbdata/NucConversion.cpp b/libcpp/pbdata/NucConversion.cpp
deleted file mode 100644
index ba46f6b..0000000
--- a/libcpp/pbdata/NucConversion.cpp
+++ /dev/null
@@ -1,409 +0,0 @@
-#include "NucConversion.hpp"
-
-int TwoBit[] = {
- 0, 1, 2, 3, 0, 1, 2, 3,
- 255,255,255,255,255,255,255,255,
- 255,255,255,255,255,255,255,255,
- 255,255,255,255,255,255,255,255,
- 255,255,255,255,255,255,255,255,
- 255,255,255,255,255,255,255,255,
- 255,255,255,255,255,255,255,255,
- 255,255,255,255,255,255,255,255,
- 255, 0,255, 1,255,255,255, 2,
- 255,255,255,255,255,255,255,255,
- 255,255,255,255, 3,255,255,255,
- 255,255,255,255,255,255,255,255,
- 255, 0,255, 1,255,255,255, 2,
- 255,255,255,255,255,255,255,255,
- 255,255,255,255, 3,255,255,255,
- 255,255,255,255,255,255,255,255,
- 255,255,255,255,255,255,255,255,
- 255,255,255,255,255,255,255,255,
- 255,255,255,255,255,255,255,255,
- 255,255,255,255,255,255,255,255,
- 255,255,255,255,255,255,255,255,
- 255,255,255,255,255,255,255,255,
- 255,255,255,255,255,255,255,255,
- 255,255,255,255,255,255,255,255,
- 255,255,255,255,255,255,255,255,
- 255,255,255,255,255,255,255,255,
- 255,255,255,255,255,255,255,255,
- 255,255,255,255,255,255,255,255,
- 255,255,255,255,255,255,255,255,
- 255,255,255,255,255,255,255,255,
- 255,255,255,255,255,255,255,255,
- 255,255,255,255,255,255,255,255
-};
-
-
-//
-// Map from charcter to 3 bit. Treat all non ACGT IUPAC as N
-// IPUAC: ACGT U M R W S Y K V H D N
-//
-
-int ThreeBit[] = {
- 0, 1, 2, 3, 4,255,255,255, // 0..3 are native nucletides, 4
- // is an 'N', which is
- // represented just fine in the 3
- // bit mode.
- 255,255,255,255,255,255,255,255, // 8
- 255,255,255,255,255,255,255,255, // 16
- 255,255,255,255,255,255,255,255, // 24
- 255,255,255,255, 5,255,255,255, // 32 define '$' for bwt.
- 255,255,255,255,255,255,255,255, // 40
- 255,255,255,255,255,255,255,255, // 48
- 255,255,255,255,255,255,255,255, // 56
- 255, 0, 4, 1, 4,255,255, 2, // 64
- 4,255,255, 4,255, 4, 4,255, // 72
- 255,255, 4, 4, 3, 4, 4, 4, // 80
- 255, 4,255,255,255,255,255, 4, // 88
- 255, 0, 4, 1, 4,255,255, 2, // 96
- 4,255,255, 4,255, 4, 4,255, // 104
- 255,255, 4, 4, 3, 4, 4, 4, // 112
- 4, 4,255,255,255,255,255,255, // 120
- 255,255,255,255,255,255,255,255, // 128
- 255,255,255,255,255,255,255,255, // 136
- 255,255,255,255,255,255,255,255, // 144
- 255,255,255,255,255,255,255,255, // 152
- 255,255,255,255,255,255,255,255, // 160
- 255,255,255,255,255,255,255,255, // 168
- 255,255,255,255,255,255,255,255, // 176
- 255,255,255,255,255,255,255,255, // 184
- 255,255,255,255,255,255,255,255, // 192
- 255,255,255,255,255,255,255,255, // 200
- 255,255,255,255,255,255,255,255, // 208
- 255,255,255,255,255,255,255,255, // 216
- 255,255,255,255,255,255,255,255, // 224
- 255,255,255,255,255,255,255,255, // 232
- 255,255,255,255,255,255,255,255, // 240
- 255,255,255,255,255,255,255,255 // 248
-};
-
-int IsACTG[] = {
- 1, 1, 1, 1, 0, 0, 0, 0,
- 0, 0, 0, 0, 0, 0, 0, 0,
- 0, 0, 0, 0, 0, 0, 0, 0,
- 0, 0, 0, 0, 0, 0, 0, 0,
- 0, 0, 0, 0, 0, 0, 0, 0,
- 0, 0, 0, 0, 0, 0, 0, 0,
- 0, 0, 0, 0, 0, 0, 0, 0,
- 0, 0, 0, 0, 0, 0, 0, 0,
- 0, 1, 0, 1, 0, 0, 0, 1,
- 0, 0, 0, 0, 0, 0, 0, 0,
- 0, 0, 0, 0, 1, 0, 0, 0,
- 0, 0, 0, 0, 0, 0, 0, 0,
- 0, 1, 0, 1, 0, 0, 0, 1,
- 0, 0, 0, 0, 0, 0, 0, 0,
- 0, 0, 0, 0, 1, 0, 0, 0,
- 0, 0, 0, 0, 0, 0, 0, 0,
- 0, 0, 0, 0, 0, 0, 0, 0,
- 0, 0, 0, 0, 0, 0, 0, 0,
- 0, 0, 0, 0, 0, 0, 0, 0,
- 0, 0, 0, 0, 0, 0, 0, 0,
- 0, 0, 0, 0, 0, 0, 0, 0,
- 0, 0, 0, 0, 0, 0, 0, 0,
- 0, 0, 0, 0, 0, 0, 0, 0,
- 0, 0, 0, 0, 0, 0, 0, 0,
- 0, 0, 0, 0, 0, 0, 0, 0,
- 0, 0, 0, 0, 0, 0, 0, 0,
- 0, 0, 0, 0, 0, 0, 0, 0,
- 0, 0, 0, 0, 0, 0, 0, 0,
- 0, 0, 0, 0, 0, 0, 0, 0,
- 0, 0, 0, 0, 0, 0, 0, 0,
- 0, 0, 0, 0, 0, 0, 0, 0,
- 0, 0, 0, 0, 0, 0, 0, 0
-};
-
-int IsLowerCase[] = {
- 0, 0, 0, 0, 0, 0, 0, 0,
- 0, 0, 0, 0, 0, 0, 0, 0,
- 0, 0, 0, 0, 0, 0, 0, 0,
- 0, 0, 0, 0, 0, 0, 0, 0,
- 0, 0, 0, 0, 0, 0, 0, 0,
- 0, 0, 0, 0, 0, 0, 0, 0,
- 0, 0, 0, 0, 0, 0, 0, 0,
- 0, 0, 0, 0, 0, 0, 0, 0,
- 0, 0, 0, 0, 0, 0, 0, 0,
- 0, 0, 0, 0, 0, 0, 0, 0,
- 0, 0, 0, 0, 0, 0, 0, 0,
- 0, 0, 0, 0, 0, 0, 0, 0,
- 0, 1, 0, 1, 0, 0, 0, 1,
- 0, 0, 0, 0, 0, 0, 0, 0,
- 0, 0, 0, 0, 1, 0, 0, 0,
- 0, 0, 0, 0, 0, 0, 0, 0,
- 0, 0, 0, 0, 0, 0, 0, 0,
- 0, 0, 0, 0, 0, 0, 0, 0,
- 0, 0, 0, 0, 0, 0, 0, 0,
- 0, 0, 0, 0, 0, 0, 0, 0,
- 0, 0, 0, 0, 0, 0, 0, 0,
- 0, 0, 0, 0, 0, 0, 0, 0,
- 0, 0, 0, 0, 0, 0, 0, 0,
- 0, 0, 0, 0, 0, 0, 0, 0,
- 0, 0, 0, 0, 0, 0, 0, 0,
- 0, 0, 0, 0, 0, 0, 0, 0,
- 0, 0, 0, 0, 0, 0, 0, 0,
- 0, 0, 0, 0, 0, 0, 0, 0,
- 0, 0, 0, 0, 0, 0, 0, 0,
- 0, 0, 0, 0, 0, 0, 0, 0,
- 0, 0, 0, 0, 0, 0, 0, 0,
- 0, 0, 0, 0, 0, 0, 0, 0
-};
-
-
-int FourBit[] = {
- 0, 1, 2, 3, 4, 5, 6, 7,
- 255,255,255,255,255,255,255,255,
- 255,255,255,255,255,255,255,255,
- 255,255,255,255,255,255,255,255,
- 255,255,255,255,255,255,255,255,
- 255,255,255,255,255,255,255,255,
- 255,255,255,255,255,255,255,255,
- 255,255,255,255,255,255,255,255,
- 255, 0,255, 1,255,255,255, 2,
- 255,255,255,255,255,255, 8,255,
- 255,255,255,255, 3,255,255,255,
- 255,255,255,255,255,255,255,255,
- 255, 4,255, 5,255,255,255, 6,
- 255,255,255,255,255,255, 8,255,
- 255,255,255,255, 7,255,255,255,
- 255,255,255,255,255,255,255,255,
- 255,255,255,255,255,255,255,255,
- 255,255,255,255,255,255,255,255,
- 255,255,255,255,255,255,255,255,
- 255,255,255,255,255,255,255,255,
- 255,255,255,255,255,255,255,255,
- 255,255,255,255,255,255,255,255,
- 255,255,255,255,255,255,255,255,
- 255,255,255,255,255,255,255,255,
- 255,255,255,255,255,255,255,255,
- 255,255,255,255,255,255,255,255,
- 255,255,255,255,255,255,255,255,
- 255,255,255,255,255,255,255,255,
- 255,255,255,255,255,255,255,255,
- 255,255,255,255,255,255,255,255,
- 255,255,255,255,255,255,255,255,
- 255,255,255,255,255,255,255,255
-};
-
-int FourBitToAscii[] = {'A', 'C', 'G', 'T', 'a', 'c', 'g', 't', 'N', 'X'};
-int ThreeBitToAscii[] = {'A', 'C', 'G', 'T', 'N', '$'};
-
-int MaskedFourBit[] = {
- 9,9,9,9,9,9,9,9,
- 9,9,9,9,9,9,9,9,
- 9,9,9,9,9,9,9,9,
- 9,9,9,9,9,9,9,9,
- 9,9,9,9,9,9,9,9,
- 9,9,9,9,9,9,9,9,
- 9,9,9,9,9,9,9,9,
- 9,9,9,9,9,9,9,9,
- 9,0,9,1,9,9,9,2,
- 9,9,9,9,9,9,8,9,
- 9,9,9,9,3,9,9,9,
- 9,9,9,9,9,9,9,9,
- 9,4,9,5,9,9,9,6,
- 9,9,9,9,9,9,8,9,
- 9,9,9,9,7,9,9,9,
- 9,9,9,9,9,9,9,9,
- 9,9,9,9,9,9,9,9,
- 9,9,9,9,9,9,9,9,
- 9,9,9,9,9,9,9,9,
- 9,9,9,9,9,9,9,9,
- 9,9,9,9,9,9,9,9,
- 9,9,9,9,9,9,9,9,
- 9,9,9,9,9,9,9,9,
- 9,9,9,9,9,9,9,9,
- 9,9,9,9,9,9,9,9,
- 9,9,9,9,9,9,9,9,
- 9,9,9,9,9,9,9,9,
- 9,9,9,9,9,9,9,9,
- 9,9,9,9,9,9,9,9,
- 9,9,9,9,9,9,9,9,
- 9,9,9,9,9,9,9,9,
- 9,9,9,9,9,9,9,9
-};
-
-unsigned char AllToUpper[] = {
- 'A','C','G','T','N','N','N','N',
- 'N','N','N','N','N','N','N','N',
- 'N','N','N','N','N','N','N','N',
- 'N','N','N','N','N','N','N','N',
- 'N','N','N','N','N','N','N','N',
- 'N','N','N','N','N','N','N','N',
- 'N','N','N','N','N','N','N','N',
- 'N','N','N','N','N','N','N','N',
- 'N','A','N','C','N','N','N','G',
- 'N','N','N','N','N','N','N','N',
- 'N','N','N','N','T','N','N','N',
- 'N','N','N','N','N','N','N','N',
- 'N','A','N','C','N','N','N','G',
- 'N','N','N','N','N','N','N','N',
- 'N','N','N','N','T','N','N','N',
- 'N','N','N','N','N','N','N','N',
- 'N','N','N','N','N','N','N','N',
- 'N','N','N','N','N','N','N','N',
- 'N','N','N','N','N','N','N','N',
- 'N','N','N','N','N','N','N','N',
- 'N','N','N','N','N','N','N','N',
- 'N','N','N','N','N','N','N','N',
- 'N','N','N','N','N','N','N','N',
- 'N','N','N','N','N','N','N','N',
- 'N','N','N','N','N','N','N','N',
- 'N','N','N','N','N','N','N','N',
- 'N','N','N','N','N','N','N','N',
- 'N','N','N','N','N','N','N','N',
- 'N','N','N','N','N','N','N','N',
- 'N','N','N','N','N','N','N','N',
- 'N','N','N','N','N','N','N','N',
- 'N','N','N','N','N','N','N','N'
-};
-char AllToLower[] = {
- 'a','c','g','t','N','N','N','N',
- 'N','N','N','N','N','N','N','N',
- 'N','N','N','N','N','N','N','N',
- 'N','N','N','N','N','N','N','N',
- 'N','N','N','N','N','N','N','N',
- 'N','N','N','N','N','N','N','N',
- 'N','N','N','N','N','N','N','N',
- 'N','N','N','N','N','N','N','N',
- 'N','a','N','c','N','N','N','g',
- 'N','N','N','N','N','N','N','N',
- 'N','N','N','N','t','N','N','N',
- 'N','N','N','N','N','N','N','N',
- 'N','a','N','c','N','N','N','g',
- 'N','N','N','N','N','N','N','N',
- 'N','N','N','N','t','N','N','N',
- 'N','N','N','N','N','N','N','N',
- 'N','N','N','N','N','N','N','N',
- 'N','N','N','N','N','N','N','N',
- 'N','N','N','N','N','N','N','N',
- 'N','N','N','N','N','N','N','N',
- 'N','N','N','N','N','N','N','N',
- 'N','N','N','N','N','N','N','N',
- 'N','N','N','N','N','N','N','N',
- 'N','N','N','N','N','N','N','N',
- 'N','N','N','N','N','N','N','N',
- 'N','N','N','N','N','N','N','N',
- 'N','N','N','N','N','N','N','N',
- 'N','N','N','N','N','N','N','N',
- 'N','N','N','N','N','N','N','N',
- 'N','N','N','N','N','N','N','N',
- 'N','N','N','N','N','N','N','N',
- 'N','N','N','N','N','N','N','N'
-};
-
-unsigned char PreserveCase[] = {
-0,1,2,3,4,5,6,7,
-8,9,10,11,12,13,14,15,
-16,17,18,19,20,21,22,23,
-24,25,26,27,28,29,30,31,
-32,33,34,35,36,37,38,39,
-40,41,42,43,44,45,46,47,
-48,49,50,51,52,53,54,55,
-56,57,58,59,60,61,62,63,
-64,65,66,67,68,69,70,71,
-72,73,74,75,76,77,78,79,
-80,81,82,83,84,85,86,87,
-88,89,90,91,92,93,94,95,
-96,97,98,99,100,101,102,103,
-104,105,106,107,108,109,110,111,
-112,113,114,115,116,117,118,119,
-120,121,122,123,124,125,126,127,
-128,129,130,131,132,133,134,135,
-136,137,138,139,140,141,142,143,
-144,145,146,147,148,149,150,151,
-152,153,154,155,156,157,158,159,
-160,161,162,163,164,165,166,167,
-168,169,170,171,172,173,174,175,
-176,177,178,179,180,181,182,183,
-184,185,186,187,188,189,190,191,
-192,193,194,195,196,197,198,199,
-200,201,202,203,204,205,206,207,
-208,209,210,211,212,213,214,215,
-216,217,218,219,220,221,222,223,
-224,225,226,227,228,229,230,231,
-232,233,234,235,236,237,238,239,
-240,241,242,243,244,245,246,247,
-248,249,250,251,252,253,254,255};
-
-
-char TwoBitToAscii[] = {'A', 'C', 'G', 'T'};
-
-
-unsigned char ReverseComplementNuc[] = {
- 3, 2, 1, 0,127,127,127,127,
- 127,127,127,127,127,127,127,127,
- 127,127,127,127,127,127,127,127,
- 127,127,127,127,127,127,127,127,
- 127,127,127,127,127,127,127,127,
- 127,127,127,127,127,127,127,127,
- 127,127,127,127,127,127,127,127,
- 127,127,127,127,127,127,127,127,
- 127,'T',127,'G',127,127,127,'C',
- 127,127,127,127,127,127,'N',127,
- 127,127,127,127,'A',127,127,127,
- 127,127,127,127,127,127,127,127,
- 127,'t',127,'g',127,127,127,'c',
- 127,127,127,127,127,127,'n',127,
- 127,127,127,127,'a',127,127,127,
- 127,127,127,127,127,127,127,127,
- 127,127,127,127,127,127,127,127,
- 127,127,127,127,127,127,127,127,
- 127,127,127,127,127,127,127,127,
- 127,127,127,127,127,127,127,127,
- 127,127,127,127,127,127,127,127,
- 127,127,127,127,127,127,127,127,
- 127,127,127,127,127,127,127,127,
- 127,127,127,127,127,127,127,127,
- 127,127,127,127,127,127,127,127,
- 127,127,127,127,127,127,127,127,
- 127,127,127,127,127,127,127,127,
- 127,127,127,127,127,127,127,127,
- 127,127,127,127,127,127,127,127,
- 127,127,127,127,127,127,127,127,
- 127,127,127,127,127,127,127,127,
- 127,127,127,127,127,127,127,127
-};
-
-//
-// HDF Column Orders: GTAC
-// A - column 2; C - column 3;
-// G - column 0; T - column 1;
-// Ascii code:
-// A=65, C=67, G=71, T=84
-// a=97, c=99, g=116, t=103
-//
-int NucToHdfColumnOrder[] = {
- 2, 3, 1, 0, 2, 3, 1, 0,
- 255,255,255,255,255,255,255,255,
- 255,255,255,255,255,255,255,255,
- 255,255,255,255,255,255,255,255,
- 255,255,255,255,255,255,255,255,
- 255,255,255,255,255,255,255,255,
- 255,255,255,255,255,255,255,255,
- 255,255,255,255,255,255,255,255,
- 255, 2,255, 3,255,255,255, 1,
- 255,255,255,255,255,255,255,255,
- 255,255,255,255, 0,255,255,255,
- 255,255,255,255,255,255,255,255,
- 255, 2,255, 3,255,255,255, 1,
- 255,255,255,255,255,255,255,255,
- 255,255,255,255, 0,255,255,255,
- 255,255,255,255,255,255,255,255,
- 255,255,255,255,255,255,255,255,
- 255,255,255,255,255,255,255,255,
- 255,255,255,255,255,255,255,255,
- 255,255,255,255,255,255,255,255,
- 255,255,255,255,255,255,255,255,
- 255,255,255,255,255,255,255,255,
- 255,255,255,255,255,255,255,255,
- 255,255,255,255,255,255,255,255,
- 255,255,255,255,255,255,255,255,
- 255,255,255,255,255,255,255,255,
- 255,255,255,255,255,255,255,255,
- 255,255,255,255,255,255,255,255,
- 255,255,255,255,255,255,255,255,
- 255,255,255,255,255,255,255,255,
- 255,255,255,255,255,255,255,255,
- 255,255,255,255,255,255,255,255
-};
diff --git a/libcpp/pbdata/NucConversion.hpp b/libcpp/pbdata/NucConversion.hpp
deleted file mode 100644
index 892dd07..0000000
--- a/libcpp/pbdata/NucConversion.hpp
+++ /dev/null
@@ -1,50 +0,0 @@
-#ifndef _BLASR_NUC_CONVERSION_HPP_
-#define _BLASR_NUC_CONVERSION_HPP_
-
-//
-// Map from ascii to 2 bit representation.
-//
-extern int TwoBit[256];
-
-//
-// Map from charcter to 3 bit. Treat all non ACGT IUPAC as N
-// IPUAC: ACGT U M R W S Y K V H D N
-//
-extern int ThreeBit[256];
-
-extern int IsACTG[256];
-
-extern int IsLowerCase[256];
-
-extern int FourBit[256];
-
-extern int FourBitToAscii[10];
-
-extern int ThreeBitToAscii[6];
-
-extern int MaskedFourBit[256];
-
-extern unsigned char AllToUpper[256];
-
-extern char AllToLower[256];
-
-extern unsigned char PreserveCase[256];
-
-extern char TwoBitToAscii[4];
-
-extern unsigned char ReverseComplementNuc[256];
-
-//
-// HDF Column Orders: GTAC
-// A - column 2; C - column 3;
-// G - column 0; T - column 1;
-// Ascii code:
-// A=65, C=67, G=71, T=84
-// a=97, c=99, g=116, t=103
-//
-extern int NucToHdfColumnOrder[256];
-
-// Convert a FASTQ character to Quality.
-const unsigned int FASTQ_CHAR_TO_QUALITY = 33;
-
-#endif // _BLASR_NUC_CONVERSION_HPP_
diff --git a/libcpp/pbdata/PackedDNASequence.cpp b/libcpp/pbdata/PackedDNASequence.cpp
deleted file mode 100644
index 957839b..0000000
--- a/libcpp/pbdata/PackedDNASequence.cpp
+++ /dev/null
@@ -1,233 +0,0 @@
-#include "utils.hpp"
-#include "PackedDNASequence.hpp"
-
-const PackedDNAWord PackedDNASequence::NucPosMask[] = {7, 56, 448,
- 3584, 28672, 229376,
- 1835008, 14680064, 117440512,
- 939524096};
-
-const PackedDNAWord PackedDNASequence::NegMask[] = { 4294967288,// 11111111 11111111 11111111 11111000
- 4294967239,// 11111111 11111111 11111111 11000111
- 4294966847, /// and so on...
- 4294963711, 4294938623, 4294737919,
- 4293132287, 4280287231, 4177526783,
- 3355443199};
-
-// Masks from the rightmost pos 'R' all to the end of the left side of
-// the word.
-const PackedDNAWord PackedDNASequence::MaskRL[] = {1073741823, 1073741816, 1073741760,
- 1073741312, 1073737728, 1073709056,
- 1073479680, 1071644672, 1056964608,
- 939524096};
-
-// Masks from starting position 'L' to the rightmost 'R'
-const PackedDNAWord PackedDNASequence::MaskLR[] = {7, 63, 511, 4095, 32767, 262143, 2097151, 16777215, 134217727, 1073741823};
-
-/*
- * Count nucleotides by Xor'ing with the complement of the bit pattern.
- */
-const PackedDNAWord PackedDNASequence::xorMask[] = {
- 1073741823, // mask A=000 by 111111111111111111111111111111
- 920350134, // mask C=001 by 110110110110110110110110110110
- 766958445, // mask G=010 by 101101101101101101101101101101
- 613566756, // mask T=011 by 100100100100100100100100100100
- 460175067, // mask N=100 by 011011011011011011011011011011
- 153391689, // mask 001001001001001001001001001001 *unused*, can mask X=110
- 306783378, // mask 010010010010010010010010010010 *unused*, can mask X'=101
- 0}; // mask 000000000000000000000000000000 *unused*, mask X''=111
-
-
-
-Nucleotide PackedDNASequence::Get(DNALength pos) {
- PackedDNAWord offset = pos% NucsPerWord;
- return (seq[pos/NucsPerWord] >> (3*offset)) & NucMask ;
-}
-
-Nucleotide PackedDNASequence::operator[](DNALength pos){
- return Get(pos);
-}
-
-PackedDNASequence::PackedDNASequence() {
- nCountInWord = 0;
- nCountNuc = 0;
- length = arrayLength = 0;
- seq = NULL;
-}
-
-PackedDNASequence::~PackedDNASequence() {
- nCountInWord = 0;
- nCountNuc = 0;
- length = arrayLength = 0;
- if (seq) {
- delete [] seq;
- seq = NULL;
- }
-}
-
-void PackedDNASequence::Allocate(DNALength numberOfNucleotides) {
- arrayLength = CeilOfFraction(numberOfNucleotides, NucsPerWord);
- length = numberOfNucleotides;
- if (seq) {delete [] seq; seq = NULL;}
- if (arrayLength > 0) {
- seq = new PackedDNAWord[arrayLength];
- std::fill(seq, seq + arrayLength, 0);
- }
-}
-
-void PackedDNASequence::CreateFromDNASequence(DNASequence &dnaSeq) {
- arrayLength = CeilOfFraction(dnaSeq.length, NucsPerWord);
- length = dnaSeq.length;
- if (seq) {delete [] seq; seq = NULL;}
- if (arrayLength > 0) {
- seq = new PackedDNAWord[arrayLength];
- DNALength pos;
- for (pos = 0; pos < dnaSeq.length; pos++) {
- Set(pos, ThreeBit[dnaSeq[pos]]);
- }
- }
-}
-
-void PackedDNASequence::Set(DNALength pos, Nucleotide threeBitValue) {
- DNALength wordPos = pos/NucsPerWord;
- DNALength wordOffset = pos%NucsPerWord;
- //
- // Pull the value to update out of memory.
- //
- PackedDNAWord word = seq[wordPos];
-
- //
- // Expand the 3 bit value into a whole word.
- //
- PackedDNAWord nuc = threeBitValue;
-
- word = word & NegMask[wordOffset];
- nuc = nuc << (3*(pos%NucsPerWord));
- word = word + nuc;
- //
- // Write back the whole word.
- //
- seq[wordPos] = word;
-}
-
-
-DNALength PackedDNASequence::CountInWord(PackedDNAWord word, PackedDNAWord wordMask, Nucleotide nuc) {
-
- /*
- * Count the number of times a nucleotide (3-mer) appears in a word.
- * This is done by a series of masking and ands.
- * The packed format is a triplet of bits (b2,b1,b0), where N is a
- * mask bit, and n1n0 specifies the nucleotide.
- *
- * The sequence CCGN appears as
- * 001001010100
- *
- * To count C's: perform xor mask with a complement mask that will
- * produce a triplet of 111 on every position where there is a C,
- * followed by an and with a stride-isolation mask.
- *
- * b0 b1 b2
- * 001001010100 001001010100 001001010100
- * xor 110110110110 110110110110 110110110110
- * ------------ ------------ ------------
- * 111111100100 111111100100 111111100100
-
- * and 001001001001 010010010010 100100100100
- * ------------ ------------ ------------
- * 001001000000 010010000010 000000000100
- *
- * Shift b1 by 1 to get parity with b0.
- * 010010000010 -> 001001000001
- * 001001000001
- * And with b0 pattern 001001000000
- * to count masked nucs. ------------
- * nuc_count= 001001000000
- * Shift the b2 by 2 to set up the and-gate.
- * 000000000100 -> 000000000001
- * and ~MASK with nuc_count to get rid of masked columns if the
- * whole word is not being calculated.
- * 111111111110 & 001001000000 = 001001000000
- * Finally, use 64-bit multiplication bit-hack to count the number
- * of set-bits:
- * CountInWord(001001000000) = 2
- *
- */
- PackedDNAWord w0,w1,w2, w;
- PackedDNAWord w01, w12;
- Nucleotide tbn = ThreeBit[nuc];
- PackedDNAWord xorMaskNuc = xorMask[tbn];
- w0 = w1 = w2 = (word ^ xorMaskNuc);
- w0 = (w0) & Mask0All;
- w1 = ((w1) & Mask1All) >> 1;
- w2 = ((w2) & Mask2All) >> 2;
- // Ideally the architecture will parallelize all these
- // Do a cascaded.
- // w01 = (w0 & w1);
- // w12 = (w1 & w2);
- // w = w01 & w12;
- w = ((w0 & w1) & w2) & wordMask;
- // ++nCountInWord;
- return CountBits(w);
-}
-
-DNALength PackedDNASequence::CountNuc(DNALength start, DNALength end, Nucleotide nuc) {
- DNALength startWordIndex, endWordIndex, wordIndex;
- DNALength startInWord, endInWord;
- Nucleotide tbn = ThreeBit[nuc];
- endInWord = NucsPerWord;
- startInWord = start % NucsPerWord;
- startWordIndex = start / NucsPerWord;
- endWordIndex = end / NucsPerWord;
-
- //
- // Process all whole words.
- //
- DNALength nNuc = 0;
- for (wordIndex = startWordIndex; wordIndex < endWordIndex; wordIndex++) {
- endInWord = NucsPerWord;
- nNuc += CountInWord(seq[wordIndex] & MaskRL[startInWord], MaskRL[startInWord], nuc);
- startInWord = 0;
- }
- /*
- * Look to see if there is extra sequence to process when the seq
- * does not end on a word boundary.
- */
- if (end % NucsPerWord != 0) {
- endInWord = end % NucsPerWord;
- nNuc += CountInWord(seq[wordIndex] & MaskRL[startInWord] & MaskLR[endInWord-1],
- MaskRL[startInWord] & MaskLR[endInWord-1],
- nuc);
- }
- // ++nCountNuc;
- return nNuc;
-}
-
-void PackedDNASequence::Write(std::ostream &out) {
- out.write((char*)&arrayLength, sizeof(arrayLength));
- out.write((char*)&length, sizeof(length));
- if (arrayLength > 0) {
- out.write((char*)seq, sizeof(PackedDNAWord)*arrayLength);
- }
-}
-
-void PackedDNASequence::Read(std::istream &in) {
- in.read((char*)&arrayLength, sizeof(arrayLength));
- in.read((char*)&length, sizeof(length));
- if (seq) {delete [] seq; seq = NULL;}
- if (arrayLength > 0) {
- seq = new PackedDNAWord[arrayLength];
- in.read((char*)seq, sizeof(PackedDNAWord)*arrayLength);
- }
-}
-
-void PackedDNASequence::PrintUnpacked(std::ostream &out, int lineLength) {
- DNALength p;
- for (p = 0; p < length; p++) {
- out << (char) ThreeBitToAscii[Get(p)];
- if (p % lineLength == lineLength-1) {
- out << std::endl;
- }
- }
- if (p % lineLength != 0) {
- out << std::endl;
- }
-}
diff --git a/libcpp/pbdata/PackedDNASequence.hpp b/libcpp/pbdata/PackedDNASequence.hpp
deleted file mode 100644
index d780c0e..0000000
--- a/libcpp/pbdata/PackedDNASequence.hpp
+++ /dev/null
@@ -1,60 +0,0 @@
-#ifndef _BLASR_PACKED_DNA_SEQUENCE_HPP_
-#define _BLASR_PACKED_DNA_SEQUENCE_HPP_
-
-#include <fstream>
-#include "DNASequence.hpp"
-#include "NucConversion.hpp"
-#include "utils/BitUtils.hpp"
-
-/*
- * Implement a structure to maintain DNA as 3 bits per nucleotide.
- * The extra bit is required for N's in the sequence. A key is that
- * this structure is read-only through the operator[]. It may be set
- * with the PackedDNASequence::Set(pos,value) command.
- */
-
-typedef unsigned int PackedDNAWord;
-
-class PackedDNASequence {
-public:
- static const PackedDNAWord Mask2All = 613566756; //100100100...
- static const PackedDNAWord Mask1All = 306783378; //010010010...
- static const PackedDNAWord Mask0All = 153391689; //001001001...
- static const PackedDNAWord xorMask[];
- static const PackedDNAWord NucPosMask[];
- static const PackedDNAWord NegMask[];
- static const PackedDNAWord MaskRL[];
- static const PackedDNAWord MaskLR[];
- static const PackedDNAWord NucMask = 7;
- static const DNALength NucsPerWord = 10;
- PackedDNAWord *seq;
- int nCountInWord;
- int nCountNuc;
- DNALength length;
- DNALength arrayLength;
-
- Nucleotide Get(DNALength pos);
-
- Nucleotide operator[](DNALength pos);
-
- PackedDNASequence();
- ~PackedDNASequence();
-
- void Allocate(DNALength numberOfNucleotides);
-
- void CreateFromDNASequence(DNASequence &dnaSeq);
-
- void Set(DNALength pos, Nucleotide threeBitValue);
-
- DNALength CountInWord(PackedDNAWord word, PackedDNAWord wordMask, Nucleotide nuc);
-
- DNALength CountNuc(DNALength start, DNALength end, Nucleotide nuc);
-
- void Write(std::ostream &out);
-
- void Read(std::istream &in);
-
- void PrintUnpacked(std::ostream &out, int lineLength = 50);
-};
-
-#endif // _BLASR_PACKED_DNA_SEQUENCE_HPP_
diff --git a/libcpp/pbdata/ReverseCompressIndex.cpp b/libcpp/pbdata/ReverseCompressIndex.cpp
deleted file mode 100644
index 5179735..0000000
--- a/libcpp/pbdata/ReverseCompressIndex.cpp
+++ /dev/null
@@ -1,40 +0,0 @@
-#include <iostream>
-#include <fstream>
-#include "ReverseCompressIndex.hpp"
-
-ReverseCompressIndex::ReverseCompressIndex() {
- index = NULL;
- indexLength = binSize = maxRun = 0;
-}
-
-ReverseCompressIndex::~ReverseCompressIndex() {
- ReverseCompressIndex::Free();
-}
-
-void ReverseCompressIndex::Free() {
- if (index) {delete [] index; index = NULL;}
- indexLength = binSize = maxRun = 0;
-}
-
-void ReverseCompressIndex::Write(std::ofstream &out) {
- out.write((char*) &indexLength, sizeof(int));
- out.write((char*) &binSize, sizeof(int));
- out.write((char*) &maxRun, sizeof(int));
- out.write((char*) index, sizeof(int) * indexLength);
-}
-
-void ReverseCompressIndex::Read(std::ifstream &in) {
- in.read((char*) &indexLength, sizeof(int));
- in.read((char*) &binSize, sizeof(int));
- in.read((char*) &maxRun, sizeof(int));
- index = new int[indexLength];
- in.read((char*) index, sizeof(int) *indexLength);
-}
-
-void ReverseCompressIndex::ShallowCopy(ReverseCompressIndex &rhs) {
- ReverseCompressIndex::Free(); // Free before shallow copy.
- index = rhs.index;
- indexLength = rhs.indexLength;
- binSize = rhs.binSize;
- maxRun = rhs.maxRun;
-}
diff --git a/libcpp/pbdata/ReverseCompressIndex.hpp b/libcpp/pbdata/ReverseCompressIndex.hpp
deleted file mode 100644
index bfa2601..0000000
--- a/libcpp/pbdata/ReverseCompressIndex.hpp
+++ /dev/null
@@ -1,25 +0,0 @@
-#ifndef _BLASR_REVERSE_COMPRESS_INDEX_HPP_
-#define _BLASR_REVERSE_COMPRESS_INDEX_HPP_
-
-class ReverseCompressIndex {
-public:
- int *index;
- int indexLength;
- int binSize;
- int maxRun;
- int size() { return indexLength;}
-
- ReverseCompressIndex();
- ~ReverseCompressIndex();
-
- void Write(std::ofstream &out);
-
- void Read(std::ifstream &in);
-
- void ShallowCopy(ReverseCompressIndex &rhs);
-
- void Free();
-};
-
-
-#endif // _BLASR_REVERSE_COMPRESS_INDEX_HPP_
diff --git a/libcpp/pbdata/SMRTSequence.cpp b/libcpp/pbdata/SMRTSequence.cpp
deleted file mode 100644
index baabf57..0000000
--- a/libcpp/pbdata/SMRTSequence.cpp
+++ /dev/null
@@ -1,283 +0,0 @@
-#include <stdlib.h>
-#include "SMRTSequence.hpp"
-
-using namespace std;
-
-void SMRTSequence::SetNull() {
- pulseIndex = NULL;
- preBaseFrames = NULL;
- widthInFrames = NULL;
- xy[0] = 0; xy[1] = 0;
- // These are not allocted by default.
- meanSignal = maxSignal = midSignal = NULL;
- classifierQV = NULL;
- startFrame = NULL;
- platform = NoPlatform;
- // By default, allow the entire read.
- lowQualityPrefix = lowQualitySuffix = 0;
- highQualityRegionScore = 0;
- // ZMWMetrics
- for (size_t i = 0; i < 4; i++) {
- hqRegionSnr[i] = -1;
- }
- readScore = -1;
- holeNumber = static_cast<UInt>(-1);
- readGroupId = "";
- copiedFromBam = false;
-#ifdef USE_PBBAM
- bamRecord = PacBio::BAM::BamRecord();
-#endif
-}
-
-SMRTSequence::SMRTSequence() : FASTQSequence() {
- SetNull();
-}
-
-void SMRTSequence::Allocate(DNALength length) {
- // Assert *this has no allocated space.
- if (not (seq == NULL && preBaseFrames == NULL &&
- widthInFrames == NULL and pulseIndex == NULL)) {
- cout << "ERROR, trying to double-allocate memory for a SMRTSequence." << endl;
- exit(1);
- }
-
- FASTQSequence::AllocateRichQualityValues(length);
- seq = new Nucleotide[length];
- qual.Allocate(length);
- preBaseFrames = new HalfWord[length];
- widthInFrames = new HalfWord[length];
- pulseIndex = new int[length];
- subreadEnd = length;
- deleteOnExit = true;
-}
-
-void SMRTSequence::SetSubreadTitle(SMRTSequence &subread, DNALength subreadStart, DNALength subreadEnd) {
- stringstream titleStream;
- titleStream << title << "/"<< subreadStart << "_" << subreadEnd;
- subread.CopyTitle(titleStream.str());
-}
-
-void SMRTSequence::SetSubreadBoundaries(SMRTSequence &subread, DNALength subreadStart, DNALength subreadEnd) {
- if (subreadEnd == -1) {
- subreadEnd = length;
- }
- assert(subreadEnd - subreadStart <= length);
- subread.subreadStart= subreadStart;
- subread.subreadEnd = subreadEnd;
- SetSubreadTitle(subread, subreadStart, subreadEnd);
-}
-
-void SMRTSequence::MakeSubreadAsMasked(SMRTSequence &subread,
- DNALength subreadStart, int subreadEnd) {
- subread.Free();
- //
- // This creates the entire subread, but masks out the portions
- // that do not correspond to this insert.
- //
- static_cast<SMRTSequence*>(&subread)->Copy(*this);
- SetSubreadBoundaries(subread, subreadStart, subreadEnd);
- DNALength pos;
- for (pos = 0; pos < subreadStart; pos++) { subread.seq[pos] = 'N'; }
- for (pos = subreadEnd; pos < length; pos++) { subread.seq[pos] = 'N'; }
- // This is newly allocated memory, free it on exit.
- assert(subread.deleteOnExit);
-}
-
-void SMRTSequence::MakeSubreadAsReference(SMRTSequence &subread,
- DNALength subreadStart, int subreadEnd) {
- subread.Free();
- //
- // Just create a reference to a substring of this read.
- //
- static_cast<FASTQSequence*>(&subread)->ReferenceSubstring(*this, subreadStart, subreadEnd - subreadStart);
- SetSubreadBoundaries(subread, subreadStart, subreadEnd);
- // The subread references this read, protect the memory.
- assert(not subread.deleteOnExit);
-}
-
-void SMRTSequence::Copy(const SMRTSequence &rhs) {
- SMRTSequence::Copy(rhs, 0, rhs.length);
-}
-
-void SMRTSequence::Copy(const SMRTSequence &rhs, int rhsPos, int rhsLength) {
- // Sanity check
- CheckBeforeCopyOrReference(rhs, "SMRTSequence");
-
- // Free this SMRTSequence before copying anything from rhs.
- SMRTSequence::Free();
-
- FASTQSequence subseq;
- // subseq.seq is referenced, while seq.title is not, we need to call
- // subseq.Free() to prevent memory leak.
- static_cast<FASTQSequence*>(&subseq)->ReferenceSubstring(rhs, rhsPos, rhsLength);
- static_cast<FASTQSequence*>(&subseq)->CopyTitle(rhs.title, rhs.titleLength);
-
- if (rhs.length == 0) {
- static_cast<FASTQSequence*>(this)->Copy(subseq);
- //
- // Make sure that no values of length 0 are allocated by returning here.
- //
- }
- else {
- assert(rhs.seq != seq);
- assert(rhsLength <= rhs.length);
- assert(rhsPos < rhs.length);
-
- // Copy seq, title and FASTQ QVs from subseq
- static_cast<FASTQSequence*>(this)->Copy(subseq);
-
- // Copy SMRT QVs
- if (rhs.preBaseFrames != NULL) {
- preBaseFrames = new HalfWord[length];
- memcpy(preBaseFrames, rhs.preBaseFrames, length*sizeof(HalfWord));
- }
- if (rhs.widthInFrames != NULL) {
- widthInFrames = new HalfWord[length];
- memcpy(widthInFrames, rhs.widthInFrames, length*sizeof(HalfWord));
- }
- if (rhs.pulseIndex != NULL) {
- pulseIndex = new int[length];
- memcpy(pulseIndex, rhs.pulseIndex, sizeof(int) * length);
- }
- }
-
- // Copy other member variables from rhs
- subreadStart = rhs.subreadStart;
- subreadEnd = rhs.subreadEnd;
- lowQualityPrefix = rhs.lowQualityPrefix;
- lowQualitySuffix = rhs.lowQualitySuffix;
- highQualityRegionScore = rhs.highQualityRegionScore;
- zmwData = rhs.zmwData;
-
- assert(deleteOnExit); // should have control over seq and all QVs
-
- subseq.Free();
- copiedFromBam = rhs.copiedFromBam;
-#ifdef USE_PBBAM
- bamRecord = rhs.bamRecord;
-#endif
-}
-
-void SMRTSequence::Print(ostream &out) {
- out << "SMRTSequence for zmw " << zmwData.holeNumber
- << ", [" << subreadStart << ", " << subreadEnd << ")" << endl;
- DNASequence::Print(out);
-}
-
-SMRTSequence& SMRTSequence::operator=(const SMRTSequence &rhs) {
- SMRTSequence::Copy(rhs);
- return *this;
-}
-
-void SMRTSequence::Free() {
- if (deleteOnExit == true) {
- if (preBaseFrames) {
- delete[] preBaseFrames;
- }
- if (widthInFrames) {
- delete[] widthInFrames;
- }
- if (pulseIndex) {
- delete[] pulseIndex;
- }
- if (startFrame) {
- delete[] startFrame;
- }
- // meanSignal, maxSignal, midSignal and classifierQV
- // need to be handled separatedly.
- }
-
- // Reset SMRT QV pointers anyway
- preBaseFrames = NULL;
- widthInFrames = NULL;
- pulseIndex = NULL;
- startFrame = NULL;
-
- // Reset member variables
- xy[0] = 0; xy[1] = 0;
- lowQualityPrefix = lowQualitySuffix = 0;
- highQualityRegionScore = 0;
- holeNumber = static_cast<UInt>(-1);
- readGroupId = "";
- copiedFromBam = false;
-#ifdef USE_PBBAM
- bamRecord = PacBio::BAM::BamRecord();
-#endif
-
- // Free seq, title and FASTQ QVs, also reset deleteOnExit.
- // Don't call FASTQSequence::Free() before freeing SMRT QVs.
- FASTQSequence::Free();
-}
-
-bool SMRTSequence::StoreXY(int16_t xyP[]) {
- xy[0] = xyP[0];
- xy[1] = xyP[1];
- return true;
-}
-
-bool SMRTSequence::StorePlatformId(PlatformId pid) {
- platform = pid;
- return true;
-}
-
-bool SMRTSequence::StoreHoleNumber(UInt holeNumberP){
- zmwData.holeNumber = holeNumber = holeNumberP;
- return true;
-}
-
-bool SMRTSequence::StoreHoleStatus(unsigned char s) {
- zmwData.holeStatus = s;
- return true;
-}
-
-bool SMRTSequence::StoreZMWData(ZMWGroupEntry &data) {
- zmwData = data;
- return true;
-}
-
-bool SMRTSequence::GetXY(int xyP[]) {
- xyP[0] = xy[0];
- xyP[1] = xy[1];
- return true;
-}
-
-bool SMRTSequence::GetHoleNumber(UInt & holeNumberP) {
- holeNumberP = holeNumber;
- return true;
-}
-
-std::string SMRTSequence::GetReadGroupId() {
- return readGroupId;
-}
-
-void SMRTSequence::SetReadGroupId(const std::string & rid) {
- readGroupId = rid;
-}
-
-#ifdef USE_PBBAM
-void SMRTSequence::Copy(const PacBio::BAM::BamRecord & record) {
- Free();
-
- copiedFromBam = true;
-
- bamRecord = PacBio::BAM::BamRecord(record);
-
- // Only copy insertionQV, deletionQV, substitutionQV, mergeQV,
- // deletionTag and substitutionTag from BamRecord to SMRTSequence.
- // Do NOT copy other SMRTQVs such as startFrame, meanSignal...
- (static_cast<FASTQSequence*>(this))->Copy(record);
-
- // Copy read group id from BamRecord.
- SetReadGroupId(record.ReadGroupId());
-
- // PacBio bam for secondary analysis does NOT carry zmw
- // info other than holeNumber, including holeStatus, holeX,
- // holeY, numEvents.
- zmwData.holeNumber = static_cast<UInt> (record.HoleNumber());
-
- // Set hq region read score
- if (record.Impl().HasTag("rq"))
- highQualityRegionScore = record.Impl().TagValue("rq").ToInt32();
-
-}
-#endif
diff --git a/libcpp/pbdata/SMRTSequence.hpp b/libcpp/pbdata/SMRTSequence.hpp
deleted file mode 100644
index f7cff1c..0000000
--- a/libcpp/pbdata/SMRTSequence.hpp
+++ /dev/null
@@ -1,115 +0,0 @@
-#ifndef _BLASR_SMRT_SEQUENCE_HPP_
-#define _BLASR_SMRT_SEQUENCE_HPP_
-
-#include <cassert>
-#include <iostream>
-#include <sstream>
-
-#include "Types.h"
-#include "Enumerations.h"
-#include "NucConversion.hpp"
-#include "FASTQSequence.hpp"
-#include "reads/RegionTable.hpp"
-#include "reads/ZMWGroupEntry.hpp"
-
-class SMRTSequence : public FASTQSequence {
-public:
- int16_t xy[2];
- UInt holeNumber;
- float hqRegionSnr[4];
- float readScore;
- ZMWGroupEntry zmwData;
- PlatformId platform;
- HalfWord *preBaseFrames;
- HalfWord *widthInFrames;
- //
- // The following are fields that are read in from the pulse file.
- // Because they are not standard in bas.h5 files, these fields
- // should not be preallocated when resizing a SMRTSequence, and
- // memory should be managed separately. For now, these fields all
- // have the same length as the number of bases, but this could
- // change so that all pulse values are stored in a SMRTSequence.
- //
- HalfWord *meanSignal, *maxSignal, *midSignal;
- float *classifierQV;
- unsigned int *startFrame;
- int *pulseIndex;
- DNALength lowQualityPrefix, lowQualitySuffix;
- int highQualityRegionScore; // High quality region score in region table.
-
-protected:
- // read group id associated with each SMRTSequence
- std::string readGroupId;
-
-public:
- // Whether or not this is originally copied from a BamRecord.
- bool copiedFromBam;
-
- void SetNull();
-
- SMRTSequence();
- inline ~SMRTSequence();
-
- void Allocate(DNALength length);
-
- void SetSubreadTitle(SMRTSequence &subread, DNALength subreadStart,
- DNALength subreadEnd);
-
- void SetSubreadBoundaries(SMRTSequence &subread, DNALength subreadStart,
- DNALength subreadEnd);
-
- void MakeSubreadAsMasked(SMRTSequence &subread, DNALength subreadStart = 0,
- int subreadEnd = -1);
-
- void MakeSubreadAsReference(SMRTSequence &subread, DNALength subreadStart = 0,
- int subreadEnd = -1);
-
- void Copy(const SMRTSequence &rhs);
-
- void Copy(const SMRTSequence &rhs, int rhsPos, int rhsLength);
-
- void Print(std::ostream &out);
-
- SMRTSequence& operator=(const SMRTSequence &rhs);
-
- void Free();
-
- bool StoreXY(int16_t xyP[]);
-
- bool StorePlatformId(PlatformId pid);
-
- bool StoreHoleNumber(UInt holeNumberP);
-
- bool StoreHoleStatus(unsigned char s);
-
- bool StoreZMWData(ZMWGroupEntry &data);
-
- bool GetXY(int xyP[]);
-
- bool GetHoleNumber(UInt & holeNumberP);
-
- // Get read group id for this sequence.
- std::string GetReadGroupId();
-
- // Set readGroup Id for this sequence.
- void SetReadGroupId(const std::string & rid);
-
-#ifdef USE_PBBAM
-public:
- // Copy read sequence, title, holeNumber, readGroupId, and QVs
- // (iq, dq, sq, mq, st, dt) from BamRecord to this SMRTSequence.
- void Copy(const PacBio::BAM::BamRecord & record);
-
- // Keep track of BamRecord from which this SMRTSequence is
- // originally copied. However, one should NOT assume
- // that this SMRTSequence has the same sequence, title, QVs as
- // the BamRecord, because this SMRTSequence may be created by
- // MakeSubreadAsMasked(...) or MakeRC(...).
- PacBio::BAM::BamRecord bamRecord;
-#endif
-};
-
-inline SMRTSequence::~SMRTSequence(){
- SMRTSequence::Free();
-}
-#endif // _BLASR_SMRT_SEQUENCE_HPP_
diff --git a/libcpp/pbdata/SeqUtils.hpp b/libcpp/pbdata/SeqUtils.hpp
deleted file mode 100644
index 8e0b087..0000000
--- a/libcpp/pbdata/SeqUtils.hpp
+++ /dev/null
@@ -1,17 +0,0 @@
-#ifndef _BLASR_SEQ_UTILS_HPP_
-#define _BLASR_SEQ_UTILS_HPP_
-
-#include "DNASequence.hpp"
-
-template< typename T_Sequence>
-int OnlyACTG(T_Sequence &seq);
-
-template< typename T_Sequence>
-DNALength CountMasked(T_Sequence &seq);
-
-template< typename T_Sequence>
-int CountNotMasked(T_Sequence &seq);
-
-#include "SeqUtilsImpl.hpp"
-
-#endif // _BLASR_SEQ_UTILS_HPP_
diff --git a/libcpp/pbdata/SeqUtilsImpl.hpp b/libcpp/pbdata/SeqUtilsImpl.hpp
deleted file mode 100644
index 35754d9..0000000
--- a/libcpp/pbdata/SeqUtilsImpl.hpp
+++ /dev/null
@@ -1,47 +0,0 @@
-#include <vector>
-#include <iostream>
-#include <stdint.h>
-#include "utils.hpp"
-#include "DNASequence.hpp"
-#include "NucConversion.hpp"
-#include "SeqUtils.hpp"
-
-template< typename T_Sequence>
-int OnlyACTG(T_Sequence &seq) {
- DNALength p;
- for (p = 0; p < seq.length; p++) {
- if (ThreeBit[seq.seq[p]] > 3)
- return 0;
- }
- return 1;
-}
-
-template< typename T_Sequence>
-DNALength CountMasked(T_Sequence &seq) {
- DNALength p;
- DNALength nMasked = 0;
- for (p = 0; p < seq.length; p++) {
- if ((seq.seq[p] >= 'a' and
- seq.seq[p] <= 'z') or
- seq.seq[p] == 'N') {
- nMasked++;
- }
- }
- return nMasked;
-}
-
-template< typename T_Sequence>
-int CountNotMasked(T_Sequence &seq) {
- int p;
- int nUnmasked = 0;
- for (p = 0; p < seq.length; p++ ) {
- if (seq.seq[p] == 'A' or
- seq.seq[p] == 'C' or
- seq.seq[p] == 'G' or
- seq.seq[p] == 'T') {
- nUnmasked++;
- }
- }
-
- return nUnmasked;
-}
diff --git a/libcpp/pbdata/StringUtils.cpp b/libcpp/pbdata/StringUtils.cpp
deleted file mode 100644
index 2b008d4..0000000
--- a/libcpp/pbdata/StringUtils.cpp
+++ /dev/null
@@ -1,133 +0,0 @@
-#include <string>
-#include <stdint.h>
-#include <vector>
-#include <sstream>
-#include "Types.h"
-#include "MD5Utils.hpp"
-#include "StringUtils.hpp"
-
-int ExactPatternMatch(string orig, string pattern) {
- string::size_type pos = orig.find(pattern);
- if (pos == orig.npos) {
- return 0;
- }
- else {
- return 1;
- }
-}
-
-void MakeMD5(const char *data, unsigned int dataLength, string &md5Str, int nChars) {
-
- MD5 md5engine;
- md5engine.update((unsigned char*) data, dataLength);
- md5engine.finalize();
-
- char *md5c_str = md5engine.hex_digest();
- assert(md5c_str != NULL);
- if (nChars == 0) {
- nChars = 32;
- }
- md5Str.assign(md5c_str, nChars);
- delete[] md5c_str;
-}
-
-
-void MakeMD5(string &data, string &md5Str, int nChars) {
- MakeMD5(data.c_str(), data.size(), md5Str, nChars);
-}
-
-
-int IsWhitespace(char c) {
- return (c == ' ' or c == '\t' or c == '\n' or c == '\r' or c == '\0');
-}
-
-int IsSpace(char c) {
- return (c == ' ' or c == '\t');
-}
-
-int ToWords(string &orig, vector<string> &words) {
- int curWordStart, curWordEnd;
- curWordStart = 0;
- while(curWordStart < orig.size()) {
- while (curWordStart < orig.size() and IsSpace(orig[curWordStart])) { curWordStart++; }
- curWordEnd = curWordStart;
- while (curWordEnd < orig.size() and !IsSpace(orig[curWordEnd])) { curWordEnd++; }
- string word;
- if (curWordEnd != curWordStart) {
- word.assign(orig, curWordStart, curWordEnd - curWordStart);
- words.push_back(word);
- }
- curWordStart = curWordEnd;
- }
- return words.size();
-}
-
-// Splice a string by pattern and save to a vector of token strings.
-int Splice(const string & orig, const string & pattern, vector<string> & tokens) {
- assert(pattern.size() > 0);
-
- tokens.clear();
- size_t search_start = 0;
- size_t find_pos = orig.find(pattern, search_start);
- while(find_pos != string::npos) {
- string x = orig.substr(search_start, find_pos - search_start);
- tokens.push_back(x);
- search_start = find_pos + pattern.size();
- find_pos = orig.find(pattern, search_start);
- }
- tokens.push_back(orig.substr(search_start));
- return tokens.size();
-}
-
-void ParseSeparatedList(const string &csl, vector<string> &values, char delim) {
- stringstream cslStrm(csl);
- string valString;
- string next;
- do {
- if (getline(cslStrm, valString, delim)) {
- if (valString.size() > 0) {
- values.push_back(valString);
- }
- }
- }
- while (cslStrm);
-}
-
-int AssignUntilFirstSpace(char *orig, int origLength, string &result) {
- int i;
- for (i = 0; i < origLength; i++ ){
- if (orig[i] == ' ' or orig[i] == '\t' or orig[i] == '\n' or orig[i] == '\r' or orig[i] == '\0') {
- break;
- }
- }
- result.assign(orig, i);
- return i;
-}
-
-string RStrip(string & fileName) {
- // Remove right-ended spaces
- int i = fileName.size();
- if (i == 0) {
- return "";
- }
- while (i >= 1) {
- i--;
- if (not IsWhitespace(fileName[i])) {
- break;
- }
- }
- return fileName.substr(0, i + 1);
-}
-
-string MakeReadGroupId(const string & movieName, const ReadType::ReadTypeEnum & readType) {
- // PBBAM spec 3.0b5:
- // Read Group Id is computed as MD5(${movieName}//${readType})[0:8], where
- // movieName is PacBio platform unit id, e.g., (m140905_042...77_s1_X0),
- // readtype is SUBREAD, CCS or UNKNOWN,
- // CCS reads for a movie named "movie32" would have
- // RGID STRING = "f5b4ffb6"
- string seed = movieName + "//" + ReadType::ToString(readType);
- string readGroupId;
- MakeMD5(seed, readGroupId, 8);
- return readGroupId;
-}
diff --git a/libcpp/pbdata/StringUtils.hpp b/libcpp/pbdata/StringUtils.hpp
deleted file mode 100644
index ea895a2..0000000
--- a/libcpp/pbdata/StringUtils.hpp
+++ /dev/null
@@ -1,71 +0,0 @@
-#ifndef UTILS_STRING_UTILS_H_
-#define UTILS_STRING_UTILS_H_
-
-#include <cassert>
-#include <string>
-#include <vector>
-#include <sstream>
-#include "Types.h"
-#include "MD5Utils.hpp"
-#include "reads/ReadType.hpp"
-
-using namespace std;
-
-int ExactPatternMatch(string orig, string pattern);
-
-void MakeMD5(const char *data, unsigned int dataLength, string &md5Str, int nChars = 0);
-
-void MakeMD5(string &data, string &md5Str, int nChars=0);
-
-int IsWhitespace(char c);
-
-int IsSpace(char c);
-
-int ToWords(string &orig, vector<string> &words);
-
-int Splice(const string & orig, const string & pattern, vector<string> &tokens);
-
-void ParseSeparatedList(const string &csl, vector<string> &values, char delim=',');
-
-int AssignUntilFirstSpace(char *orig, int origLength, string &result);
-
-template<typename T_Value>
-void ParseSeparatedList(const string &csl, vector<T_Value> &values, char delim, int maxVals) {
- //Parse up to 'maxVals' lines of lists.
- stringstream cslStrm(csl);
- T_Value val;
- string valString;
- string next;
- int valIndex = 0;
- do {
- if (maxVals == 0 or valIndex < maxVals - 1 ) {
- getline(cslStrm, valString, delim);
- }
- else {
- // If on last value, get the rest of the line.
- getline(cslStrm, valString);
- }
- if (cslStrm and valString.size() > 0) {
- stringstream valStrm(valString);
- if (! (valStrm >> val) ) {
- cout << "Error, value " << valString << " is malformatted." << endl;
- }
- else {
- values.push_back(val);
- }
- }
- valIndex++;
- }
- while (cslStrm);
-}
-
-template<typename T_Value>
-void ParseSeparatedList(const string &csl, vector<T_Value> &values, char delim=',') {
- ParseSeparatedList(csl, values, delim, 0);
-}
-
-string RStrip(string & fileName);
-
-/// \returns Read Group Id, given movieName and readType.
-string MakeReadGroupId(const string & movieName, const ReadType::ReadTypeEnum & readType);
-#endif
diff --git a/libcpp/pbdata/Types.h b/libcpp/pbdata/Types.h
deleted file mode 100644
index 54fb856..0000000
--- a/libcpp/pbdata/Types.h
+++ /dev/null
@@ -1,21 +0,0 @@
-#ifndef _BLASR_TYPES_H_
-#define _BLASR_TYPES_H_
-
-#include <stdint.h>
-
-typedef unsigned long ULong;
-
-// Move DNA sequence related definitions.
-typedef uint32_t DNALength;
-typedef unsigned char Nucleotide;
-
-//
-// Add definitions to handle 64/32 bit computing environments
-//
-typedef uint32_t VectorIndex;
-typedef uint32_t UInt;
-typedef uint8_t Byte;
-typedef uint8_t UChar;
-typedef uint16_t HalfWord;
-typedef float MatchWeight;
-#endif // _BLASR_TYPES_H_
diff --git a/libcpp/pbdata/VectorUtils.hpp b/libcpp/pbdata/VectorUtils.hpp
deleted file mode 100644
index c654c9d..0000000
--- a/libcpp/pbdata/VectorUtils.hpp
+++ /dev/null
@@ -1,17 +0,0 @@
-#ifndef _BLASR_VECTOR_UTILS_HPP_
-#define _BLASR_VECTOR_UTILS_HPP_
-
-#include <vector>
-
-// Clear all memory allocated by this vector
-template <typename T>
-void ClearMemory(std::vector<T> & vt) {
- // Create an empty vector
- std::vector<T> emptyVector;
- // First clear the content
- vt.clear();
- // Then swap vt with the empty vector
- vt.swap(emptyVector);
-}
-
-#endif // _BLASR_VECTOR_UTILS_HPP_
diff --git a/libcpp/pbdata/alignment/CmpAlignment.cpp b/libcpp/pbdata/alignment/CmpAlignment.cpp
deleted file mode 100644
index d3569d4..0000000
--- a/libcpp/pbdata/alignment/CmpAlignment.cpp
+++ /dev/null
@@ -1,219 +0,0 @@
-#include "CmpAlignment.hpp"
-
-std::map<std::string,int> CmpAlignmentBase::columnNameToIndex;
-
-unsigned int* CmpAlignmentBase::GetAlignmentIndex() {
- return &alignmentIndex[0];
-}
-int CmpAlignmentBase::GetAlignmentIndexSize() {
- return alignmentIndex.size();
-}
-unsigned int CmpAlignmentBase::GetAlignedStrand() {
- return LookupColumnValue("AlignedStrand");
-}
-
-unsigned int CmpAlignmentBase::GetRCRefStrand() {
- return LookupColumnValue("RCRefStrand");
-}
-
-// synonym
-unsigned int CmpAlignmentBase::GetTStrand() {
- return GetRCRefStrand();
-}
-
-bool CmpAlignmentBase::GetX(int &xp) {
- if (alignmentIndex.size() > 0) {
- xp = alignmentIndex[columnNameToIndex["x"]];
- return true;
- }
- else {
- xp = -1;
- return false;
- }
-}
-
-unsigned int CmpAlignmentBase::GetAlignmentId() {
- return LookupColumnValue("AlnID");
-}
-
-unsigned int CmpAlignmentBase::GetX() {
- return LookupColumnValue("x");
-}
-
-unsigned int CmpAlignmentBase::GetY() {
- return LookupColumnValue("y");
-}
-
-unsigned int CmpAlignmentBase::GetMovieId() {
- return LookupColumnValue("MovieId");
-}
-
-unsigned int CmpAlignmentBase::GetAlnGroupId() {
- return LookupColumnValue("AlnGroupId");
-}
-
-unsigned int CmpAlignmentBase::GetReadGroupId() {
- return LookupColumnValue("ReadGroupId");
-}
-
-
-unsigned int CmpAlignmentBase::LookupColumnValue(const char * columnName) {
- if (columnNameToIndex.find(columnName) != columnNameToIndex.end()) {
- int columnIndex = columnNameToIndex[columnName];
- return alignmentIndex[columnIndex];
- }
- else {
- std::cout << "ERROR, For now cmp files must contain a column " << columnName << std::endl;
- std::cout << "size of columnNameToIndex: " << columnNameToIndex.size() << std::endl;
- assert(0);
- }
-}
-
-
-void CmpAlignmentBase::InitializeColumnNameToIndex(std::vector<std::string> &columnNames) {
- int i;
- for (i = 0; i < columnNames.size(); i++ ){
- columnNameToIndex[columnNames[i]] = i;
- }
-}
-
-
-unsigned int CmpAlignmentBase::GetHoleNumber() {
- return LookupColumnValue("HoleNumber");
-}
-
-unsigned int CmpAlignmentBase::GetRefGroupId() {
- return LookupColumnValue("RefGroupId");
-}
-
-unsigned int CmpAlignmentBase::GetRefSeqId() {
- return LookupColumnValue("RefSeqId");
-}
-
-unsigned int CmpAlignmentBase::GetOffsetBegin() {
- return LookupColumnValue("offset_begin");
-}
-
-unsigned int CmpAlignmentBase::GetOffsetEnd() {
- return LookupColumnValue("offset_end");
-}
-
-unsigned int CmpAlignmentBase::GetQueryStart() {
- return LookupColumnValue("rStart");
-}
-
-unsigned int CmpAlignmentBase::GetQueryEnd() {
- return LookupColumnValue("rEnd");
-}
-
-unsigned int CmpAlignmentBase::GetRefStart() {
- return LookupColumnValue("tStart");
-}
-
-unsigned int CmpAlignmentBase::GetRefEnd() {
- return LookupColumnValue("tEnd");
-}
-
-unsigned int CmpAlignmentBase::GetNMatch() {
- return LookupColumnValue("nM");
-}
-
-unsigned int CmpAlignmentBase::GetNMismatch() {
- return LookupColumnValue("nMM");
-}
-
-unsigned int CmpAlignmentBase::GetNInsertions() {
- return LookupColumnValue("nIns");
-}
-
-unsigned int CmpAlignmentBase::GetNDeletions() {
- return LookupColumnValue("nDel");
-}
-
-unsigned int CmpAlignmentBase::GetMapQV() {
- return LookupColumnValue("MapQV");
-}
-
-unsigned int CmpAlignmentBase::GetSubreadId() {
- return LookupColumnValue("SubreadId");
-}
-
-unsigned int CmpAlignmentBase::GetStrobeNumber() {
- return LookupColumnValue("StrobeNumber");
-}
-
-unsigned int CmpAlignmentBase::GetSetNumber() {
- return LookupColumnValue("SetNumber");
-}
-
-CmpAlignmentBase::CmpAlignmentBase(PlatformId platformIdP) {
- platformId = platformIdP;
-}
-
-void CmpAlignmentBase::SetPlatformId(PlatformId platformIdP) {
- platformId = platformIdP;
-}
-
-// CmpAlignment
-
-CmpAlignment::CmpAlignment(PlatformId pid) : CmpAlignmentBase(pid) {
-}
-
-void CmpAlignment::StoreAlignmentIndex(unsigned int *alignmentIndexPtr,
- int alignmentIndexLength) {
-
- alignmentIndex.clear();
- alignmentIndex.insert(alignmentIndex.begin(), &alignmentIndexPtr[0],
- &alignmentIndexPtr[alignmentIndexLength]);
-}
-
-void CmpAlignment::StoreAlignmentArray(unsigned char* alignmentArrayPtr,
- int alignmentArrayLength) {
-
- alignmentArray.resize(alignmentArrayLength);
- unsigned int a;
- for (a = 0; a < alignmentArrayLength; a++ ){
- alignmentArray[a] = alignmentArrayPtr[a];
- }
-}
-
-CmpAlignment &CmpAlignment::operator=(const CmpAlignment &rhs) {
- // deep copy the alignment index
- alignmentIndex.resize(rhs.alignmentIndex.size());
- copy(rhs.alignmentIndex.begin(), rhs.alignmentIndex.end(), alignmentIndex.begin());
- // deep copy the alignment array
- alignmentArray.resize(rhs.alignmentIndex.size());
- copy(rhs.alignmentArray.begin(), rhs.alignmentArray.end(), alignmentArray.begin());
- // copy fields
- Z = rhs.Z;
- index = rhs.index; readGroupId = rhs.readGroupId; movieId = rhs.movieId;
- refSeqId = rhs.refSeqId;
- expId = rhs.expId; runId = rhs.runId; panel = rhs.panel;
- x = rhs.x; y = rhs.y;
- rcRefStrand = rhs.rcRefStrand;
- holeNumber = rhs.holeNumber;
- offsetBegin = rhs.offsetBegin; offsetEnd = rhs.offsetEnd;
- setNumber = rhs.setNumber, strobeNumber = rhs.strobeNumber, mapQV = rhs.mapQV, nBackRead = rhs.nBackRead, nReadOverlap = rhs.nReadOverlap;
- subreadId = rhs.subreadId;
- nMatch = rhs.nMatch, nMismatch = rhs.nMismatch, nIns = rhs.nIns, nDel = rhs.nDel;
- return *this;
-}
-
-int CmpAlignment::operator<(const CmpAlignment &rhs) const {
- if (alignmentArray[1] == rhs.alignmentArray[1]) {
- if (alignmentArray[2] == rhs.alignmentArray[2]) {
- if (alignmentArray[10] == rhs.alignmentArray[10]) {
- return (alignmentArray[4] < rhs.alignmentArray[4]);
- }
- else {
- return alignmentArray[10] < rhs.alignmentArray[10];
- }
- }
- else {
- return alignmentArray[2] < rhs.alignmentArray[2];
- }
- }
- else {
- return alignmentArray[1] < rhs.alignmentArray[1];
- }
-}
diff --git a/libcpp/pbdata/alignment/CmpAlignment.hpp b/libcpp/pbdata/alignment/CmpAlignment.hpp
deleted file mode 100644
index 484bfa1..0000000
--- a/libcpp/pbdata/alignment/CmpAlignment.hpp
+++ /dev/null
@@ -1,126 +0,0 @@
-#ifndef DATASTRUCTURES_ALIGNMENT_CMP_ALIGNMENT_H_
-#define DATASTRUCTURES_ALIGNMENT_CMP_ALIGNMENT_H_
-#include <map>
-#include <vector>
-#include <string>
-#include <iostream>
-#include <assert.h>
-#include <algorithm>
-
-#include "Types.h"
-#include "Enumerations.h"
-
-class CmpAlignmentBase {
-public:
- //
- // For use in referencing alignment sets. TODO: subclass.
- //
- PlatformId platformId;
- int Z;
- unsigned int index, readGroupId, movieId, refSeqId;
- unsigned int expId, runId, panel;
- unsigned int x, y;
- unsigned int rcRefStrand;
- unsigned int holeNumber;
- unsigned int offsetBegin, offsetEnd;
- unsigned int setNumber, strobeNumber, mapQV, nBackRead, nReadOverlap;
- unsigned int subreadId;
- unsigned int nMatch, nMismatch, nIns, nDel;
- std::vector<unsigned char> alignmentArray;
- std::vector<unsigned int> alignmentIndex;
- static std::map<std::string,int> columnNameToIndex;
- static bool initializedColumnNameToIndex;
- std::map<std::string, std::vector<UChar> > fields;
-
- unsigned int *GetAlignmentIndex();
-
- int GetAlignmentIndexSize();
-
- unsigned int GetAlignedStrand();
-
- unsigned int GetRCRefStrand();
-
- // synonym
- unsigned int GetTStrand();
-
- bool GetX(int &xp);
-
- unsigned int GetAlignmentId();
-
- unsigned int GetX();
-
- unsigned int GetY();
-
- unsigned int GetMovieId();
-
- unsigned int GetAlnGroupId();
-
- unsigned int GetReadGroupId();
-
- unsigned int LookupColumnValue(const char * columnName);
-
- void InitializeColumnNameToIndex(std::vector<std::string> &columnNames);
-
- unsigned int GetHoleNumber();
-
- unsigned int GetRefGroupId();
-
- unsigned int GetRefSeqId();
-
- unsigned int GetOffsetBegin();
-
- unsigned int GetOffsetEnd();
-
- unsigned int GetQueryStart();
-
- unsigned int GetQueryEnd();
-
- unsigned int GetRefStart();
-
- unsigned int GetRefEnd();
-
- unsigned int GetNMatch();
-
- unsigned int GetNMismatch();
-
- unsigned int GetNInsertions();
-
- unsigned int GetNDeletions();
-
- unsigned int GetMapQV();
-
- unsigned int GetSubreadId();
-
- unsigned int GetStrobeNumber();
-
- unsigned int GetSetNumber();
-
- CmpAlignmentBase(PlatformId platformIdP=Springfield);
-
- void SetPlatformId(PlatformId platformIdP);
-};
-
-class CmpAlignment : public CmpAlignmentBase {
-public:
- int qStrand, tStrand;
- int qStart, qLength;
- int tStart, tLength;
- //
- // Default constructor just calls the base constructor to initialize platoformType
- CmpAlignment(PlatformId pid=Springfield);
-
- void StoreAlignmentIndex(unsigned int *alignmentIndexPtr, int alignmentIndexLength);
-
- void StoreAlignmentArray(unsigned char* alignmentArrayPtr, int alignmentArrayLength);
-
- template<typename T_Field>
- void StoreField(std::string fieldName, T_Field* fieldValues, int length);
-
- CmpAlignment &operator=(const CmpAlignment &rhs);
-
- int operator<(const CmpAlignment &rhs) const;
-
-};
-
-#include "CmpAlignmentImpl.hpp"
-#endif
diff --git a/libcpp/pbdata/alignment/CmpAlignmentImpl.hpp b/libcpp/pbdata/alignment/CmpAlignmentImpl.hpp
deleted file mode 100644
index e8b9a5f..0000000
--- a/libcpp/pbdata/alignment/CmpAlignmentImpl.hpp
+++ /dev/null
@@ -1,6 +0,0 @@
-
-template<typename T_Field>
-void CmpAlignment::StoreField(std::string fieldName, T_Field* fieldValues, int length) {
- fields[fieldName].resize(length);
- memcpy(&fields[fieldName][0], fieldValues, length * sizeof(T_Field));
-}
diff --git a/libcpp/pbdata/amos/AfgBasWriter.cpp b/libcpp/pbdata/amos/AfgBasWriter.cpp
deleted file mode 100644
index 2817bce..0000000
--- a/libcpp/pbdata/amos/AfgBasWriter.cpp
+++ /dev/null
@@ -1,102 +0,0 @@
-#include "AfgBasWriter.hpp"
-
-unsigned char AfgBasWriter::pacbioQVtoPhredQV(unsigned char pacbio){
- return (unsigned char) floor( 10.0 * log10( 1.0 + pow(10.0, pacbio / 100.0) ) + 0.5 );
-}
-
-AfgBasWriter::AfgBasWriter() {
- firstRecord = true;
- recordCount = 1;
- defaultQuality = 5;
-}
-
-AfgBasWriter::~AfgBasWriter() {
- firstRecord = true;
- recordCount = 1;
- defaultQuality = 5;
-}
-
-void AfgBasWriter::Initialize(std::string _afgFileName){
- afgFileName = _afgFileName;
- CrucialOpen(afgFileName, afgOut);
-}
-
-void AfgBasWriter::Close() {
- afgOut.close();
-}
-
-void AfgBasWriter::SetDefaultQuality(int _defaultQuality){
- defaultQuality = _defaultQuality;
-}
-
-int AfgBasWriter::Write(SMRTSequence &seq) {
- if (firstRecord){
- WriteHeader();
- firstRecord = false;
- }
- WriteOpen(seq);
- WriteIdentifier(seq);
- WriteBases(seq);
- WriteQualities(seq);
- WriteClose();
- return 1;
-}
-
-void AfgBasWriter::WriteHeader() {
- afgOut << "{UNV" << std::endl;
- afgOut << "iid:1" << std::endl;
- afgOut << "com:" << std::endl;
- afgOut << "generated by AfgBasWriter" << std::endl;
- afgOut << "Mon Jun 28 14:43:52 2010" << std::endl; // TODO put in real date
- afgOut << "." << std::endl << "}" << std::endl;
- afgOut << "{LIB" << std::endl << "iid:1" << std::endl;
- afgOut << "{DST" << std::endl << "mea:0" << std::endl << "std:0" << std::endl << "}" << std::endl << "}" << std::endl;
-}
-
-void AfgBasWriter::WriteOpen(SMRTSequence &seq) {
- afgOut << "{RED" << std::endl;
- afgOut << "frg:" << recordCount + 1 << std::endl;
- afgOut << "iid:" << recordCount << std::endl;
-}
-
-void AfgBasWriter::WriteIdentifier(SMRTSequence &seq) {
- afgOut << "clr:0," << seq.length << std::endl;
-
- afgOut << "eid:";
- std::string fastaTitle;
- seq.GetFASTATitle(fastaTitle);
- afgOut << fastaTitle << std::endl;
-}
-
-void AfgBasWriter::WriteClose() {
- recordCount++;
- afgOut << "}" << std::endl;
- afgOut << "{FRG" << std::endl;
- afgOut << "iid:" << recordCount << std::endl;
- afgOut << "lib:1" << std::endl << "typ:I" << std::endl << "}" << std::endl;
- recordCount++;
-}
-
-void AfgBasWriter::WriteBases(SMRTSequence &seq) {
- afgOut << "seq:" << std::endl;
- (static_cast<DNASequence*>(&seq))->PrintSeq( afgOut, lineLength );
- afgOut << "." << std::endl;
-}
-
-void AfgBasWriter::WriteQualities(SMRTSequence &seq) {
- afgOut << "qlt:" << std::endl;
- int i;
- for (i = 0; i < seq.length; i++ ){
- unsigned char quality = seq.qual.data ? seq.qual[i] : defaultQuality;
- quality = quality + charToQuality;
- quality = quality > maxAfgQuality ? maxAfgQuality : quality;
- quality = quality < minAfgQuality ? minAfgQuality : quality;
- afgOut << quality;
- if (i > 0 and (i+1) % lineLength == 0)
- afgOut << std::endl;
- }
- if (i == 0 or i % lineLength != 0) {
- afgOut << std::endl;
- }
- afgOut << "." << std::endl;
-}
diff --git a/libcpp/pbdata/amos/AfgBasWriter.hpp b/libcpp/pbdata/amos/AfgBasWriter.hpp
deleted file mode 100644
index c945f88..0000000
--- a/libcpp/pbdata/amos/AfgBasWriter.hpp
+++ /dev/null
@@ -1,59 +0,0 @@
-#ifndef _BLASR_AMOS_AFG_BAS_WRITER_HPP_
-#define _BLASR_AMOS_AFG_BAS_WRITER_HPP_
-
-#include <cmath>
-#include <fstream>
-#include <sstream>
-#include "SMRTSequence.hpp"
-#include "qvs/QualityValueVector.hpp"
-
-class AfgBasWriter {
- // TODO correct file type? outFile
- // TODO change SMRTSequence to FASTQ sequence? then maybe fasta2afg would be
- // easier to write
- std::string afgFileName;
- std::ofstream afgOut;
- bool firstRecord;
- int recordCount;
- int defaultQuality;
- // Use 122 = '{' - 1 because '{' and '}' are the message delimiters in AMOS.
- static const unsigned char maxAfgQuality = 122;
- static const unsigned char charToQuality = 48;
- static const unsigned char minAfgQuality = charToQuality + 1;
- static const int lineLength = 80;
-
- private:
-
- unsigned char pacbioQVtoPhredQV(unsigned char pacbio);
-
- public:
- // Assume that closing the afg file must be done
- // manually and not in a destructor.
- ~AfgBasWriter();
-
- AfgBasWriter();
-
- void Initialize(std::string _afgFileName);
-
- void Close();
-
- int Write(SMRTSequence &seq);
-
- void SetDefaultQuality(int _defaultQuality);
-
- private:
-
- void WriteHeader();
-
- void WriteOpen(SMRTSequence &seq);
-
- void WriteIdentifier(SMRTSequence &seq);
-
- void WriteClose();
-
- void WriteBases(SMRTSequence &seq);
-
- void WriteQualities(SMRTSequence &seq);
-};
-
-#endif
diff --git a/libcpp/pbdata/build.mk b/libcpp/pbdata/build.mk
deleted file mode 120000
index 2247f36..0000000
--- a/libcpp/pbdata/build.mk
+++ /dev/null
@@ -1 +0,0 @@
-makefile
\ No newline at end of file
diff --git a/libcpp/pbdata/defs.h b/libcpp/pbdata/defs.h
deleted file mode 100644
index c01d625..0000000
--- a/libcpp/pbdata/defs.h
+++ /dev/null
@@ -1,19 +0,0 @@
-#ifndef DEFS_H_
-#define DEFS_H_
-
-#ifndef MIN
-#define MIN(a, b) ((a) < (b) ? (a) : (b))
-#endif
-
-
-#ifndef MAX
-#define MAX(a, b) ((a) > (b) ? (a) : (b))
-#endif
-
-#define SWAP(a, b) (((a) == (b)) ? 0 : ((a) ^= (b), (b) ^= (a), (a) ^= (b)))
-
-#ifndef INF_INT
-#define INF_INT INT_MAX
-#endif
-
-#endif
diff --git a/libcpp/pbdata/loadpulses/MetricField.cpp b/libcpp/pbdata/loadpulses/MetricField.cpp
deleted file mode 100644
index 1e95a46..0000000
--- a/libcpp/pbdata/loadpulses/MetricField.cpp
+++ /dev/null
@@ -1,87 +0,0 @@
-#include "MetricField.hpp"
-
-Field::Field(std::string n, FieldType t) {
- name = n;
- type = t;
-}
-
-bool Field::operator==(const Field &another) const {
- return (name == another.name &&
- type == another.type);
-}
-
-FieldsRequirement::FieldsRequirement(const std::string & m) {
- metric = m;
- if (metric == "QualityValue" || metric == "InsertionQV" ||
- metric == "MergeQV" || metric == "DeletionQV" ||
- metric == "DeletionTag" || metric == "SubstitutionTag" ||
- metric == "SubstitutionQV" || metric == "PreBaseFrames" ||
- metric == "PulseIndex" || metric == "Basecall") {
- fieldsUseBasFile.push_back(Field (metric , BasField));
-
- } else if (metric == "ClassifierQV") {
- fieldsUsePlsFile.push_back(Field (metric , PlsField));
- fieldsUsePlsFile.push_back(Field ("NumEvent" , PlsField));
- fieldsUsePlsFile.push_back(Field ("PulseIndex" , BasField));
-
- } else if (metric == "StartTimeOffset") {
- fieldsUsePlsFile.push_back(Field ("StartFrame" , PlsField));
- fieldsUsePlsFile.push_back(Field ("NumEvent" , PlsField));
- fieldsUsePlsFile.push_back(Field ("PulseIndex" , BasField));
-
- } else if (metric == "StartFramePulse") {// Compute StartFrame from PulseCalls only
- fieldsUsePlsFile.push_back(Field ("StartFrame" , PlsField));
- fieldsUsePlsFile.push_back(Field ("NumEvent" , PlsField));
- fieldsUsePlsFile.push_back(Field ("PulseIndex" , BasField));
-
- } else if (metric == "StartFrameBase") {// Compute StartFrame from BaseCalls only
- fieldsUseBasFile.push_back(Field ("PreBaseFrames", BasField));
- fieldsUseBasFile.push_back(Field ("WidthInFrames", BasField));
-
- } else if (metric == "WhenStarted") {
- // WhenStarted does not require any field because it only requires an attribute
-
- } else if (metric == "pkmid") {
- fieldsUsePlsFile.push_back(Field ("MidSignal" , PlsField));
- fieldsUsePlsFile.push_back(Field ("NumEvent" , PlsField));
- fieldsUsePlsFile.push_back(Field ("PulseIndex" , BasField));
-
- } else if (metric == "Light") {
- fieldsUsePlsFile.push_back(Field ("WidthInFrames", PlsField));
- fieldsUsePlsFile.push_back(Field ("MeanSignal" , PlsField));
- fieldsUsePlsFile.push_back(Field ("NumEvent" , PlsField));
- fieldsUsePlsFile.push_back(Field ("PulseIndex" , BasField));
-
- } else if (metric == "PulseWidth" || metric == "WidthInFrames") {
- // Both metrics require a field "WidthInFrames", which can be read from
- // either bas.h5 or pls.h5.
- fieldsUseBasFile.push_back(Field ("WidthInFrames", BasField));
-
- fieldsUsePlsFile.push_back(Field ("WidthInFrames", PlsField));
- fieldsUsePlsFile.push_back(Field ("NumEvent" , PlsField));
- fieldsUsePlsFile.push_back(Field ("PulseIndex" , BasField));
-
- } else if (metric == "StartFrame") {
- // Compute StartFrame from either PulseCalls or BaseCalls
- fieldsUseBasFile.push_back(Field ("PreBaseFrames", BasField));
- fieldsUseBasFile.push_back(Field ("WidthInFrames", BasField));
-
- fieldsUsePlsFile.push_back(Field ("StartFrame" , PlsField));
- fieldsUsePlsFile.push_back(Field ("NumEvent" , PlsField));
- fieldsUsePlsFile.push_back(Field ("PulseIndex" , BasField));
- } else if (metric == "IPD") {
- // IPD can be obtained from basFile.PreBaseFrames or computed from
- // plsFile.WidthInFrames and plsFile.StartFrame. Use the second method if possible
- fieldsUseBasFile.push_back(Field ("PreBaseFrames", BasField));
-
- fieldsUsePlsFile.push_back(Field ("StartFrame" , PlsField));
- fieldsUsePlsFile.push_back(Field ("WidthInFrames", PlsField));
- fieldsUsePlsFile.push_back(Field ("NumEvent" , PlsField));
- fieldsUsePlsFile.push_back(Field ("PulseIndex" , BasField));
- } else if (metric == "") {
- // No metric, no required fields.
- } else {
- std::cout << "ERROR, metric [" << metric << "] is not supported." << std::endl;
- exit(1);
- }
-}
diff --git a/libcpp/pbdata/loadpulses/MetricField.hpp b/libcpp/pbdata/loadpulses/MetricField.hpp
deleted file mode 100644
index a930017..0000000
--- a/libcpp/pbdata/loadpulses/MetricField.hpp
+++ /dev/null
@@ -1,115 +0,0 @@
-#ifndef _LOADPULSES_METRICFIELD_HPP_
-#define _LOADPULSES_METRICFIELD_HPP_
-#include <iostream>
-#include <string>
-#include <vector>
-
-#include <stdlib.h>
-
-#include "Types.h"
-
-enum FieldType {BasField, PlsField};
-
-class Field {
-public:
- std::string name;
- FieldType type;
- Field(std::string n, FieldType t);
- bool operator == (const Field &another) const;
-};
-
-class FieldsRequirement {
-public:
- std::string metric;
- std::vector<Field> fieldsUseBasFile;
- std::vector<Field> fieldsUsePlsFile;
-
- // Return fields that are required for computing this metric.
- // Eighteen metrics are supported in total.
- // [1/18] metric requires only an attribute (not a field):
- // WhenStarted
- //
- // [9/18] metrics require exactly one BaseCall field
- // QualityValue InsertionQV MergeQV DeletionQV
- // DeletionTag SubstitutionTag SubstitutionQV PreBaseFrames
- // PulseIndex
- //
- // [4/18] metrics require more than one field and can be computed using
- // only one method:
- // BaseCall PulseCall
- // ----------------------------------------------------
- // ClassifierQV PulseIndex NumEvent
- // ClassifierQV
- // ----------------------------------------------------
- // pkmid PulseIndex NumEvent
- // MidSignal
- // ----------------------------------------------------
- // Light PulseIndex NumEvent
- // WidthInFrames
- // MeanSignal
- // ----------------------------------------------------
- // StartTimeOffset PulseIndex NumEvent
- // StartFrame
- // ----------------------------------------------------
- // [4/18] metrics can be computed from both BaseCalls and PulseCalls.
- // But sometimes the value computed from BaseCalls can be wrong,
- // because the value of BaseCalls/PreBaseFrames may exceed 2^16-1.
- // Method BaseCall PulseCall
- // ----------------------------------------------------
- // PulseWidth (1) WidthInFrames
- // =======================================
- // (2) PulseIndex NumEvent
- // WidthInFrames
- // ----------------------------------------------------
- // WidthInFrames : The same as PulseWidth
- // ----------------------------------------------------
- // StartFrame (1) PreBaseFrames
- // WidthInFrames
- // =======================================
- // (2) PulseIndex NumEvent
- // StartFrame
- // ----------------------------------------------------
- // IPD (1) PreBaseFrames
- // =======================================
- // (2) PulseIndex NumEvent
- // StartFrame
- // WidthInFrames
- // ----------------------------------------------------
- // Note: PulseWidth and WidthInFrames have the same meaning and are
- // computed in the same way.
- //
- // Note: StartFrame can be loaded for both bas.h5 and pls.h5 files
- // for bas.h5, StartFrame is computed from PreBaseFrames and WidthInFrames
- // Let x = PreBaseFrames for bases 0 ... n-1, where x[0] is 0 and
- // x[i] is the inter-pulse distance between start of pulse
- // for base i and end of pulse for base i-1
- // Let y = WidthInFrames for bases 0 ... n-1, where y[i] is the
- // number of pulses within base i
- // Then,
- // StartFrame[0] = x[0]
- // StartFrame[i] = sum(x[0] ... x[i]) + sum(y[0] ... y[i-1])
- // for i in [1 ... n-1]
- // for pls.h5, StartFrame can be directly read from dataset
- // /PulseData/PulseCalls/StartFrame
- //
- // Note: StartTimeOffset is the StartFrame for the very first base of a read, it
- // can only be computed from PulseCalls
- //
- // Note: IPD has the same meaning as PreBaseFrames:
- // = the inter-pulse distance between this base and end of last base,
- // = the number of Frames between the ending pulse of the last base and
- // the starting pulse of this base.
- // However, PreBaseFrames can only be read directly from BaseCalls, while
- // IPD can also be computed from PulseCalls
- // If use BaseCalls,
- // IPD[i] = PreBaseFrames[i] for i in [0 ... n-1]
- // If use PulseCalls,
- // IPD[0] = 0
- // IPD[i] = StartFrame[i] - StartFrame[i-1] - WidthInFrames[i-1]
- // for i in [1 ... n-1]
- //
- //void GetRequiredFieldsForMetric(const string & metric, FieldType & field){
- FieldsRequirement(const std::string & m);
-};
-
-#endif
diff --git a/libcpp/pbdata/loadpulses/MovieAlnIndexLookupTable.cpp b/libcpp/pbdata/loadpulses/MovieAlnIndexLookupTable.cpp
deleted file mode 100644
index 51140d3..0000000
--- a/libcpp/pbdata/loadpulses/MovieAlnIndexLookupTable.cpp
+++ /dev/null
@@ -1,54 +0,0 @@
-#include "MovieAlnIndexLookupTable.hpp"
-
-
-MovieAlnIndexLookupTable::MovieAlnIndexLookupTable() {
- skip = true;
- //skip this alignment unless we can find all the information
-}
-
-void MovieAlnIndexLookupTable::SetValue(
- const bool & skipP,
- const int & movieAlignmentIndexP,
- const UInt & alignmentIndexP,
- const int & refGroupIndexP,
- const int & readGroupIndexP,
- const UInt & holeNumberP,
- const UInt & offsetBeginP,
- const UInt & offsetEndP,
- const int & queryStartP,
- const int & queryEndP,
- const int & readIndexP,
- const int & readStartP,
- const int & readLengthP,
- const int & plsReadIndexP) {
- skip = skipP;
- movieAlignmentIndex = movieAlignmentIndexP;
- alignmentIndex = alignmentIndexP;
- refGroupIndex = refGroupIndexP;
- readGroupIndex = readGroupIndexP;
- holeNumber = holeNumberP;
- offsetBegin = offsetBeginP;
- offsetEnd = offsetEndP;
- queryStart = queryStartP;
- queryEnd = queryEndP;
- readIndex = readIndexP;
- readStart = readStartP;
- readLength = readLengthP;
- plsReadIndex = plsReadIndexP;
-}
-
-
-void MovieAlnIndexLookupTable::print() {
- // Print this lookup table for debugging .
- if (skip)
- std::cout << "skip = True, ";
- else
- std::cout << "skip = False, ";
- std::cout << "movieAlnIndex = " << alignmentIndex << ", refGroupIndex = " << refGroupIndex
- << ", readGroupIndex = " << readGroupIndex << ", holeNumber = " << holeNumber
- << ", offsetBegin = " << offsetBegin << ", offsetEnd = " << offsetEnd
- << ", queryStart = " << queryStart << ", queryEnd = " << queryEnd
- << ", readIndex = " << readIndex << ", readStart = " << readStart
- << ", readLength = " << readLength << ", plsReadIndex = " << plsReadIndex
- << std::endl;
-}
diff --git a/libcpp/pbdata/loadpulses/MovieAlnIndexLookupTable.hpp b/libcpp/pbdata/loadpulses/MovieAlnIndexLookupTable.hpp
deleted file mode 100644
index f69811c..0000000
--- a/libcpp/pbdata/loadpulses/MovieAlnIndexLookupTable.hpp
+++ /dev/null
@@ -1,117 +0,0 @@
-/*
- * =====================================================================================
- *
- * Filename: MovieAlnIndexLookupTable.h
- *
- * Description: For cpp/pbihdfutils/LoadPulses.cpp use only.
- * Cache all the information required for loading metric from pls/bas
- * to cmp file.
- * mapping movieAlignmentIndex in movieIndexSets[movieIndex] to:
- * alignmentIndex: index of this alignment in cmpFile.alnInfo.alignments
- * refGroupIndex : index of this alignment in cmpReader.refAlignGroups
- * readGroupIndex: index of this alignment in cmpReader.refAlignGroups\
- * [refGroupIndex]->readGroupds[readGroupIndex]
- * offsetBegin : offset begin for this alignment in cmpFile
- * dataset /ref/movie/AlnArray
- * offsetEnd : offset enda
- * queryStart : start position of query of this alignment
- * queryEnd : end position of query of this alignment
- * readIndex : index of this alignment in baseFile.readStartPositions
- * readStart : start position of this alignment in baseFile
- * readLength : read length of this alignment in baseFile
- * plsReadIndex : index of this alignment in pulseFile.pulseStartPositions
- * alignedSequence
- * : aligned sequence of this alignment
- *
- * Version: 1.0
- * Created: 12/19/2012 03:50:21 PM
- * Revision: none
- * Compiler: gcc
- *
- * Author: Yuan Li (yli), yli at pacificbiosciences.com
- * Company: Pacific Biosciences
- *
- * =====================================================================================
- */
-
-#ifndef _LOADPULSES_MovieAlnIndexLookupTable_HPP_
-#define _LOADPULSES_MovieAlnIndexLookupTable_HPP_
-#include <iostream>
-#include <string>
-
-#include "Types.h"
-
-class MovieAlnIndexLookupTable {
-public:
- bool skip;
- // as movies may split into multiple parts, skip=true if
- // this alignment is not found in the movie
-
- int movieAlignmentIndex;
- // movieIndexSets[movieIndex][toFrom[movieAlignmentIndex]]
-
- UInt alignmentIndex;
- // cmpFile.alnInfo.alignments[alignmentIndex]
-
- UInt holeNumber;
- // holeNumber corresponding to this alignment in baseFile
-
- int refGroupIndex;
- // cmpReader.refAlignGroups[refGroupIndex]
-
- int readGroupIndex;
- // cmpReader.refAlignGroups[refGroupIndex]->readGroups[readGroupIndex]
-
- UInt offsetBegin, offsetEnd;
- // offset begin and end for this alignment in /ref/movie/AlnArray
- // = cmpFile.alnInfo.alignments[alignmentIndex].GetOffsetBegin/End()
-
- int queryStart, queryEnd;
- // start/end for this read = cmpFile.alnInfo.
- // alignments[alignmentIndex].GetQueryStart/End()
-
- int readIndex;
- // index of this alignment in baseFile.readStartPositions
- // = index of this hole number in BaseCalls/ZMW/HoleNumber
- // baseFile.LookupReadIndexByHoleNumber(holeNumber, out=readIndex)
-
- int readStart;
- // start pos of this alignment in baseFile
- // = baseFile.readStartPositions[readIndex]
-
- int readLength;
- // read length of this alignment in baseFile
- // = baseFile.readStartPositions[readIndex+1] - readStart
-
- int plsReadIndex;
- // index of this alignment in pulseFile.pulseStartPositions
- // = index of this hole number in PulseCalls/ZMW/HoleNumbers
- // = pulseFile.LookupReadIndexByHoleNumber(holeNumber, out=plsReadIndex)
-
- // vector<int> baseToAlignmentMap;
- // keep all the baseToAlignmentMap in memory for now
- // Note that baseToAlignmentMap is not initialized when
- // BuildLookupTable is called.
-
- std::string alignedSequence;
-
- MovieAlnIndexLookupTable();
-
- void SetValue(const bool & skipP,
- const int & movieAlignmentIndexP,
- const UInt & alignmentIndexP,
- const int & refGroupIndexP,
- const int & readGroupIndexP,
- const UInt & holeNumberP,
- const UInt & offsetBeginP,
- const UInt & offsetEndP,
- const int & queryStartP,
- const int & queryEndP,
- const int & readIndexP,
- const int & readStartP,
- const int & readLengthP,
- const int & plsReadIndexP);
-
- void print();
-};
-#endif
diff --git a/libcpp/pbdata/makefile b/libcpp/pbdata/makefile
deleted file mode 100644
index fd4a65c..0000000
--- a/libcpp/pbdata/makefile
+++ /dev/null
@@ -1,40 +0,0 @@
-all:
-
-include ../rules.mk
-include ../defines.mk
-
-CXXOPTS += -std=c++11 -pedantic -MMD -MP
-CPPFLAGS += -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment
-INCLUDES += ${PBBAM_INCLUDE} ${HTSLIB_INCLUDE} ${BOOST_INCLUDE}
-DEP_LIBS += ${PBBAM_LIB} ${HTSLIB_LIB}
-LDFLAGS += $(patsubst %,$(dirname %),${DEP_LIBS})
-
-all: libpbdata.a libpbdata.so
-
-sources := $(wildcard *.cpp) \
- $(wildcard matrix/*.cpp) \
- $(wildcard reads/*.cpp) \
- $(wildcard metagenome/*.cpp) \
- $(wildcard qvs/*.cpp) \
- $(wildcard saf/*.cpp) \
- $(wildcard utils/*.cpp) \
- $(wildcard loadpulses/*.cpp) \
- $(wildcard alignment/*.cpp) \
- $(wildcard amos/*.cpp) \
- $(wildcard sam/*.cpp)
-
-objects := $(sources:.cpp=.o)
-shared_objects := $(sources:.cpp=.shared.o)
-dependencies := $(objects:.o=.d) $(shared_objects:.o=.d)
-
-libpbdata.a: $(objects)
- $(AR) $(ARFLAGS) $@ $^
-
-libpbdata.so: $(shared_objects) $(DEP_LIBS)
- $(CXX) $(LD_SHAREDFLAGS) -o $@ -Wl,-soname,$@ $^
-
-clean:
- @rm -f libpbdata.a libpbdata.so
- @rm -f $(objects) $(shared_objects) $(dependencies)
-
--include $(dependencies)
diff --git a/libcpp/pbdata/matrix/FlatMatrix.hpp b/libcpp/pbdata/matrix/FlatMatrix.hpp
deleted file mode 100644
index 1664f9e..0000000
--- a/libcpp/pbdata/matrix/FlatMatrix.hpp
+++ /dev/null
@@ -1,98 +0,0 @@
-#ifndef _BLASR_FLAT_MATRIX_HPP_
-#define _BLASR_FLAT_MATRIX_HPP_
-
-#define rc2index(r, c, rowSize) ( (r) * (rowSize) + c)
-
-template<typename T>
-void CreateFlatMatrix(int rows, int cols, std::vector<T> &matrix);
-
-template<typename T>
-void PrintFlatMatrix(std::vector<T> &matrix, int rows, int cols, std::ostream &out, int width=6);
-
-template<typename T>
-void PrintFlatMatrix(const T* matrix, int rows, int cols, std::ostream &out, int width=6);
-
-template<typename T>
-class FlatMatrix2D {
- public:
- T* matrix;
- int nRows, nCols;
- int totalSize;
- int RC2Index(int row, int col);
-
- FlatMatrix2D();
-
- ~FlatMatrix2D();
-
- T* operator[](int row);
-
- T operator()(int row, int col);
-
- unsigned int Size();
-
- void Fill(T value) {
- fill(matrix, &matrix[totalSize], value);
- }
-
- void Resize(int _nRows, int _nCols) {
- Grow(_nRows, _nCols);
- }
-
- void Resize(unsigned int totalSize);
-
- FlatMatrix2D(int _nRows, int _nCols);
-
- void Clear() {
- if (matrix) {delete[] matrix;}
- matrix = NULL;
- nRows = nCols = 0;
- totalSize = 0;
- }
-
-
- void Grow(int _nRows, int _nCols);
-
- T Get(int r, int c);
-
- T Set(int r, int c, T v);
-
- int Index(int r, int c);
-
- void Print(std::ostream &out);
-
- void Allocate(UInt _nRows, UInt _nCols);
-
- void Initialize(T value);
-};
-
-
-template<typename T>
-class FlatMatrix3D {
- public:
- T* matrix;
- //
- // For some reason it makes sense to go from rows,cols to x,y,z
- // for referencing coordinates.
- //
- int nx, ny, nz;
- int xy;
- int totalSize;
-
- FlatMatrix3D();
-
- FlatMatrix3D(int _nx, int _ny, int _nz);
-
- void Grow(int _nx, int _ny, int _nz);
-
- int Index(int x, int y, int z);
-
- T Get(int x, int y, int z);
-
- T Set(int x, int y, int z, T v);
-
- ~FlatMatrix3D();
-};
-
-#include "FlatMatrixImpl.hpp"
-
-#endif // _BLASR_FLAT_MATRIX_HPP_
diff --git a/libcpp/pbdata/matrix/FlatMatrixImpl.hpp b/libcpp/pbdata/matrix/FlatMatrixImpl.hpp
deleted file mode 100644
index 5536cb7..0000000
--- a/libcpp/pbdata/matrix/FlatMatrixImpl.hpp
+++ /dev/null
@@ -1,192 +0,0 @@
-#include <stdint.h>
-#include <vector>
-#include <iostream>
-#include <assert.h>
-#include "Types.h"
-#include "FlatMatrix.hpp"
-
-template<typename T>
-void CreateFlatMatrix(int rows, int cols, std::vector<T> &matrix) {
- matrix.resize(rows*cols);
-}
-
-template<typename T>
-void PrintFlatMatrix(std::vector<T> &matrix, int rows, int cols, std::ostream &out, int width) {
- PrintFlatMatrix((const T*) &matrix[0], rows, cols, out, width);
-}
-
-template<typename T>
-void PrintFlatMatrix(const T* matrix, int rows, int cols, std::ostream &out, int width) {
- int r, c, i;
- i = 0;
- for (r = 0; r < rows; r++ ) {
- for (c = 0; c < cols; c++ ) {
- out.width(width);
- out << matrix[i] << " ";
- i++;
- }
- out << std::endl;
- }
-}
-
-template<typename T>
-int FlatMatrix2D<T>::RC2Index(int row, int col) {
- return row * nCols + col;
-}
-
-template<typename T>
-T* FlatMatrix2D<T>::operator[](int row) {
- return &matrix[row*nCols];
-}
-
-template<typename T>
-T FlatMatrix2D<T>::operator()(int row, int col) {
- int index = RC2Index(row,col);
- return matrix[index];
-}
-
-template<typename T>
-FlatMatrix2D<T>::FlatMatrix2D() {
- matrix = NULL;
- nRows = nCols = totalSize = 0;
-}
-
-template<typename T>
-unsigned int FlatMatrix2D<T>::Size() {
- return nRows * nCols;
-}
-
-template<typename T>
-void FlatMatrix2D<T>::Resize(unsigned int _totalSize) {
- if (matrix != NULL) {
- delete[] matrix;
- }
- matrix = new T[_totalSize];
- totalSize = _totalSize;
-}
-
-template<typename T>
-FlatMatrix2D<T>::FlatMatrix2D(int _nRows, int _nCols) {
- totalSize = 0;
- matrix = NULL;
- // assert(_nRows > 0);
- // assert(_nCols > 0);
- if (_nRows == 0 or _nCols == 0) {
- nRows = _nRows; nCols = _nCols;
- return;
- }
- else {
- Grow(_nRows, _nCols);
- }
-}
-template<typename T>
-void FlatMatrix2D<T>::Grow(int _nRows, int _nCols) {
- nRows = _nRows;
- nCols = _nCols;
- if (nRows * nCols > totalSize) {
- if (totalSize != 0 && matrix)
- delete[] matrix;
- totalSize = nRows * nCols;
- matrix = new T[totalSize];
- }
-}
-
-template<typename T>
-T FlatMatrix2D<T>::Get(int r, int c) {
- return matrix[r * nCols + c];
-}
-
-template<typename T>
-T FlatMatrix2D<T>::Set(int r, int c, T v) {
- return matrix[r*nCols+c] = v;
-}
-
-template<typename T>
-int FlatMatrix2D<T>::Index(int r, int c) {
- return r*nCols + c;
-}
-
-template<typename T>
-void FlatMatrix2D<T>::Print(std::ostream &out) {
- PrintFlatMatrix(matrix, nRows, nCols, out);
-}
-
-template<typename T>
-void FlatMatrix2D<T>::Allocate(UInt _nRows, UInt _nCols) {
- nRows = _nRows;
- nCols = _nCols;
- matrix = new T[nRows * nCols];
-}
-
-template<typename T>
-void FlatMatrix2D<T>::Initialize(T value) {
- T* matPtr, *matEnd;
- matEnd = &matrix[nRows*nCols];
- for (matPtr = &matrix[0]; matPtr != matEnd; ++matPtr) {
- *matPtr = value;
- }
-}
-
-template<typename T>
-FlatMatrix2D<T>::~FlatMatrix2D(){
- if (matrix != NULL) {
- delete [] matrix;
- matrix = NULL;
- }
-}
-
-template<typename T>
-FlatMatrix3D<T>::FlatMatrix3D() {
- nx = 0, ny = 0, nz = 0;
- xy = 0;
- totalSize = 0;
- matrix = NULL;
-}
-
-template<typename T>
-FlatMatrix3D<T>::FlatMatrix3D(int _nx, int _ny, int _nz) {
- totalSize = 0;
- matrix =NULL;
- assert(_nx > 0);
- assert(_ny > 0);
- assert(_nz > 0);
- Grow(_nx, _ny, _nz);
-}
-
-template<typename T>
-void FlatMatrix3D<T>::Grow(int _nx, int _ny, int _nz) {
- nx = _nx;
- ny = _ny;
- nz = _nz;
- if (nx * ny * nz > totalSize) {
- if (matrix != NULL) {
- delete[] matrix;
- }
- totalSize = nx*ny*nz;
- matrix = new T[totalSize];
- }
- xy = nx*ny;
-}
-
-template<typename T>
-int FlatMatrix3D<T>::Index(int x, int y, int z) {
- return z * xy + y * nx + x;
-}
-
-template<typename T>
-T FlatMatrix3D<T>::Get(int x, int y, int z) {
- return matrix[Index(x,y,z)];
-}
-
-template<typename T>
-T FlatMatrix3D<T>::Set(int x, int y, int z, T v){
- return matrix[Index(x,y,z)] = v;
-}
-
-template<typename T>
-FlatMatrix3D<T>::~FlatMatrix3D() {
- if (matrix != NULL) {
- delete [] matrix;
- matrix = NULL;
- }
-}
diff --git a/libcpp/pbdata/matrix/Matrix.hpp b/libcpp/pbdata/matrix/Matrix.hpp
deleted file mode 100644
index 3ef6bca..0000000
--- a/libcpp/pbdata/matrix/Matrix.hpp
+++ /dev/null
@@ -1,50 +0,0 @@
-#ifndef _BLASR_MATRIX_HPP_
-#define _BLASR_MATRIX_HPP_
-
-#include <vector>
-#include "Types.h"
-
-template<typename T>
-void CreateMatrix(int rows, int cols, std::vector<T*> matrix);
-
-/*
- * Implement a matrix as an array into a large allocated buffer of size
- * nRows * nCols.
- */
-
-template<typename T>
-class Matrix {
-private:
- VectorIndex nRows;
- VectorIndex nCols;
- T** matrix;
- VectorIndex matrixBufferSize;
- VectorIndex matrixSize;
- VectorIndex rowsBufferSize;
-public:
- Matrix();
-
- unsigned int size();
-
- unsigned int GetNCols();
-
- unsigned int GetNRows();
-
- void Resize(VectorIndex nRowsP, VectorIndex nColsP);
-
- Matrix(VectorIndex nRowsP, VectorIndex nColsP);
-
- void Reference(Matrix<T> &rhs);
-
- void Initialize(T value);
-
- T* operator[](VectorIndex rowIndex);
-
- void Free();
-
- void Print(std::ofstream &out);
-};
-
-#include "MatrixImpl.hpp"
-
-#endif // _BLASR_MATRIX_HPP_
diff --git a/libcpp/pbdata/matrix/MatrixImpl.hpp b/libcpp/pbdata/matrix/MatrixImpl.hpp
deleted file mode 100644
index c66aaf4..0000000
--- a/libcpp/pbdata/matrix/MatrixImpl.hpp
+++ /dev/null
@@ -1,117 +0,0 @@
-#ifndef _BLASR_MATRIX_IMPL_HPP
-#define _BLASR_MATRIX_IMPL_HPP
-#include <cassert>
-#include <vector>
-#include <iostream>
-#include <fstream>
-#include <stdint.h>
-#include "Types.h"
-
-template<typename T>
-void CreateMatrix(int rows, int cols, std::vector<T*> matrix) {
- matrix.resize(rows);
- if (matrix[0]) {delete [] matrix[0]; matrix[0] = NULL;}
- matrix[0] = new T[rows*cols];
- VectorIndex r = 1;
- for (r = 1; r < rows; r++) {
- matrix[r] = &matrix[cols * r];
- }
-}
-
-template<typename T>
-Matrix<T>::Matrix() {
- nRows = 0;
- rowsBufferSize = 0;
- nCols = 0;
- matrixBufferSize = 0;
- matrix = NULL;
-}
-
-template<typename T>
-unsigned int Matrix<T>::size() {
- return nRows * nCols;
-}
-
-template<typename T>
-unsigned int Matrix<T>::GetNCols() {
- return nCols;
-}
-
-template<typename T>
-unsigned int Matrix<T>::GetNRows() {
- return nRows;
-}
-
-template<typename T>
-void Matrix<T>::Resize(VectorIndex nRowsP, VectorIndex nColsP) {
-
- nRows = nRowsP;
- nCols = nColsP;
- matrixSize = nRows * nCols;
- if (nRows * nCols > matrixBufferSize) {
- matrixBufferSize = nRows * nCols;
- if (nRows > rowsBufferSize) {
- if (matrix != NULL) {
- delete[] matrix; matrix = NULL;
- }
- }
- if (matrix == NULL) {
- matrix = new T*[nRows];
- }
- else {
- if (matrix[0] != NULL) {
- delete[] matrix[0]; matrix[0] = NULL;
- }
- }
- matrix[0] = new T[matrixBufferSize];
- VectorIndex rowIndex;
- for (rowIndex = 1; rowIndex < nRows; rowIndex++ ){
- matrix[rowIndex] = &matrix[0][nCols * rowIndex];
- }
- }
-}
-
-template<typename T>
-Matrix<T>::Matrix(VectorIndex nRowsP, VectorIndex nColsP) {
- Resize(nRowsP, nColsP);
-}
-
-template<typename T>
-void Matrix<T>::Reference(Matrix<T> &rhs) {
- matrix = rhs.matrix;
-}
-
-template<typename T>
-void Matrix<T>::Initialize(T value) {
- std::fill(&matrix[0][0], &matrix[0][matrixSize], value);
-}
-
-template<typename T>
-T* Matrix<T>::operator[](VectorIndex rowIndex) {
- assert(rowIndex < nRows);
- return matrix[rowIndex];
-}
-
-template<typename T>
-void Matrix<T>::Free() {
- if (matrix != NULL) {
- if (matrix[0] != NULL) {
- delete[] matrix[0];
- }
- delete[] matrix;
- }
- matrix = NULL;
-}
-
-template<typename T>
-void Matrix<T>::Print(std::ofstream &out) {
- VectorIndex i;
- VectorIndex j;
- for (i = 0; i < nRows; i++) {
- for (j = 0; j < nCols; j++ ){
- out << matrix[i][j] << " ";
- }
- out << std::endl;
- }
-}
-#endif
diff --git a/libcpp/pbdata/metagenome/FindRandomSequence.hpp b/libcpp/pbdata/metagenome/FindRandomSequence.hpp
deleted file mode 100644
index cb5ab3c..0000000
--- a/libcpp/pbdata/metagenome/FindRandomSequence.hpp
+++ /dev/null
@@ -1,70 +0,0 @@
-#ifndef _FIND_RANDOM_SEQUENCE_HPP_
-#define _FIND_RANDOM_SEQUENCE_HPP_
-
-#include <vector>
-#include "DNASequence.hpp"
-#include "statistics/StatUtils.hpp"
-
-
-template<typename T_Sequence>
-void FindRandomPos(vector<T_Sequence> &sequences, DNALength &seqIndex, DNALength &seqPos, DNALength seqLength=0 ) {
- vector<UInt> cumulativeLengths;
- cumulativeLengths.resize(sequences.size());
- int i;
- if (sequences.size() == 0) {
- return;
- }
- DNALength cumulativeLength;
- cumulativeLengths[0] = sequences[0].length;
- cumulativeLength = cumulativeLengths[0];
- for (i = 1; i < sequences.size(); i++) {
- cumulativeLengths[i] = cumulativeLength = cumulativeLengths[i-1] + sequences[i].length;
- }
- bool validPosFound = false;
- int iter = 0;
- int max_iter = 100000;
- while (validPosFound == false and iter < max_iter) {
- ++iter;
- if (seqLength > cumulativeLength) {
- validPosFound = false;
- iter = max_iter;
- break;
- }
- DNALength pos = RandomUnsignedInt(cumulativeLength - seqLength);
- // Make sure this sequence fits
- for (seqIndex = 0; seqIndex < sequences.size(); seqIndex++) {
- if (cumulativeLengths[seqIndex] > pos) break;
- }
- if (cumulativeLengths[seqIndex] - pos < seqLength) {
- continue;
- }
- UInt pi;
- if (seqIndex == 0) {
- seqPos = pos;
- }
- else {
- seqPos = pos - cumulativeLengths[seqIndex-1];
- }
- bool seqContainsN = false;
- for (pi = seqPos; pi < seqPos + seqLength; pi++) {
- if (toupper(sequences[seqIndex].seq[pi]) == 'N') {
- seqContainsN = true;
- break;
- }
- }
- if (seqContainsN) {
- continue;
- }
- else {
- validPosFound = true;
- }
- }
- if (iter == max_iter) {
- cout << "ERROR! Unable to generate a random seq/pos pair!, maybe length " << seqLength << endl
- << " is too high, or there are too many N's in the references." << endl;
- exit(1);
- }
-}
-
-
-#endif
diff --git a/libcpp/pbdata/metagenome/SequenceIndexDatabase.hpp b/libcpp/pbdata/metagenome/SequenceIndexDatabase.hpp
deleted file mode 100644
index 7a43cba..0000000
--- a/libcpp/pbdata/metagenome/SequenceIndexDatabase.hpp
+++ /dev/null
@@ -1,96 +0,0 @@
-#ifndef _BLASR_SEQUENCE_INDEX_DATABASE_HPP_
-#define _BLASR_SEQUENCE_INDEX_DATABASE_HPP_
-
-#include <fstream>
-#include <iostream>
-#include <vector>
-#include <assert.h>
-#include <stdlib.h>
-#include <sstream>
-#include <cstring>
-#include <algorithm>
-#include "Types.h"
-#include "DNASequence.hpp"
-#include "StringUtils.hpp"
-
-
-#define SEQUENCE_INDEX_DATABASE_MAGIC 1233211233
-
-template<typename TSeq>
-class SequenceIndexDatabase {
-public:
- std::vector<DNALength> growableSeqStartPos;
- std::vector<std::string> growableName;
-
- DNALength *seqStartPos;
- bool deleteSeqStartPos;
- char **names;
- bool deleteNames;
- int *nameLengths;
- bool deleteNameLengths;
- int nSeqPos;
- bool deleteStructures;
- //
- // This is stored after reading in the sequence.
- //
- std::vector<std::string> md5;
-
- SequenceIndexDatabase(int final=0);
- ~SequenceIndexDatabase();
-
- DNALength GetLengthOfSeq(int seqIndex);
-
- // Return index of a reference sequence with name "seqName".
- int GetIndexOfSeqName(std::string seqName);
-
- void GetName(int seqIndex, std::string &name);
-
- void MakeSAMSQString(std::string &sqString);
-
- DNALength ChromosomePositionToGenome(int chrom, DNALength chromPos);
-
- int SearchForIndex(DNALength pos);
-
- std::string GetSpaceDelimitedName(unsigned int index);
-
- int SearchForStartBoundary(DNALength pos);
-
- int SearchForEndBoundary(DNALength pos);
-
- DNALength SearchForStartAndEnd(DNALength pos, DNALength &start,
- DNALength &end);
-
- void WriteDatabase(ofstream &out);
-
- void ReadDatabase(ifstream &in);
-
- void SequenceTitleLinesToNames();
-
- VectorIndex AddSequence(TSeq &sequence);
-
- void Finalize();
-
- void FreeDatabase();
-};
-
-
-template< typename TSeq >
-class SeqBoundaryFtr {
-public:
- SequenceIndexDatabase<TSeq> *seqDB;
-
- SeqBoundaryFtr(SequenceIndexDatabase<TSeq> *_seqDB);
-
- int GetIndex(DNALength pos);
-
- int GetStartPos(int index);
-
- DNALength operator()(DNALength pos);
-
- // This is misuse of a functor, but easier interface coding for now.
- DNALength Length(DNALength pos);
-};
-
-#include "metagenome/SequenceIndexDatabaseImpl.hpp"
-
-#endif
diff --git a/libcpp/pbdata/metagenome/SequenceIndexDatabaseImpl.hpp b/libcpp/pbdata/metagenome/SequenceIndexDatabaseImpl.hpp
deleted file mode 100644
index e26f61e..0000000
--- a/libcpp/pbdata/metagenome/SequenceIndexDatabaseImpl.hpp
+++ /dev/null
@@ -1,347 +0,0 @@
-#ifndef _BLASR_SEQUENCE_INDEX_DATABASE_IMPL_HPP_
-#define _BLASR_SEQUENCE_INDEX_DATABASE_IMPL_HPP_
-
-template<typename TSeq>
-SequenceIndexDatabase<TSeq>::
-SequenceIndexDatabase(int final) {
- nSeqPos = 0;
- if (!final) {
- growableSeqStartPos.push_back(0);
- }
- names = NULL; deleteNames = false;
- nameLengths = NULL; deleteNameLengths = false;
- seqStartPos = NULL; deleteSeqStartPos = false;
- deleteStructures = false;
-}
-
-template<typename TSeq>
-SequenceIndexDatabase<TSeq>::
-~SequenceIndexDatabase() {
- FreeDatabase();
-}
-
-template<typename TSeq>
-DNALength SequenceIndexDatabase<TSeq>::
-GetLengthOfSeq(int seqIndex) {
- assert(seqIndex < nSeqPos-1);
- return seqStartPos[seqIndex+1] - seqStartPos[seqIndex] - 1;
-}
-
-// Return index of a reference sequence with name "seqName".
-template<typename TSeq>
-int SequenceIndexDatabase<TSeq>::
-GetIndexOfSeqName(std::string seqName) {
- for(int i = 0; i < nSeqPos - 1; i++) {
- if (seqName == std::string(names[i])) {
- return i;
- }
- }
- return -1;
-}
-
-template<typename TSeq>
-void SequenceIndexDatabase<TSeq>::
-GetName(int seqIndex, std::string &name) {
- assert(seqIndex < nSeqPos-1);
- name = names[seqIndex];
-}
-
-template<typename TSeq>
-void SequenceIndexDatabase<TSeq>::
-MakeSAMSQString(std::string &sqString) {
- std::stringstream st;
- int i;
- for (i = 0; i < nSeqPos-1; i++) {
- st << "@SQ\tSN:" << names[i] << "\tLN:" << GetLengthOfSeq(i);
- if (md5.size() == nSeqPos-1) {
- st << "\tM5:" << md5[i];
- }
- st << endl;
- }
- sqString = st.str();
-}
-
-template<typename TSeq>
-DNALength SequenceIndexDatabase<TSeq>::
-ChromosomePositionToGenome(int chrom, DNALength chromPos) {
- assert(chrom < nSeqPos);
- return seqStartPos[chrom] + chromPos;
-
-}
-
-template<typename TSeq>
-int SequenceIndexDatabase<TSeq>::
-SearchForIndex(DNALength pos) {
- // The default behavior for the case
- // that there is just one genome.
- if (nSeqPos == 1) {
- return 0;
- }
-
- DNALength* seqPosIt = upper_bound(seqStartPos+1,
- seqStartPos + nSeqPos, pos);
-
- return seqPosIt - seqStartPos - 1;
-}
-
-template<typename TSeq>
-std::string SequenceIndexDatabase<TSeq>::
-GetSpaceDelimitedName(unsigned int index) {
- int pos;
- assert(index < nSeqPos);
- std::string name;
- for (pos = 0; pos < nameLengths[index]; pos++) {
- if (names[index][pos] == ' ' or
- names[index][pos] == '\t' or
- names[index][pos] == '\0') {
- break;
- }
- }
- name.assign(names[index], pos);
- return name;
-}
-
-template<typename TSeq>
-int SequenceIndexDatabase<TSeq>::
-SearchForStartBoundary(DNALength pos) {
-
- int index = SearchForIndex(pos);
- if (index != -1) {
- return seqStartPos[index];
- }
- else {
- return -1;
- }
-}
-
-
-template<typename TSeq>
-int SequenceIndexDatabase<TSeq>::
-SearchForEndBoundary(DNALength pos) {
-
- int index = SearchForIndex(pos);
- if (index != -1) {
- return seqStartPos[index + 1];
- }
- else {
- return -1;
- }
-}
-
-
-template<typename TSeq>
-DNALength SequenceIndexDatabase<TSeq>::
-SearchForStartAndEnd(DNALength pos, DNALength &start, DNALength &end) {
- int index = SearchForIndex(pos);
- if (index != -1) {
- start = seqStartPos[index];
- end = seqStartPos[index+1];
- return 1;
- }
- else {
- start = end = -1;
- return 0;
- }
-}
-
-
-template<typename TSeq>
-void SequenceIndexDatabase<TSeq>::
-WriteDatabase(std::ofstream &out) {
- int mn = SEQUENCE_INDEX_DATABASE_MAGIC;
- out.write((char*) &mn, sizeof(int));
- out.write((char*) &nSeqPos, sizeof(int));
- out.write((char*) seqStartPos, sizeof(DNALength) * nSeqPos);
- int nSeq = nSeqPos - 1;
- out.write((char*) nameLengths, sizeof(int) * nSeq);
- int i;
- //
- // The number of sequences is 1 less than the number of positions
- // since the positions include 0 as a boundary.
- //
- char nullchar = '\0';
- for (i = 0; i < nSeq; i++) {
- //
- // nameLengths has space for the null char, so the length of the
- // name = nameLengths[i]-1. Write a nullchar to disk so that it
- // may be read in later with no work.
- //
- out.write((char*) names[i], sizeof(char) * (nameLengths[i]-1));
- out.write((char*) &nullchar, sizeof(char));
- }
-}
-
-
-template<typename TSeq>
-void SequenceIndexDatabase<TSeq>::
-ReadDatabase(std::ifstream &in) {
- int mn;
- // Make sure this is a read database, since the binary input
- // is not syntax checked.
- in.read((char*) &mn, sizeof(int));
- if (mn != SEQUENCE_INDEX_DATABASE_MAGIC) {
- std::cout << "ERROR: Sequence index database is corrupt!" << std::endl;
- exit(1);
- }
-
- //
- // Read in the boundaries of each sequence.
- //
- deleteStructures = true;
-
- in.read((char*) &nSeqPos, sizeof(int));
- assert(seqStartPos == NULL);
- seqStartPos = new DNALength[nSeqPos];
- deleteSeqStartPos = true;
- in.read((char*) seqStartPos, sizeof(DNALength) * nSeqPos);
- int nSeq = nSeqPos - 1;
-
- // Get the lengths of the strings to read.
- assert(nameLengths == NULL);
- nameLengths = new int[nSeq];
- deleteNameLengths = true;
- in.read((char*)nameLengths, sizeof(int) * nSeq);
-
- // Get the titles of the sequences.
- assert(names == NULL); // Otherwise need to delete names;
- names = new char*[nSeq];
- deleteNames = true;
- char *namePtr;
- int i;
- for (i = 0; i < nSeq; i++) {
- namePtr = new char[nameLengths[i]];
- if (nameLengths[i] > 0) {
- in.read(namePtr, nameLengths[i]);
- }
- namePtr[nameLengths[i]-1] = '\0';
- names[i] = namePtr;
- }
-}
-
-template<typename TSeq>
-void SequenceIndexDatabase<TSeq>::
-SequenceTitleLinesToNames() {
- int seqIndex;
- std::vector<std::string> tmpNameArray;
- for (seqIndex = 0; seqIndex < nSeqPos-1; seqIndex++) {
- std::string tmpName;
- AssignUntilFirstSpace(names[seqIndex], nameLengths[seqIndex], tmpName);
- if (names[seqIndex]) {delete[] names[seqIndex];}
- names[seqIndex] = new char[tmpName.size()+1];
- strcpy(names[seqIndex], tmpName.c_str());
- names[seqIndex][tmpName.size()] = '\0';
- nameLengths[seqIndex] = tmpName.size();
- tmpNameArray.push_back(tmpName);
- }
- // Make sure that reference names are unique.
- sort(tmpNameArray.begin(), tmpNameArray.end());
- for(int j = 0; j < tmpNameArray.size() - 1; j++) {
- if (tmpNameArray[j] == tmpNameArray[j+1]) {
- std::cout << "Error, reference with name \""
- << tmpNameArray[j]
- << "\" in the reference genome is not unique"
- << std::endl;
- exit(1);
- }
- }
-}
-
-template<typename TSeq>
-VectorIndex SequenceIndexDatabase<TSeq>::
-AddSequence(TSeq &sequence) {
- int endPos = growableSeqStartPos[growableSeqStartPos.size() - 1];
- int growableSize = growableSeqStartPos.size();
- growableSeqStartPos.push_back(endPos + sequence.length + 1);
- std::string fastaTitle;
- sequence.GetFASTATitle(fastaTitle);
- growableName.push_back(fastaTitle);
- return growableName.size();
-}
-
-template<typename TSeq>
-void SequenceIndexDatabase<TSeq>::
-Finalize() {
- deleteStructures = true;
- seqStartPos = &growableSeqStartPos[0];
- nSeqPos = growableSeqStartPos.size();
- int nSeq = nSeqPos - 1;
-
- assert(names==NULL);
- names = new char*[nSeq];
- deleteNames = true;
- unsigned int i;
- if (nameLengths) {delete [] nameLengths; nameLengths = NULL;}
- nameLengths = new int[nSeq];
- deleteNameLengths = true;
- for (i = 0; i < nSeq; i++) {
- names[i] = new char[growableName[i].size() + 1];
-
- memcpy((char*) names[i], (char*) growableName[i].c_str(),
- growableName[i].size());
-
- names[i][growableName[i].size()] = '\0';
- nameLengths[i] = growableName[i].size() + 1;
- }
-}
-
-
-template<typename TSeq>
-void SequenceIndexDatabase<TSeq>::
-FreeDatabase() {
- int i;
- if (deleteStructures == false) {
- return;
- }
- if (names != NULL and deleteNames) {
- int nSeq = nSeqPos - 1;
- for (i = 0; i < nSeq; i++ ){
- delete[] names[i];
- }
- delete[] names;
- names = NULL;
- }
- if (nameLengths != NULL and deleteNameLengths) {
- delete[] nameLengths;
- nameLengths = NULL;
- }
- if (seqStartPos != NULL and deleteSeqStartPos) {
- delete[] seqStartPos;
- seqStartPos = NULL;
- }
-}
-
-
-template< typename TSeq >
-SeqBoundaryFtr<TSeq>::
-SeqBoundaryFtr(SequenceIndexDatabase<TSeq> *_seqDB) {
- seqDB = _seqDB;
-}
-
-template< typename TSeq >
-int SeqBoundaryFtr<TSeq>::
-GetIndex(DNALength pos) {
- return seqDB->SearchForIndex(pos);
-}
-
-template< typename TSeq >
-int SeqBoundaryFtr<TSeq>::
-GetStartPos(int index) {
- assert(index < seqDB->nSeqPos);
- return seqDB->seqStartPos[index];
-}
-
-template< typename TSeq >
-DNALength SeqBoundaryFtr<TSeq>::
- operator()(DNALength pos) {
- return seqDB->SearchForStartBoundary(pos);
-}
-
-template< typename TSeq >
-DNALength SeqBoundaryFtr<TSeq>::
-Length(DNALength pos) {
- DNALength start, end;
- seqDB->SearchForStartAndEnd(pos, start, end);
- return end - start;
-}
-
-#endif
diff --git a/libcpp/pbdata/metagenome/TitleTable.cpp b/libcpp/pbdata/metagenome/TitleTable.cpp
deleted file mode 100644
index 078da23..0000000
--- a/libcpp/pbdata/metagenome/TitleTable.cpp
+++ /dev/null
@@ -1,109 +0,0 @@
-#include "TitleTable.hpp"
-
-TitleTable::TitleTable() {
- table = NULL;
- tableLength = 0;
-}
-
-TitleTable::~TitleTable() {
- Free();
-}
-
-void TitleTable::Copy(char **src, int nSrc) {
- Free(); //Free before copy
- table = new char*[nSrc];
- tableLength = nSrc;
- int i;
- for (i = 0; i < nSrc; i++ ){
- int lenStrI = strlen(src[i]);
- table[i] = new char[lenStrI+1];
- memcpy(table[i], src[i], lenStrI);
- table[i][lenStrI] = '\0';
- }
-}
-
-void TitleTable::Write(std::string &name) {
- std::ofstream out;
- CrucialOpen(name, out, std::ios::out);
- Write(out);
-}
-
-void TitleTable::Write(std::ofstream &out) {
- int i;
- for (i = 0; i < tableLength;i++) {
- out << table[i] << std::endl;
- }
-}
-
-void TitleTable::Read(std::string &inFileName) {
- std::ifstream in;
- CrucialOpen(inFileName, in, std::ios::in);
- Read(in);
-}
-
-void TitleTable::CopyFromVector(std::vector<std::string> &titles) {
- Free(); //Free before copy.
- tableLength = titles.size();
- table = new char*[tableLength];
- int i;
- for (i = 0; i < tableLength; i++) {
- table[i] = new char[titles[i].size() + 1];
- memcpy(table[i], titles[i].c_str(), titles[i].size());
- table[i][titles[i].size()] = '\0';
- }
-}
-
-void TitleTable::Read(std::ifstream &in) {
- std::vector<std::string> titles;
- while(in) {
- char title[1024];
- in.getline(title, 1024);
- if (not std::string(title).empty())
- titles.push_back(title);
- }
- if (titles.size() > 0) {
- CopyFromVector(titles);
- }
- else {
- tableLength = 0;
- table = NULL;
- }
-}
-
-void TitleTable::Free() {
- int i;
- for (i = 0; i < tableLength; i++) {
- if (table[i]) {delete[] table[i]; table[i] = NULL;}
- }
- if (table) {delete[] table;};
- table = NULL;
- tableLength = 0;
-}
-
-bool TitleTable::Lookup(std::string title, int &index) {
- int i;
- for (i = 0; i < tableLength; i++) {
- if (table[i] == title) {
- index = i;
- return true;
- }
- }
- return false;
-}
-
-void TitleTable::ResetTableToIntegers(char **table,
- int *tableLengths, int nTable) {
-
- int i;
- for (i = 0; i < nTable; i++ ) {
- delete[] table[i];
- std::stringstream namestrm;
- namestrm << i;
- std::string name;
- name = namestrm.str();
- table[i] = new char[name.size()+1];
- memcpy( table[i], name.c_str(), name.size());
- table[i][name.size()] = '\0';
- tableLengths[i] = (int) name.size() + 1;
- }
-}
diff --git a/libcpp/pbdata/metagenome/TitleTable.hpp b/libcpp/pbdata/metagenome/TitleTable.hpp
deleted file mode 100644
index 14b23a7..0000000
--- a/libcpp/pbdata/metagenome/TitleTable.hpp
+++ /dev/null
@@ -1,39 +0,0 @@
-#ifndef _BLASR_TITLE_TABLE_HPP_
-#define _BLASR_TITLE_TABLE_HPP_
-
-#include <sstream>
-#include <iostream>
-#include <fstream>
-#include <string>
-#include <string.h>
-#include <vector>
-#include "utils.hpp"
-
-class TitleTable {
-public:
- char **table;
- int tableLength;
- TitleTable();
- ~TitleTable();
-
- void Copy(char **src, int nSrc);
-
- void Write(std::string &name);
-
- void Write(std::ofstream &out);
-
- void Read(std::string &inFileName);
-
- void CopyFromVector(std::vector<std::string> &titles);
-
- void Read(std::ifstream &in);
-
- void Free();
-
- bool Lookup(std::string title, int &index) ;
-
- static void ResetTableToIntegers(char **table,
- int *tableLengths, int nTable);
-};
-
-#endif
diff --git a/libcpp/pbdata/mklibconfig.sh b/libcpp/pbdata/mklibconfig.sh
deleted file mode 100755
index e438893..0000000
--- a/libcpp/pbdata/mklibconfig.sh
+++ /dev/null
@@ -1,32 +0,0 @@
-#!/bin/bash
-fn=$1
-use_pbbam=$2
-# If $fn exists, then guarantee its contents are correct.
-# If not, write the proper contents.
-# This way, 'make' will not have to re-create a perfectly fine file,
-# which would cause all other targets to be remade.
-
-use0=$(cat <<'EOF'
-EOF
-)
-
-use1=$(cat <<'EOF'
-#define USE_PBBAM
-EOF
-)
-
-if [ "${use_pbbam}" == "YES" ]; then
- wanted=$use1
-else
- wanted=$use0
-fi
-
-if [ -r $fn ]; then
- actual=$(<"${fn}")
-else
- actual="EMPTY"
-fi
-
-if [ "$wanted" != "$actual" ]; then
- echo "$wanted" > $fn
-fi
diff --git a/libcpp/pbdata/old.Makefile b/libcpp/pbdata/old.Makefile
deleted file mode 100644
index a01c77e..0000000
--- a/libcpp/pbdata/old.Makefile
+++ /dev/null
@@ -1,87 +0,0 @@
-# Let common.mk know that that the third party checks should be ignored
-COMMON_NO_THIRD_PARTY_REQD := true
-
-include ../common.mk
-
-CXXOPTS := -std=c++11 -pedantic -MMD -MP
-INCLUDES := -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment
-
-# To enable building a shared library, invoke as "make SHARED_LIB=true ..."
-ifneq ($(SHARED_LIB),)
- # Generating shared library
- CXX_SHAREDFLAGS := -fPIC
- LD_SHAREDFLAGS := -shared -fPIC
- TARGET_LIB := libpbdata.so
- # Developers should set these to appropriate defaults (other systems
- # will override these on the command line):
- PBBAM_LIB := ../../../staging/PostPrimary/pbbam/_output/install-build/lib/libpbbam.so
- HTSLIB_LIB := ../../../staging/PostPrimary/htslib/_output/install-build/lib/libhts.so
-else
- # Generating static library
- CXX_SHAREDFLAGS :=
- TARGET_LIB := libpbdata.a
- LD_SHAREDFLAGS :=
- HTSLIB_LIB :=
- PBBAM_LIB :=
-endif
-
-DEP_LIBS := $(HTSLIB_LIB) $(PBBAM_LIB)
-
-PBBAM_INCLUDE := $(PBBAM)/include
-HTSLIB_INCLUDE ?= $(HTSLIB)
-
-sources := $(wildcard *.cpp) \
- $(wildcard matrix/*.cpp) \
- $(wildcard reads/*.cpp) \
- $(wildcard metagenome/*.cpp) \
- $(wildcard qvs/*.cpp) \
- $(wildcard saf/*.cpp) \
- $(wildcard utils/*.cpp) \
- $(wildcard loadpulses/*.cpp) \
- $(wildcard alignment/*.cpp) \
- $(wildcard amos/*.cpp) \
- $(wildcard sam/*.cpp)
-
-objects := $(sources:.cpp=.o)
-shared_objects := $(sources:.cpp=.shared.o)
-dependencies := $(objects:.o=.d) $(shared_objects:.o=.d)
-
-all : CXXFLAGS ?= -O3
-
-debug : CXXFLAGS ?= -g -ggdb -fno-inline
-
-profile : CXXFLAGS ?= -Os -pg
-
-g: CXXFLAGS = -g -ggdb -fno-inline -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer
-
-all debug profile g: mklibconfig $(TARGET_LIB)
-
-ifeq ($(origin nopbbam), undefined)
- INCLUDES += -I$(PBBAM_INCLUDE) -I$(HTSLIB_INCLUDE) -I$(BOOST_INCLUDE)
- USE_PBBAM:=YES
-else
- USE_PBBAM:=NO
-endif
-
-mklibconfig:
- ./mklibconfig.sh libconfig.h ${USE_PBBAM}
-
-libpbdata.a: $(objects)
- $(AR_pp) $(ARFLAGS) $@ $^
-
-libpbdata.so: $(shared_objects) $(DEP_LIBS)
- $(CXX_pp) $(LD_SHAREDFLAGS) -o $@ $^
-
-%.o: %.cpp
- $(CXX_pp) $(CXXOPTS) $(CXXFLAGS) $(INCLUDES) -MF"$(@:%.o=%.d)" -MT"$(@:%.o=%.o) $(@:%.o=%.d)" -c $< -o $@
-
-%.shared.o: %.cpp
- $(CXX_pp) $(CXX_SHAREDFLAGS) $(CXXOPTS) $(CXXFLAGS) $(INCLUDES) -MF"$(@:%.o=%.d)" -MT"$(@:%.o=%.o) $(@:%.o=%.d)" -c $< -o $@
-
-# .INTERMEDIATE: $(objects)
-
-clean:
- @rm -f libpbdata.a libpbdata.so
- @rm -f $(objects) $(shared_objects) $(dependencies)
-
--include $(dependencies)
diff --git a/libcpp/pbdata/qvs/QualityTransform.cpp b/libcpp/pbdata/qvs/QualityTransform.cpp
deleted file mode 100644
index 45ec117..0000000
--- a/libcpp/pbdata/qvs/QualityTransform.cpp
+++ /dev/null
@@ -1,23 +0,0 @@
-#include <cassert>
-#include "QualityTransform.hpp"
-/*
-* Base lookup table class for quality values.
-*/
-
-float QualityToProb::operator()(int index) {
- assert(index >= 0);
- assert(index <= MAX_QUALITY_VALUE);
- return prob[index];
-}
-
-/*
-* Create a lookup table for transforming from quality value
-* to p-value using Patrick Marks' low-end expand qv = -100*log10(p/(1-p))
-*/
-void LowEndExpandQualityTransform::operator()(QualityToProb &qt) {
- int i;
- for (i = MIN_QUALITY_VALUE; i <= MAX_QUALITY_VALUE; i++) {
- float v = pow(10,i/-100.0);
- qt.prob[i] = 1 - v/(1+v);
- }
-}
diff --git a/libcpp/pbdata/qvs/QualityTransform.hpp b/libcpp/pbdata/qvs/QualityTransform.hpp
deleted file mode 100644
index 73c8f27..0000000
--- a/libcpp/pbdata/qvs/QualityTransform.hpp
+++ /dev/null
@@ -1,26 +0,0 @@
-#ifndef _BLASR_QVS_QUALITY_TRANSFORM_HPP_
-#define _BLASR_QVS_QUALITY_TRANSFORM_HPP_
-
-#include <math.h>
-#include "QualityValue.hpp"
-
-/*
- * Base lookup table class for quality values.
- */
-class QualityToProb {
-public:
- float prob[MAX_QUALITY_VALUE - MIN_QUALITY_VALUE + 1];
- float operator()(int index);
-};
-
-/*
- * Create a lookup table for transforming from quality value
- * to p-value using Patrick Marks' low-end expand qv = -100*log10(p/(1-p))
- */
-class LowEndExpandQualityTransform {
-public:
- void operator()(QualityToProb &qt);
-};
-
-
-#endif // _BLASR_QVS_QUALITY_TRANSFORM_HPP_
diff --git a/libcpp/pbdata/qvs/QualityValue.cpp b/libcpp/pbdata/qvs/QualityValue.cpp
deleted file mode 100644
index e9f1775..0000000
--- a/libcpp/pbdata/qvs/QualityValue.cpp
+++ /dev/null
@@ -1,65 +0,0 @@
-#include <math.h>
-#include "defs.h"
-#include <assert.h>
-#include "QualityValue.hpp"
-
-QualityValue
-ProbabilityToQualityValue(QualityProbability pErr, QVScale qvScale) {
- if (qvScale == POverOneMinusP) {
- QualityProbability pe;
- QualityProbability maxReportedErrorProb = 0.499;
- pe = MIN(pErr, maxReportedErrorProb);
- return MIN(255, -100*log10(pe/(1-pe)));
- }
- else if (qvScale == PHRED) {
- return -10*log10(pErr);
- } else {
- assert(false);
- }
-}
-
-QualityValue
-PacBioQVToPhred(QualityValue pbQV) {
- // yanked from Aaron's code.
- return (unsigned char) floor( 10.0 * log10( 1.0 + pow(10.0, pbQV / 100.0) ) + 0.5 );
-}
-
-QualityValue
-ToPhred(QualityValue qv, QVScale qvScale) {
- //
- // Nothing to do when the quality is already in phred.
- //
- if (qvScale == PHRED) {
- return qv;
- }
- else {
- return PacBioQVToPhred(qv);
- }
-}
-
-
-QualityProbability
-QualityValueToProbability(QualityValue qv, QVScale qvScale) {
- if (qvScale == POverOneMinusP) {
- QualityProbability pp;
- pp = pow(10, qv/-100.0);
- return pp/(1+pp);
- }
- else if (qvScale == PHRED) {
- return pow(10, qv/-10.0);
- } else {
- assert(false);
- }
-}
-
-QVScale DetermineQVScaleFromChangeListID(ChangeListID &cl) {
- ChangeListID phredCL;
- phredCL.intVer.resize(3);
- phredCL.intVer[0] = 1; phredCL.intVer[1] = 2; phredCL.intVer[2] = 2;
- if (cl.LessThan(phredCL)) {
- return POverOneMinusP;
- }
- else {
- return PHRED;
- }
-}
diff --git a/libcpp/pbdata/qvs/QualityValue.hpp b/libcpp/pbdata/qvs/QualityValue.hpp
deleted file mode 100644
index 9def8e5..0000000
--- a/libcpp/pbdata/qvs/QualityValue.hpp
+++ /dev/null
@@ -1,31 +0,0 @@
-#ifndef _BLASR_QUALITY_VALUE_HPP_
-#define _BLASR_QUALITY_VALUE_HPP_
-
-#include <stdint.h>
-#include "ChangeListID.hpp"
-
-typedef unsigned char QualityValue;
-typedef float QualityProbability;
-
-#define MIN_QUALITY_VALUE 0
-#define MAX_QUALITY_VALUE 255
-
-#ifndef _QVScale_
-#define _QVScale_
-enum QVScale {POverOneMinusP, // popularized by Illumina
- PHRED};
-#endif
-
-QualityValue ProbabilityToQualityValue(
- QualityProbability pErr, QVScale qvScale=POverOneMinusP);
-
-QualityValue PacBioQVToPhred(QualityValue pbQV);
-
-QualityValue ToPhred(QualityValue qv, QVScale qvScale=POverOneMinusP);
-
-QualityProbability QualityValueToProbability(QualityValue qv,
- QVScale qvScale=POverOneMinusP);
-
-QVScale DetermineQVScaleFromChangeListID(ChangeListID &cl);
-
-#endif // _BLASR_QUALITY_VALUE_HPP_
diff --git a/libcpp/pbdata/qvs/QualityValueVector.hpp b/libcpp/pbdata/qvs/QualityValueVector.hpp
deleted file mode 100644
index 8e3ae5d..0000000
--- a/libcpp/pbdata/qvs/QualityValueVector.hpp
+++ /dev/null
@@ -1,47 +0,0 @@
-#ifndef _BLASR_QUALITY_VALUE_VECTOR_HPP_
-#define _BLASR_QUALITY_VALUE_VECTOR_HPP_
-#include <stdint.h>
-#include <cstddef>
-#include <ostream>
-#include <cstring>
-#include "Types.h"
-#include "utils.hpp"
-#include "QualityValue.hpp"
-
-template<typename T_QV>
-class QualityValueVector {
-public:
- T_QV *data;
- QVScale qvScale;
-
- T_QV &operator[](unsigned int pos) const;
-
- QualityValueVector();
-
- QualityProbability ToProbability(unsigned int pos);
-
- T_QV ToPhred(unsigned int pos);
-
- void Copy(const QualityValueVector<T_QV> &rhs, const DNALength length);
-
- void Copy(const std::string & rhs);
-
- void Free();
-
- void Allocate(unsigned int length);
-
- bool Empty() const;
-
- void ShallowCopy(const QualityValueVector<T_QV> &ref, int pos, const DNALength & length);
-
- std::string ToString(void);
-
- // Returns data length
- DNALength Length(void);
-
-private:
- DNALength _length;
-};
-
-#include "QualityValueVectorImpl.hpp"
-#endif // _BLASR_QUALITY_VALUE_VECTOR_HPP_
diff --git a/libcpp/pbdata/qvs/QualityValueVectorImpl.hpp b/libcpp/pbdata/qvs/QualityValueVectorImpl.hpp
deleted file mode 100644
index 7d33266..0000000
--- a/libcpp/pbdata/qvs/QualityValueVectorImpl.hpp
+++ /dev/null
@@ -1,99 +0,0 @@
-#ifndef _BLASR_QUALITY_VALUE_VECTOR_IMPL_HPP_
-#define _BLASR_QUALITY_VALUE_VECTOR_IMPL_HPP_
-#include "NucConversion.hpp"
-
-template<typename T_QV>
-T_QV& QualityValueVector<T_QV>::operator[](unsigned int pos) const {
- return data[pos];
-}
-
-template<typename T_QV>
-QualityValueVector<T_QV>::QualityValueVector() {
- data = NULL;
- // Default to phred.
- qvScale = PHRED;
- _length = 0;
-}
-
-template<typename T_QV>
-QualityProbability QualityValueVector<T_QV>::ToProbability(unsigned int pos) {
- return QualityValueToProbability(data[pos], qvScale);
-}
-
-template<typename T_QV>
-T_QV QualityValueVector<T_QV>::ToPhred(unsigned int pos) {
- if (qvScale == PHRED) {
- return data[pos];
- }
- else {
- return PacBioQVToPhred(data[pos]);
- }
-}
-
-template<typename T_QV>
-void QualityValueVector<T_QV>::Copy(const QualityValueVector<T_QV> &rhs, const DNALength length) {
- Free();
- if (rhs.Empty()) {
- return;
- }
- Allocate(length);
- std::memcpy(data, rhs.data, length * sizeof(T_QV));
-}
-
-template<typename T_QV>
-void QualityValueVector<T_QV>::Copy(const std::string & rhs) {
-// Char to QualityValue
- Free();
- if (rhs.size() == 0) return;
- Allocate(static_cast<DNALength>(rhs.size()));
- for (size_t i = 0; i < rhs.size(); i++) {
- data[i] = static_cast<T_QV>(rhs[i] - FASTQ_CHAR_TO_QUALITY);
- }
-}
-
-template<typename T_QV>
-void QualityValueVector<T_QV>::Free() {
- if (data != NULL) {
- delete[] data;
- data = NULL;
- }
- _length = 0;
-}
-
-template<typename T_QV>
-void QualityValueVector<T_QV>::Allocate(unsigned int length) {
- data = ProtectedNew<T_QV>(length);
- _length = static_cast<DNALength>(length);
-}
-
-template<typename T_QV>
-bool QualityValueVector<T_QV>::Empty() const {
- return data == NULL;
-}
-
-template<typename T_QV>
-void QualityValueVector<T_QV>::ShallowCopy(const QualityValueVector<T_QV> &ref, int pos, const DNALength & length) {
- data = &ref.data[pos];
- qvScale = ref.qvScale;
- _length = static_cast<DNALength>(length);
-}
-
-template<typename T_QV>
-std::string QualityValueVector<T_QV>::ToString(void) {
- if (data == NULL) { return "";}
-
- std::string str(static_cast<size_t>(_length), '0');
- for (DNALength i = 0; i < _length; i++) {
- str[i] = static_cast<char>(data[i] + FASTQ_CHAR_TO_QUALITY);
- }
- return str;
-}
-
-template<typename T_QV>
-DNALength QualityValueVector<T_QV>::Length(void) {
- return _length;
-}
-
-template class QualityValueVector<QualityValue>;
-
-#endif
diff --git a/libcpp/pbdata/reads/BaseFile.cpp b/libcpp/pbdata/reads/BaseFile.cpp
deleted file mode 100644
index bf4c56a..0000000
--- a/libcpp/pbdata/reads/BaseFile.cpp
+++ /dev/null
@@ -1,82 +0,0 @@
-#include <algorithm>
-#include "BaseFile.hpp"
-
-bool CompareHoleXY::operator()(const HoleXY &lhs, const HoleXY &rhs) const {
- if (lhs.xy[0] == rhs.xy[0]) {
- return lhs.xy[1] < rhs.xy[1];
- }
- else {
- return lhs.xy[0] < rhs.xy[0];
- }
-}
-
-bool BaseFile::LookupReadIndexByXY(uint16_t x, uint16_t y, int &index) {
- int16_t xy[2];
- xy[0] = x; xy[1] = y;
- std::vector<HoleXY>::iterator holeIt;
- holeIt = lower_bound(holeXY.begin(), holeXY.end(), xy);
- if ((*holeIt).xy[0] == xy[0] and (*holeIt).xy[1] == xy[1]) {
- index = holeIt - holeXY.begin();
- return true;
- }
- else {
- return false;
- }
-}
-
-
-void BaseFile::CopyReadAt(uint32_t readIndex, SMRTSequence &read) {
- assert(holeNumbers.size() > readIndex);
- read.zmwData.holeNumber = holeNumbers[readIndex];
- if (holeXY.size() > 0) {
- assert(holeXY.size() > readIndex);
- read.zmwData.x = holeXY[readIndex].xy[0];
- read.zmwData.y = holeXY[readIndex].xy[1];
- }
-
- int startPos = readStartPositions[readIndex];
- int readLength = readLengths[readIndex];
- read.length = readLength;
- read.Allocate(readLength);
- if (baseCalls.size() > 0) {
- assert(baseCalls.size() >= readLength + startPos);
- CopyArray(baseCalls, startPos, readLength, read.seq);
- }
- if (qualityValues.size() > 0) {
- assert(qualityValues.size() >= readLength + startPos);
- CopyArray(qualityValues, startPos, readLength, read.qual.data);
- }
- if (basWidthInFrames.size() > 0) {
- assert(basWidthInFrames.size() >= readLength + startPos);
- CopyArray(basWidthInFrames, startPos, readLength, read.widthInFrames);
- }
- if (deletionQV.size() > 0) {
- assert(deletionQV.size() >= readLength + startPos);
- CopyArray(deletionQV, startPos, readLength, read.deletionQV.data);
- }
- if (deletionTag.size() > 0) {
- assert(deletionTag.size() >= readLength + startPos);
- CopyArray(deletionTag, startPos, readLength, read.deletionTag);
- }
- if (insertionQV.size() > 0) {
- assert(insertionQV.size() >= readLength + startPos);
- CopyArray(insertionQV, startPos, readLength, read.insertionQV.data);
- }
- if (substitutionQV.size() > 0) {
- assert(substitutionQV.size() >= readLength + startPos);
- CopyArray(substitutionQV, startPos, readLength, read.substitutionQV.data);
- }
- if (mergeQV.size() > 0) {
- assert(mergeQV.size() >= readLength + startPos);
- CopyArray(mergeQV, startPos, readLength, read.mergeQV.data);
- }
- if (substitutionTag.size() > 0) {
- assert(substitutionTag.size() >= readLength + startPos);
- CopyArray(substitutionTag, startPos, readLength, read.substitutionTag);
- }
- if (preBaseFrames.size() > 0) {
- assert(preBaseFrames.size() >= readLength + startPos);
- CopyArray(preBaseFrames, startPos, readLength, read.preBaseFrames);
- }
-
-}
diff --git a/libcpp/pbdata/reads/BaseFile.hpp b/libcpp/pbdata/reads/BaseFile.hpp
deleted file mode 100644
index d3b6afb..0000000
--- a/libcpp/pbdata/reads/BaseFile.hpp
+++ /dev/null
@@ -1,49 +0,0 @@
-#ifndef _BLASR_BASE_FILE_HPP_
-#define _BLASR_BASE_FILE_HPP_
-
-#include <stdint.h>
-#include <vector>
-#include "Enumerations.h"
-#include "SMRTSequence.hpp"
-
-#include "HoleXY.hpp"
-#include "PulseBaseCommon.hpp"
-#include "ScanData.hpp"
-
-class CompareHoleXY {
-public:
- bool operator()(const HoleXY &lhs, const HoleXY &rhs) const;
-};
-
-class BaseFile : public PulseBaseCommon {
-public:
- std::vector<unsigned char> baseCalls;
- std::vector<uint8_t> holeStatus;
- std::vector<HoleXY> holeXY;
- std::vector<uint16_t> basWidthInFrames;
- std::vector<uint16_t> preBaseFrames;
- std::vector<int> pulseIndex;
- std::vector<unsigned char> qualityValues;
- std::vector<unsigned char> deletionQV;
- std::vector<unsigned char> deletionTag;
- std::vector<unsigned char> insertionQV;
- std::vector<unsigned char> substitutionQV;
- std::vector<unsigned char> substitutionTag;
- std::vector<unsigned char> mergeQV;
- std::vector<int> readLengths;
- std::vector<int> readStartPositions;
- int nReads;
- int nBases;
-
- bool LookupReadIndexByXY(uint16_t x, uint16_t y, int &index);
-
- void CopyReadAt(uint32_t readIndex, SMRTSequence &read);
-
- template<typename T>
- void CopyArray(std::vector<T> &fullArray, int pos, int length, T*dest);
-
-};
-
-#include "BaseFileImpl.hpp"
-
-#endif // _BLASR_BASE_FILE_HPP_
diff --git a/libcpp/pbdata/reads/BaseFileImpl.hpp b/libcpp/pbdata/reads/BaseFileImpl.hpp
deleted file mode 100644
index b09c927..0000000
--- a/libcpp/pbdata/reads/BaseFileImpl.hpp
+++ /dev/null
@@ -1,11 +0,0 @@
-#ifndef _BLASR_BASE_FILE_IMPL_HPP_
-#define _BLASR_BASE_FILE_IMPL_HPP_
-
-#include "BaseFile.hpp"
-
-template<typename T>
-void BaseFile::CopyArray(std::vector<T> &fullArray, int pos, int length, T*dest) {
- memcpy(dest, &fullArray[pos], sizeof(T) * length);
-}
-
-#endif
diff --git a/libcpp/pbdata/reads/HoleXY.cpp b/libcpp/pbdata/reads/HoleXY.cpp
deleted file mode 100644
index ff9d1f7..0000000
--- a/libcpp/pbdata/reads/HoleXY.cpp
+++ /dev/null
@@ -1,14 +0,0 @@
-#include "HoleXY.hpp"
-
-bool HoleXY::operator<(const HoleXY &rhs) const {
- return *this < rhs.xy;
-}
-
-bool HoleXY::operator<(const int16_t xyP[2]) const {
- if (xy[0] == xyP[0]) {
- return xy[1] < xyP[1];
- }
- else {
- return xy[0] < xyP[0];
- }
-}
diff --git a/libcpp/pbdata/reads/HoleXY.hpp b/libcpp/pbdata/reads/HoleXY.hpp
deleted file mode 100644
index 5386c72..0000000
--- a/libcpp/pbdata/reads/HoleXY.hpp
+++ /dev/null
@@ -1,14 +0,0 @@
-#ifndef _BLASR_HOLE_XY_HPP_
-#define _BLASR_HOLE_XY_HPP_
-
-#include <stdlib.h>
-
-class HoleXY {
-public:
- int16_t xy[2];
- bool operator<(const HoleXY &rhs) const;
-
- bool operator<(const int16_t xyP[2]) const;
-};
-
-#endif // _BLASR_HOLE_XY_HPP_
diff --git a/libcpp/pbdata/reads/PulseBaseCommon.cpp b/libcpp/pbdata/reads/PulseBaseCommon.cpp
deleted file mode 100644
index 437a0fb..0000000
--- a/libcpp/pbdata/reads/PulseBaseCommon.cpp
+++ /dev/null
@@ -1,37 +0,0 @@
-#include <vector>
-#include <algorithm>
-#include "PulseBaseCommon.hpp"
-
-float PulseBaseCommon::GetFrameRate() {
- return scanData.frameRate;
-}
-
-unsigned int PulseBaseCommon::GetNumFrames() {
- return scanData.numFrames;
-}
-
-std::string PulseBaseCommon::GetMovieName() {
- return scanData.movieName;
-}
-
-std::map<char, int> PulseBaseCommon::GetBaseMap() {
- return scanData.baseMap;
-}
-
-bool PulseBaseCommon::LookupReadIndexByHoleNumber(uint32_t holeNumber, int &readIndex) {
- std::vector<uint32_t>::iterator holeIt;
- if (holeNumbers.size() == 0) {
- return false;
- }
- holeIt = lower_bound(holeNumbers.begin(), holeNumbers.end(), holeNumber);
- if (holeIt == holeNumbers.end()) {
- return false;
- }
- if (*holeIt == holeNumber) {
- readIndex = holeIt - holeNumbers.begin();
- return true;
- }
- else {
- return false;
- }
-}
diff --git a/libcpp/pbdata/reads/PulseBaseCommon.hpp b/libcpp/pbdata/reads/PulseBaseCommon.hpp
deleted file mode 100644
index e8b86fc..0000000
--- a/libcpp/pbdata/reads/PulseBaseCommon.hpp
+++ /dev/null
@@ -1,26 +0,0 @@
-#ifndef DATASTRUCTURES_READS_PULSE_BASE_COMMON_H_
-#define DATASTRUCTURES_READS_PULSE_BASE_COMMON_H_
-
-//
-// This includes values that both pulse and base files must have.
-//
-#include <stdint.h>
-#include "ScanData.hpp"
-
-class PulseBaseCommon {
-public:
- ScanData scanData;
- std::vector<uint32_t> holeNumbers;
-
- float GetFrameRate();
-
- unsigned int GetNumFrames();
-
- std::string GetMovieName();
-
- std::map<char, int> GetBaseMap();
-
- bool LookupReadIndexByHoleNumber(uint32_t holeNumber, int &readIndex);
-};
-
-#endif
diff --git a/libcpp/pbdata/reads/PulseFile.cpp b/libcpp/pbdata/reads/PulseFile.cpp
deleted file mode 100644
index 7d2db0b..0000000
--- a/libcpp/pbdata/reads/PulseFile.cpp
+++ /dev/null
@@ -1,76 +0,0 @@
-#include "PulseFile.hpp"
-
-
-void PulseFile::CopySignal(HalfWord *signalData, // either a vector or matrix
- int signalNDims,
- int pulseStartPos, // 0 if baseToPulseIndex maps to abs position
- int *baseToPulseIndex,
- Nucleotide *readSeq,
- int readLength,
- HalfWord *readData) {
- // if baseToPulseIndex maps bases to absolute pulse postions
- // pulseStartPos must be 0;
- // otherwise, pulseStartPos is pulseStartPositions[holeIndex]
-
- std::map<char, int> baseMap = GetBaseMap();
- int i;
- if (signalNDims == 1) {
- for (i = 0; i < readLength; i++) {
- readData[i] = signalData[pulseStartPos + baseToPulseIndex[i] ];
- }
- }
- else {
- for (i = 0; i < readLength; i++) {
- readData[i] = signalData[baseToPulseIndex[i]*4 + baseMap[readSeq[i]]];
- }
- }
-}
-
-void PulseFile::CopyReadAt(uint32_t plsReadIndex, int *baseToPulseIndex, SMRTSequence &read) {
- int pulseStartPos = pulseStartPositions[plsReadIndex];
- bool allocResult;
- if (midSignal.size() > 0) {
- assert(midSignal.size() > pulseStartPos);
- allocResult = Realloc(read.midSignal, read.length);
- CopySignal(&midSignal[0],
- midSignalNDims,
- pulseStartPos,
- baseToPulseIndex,
- read.seq, read.length,
- read.midSignal);
- }
-
- if (maxSignal.size() > 0) {
- assert(maxSignal.size() > pulseStartPos);
- Realloc(read.maxSignal, read.length);
- CopySignal(&maxSignal[0],
- maxSignalNDims,
- pulseStartPos,
- baseToPulseIndex,
- read.seq, read.length,
- read.maxSignal);
- }
-
- if (meanSignal.size() > 0) {
- assert(meanSignal.size() > pulseStartPos);
- Realloc(read.meanSignal, read.length);
- CopySignal(&meanSignal[0],
- meanSignalNDims,
- pulseStartPos,
- baseToPulseIndex,
- read.seq, read.length,
- read.meanSignal);
- }
- if (plsWidthInFrames.size() > 0) {
- Realloc(read.widthInFrames, read.length);
- StoreField(plsWidthInFrames, baseToPulseIndex, read.widthInFrames, read.length);
- }
- if (classifierQV.size() > 0) {
- Realloc(read.classifierQV, read.length);
- StoreField(classifierQV, baseToPulseIndex, read.classifierQV, read.length);
- }
- if (startFrame.size() > 0) {
- Realloc(read.startFrame, read.length);
- StoreField(startFrame, baseToPulseIndex, read.startFrame, read.length);
- }
-}
diff --git a/libcpp/pbdata/reads/PulseFile.hpp b/libcpp/pbdata/reads/PulseFile.hpp
deleted file mode 100644
index d5c4d89..0000000
--- a/libcpp/pbdata/reads/PulseFile.hpp
+++ /dev/null
@@ -1,53 +0,0 @@
-#ifndef _BLASR_PULSE_FILE_HPP_
-#define _BLASR_PULSE_FILE_HPP_
-
-#include <map>
-#include <vector>
-#include "Types.h"
-#include "Enumerations.h"
-#include "DNASequence.hpp"
-#include "SMRTSequence.hpp"
-#include "PulseBaseCommon.hpp"
-#include "ScanData.hpp"
-
-class PulseFile : public PulseBaseCommon {
- public:
- unsigned int numFrames;
- PlatformId platformId;
- std::vector<unsigned int> startFrame;
- std::vector<uint16_t> plsWidthInFrames;
- int midSignalNDims, maxSignalNDims, meanSignalNDims;
- std::vector<uint16_t> midSignal;
- std::vector<uint16_t> maxSignal;
- std::vector<uint16_t> meanSignal;
- std::vector<int> numEvent;
- std::vector<int> pulseStartPositions;
- std::vector<float> classifierQV;
-
- PulseFile(){numFrames = 0; platformId = Springfield;}
-
- void CopySignal(HalfWord *signalData, // either a vector or matrix
- int signalNDims,
- int pulseStartPos, // 0 if baseToPulseIndex maps to abs position
- int *baseToPulseIndex,
- Nucleotide *readSeq,
- int readLength,
- HalfWord *readData);
-
- // plsReadIndex: index of this hole number in /PulseCalls/ZMW/HoleNumber.
- // baseToPulseIndex: index from pulse to base from the beginning of the read.
- // read: a SMRTSequence.
- void CopyReadAt(uint32_t plsReadIndex, int *baseToPulseIndex, SMRTSequence &read);
-
- template<typename T_FieldType>
- void StoreField(std::vector<T_FieldType> &source, int *basToPlsIndex, T_FieldType *dest, int destLength);
-
- template <typename T>
- bool Realloc(T *&ptr, int length);
-
-
-};
-
-#include "PulseFileImpl.hpp"
-
-#endif
diff --git a/libcpp/pbdata/reads/PulseFileImpl.hpp b/libcpp/pbdata/reads/PulseFileImpl.hpp
deleted file mode 100644
index 7fc1f8d..0000000
--- a/libcpp/pbdata/reads/PulseFileImpl.hpp
+++ /dev/null
@@ -1,21 +0,0 @@
-#ifndef _BLASR_PULSE_FILE_IMPL_HPP_
-#define _BLASR_PULSE_FILE_IMPL_HPP_
-
-template<typename T_FieldType>
- void PulseFile::StoreField(std::vector<T_FieldType> &source, int *basToPlsIndex, T_FieldType *dest, int destLength) {
- int i;
- for (i = 0 ; i < destLength; i++) {
- dest[i] = source[basToPlsIndex[i]];
- }
-}
-
-template <typename T>
- bool PulseFile::Realloc(T *&ptr, int length) {
- if (ptr != NULL) {
- delete[] ptr;
- }
- ptr = new T[length];
- return ptr != NULL;
-}
-
-#endif
diff --git a/libcpp/pbdata/reads/ReadInterval.hpp b/libcpp/pbdata/reads/ReadInterval.hpp
deleted file mode 100644
index c21838f..0000000
--- a/libcpp/pbdata/reads/ReadInterval.hpp
+++ /dev/null
@@ -1,18 +0,0 @@
-#ifndef _BLASR_READ_INTERVAL_HPP_
-#define _BLASR_READ_INTERVAL_HPP_
-
-class ReadInterval {
-public:
- int start;
- int end;
- int score;
- ReadInterval(int s, int e, int sc=0) : start(s), end(e), score(sc) {};
- ReadInterval& operator=(const ReadInterval &rhs) {
- start = rhs.start;
- end = rhs.end;
- score = rhs.score;
- return *this;
- }
-};
-
-#endif
diff --git a/libcpp/pbdata/reads/ReadType.cpp b/libcpp/pbdata/reads/ReadType.cpp
deleted file mode 100644
index 7e15ce0..0000000
--- a/libcpp/pbdata/reads/ReadType.cpp
+++ /dev/null
@@ -1,43 +0,0 @@
-#include "ReadType.hpp"
-
-ReadType::ReadTypeEnum ReadType::ParseReadType(std::string &readTypeString) {
- if (readTypeString == "Standard") {
- return ReadType::Standard;
- }
- else if (readTypeString == "CCS") {
- return ReadType::CCS;
- }
- else if (readTypeString == "RCCS") {
- return ReadType::RCCS;
- }
- else if (readTypeString == "POLYMERASE") {
- return ReadType::POLYMERASE;
- }
- else if (readTypeString == "HQREGION") {
- return ReadType::HQREGION;
- }
- else if (readTypeString == "SUBREAD") {
- return ReadType::SUBREAD;
- }
- else if (readTypeString == "SCRAP") {
- return ReadType::SCRAP;
- }
- else if (readTypeString == "UNKNOWN") {
- return ReadType::UNKNOWN;
- }
- else {
- return ReadType::NoReadType;
- }
-}
-
-std::string ReadType::ToString(const ReadType::ReadTypeEnum & readType) {
- if (readType == ReadType::Standard) return "Standard";
- if (readType == ReadType::CCS) return "CCS";
- if (readType == ReadType::RCCS) return "RCCS";
- if (readType == ReadType::HQREGION) return "HQREGION";
- if (readType == ReadType::POLYMERASE) return "POLYMERASE";
- if (readType == ReadType::SUBREAD) return "SUBREAD";
- if (readType == ReadType::SCRAP) return "SCRAP";
- if (readType == ReadType::UNKNOWN) return "UNKNOWN";
- return "NoReadType";
-}
diff --git a/libcpp/pbdata/reads/ReadType.hpp b/libcpp/pbdata/reads/ReadType.hpp
deleted file mode 100644
index 02279da..0000000
--- a/libcpp/pbdata/reads/ReadType.hpp
+++ /dev/null
@@ -1,18 +0,0 @@
-#ifndef _BLASR_READ_TYPE_HPP
-#define _BLASR_READ_TYPE_HPP
-
-#include <string>
-
-class ReadType {
- public:
- enum ReadTypeEnum {NoReadType=0, Standard=1, CCS=2, RCCS=3, POLYMERASE=4, HQREGION=5, SUBREAD=6, SCRAP=7, UNKNOWN=8};
- static ReadTypeEnum ParseReadType(std::string &readTypeString);
- static std::string ToString(const ReadType::ReadTypeEnum & readType);
-};
-
-
-//The READTYPE values encountered in secondary analysis will be limited to SUBREAD and CCS.
-//POLYMERASE, HQREGION, SCRAP, and UNKNOWN will only be encountered in intermediate steps before
-//secondary analysis.
-//NoReadType, Standard and RCCS were used in CMP.H5 deprecated.
-#endif
diff --git a/libcpp/pbdata/reads/RegionTable.cpp b/libcpp/pbdata/reads/RegionTable.cpp
deleted file mode 100644
index 54582a7..0000000
--- a/libcpp/pbdata/reads/RegionTable.cpp
+++ /dev/null
@@ -1,159 +0,0 @@
-#include <algorithm>
-#include "RegionTable.hpp"
-
-using namespace std;
-
-RegionAnnotation& RegionAnnotation::operator=(const RegionAnnotation &rhs) {
- memcpy(row, rhs.row, sizeof(int)*NCOLS);
- return *this;
-}
-int RegionAnnotation::GetHoleNumber() {
- return row[HoleNumber];
-}
-
-void RegionAnnotation::SetHoleNumber(int holeNumber) {
- row[HoleNumber] = holeNumber;
-}
-
-int RegionAnnotation::GetType() const {
- return row[RegionType];
-}
-
-void RegionAnnotation::SetType(int regionType) {
- row[RegionType] = regionType;
-}
-
-int RegionAnnotation::GetStart() {
- return row[RegionStart];
-}
-
-void RegionAnnotation::SetStart(int start) {
- row[RegionStart] = start;
-}
-int RegionAnnotation::GetEnd() {
- return row[RegionEnd];
-}
-
-void RegionAnnotation::SetEnd(int end) {
- row[RegionEnd] = end;
-}
-
-int RegionAnnotation::GetScore() {
- return row[RegionScore];
-}
-
-void RegionAnnotation::SetScore(int score) {
- row[RegionScore] = score;
-}
-
-int RegionTable::LookupRegionsByHoleNumber(int holeNumber, int &low, int &high) const {
- std::vector<RegionAnnotation>::const_iterator lowIt, highIt;
- lowIt = std::lower_bound(table.begin(), table.end(), holeNumber);
- highIt = std::lower_bound(table.begin(), table.end(), holeNumber+1);
- low = lowIt - table.begin();
- high = highIt - table.begin();
- return high-low;
-}
-
-//
-// Define a bunch of accessor functions.
-//
-
-//
-// Different region tables have different ways of encoding regions.
-// This maps from the way they are encoded in the rgn table to a
-// standard encoding.
-//
-
-RegionType RegionTable::GetType(int regionIndex) const {
- assert(regionIndex < table.size());
- assert(regionIndex >= 0);
- return (RegionType) regionTypeEnums[table[regionIndex].GetType()];
-}
-
-int RegionTable::GetStart(int regionIndex) {
- assert(regionIndex < table.size());
- assert(regionIndex >= 0);
- return table[regionIndex].GetStart();
-}
-
-void RegionTable::SetStart(int regionIndex, int start) {
- assert(regionIndex < table.size());
- assert(regionIndex >= 0);
- table[regionIndex].SetStart(start);
-}
-
-int RegionTable::GetEnd(int regionIndex) {
- assert(regionIndex < table.size());
- assert(regionIndex >= 0);
- return table[regionIndex].GetEnd();
-}
-
-void RegionTable::SetEnd(int regionIndex, int end) {
- assert(regionIndex < table.size());
- assert(regionIndex >= 0);
- table[regionIndex].SetEnd(end);
-}
-
-int RegionTable::GetHoleNumber(int regionIndex) {
- assert(regionIndex < table.size());
- assert(regionIndex >= 0);
- return table[regionIndex].GetHoleNumber();
-}
-
-void RegionTable::SetHoleNumber(int regionIndex, int holeNumber) {
- assert(regionIndex < table.size());
- assert(regionIndex >= 0);
- table[regionIndex].SetHoleNumber(holeNumber);
-}
-
-int RegionTable::GetScore(int regionIndex) {
- assert(regionIndex < table.size());
- assert(regionIndex >= 0);
- return table[regionIndex].row[RegionAnnotation::RegionScore];
-}
-
-void RegionTable::SetScore(int regionIndex, int score) {
- assert(regionIndex < table.size());
- assert(regionIndex >= 0);
- table[regionIndex].row[RegionAnnotation::RegionScore] = score;
-}
-
-void RegionTable::SortTableByHoleNumber() {
- std::stable_sort(table.begin(), table.end());
-}
-
-void RegionTable::Reset() {
- table.clear();
- columnNames.clear();
- regionTypes.clear();
- regionDescriptions.clear();
- regionSources.clear();
- regionTypeEnums.clear();
-}
-
-void RegionTable::CreateDefaultAttributes() {
- columnNames.clear();
- columnNames.push_back("HoleNumber");
- columnNames.push_back("Region type index");
- columnNames.push_back("Region start in bases");
- columnNames.push_back("Region end in bases");
- columnNames.push_back("Region score");
-
- regionTypes.push_back("Adapter");
- regionTypes.push_back("Insert");
- regionTypes.push_back("HQRegion");
-
- regionDescriptions.push_back("Adapter Hit");
- regionDescriptions.push_back("Insert Region");
- regionDescriptions.push_back("High Quality bases region. Score is 1000 * "
- "predicted accuracy, where predicted accuary is 0 to 1.0");
-
- regionSources.push_back("AdapterFinding");
- regionSources.push_back("AdapterFinding");
- regionSources.push_back("PulseToBase Region classifer");
-
- regionTypeEnums.push_back(Adapter);
- regionTypeEnums.push_back(Insert);
- regionTypeEnums.push_back(HQRegion);
-}
diff --git a/libcpp/pbdata/reads/RegionTable.hpp b/libcpp/pbdata/reads/RegionTable.hpp
deleted file mode 100644
index 497e625..0000000
--- a/libcpp/pbdata/reads/RegionTable.hpp
+++ /dev/null
@@ -1,95 +0,0 @@
-#ifndef _BLASR_REGION_TABLE_HPP_
-#define _BLASR_REGION_TABLE_HPP_
-
-#include <cassert>
-#include <cstring>
-#include <string>
-#include <vector>
-#include "Enumerations.h"
-
-class RegionAnnotation {
-public:
- typedef enum T_AnnotationRow {HoleNumber, RegionType, RegionStart,
- RegionEnd, RegionScore} AnnotationRow;
- static const int NCOLS=5;
- int row[NCOLS];
-
- inline
- bool operator<(const RegionAnnotation &rhs) const
- { return row[HoleNumber] < rhs.row[HoleNumber]; }
-
- inline
- bool operator<(int holeNumber) const
- { return row[HoleNumber] < holeNumber; }
-
- RegionAnnotation& operator=(const RegionAnnotation &rhs);
-
- int GetHoleNumber();
-
- void SetHoleNumber(int holeNumber);
-
- int GetType() const;
-
- void SetType(int regionType);
-
- int GetStart();
-
- void SetStart(int start);
-
- int GetEnd();
-
- void SetEnd(int end);
-
- int GetScore();
-
- void SetScore(int score);
-};
-
-class RegionTable {
-public:
- std::vector<RegionAnnotation> table;
- std::vector<std::string> columnNames;
- std::vector<std::string> regionTypes;
- std::vector<std::string> regionDescriptions;
- std::vector<std::string> regionSources;
- std::vector<RegionType> regionTypeEnums;
-
- int LookupRegionsByHoleNumber(int holeNumber, int &low, int &high) const;
-
- //
- // Define a bunch of accessor functions.
- //
-
- //
- // Different region tables have different ways of encoding regions.
- // This maps from the way they are encoded in the rgn table to a
- // standard encoding.
- //
-
- RegionType GetType(int regionIndex) const;
-
- int GetStart(int regionIndex);
-
- void SetStart(int regionIndex, int start);
-
- int GetEnd(int regionIndex);
-
- void SetEnd(int regionIndex, int end);
-
- int GetHoleNumber(int regionIndex);
-
- void SetHoleNumber(int regionIndex, int holeNumber);
-
- int GetScore(int regionIndex);
-
- void SetScore(int regionIndex, int score);
-
- void SortTableByHoleNumber();
-
- void Reset();
-
- void CreateDefaultAttributes();
-};
-
-
-#endif // _BLASR_REGION_TABLE_HPP_
diff --git a/libcpp/pbdata/reads/ScanData.cpp b/libcpp/pbdata/reads/ScanData.cpp
deleted file mode 100644
index 3114376..0000000
--- a/libcpp/pbdata/reads/ScanData.cpp
+++ /dev/null
@@ -1,12 +0,0 @@
-#include "ScanData.hpp"
-
-ScanData::ScanData() {
- platformId = NoPlatform;
- frameRate = numFrames = 0;
- movieName = runCode = whenStarted = "";
- baseMap.clear();
-}
-
-std::string ScanData::GetMovieName() {
- return movieName;
-}
diff --git a/libcpp/pbdata/reads/ScanData.hpp b/libcpp/pbdata/reads/ScanData.hpp
deleted file mode 100644
index 8cf07ea..0000000
--- a/libcpp/pbdata/reads/ScanData.hpp
+++ /dev/null
@@ -1,20 +0,0 @@
-#ifndef DATASTRUCTURES_READS_SCAN_DATA_H_
-#define DATASTRUCTURES_READS_SCAN_DATA_H_
-
-#include <string>
-#include <map>
-#include "Enumerations.h"
-
-class ScanData {
-public:
- PlatformId platformId;
- float frameRate;
- unsigned int numFrames;
- std::string movieName, runCode;
- std::string whenStarted;
- std::map<char, int> baseMap;
- ScanData();
- std::string GetMovieName();
-};
-
-#endif
diff --git a/libcpp/pbdata/reads/ZMWGroupEntry.cpp b/libcpp/pbdata/reads/ZMWGroupEntry.cpp
deleted file mode 100644
index 64381ed..0000000
--- a/libcpp/pbdata/reads/ZMWGroupEntry.cpp
+++ /dev/null
@@ -1,8 +0,0 @@
-#include <stdint.h>
-#include "Types.h"
-#include "ZMWGroupEntry.hpp"
-ZMWGroupEntry::ZMWGroupEntry() {
- holeNumber = x = y = 0;
- numEvents = 0;
- holeStatus = '0';
-}
diff --git a/libcpp/pbdata/reads/ZMWGroupEntry.hpp b/libcpp/pbdata/reads/ZMWGroupEntry.hpp
deleted file mode 100644
index 05234df..0000000
--- a/libcpp/pbdata/reads/ZMWGroupEntry.hpp
+++ /dev/null
@@ -1,17 +0,0 @@
-#ifndef _BLASR_ZMW_GROUP_ENTRY_HPP_
-#define _BLASR_ZMW_GROUP_ENTRY_HPP_
-
-#include "Types.h"
-
-class ZMWGroupEntry {
- public:
- UInt holeNumber;
- UInt x;
- UInt y;
- int numEvents;
- unsigned char holeStatus;
- ZMWGroupEntry();
-};
-
-
-#endif // _BLASR_ZMW_GROUP_ENTRY_HPP_
diff --git a/libcpp/pbdata/saf/AlnGroup.cpp b/libcpp/pbdata/saf/AlnGroup.cpp
deleted file mode 100644
index 9f680cb..0000000
--- a/libcpp/pbdata/saf/AlnGroup.cpp
+++ /dev/null
@@ -1,12 +0,0 @@
-#include "AlnGroup.hpp"
-
-int AlnGroup::FindPath(int idKey, std::string &val) {
- int i;
- for (i = 0; i < id.size(); i++) {
- if (idKey == id[i]) {
- val = path[i];
- return 1;
- }
- }
- return 0;
-}
diff --git a/libcpp/pbdata/saf/AlnGroup.hpp b/libcpp/pbdata/saf/AlnGroup.hpp
deleted file mode 100644
index e941b19..0000000
--- a/libcpp/pbdata/saf/AlnGroup.hpp
+++ /dev/null
@@ -1,14 +0,0 @@
-#ifndef _BLASR_ALN_GROUP_HPP_
-#define _BLASR_ALN_GROUP_HPP_
-
-#include <vector>
-#include <string>
-
-class AlnGroup {
- public:
- std::vector<unsigned int> id;
- std::vector<std::string> path;
- int FindPath(int idKey, std::string &val);
-};
-
-#endif // _BLASR_ALN_GROUP_HPP_
diff --git a/libcpp/pbdata/saf/AlnInfo.hpp b/libcpp/pbdata/saf/AlnInfo.hpp
deleted file mode 100644
index 6d59ad2..0000000
--- a/libcpp/pbdata/saf/AlnInfo.hpp
+++ /dev/null
@@ -1,17 +0,0 @@
-#ifndef DATASTRUCTURES_SAF_ALN_INFO_H_
-#define DATASTRUCTURES_SAF_ALN_INFO_H_
-
-#include <cstdint>
-#include <vector>
-#include "Types.h"
-#include "alignment/CmpAlignment.hpp"
-
-class AlnInfo {
-public:
- std::vector<CmpAlignment> alignments;
- UInt nAlignments;
- uint64_t lastRow;
-};
-
-
-#endif
diff --git a/libcpp/pbdata/saf/MovieInfo.cpp b/libcpp/pbdata/saf/MovieInfo.cpp
deleted file mode 100644
index f76a386..0000000
--- a/libcpp/pbdata/saf/MovieInfo.cpp
+++ /dev/null
@@ -1,13 +0,0 @@
-#include "MovieInfo.hpp"
-
-
-int MovieInfo::FindMovie(int idKey, string &nameVal) {
- int i;
- for (i = 0; i < id.size(); i++) {
- if (id[i] == idKey) {
- nameVal = name[i];
- return 1;
- }
- }
- return 0;
-}
diff --git a/libcpp/pbdata/saf/MovieInfo.hpp b/libcpp/pbdata/saf/MovieInfo.hpp
deleted file mode 100644
index c92f819..0000000
--- a/libcpp/pbdata/saf/MovieInfo.hpp
+++ /dev/null
@@ -1,19 +0,0 @@
-#ifndef DATASTRUCTURES_SAF_HDF_MOVIE_INFO_H_
-#define DATASTRUCTURES_SAF_HDF_MOVIE_INFO_H_
-
-#include "Types.h"
-#include <string>
-#include <vector>
-
-using namespace std;
-
-class MovieInfo {
- public:
- vector<string> name;
- vector<UInt> run;
- vector<UInt> experiment;
- vector<UInt> id;
- int FindMovie(int idKey, string &nameVal);
-};
-
-#endif
diff --git a/libcpp/pbdata/saf/RefGroup.cpp b/libcpp/pbdata/saf/RefGroup.cpp
deleted file mode 100644
index fcd9bbf..0000000
--- a/libcpp/pbdata/saf/RefGroup.cpp
+++ /dev/null
@@ -1,25 +0,0 @@
-#include "RefGroup.hpp"
-
-
-bool RefGroup::IdToIndex(int idKey, int &idIndex) {
- int i;
- for (i = 0; i < refInfoId.size(); i++) {
- if (refInfoId[i] == idKey) {
- idIndex = i; return true;
- }
- }
- return false;
-}
-
-
-int RefGroup::FindPath(int idKey, string &pathVal, string &groupNameVal) {
- int i;
- for (i = 0; i < id.size(); i++) {
- if (id[i] == idKey) {
- pathVal = path[i];
- groupNameVal = refGroupName[i];
- return 1;
- }
- }
- return 0;
-}
diff --git a/libcpp/pbdata/saf/RefGroup.hpp b/libcpp/pbdata/saf/RefGroup.hpp
deleted file mode 100644
index 7c3b012..0000000
--- a/libcpp/pbdata/saf/RefGroup.hpp
+++ /dev/null
@@ -1,21 +0,0 @@
-#ifndef _BLASR_REF_GROUP_HPP_
-#define _BLASR_REF_GROUP_HPP_
-
-#include <string>
-#include <vector>
-
-#include <stdint.h>
-
-using namespace std;
-class RefGroup {
- public:
- vector<uint32_t> id;
- vector<string> path;
- vector<string> refGroupName;
- vector<uint32_t> refInfoId;
-
- bool IdToIndex(int idKey, int &idIndex);
- int FindPath(int idKey, string &pathVal, string &groupNameVal);
-};
-
-#endif
diff --git a/libcpp/pbdata/saf/RefInfo.cpp b/libcpp/pbdata/saf/RefInfo.cpp
deleted file mode 100644
index 48259a7..0000000
--- a/libcpp/pbdata/saf/RefInfo.cpp
+++ /dev/null
@@ -1,20 +0,0 @@
-#include "RefInfo.hpp"
-
-OneRefInfo::OneRefInfo() {
- fullName = md5 = "";
- id = length = 0;
-}
-
-bool RefInfo::RefIdToIndex(uint32_t qid, int &index) {
-/*
- * Translate from external id to position in array.
- */
- int i;
- for (i = 0; i < id.size(); i++) {
- if (id[i] == qid) {
- index = i;
- return true;
- }
- }
- return false;
-}
diff --git a/libcpp/pbdata/saf/RefInfo.hpp b/libcpp/pbdata/saf/RefInfo.hpp
deleted file mode 100644
index 39cda75..0000000
--- a/libcpp/pbdata/saf/RefInfo.hpp
+++ /dev/null
@@ -1,26 +0,0 @@
-#ifndef _BLASR_REF_INFO_HPP_
-#define _BLASR_REF_INFO_HPP_
-
-#include <string>
-#include <vector>
-#include <stdint.h>
-
-class OneRefInfo {
- public:
- std::string fullName;
- unsigned int id;
- unsigned int length;
- std::string md5;
- OneRefInfo();
-};
-
-
-class RefInfo {
- public:
- std::vector<std::string> fullName;
- std::vector<uint32_t> id;
- std::vector<uint32_t> length;
- std::vector<std::string> md5;
- bool RefIdToIndex(uint32_t qid, int &index);
-};
-#endif
diff --git a/libcpp/pbdata/sam/AlignmentSet.hpp b/libcpp/pbdata/sam/AlignmentSet.hpp
deleted file mode 100644
index 6e8bc49..0000000
--- a/libcpp/pbdata/sam/AlignmentSet.hpp
+++ /dev/null
@@ -1,31 +0,0 @@
-#ifndef _BLASR_SAM_ALIGNMENT_SET_HPP_
-#define _BLASR_SAM_ALIGNMENT_SET_HPP_
-
-#include <map>
-#include <string>
-#include <vector>
-
-#include "FASTASequence.hpp"
-#include "sam/ReadGroup.hpp"
-#include "sam/ReferenceSequence.hpp"
-#include "sam/SAMAlignment.hpp"
-#include "sam/SAMHeader.hpp"
-
-template<typename T_ReferenceSequence=SAMReferenceSequence, typename T_ReadGroup=SAMReadGroup, typename T_Alignment=SAMAlignment>
-class AlignmentSet {
- public:
- SAMHeader header;
- std::vector<T_ReferenceSequence> references;
- std::vector<T_ReadGroup> readGroups;
- std::vector<T_Alignment> alignments;
-
- //
- // Rearrange references such that they are placed in the same order
- // as fastaReferences
- //
- void RearrangeReferences(std::vector<FASTASequence> & fastaReferences);
-};
-
-#include "AlignmentSetImpl.hpp"
-
-#endif
diff --git a/libcpp/pbdata/sam/AlignmentSetImpl.hpp b/libcpp/pbdata/sam/AlignmentSetImpl.hpp
deleted file mode 100644
index ddd0e5d..0000000
--- a/libcpp/pbdata/sam/AlignmentSetImpl.hpp
+++ /dev/null
@@ -1,31 +0,0 @@
-#include "AlignmentSet.hpp"
-
-template<typename T_ReferenceSequence, typename T_ReadGroup, typename T_Alignment>
-void AlignmentSet<T_ReferenceSequence, T_ReadGroup, T_Alignment>::RearrangeReferences(std::vector<FASTASequence> &fastaReferences) {
- int i = 0;
- std::map<std::string, int> fastaRefToIndex;
- std::map<std::string, int>::iterator it;
- for (i = 0; i<fastaReferences.size(); i++) {
- it = fastaRefToIndex.find(fastaReferences[i].GetName());
- if (it != fastaRefToIndex.end()) {
- std::cout<<"Error, reference with name \""<<fastaReferences[i].GetName()
- <<"\" in the reference genome is not unique"<<std::endl;
- exit(1);
- }
- fastaRefToIndex[fastaReferences[i].GetName()] = i;
- }
- std::vector<T_ReferenceSequence> newreferences;
- for (i = 0; i < references.size(); i++) {
- newreferences.push_back(T_ReferenceSequence());
- }
- for (i = 0; i < references.size(); i++) {
- it = fastaRefToIndex.find(references[i].sequenceName);
- if (it == fastaRefToIndex.end()) {
- std::cout<<"Error, can not find reference name "<<references[i].sequenceName
- <<" in the reference genome."<<std::endl;
- exit(1);
- }
- newreferences[(*it).second] = references[i];
- }
- references = newreferences;
-}
diff --git a/libcpp/pbdata/sam/CigarString.h b/libcpp/pbdata/sam/CigarString.h
deleted file mode 100644
index 979e125..0000000
--- a/libcpp/pbdata/sam/CigarString.h
+++ /dev/null
@@ -1,23 +0,0 @@
-#ifndef _BLASR_SAM_CIGAR_STRING_HPP_
-#define _BLASR_SAM_CIGAR_STRING_HPP_
-
-#include <string>
-#include <sstream>
-
-class CigarString : public std::string {
-public:
- void Vectorize(std::vector<int> &lengths, std::vector<char> &operations) {
- std::stringstream strm;
- strm.str(*this);
- while (strm) {
- int l;
- char o;
- if ((strm >> l >> o)) {
- lengths.push_back(l);
- operations.push_back(o);
- }
- }
- }
-};
-
-#endif
diff --git a/libcpp/pbdata/sam/ReadGroup.cpp b/libcpp/pbdata/sam/ReadGroup.cpp
deleted file mode 100644
index 161e2c3..0000000
--- a/libcpp/pbdata/sam/ReadGroup.cpp
+++ /dev/null
@@ -1,51 +0,0 @@
-#include "ReadGroup.hpp"
-
-void SAMReadGroup::StoreValues(std::vector<SAMKeywordValuePair> &kvPairs,
- int lineNumber) {
- int i;
- bool idIsStored = false;
- for (i = 0; i < kvPairs.size(); i++ ){
- if (kvPairs[i].key == "ID") {
- id = kvPairs[i].value;
- idIsStored = true;
- }
- }
- if (idIsStored == false) {
- std::cout << "ReadGroup missing id at " << lineNumber << std::endl;
- exit(1);
- }
-}
-
-void SAMFullReadGroup::StoreValues(vector<SAMKeywordValuePair> &kvPairs,
- int lineNumber) {
- SAMReadGroup::StoreValues(kvPairs, lineNumber);
- std::string kwPair;
- std::string key, valueStr;
- int i;
- for (i = 0; i < kvPairs.size(); i++) {
- if (kvPairs[i].key == "CN") {
- centerName = kvPairs[i].value;
- }
- else if (kvPairs[i].key == "DS") {
- description = kvPairs[i].value;
- }
- else if (kvPairs[i].key == "DT") {
- date = kvPairs[i].value;
- }
- else if (kvPairs[i].key == "FO") {
- flowOrder = kvPairs[i].value;
- }
- else if (kvPairs[i].key == "LB") {
- library = kvPairs[i].value;
- }
- else if (kvPairs[i].key == "PG") {
- processingProgram = kvPairs[i].value;
- }
- else if (kvPairs[i].key == "PI") {
- StoreValue(kvPairs[i].value, insertSize);
- }
- else if (kvPairs[i].key == "SM") {
- sample = kvPairs[i].value;
- }
- }
-}
diff --git a/libcpp/pbdata/sam/ReadGroup.hpp b/libcpp/pbdata/sam/ReadGroup.hpp
deleted file mode 100644
index 24d6941..0000000
--- a/libcpp/pbdata/sam/ReadGroup.hpp
+++ /dev/null
@@ -1,40 +0,0 @@
-#ifndef _BLASR_SAM_READ_GROUP_HPP_
-#define _BLASR_SAM_READ_GROUP_HPP_
-
-#include <string>
-
-/*
- * Minimal components of read group. Define only required items. Use
- * if memory is scarce.
- */
-#include "SAMKeywordValuePair.hpp"
-
-class SAMReadGroup {
- public:
- std::string id;
- void StoreValues(std::vector<SAMKeywordValuePair> &kvPairs,
- int lineNumber = 0);
-};
-
-/*
- * Full read group. Use when all data are required.
- */
-class SAMFullReadGroup : public SAMReadGroup {
- public:
- std::string centerName;
- std::string description;
- std::string date;
- std::string flowOrder;
- std::string keySequence;
- std::string library;
- std::string processingProgram;
- int insertSize;
- std::string platform;
- std::string platformUnit;
- std::string sample;
-
- void StoreValues(std::vector<SAMKeywordValuePair> &kvPairs,
- int lineNumber = 0);
-};
-
-#endif
diff --git a/libcpp/pbdata/sam/ReferenceSequence.cpp b/libcpp/pbdata/sam/ReferenceSequence.cpp
deleted file mode 100644
index 6da44b9..0000000
--- a/libcpp/pbdata/sam/ReferenceSequence.cpp
+++ /dev/null
@@ -1,47 +0,0 @@
-#include "ReferenceSequence.hpp"
-
-const char* SAMReferenceSequence::SAMReferenceSequenceFieldNames[] = {"SN", "LN"};
-
-void SAMReferenceSequence::StoreValues(std::vector<SAMKeywordValuePair> &kvPairs, int lineNumber) {
- int i;
- std::vector<bool> usedFields;
- usedFields.resize(SQ_LN);
- std::fill(usedFields.begin(), usedFields.end(), false);
- for (i = 0; i < kvPairs.size(); i++) {
- if (kvPairs[i].key == "SN") {
- sequenceName = kvPairs[i].value;
- usedFields[SQ_SN] = true;
- }
- else if (kvPairs[i].key == "LN") {
- StoreValue(kvPairs[i].value, length);
- usedFields[SQ_SN] = true;
- }
- }
- for (i = 0; i < usedFields.size(); i++) {
- if (usedFields[i] == false) {
- std::cout << "SQ specifier missing " << SAMReferenceSequenceFieldNames[i] << std::endl;
- }
- }
-}
-
-const char* SAMFullReferenceSequence::SAMFullReferenceSequenceFieldNames[] = {"AS", "M5", "SP", "UR"};
-
-void SAMFullReferenceSequence::StoreValues(std::vector<SAMKeywordValuePair> &kvPairs,
- int lineNumber) {
- SAMReferenceSequence::StoreValues(kvPairs, lineNumber);
- int i;
- for (i = 0; i < kvPairs.size(); i++ ){
- if (kvPairs[i].key == "AS") {
- genomeAssembly = kvPairs[i].value;
- }
- else if (kvPairs[i].key == "M5") {
- md5 = kvPairs[i].value;
- }
- else if (kvPairs[i].key == "SP") {
- species = kvPairs[i].value;
- }
- else if (kvPairs[i].key == "UR") {
- uri = kvPairs[i].value;
- }
- }
-}
diff --git a/libcpp/pbdata/sam/ReferenceSequence.hpp b/libcpp/pbdata/sam/ReferenceSequence.hpp
deleted file mode 100644
index b5bb380..0000000
--- a/libcpp/pbdata/sam/ReferenceSequence.hpp
+++ /dev/null
@@ -1,72 +0,0 @@
-#ifndef _BLASR_SAM_REFERENCE_SEQUENCE_HPP_
-#define _BLASR_SAM_REFERENCE_SEQUENCE_HPP_
-
-#include <string>
-
-#include "sam/SAMKeywordValuePair.hpp"
-
-class SAMReferenceSequence {
- public:
- std::string sequenceName;
- unsigned int length;
- std::string GetSequenceName() {
- return sequenceName;
- }
- //
- // By definining accessor functions here but no data, we can
- // economize on the amount of space used for each element. This is
- // no big deal for references, but for pairwise alignments, it is
- // big.
- //
- std::string GetMD5() {
- return "";
- }
- unsigned int GetLength() {
- return length;
- }
- std::string GetGenomeAssembly() {
- return "";
- }
- std::string GetSpecies() {
- return "";
- }
- std::string GetURI() {
- return "";
- }
-
- enum SAMReferenceSequenceRequiredFields { SQ_SN, SQ_LN };
-
- static const char* SAMReferenceSequenceFieldNames[];
-
- void StoreValues(std::vector<SAMKeywordValuePair> &kvPairs,
- int lineNumber=0);
-};
-
-class SAMFullReferenceSequence : public SAMReferenceSequence {
- public:
- std::string md5;
- std::string species;
- std::string uri;
- std::string genomeAssembly;
- std::string GetMD5() {
- return md5;
- }
- std::string GetSpecies() {
- return species;
- }
- std::string GetURI() {
- return uri;
- }
- std::string GetGenomeAssembly() {
- return genomeAssembly;
- }
-
- enum FullReferenceSequenceRequiredFields { SQ_AS, SQ_M5, SQ_SP, SQ_UR };
-
- static const char* SAMFullReferenceSequenceFieldNames[];
-
- void StoreValues(std::vector<SAMKeywordValuePair> &kvPairs, int lineNumber=0);
-};
-
-
-#endif
diff --git a/libcpp/pbdata/sam/SAMAlignment.cpp b/libcpp/pbdata/sam/SAMAlignment.cpp
deleted file mode 100644
index e362d65..0000000
--- a/libcpp/pbdata/sam/SAMAlignment.cpp
+++ /dev/null
@@ -1,199 +0,0 @@
-#include "SAMAlignment.hpp"
-
-SAMAlignment::SAMAlignment() {
- score = xs = xe = as = xt = xq = nm = fi = xl = 0;
- rg = optTagStr = "";
-}
-
-void SAMAlignment::PrintSAMAlignment(std::ostream & out) {
- out << qName << "\t" << flag << "\t" << rName << "\t"
- << pos << "\t" << mapQV << "\t" << cigar << "\t"
- << rNext << "\t" << pNext << "\t" << tLen << "\t"
- << seq << "\t" << qual << "\t" << optTagStr
- << std::endl;
-}
-
-int SAMAlignment::FindPosOfNthChar(std::string str, int n, char c) {
- if (n < 1) {
- std::cout << "Nth should be a positive integer." << std::endl;
- exit(0);
- }
- int count = 1;
- int pos = str.find(c, 0);
- // pos is the position of the first character c;
- while(count < n and pos != std::string::npos) {
- pos = str.find(c, pos+1);
- count ++;
- }
- return pos;
-}
-
-std::string SAMAlignment::TrimStringEnd(std::string str) {
- std::string newStr = str;
- while(newStr[newStr.size()-1] == '\r' or
- newStr[newStr.size()-1] == '\n') {
- newStr.erase(newStr.size()-1, 1);
- }
- return newStr;
-}
-
-bool SAMAlignment::StoreValues(std::string &line, int lineNumber) {
- std::stringstream strm(line);
- std::vector<bool> usedFields;
- usedFields.resize(S_QUAL);
- fill(usedFields.begin(), usedFields.end(), false);
- std::string kvPair;
- int i;
- bool parseError = false;
- SAMAlignmentRequiredFields field;
- //
- // Define a temporary mapqv value that gets over a GMAP bug that prints a mapqv < 0.
- //
- int tmpMapQV;
- if (!(strm >> qName)) {
- parseError = true;
- field = S_QNAME;
- }
- else if (! (strm >> flag) ){
- parseError = true;
- field = S_FLAG;
- }
- else if (! (strm >> rName) ) {
- parseError = true;
- field = S_RNAME;
- }
- else if (! (strm >> pos) ) {
- parseError = true;
- field = S_POS;
- }
- else if (! (strm >> tmpMapQV)) {
- parseError = true; field = S_MAPQV;
- }
- else if (! (strm >> cigar)) {
- parseError = true; field = S_CIGAR;
- }
-
- else if (! (strm >> rNext)) {
- parseError = true; field = S_RNEXT;
- }
-
- else if (! (strm >> pNext)) {
- parseError = true; field = S_PNEXT;
- }
- else if (! (strm >> tLen)) {
- parseError = true; field = S_TLEN;
- }
- else if (! (strm >> seq)) {
- parseError = true; field = S_SEQ;
- }
- else if (! (strm >> qual)) {
- parseError = true; field = S_QUAL;
- }
-
- mapQV = (unsigned char) tmpMapQV;
-
- // Find posisition of the 11th tab.
- int optTagsStartPos = FindPosOfNthChar(strm.str(), 11, '\t');
- // Save all optional tags.
- if (optTagsStartPos != std::string::npos) {
- optTagStr = strm.str().substr(optTagsStartPos+1);
- optTagStr = TrimStringEnd(optTagStr);
- }
-
- //
- // If not aligned, stop trying to read in elements from the sam string.
- //
- if (rName == "*") {
- return true;
- }
-
- if (parseError) {
- std::cout << "Error parsing alignment line " << lineNumber << ". Missing or error in field " << SAMAlignmentRequiredFieldNames[field] << std::endl;
- exit(1);
- }
-
- //
- // Now parse optional data.
- //
- while (strm) {
- std::string kvName, kvType, kvValue;
- std::string typedKVPair;
- if (!(strm >> typedKVPair)) {
- break;
- }
- if (TypedKeywordValuePair::Separate(typedKVPair, kvName, kvType, kvValue)) {
- std::stringstream strm(kvValue);
- if (kvName == "RG") {
- rg = kvValue;
- }
- else if (kvName == "AS") {
- strm >> as;
- }
- else if (kvName == "XS") {
- strm >> xs;
- }
- else if (kvName == "XE") {
- strm >> xe;
- }
- else if (kvName == "XL") {
- strm >> xl;
- }
- else if (kvName == "XT") {
- strm >> xt;
- }
- else if (kvName == "NM") {
- strm >> nm;
- }
- else if (kvName == "FI") {
- strm >> fi;
- }
- else if (kvName == "XQ") {
- strm >> xq;
- } // Add quality values, including QualityValue?,
- // InsertionQV, DeletionQV, SubstitutionQV,
- // MergeQV and SubstitutionTag and DeletionTag
- else if (kvName == "iq") {
- strm >> iq;
- }
- else if (kvName == "dq") {
- strm >> dq;
- }
- else if (kvName == "sq") {
- strm >> sq;
- }
- else if (kvName == "mq") {
- strm >> mq;
- }
- else if (kvName == "st") {
- strm >> st;
- }
- else if (kvName == "dt") {
- strm >> dt;
- }
- }
- else {
- std::cout << "ERROR. Could not parse typed keyword value " << typedKVPair << std::endl;
- exit(0);
- }
- }
- return true;
-}
-
-void SAMAlignment::CopyQVs(std::vector<std::string> *optionalQVs) {
- optionalQVs->clear();
- optionalQVs->push_back(iq);
- optionalQVs->push_back(dq);
- optionalQVs->push_back(sq);
- optionalQVs->push_back(mq);
- optionalQVs->push_back(st);
- optionalQVs->push_back(dt);
-}
-
-const char* SAMAlignment::SAMAlignmentRequiredFieldNames[] = { "QNAME", "FLAG",
- "RNAME", "POS",
- "MAPQV", "CIGAR",
- "RNEXT", "PNEXT",
- "TLEN", "SEQ", "QUAL"} ;
-const char* optionalQVTags[] = {"iq", "dq", "sq", "mq", "st", "dt"};
-const char* optionalQVNames[] = {"InsertionQV", "DeletionQV", "SubstitutionQV",
- "MergeQV", "SubstitutionTag", "DeletionTag"};
diff --git a/libcpp/pbdata/sam/SAMAlignment.hpp b/libcpp/pbdata/sam/SAMAlignment.hpp
deleted file mode 100644
index a4183fd..0000000
--- a/libcpp/pbdata/sam/SAMAlignment.hpp
+++ /dev/null
@@ -1,97 +0,0 @@
-#ifndef _BLASR_SAM_ALIGNMENT_HPP_
-#define _BLASR_SAM_ALIGNMENT_HPP_
-
-#include <string>
-#include <sstream>
-
-#include "sam/SAMKeywordValuePair.hpp"
-#include "sam/CigarString.h"
-
-class SAMAlignment {
- public:
- enum SAMAlignmentRequiredFields {
- S_QNAME,
- S_FLAG,
- S_RNAME,
- S_POS,
- S_MAPQV,
- S_CIGAR,
- S_RNEXT,
- S_PNEXT,
- S_TLEN,
- S_SEQ,
- S_QUAL};
-
- static const char* SAMAlignmentRequiredFieldNames[];
-
- std::string qName;
- unsigned int flag;
- std::string rName;
- unsigned int pos;
- short mapQV;
- CigarString cigar;
- std::string rNext;
- int pNext;
- int tLen;
- std::string seq;
- std::string qual;
-
- // Optional tags defined in blasr:
- // "RG" read group Id
- // "AS" alignment score
- // "XS" read alignment start position without counting previous soft clips (1 based)
- // "XE" read alignment end position without counting previous soft clips (1 based)
- // "XL" aligned read length
- // "XQ" query read length
- // "XT" # of continues reads, always 1 for blasr
- // "NM" # of subreads
- // "FI" read alignment start position (1 based)
- //
- float score;
- int xs, xe;
- int xl;
- int xq;
-
- std::string rg;
- int as;
- int xt;
- int nm;
- int fi;
- std::string optTagStr;
- //
- // Quality values.
- //
- std::string iq, dq, sq, mq, st, dt;
- static const char* optionalQVTags[];
- static const char* optionalQVNames[];
-
- //
- // Initialize all optional fields. Required fields will be
- // assigned a value later.
- //
- SAMAlignment();
-
- void PrintSAMAlignment(std::ostream &out = std::cout);
-
- // Find position of the nth character in a string.
- int FindPosOfNthChar(std::string str, int n, char c);
-
- // Trim the end '\n\r' characters from a string.
- std::string TrimStringEnd(std::string str);
-
- bool StoreValues(std::string &line, int lineNumber=0);
-
- // CopyQVs writes the strings from the optional QV tags to a vector. The
- // order of QVs in the vector is given by optionalQVNames[]
- void CopyQVs(std::vector<std::string> *optionalQVs);
-};
-
-
-class SAMPosAlignment : public SAMAlignment {
- public:
- unsigned int qStart, qEnd;
- unsigned int tStart, tEnd;
- int qStrand, tStrand;
-};
-
-#endif
diff --git a/libcpp/pbdata/sam/SAMFlag.h b/libcpp/pbdata/sam/SAMFlag.h
deleted file mode 100644
index 10b311d..0000000
--- a/libcpp/pbdata/sam/SAMFlag.h
+++ /dev/null
@@ -1,48 +0,0 @@
-#ifndef SAM_FLAG_H_
-#define SAM_FLAG_H_
-
-inline bool IsMultipleSegment(unsigned int flag) {
- return flag & 0x1;
-}
-
-inline bool AllSegmentsMapped(unsigned int flag) {
- return flag & 0x2;
-}
-
-inline bool SegmentUnmapped(unsigned int flag) {
- return flag & 0x4;
-}
-
-inline bool NextUnmapped(unsigned int flag) {
- return flag & 0x8;
-}
-
-inline bool IsReverseComplement(unsigned int flag) {
- return flag & 0x10;
-}
-
-inline bool IsNextReverseComplement(unsigned int flag) {
- return flag & 0x20;
-}
-
-inline bool IsSegemntFirst(unsigned int flag) {
- return flag & 0x40;
-}
-
-inline bool IsSegmentLast(unsigned int flag) {
- return flag & 0x80;
-}
-
-inline bool IsSecondaryAlignment(unsigned int flag) {
- return flag & 0x100;
-}
-
-inline bool IsNotPassedQuality(unsigned int flag) {
- return flag & 0x200;
-}
-
-inline bool IsDuplicate(unsigned int flag) {
- return flag & 0x400;
-}
-
-#endif
diff --git a/libcpp/pbdata/sam/SAMHeader.cpp b/libcpp/pbdata/sam/SAMHeader.cpp
deleted file mode 100644
index 00c3d33..0000000
--- a/libcpp/pbdata/sam/SAMHeader.cpp
+++ /dev/null
@@ -1,31 +0,0 @@
-#include "SAMHeader.hpp"
-#include <algorithm>
-
-void SAMHeader::StoreValues(std::vector<SAMKeywordValuePair> &kvPairs,
- int lineNumber) {
- int i;
- for ( i = 0; i < kvPairs.size(); i++) {
- if (kvPairs[i].key == "VN") {
- formatVersion = kvPairs[i].value;
- }
- else if (kvPairs[i].key == "SO") {
- string value = kvPairs[i].value;
- std::transform(value.begin(), value.end(), value.begin(), ::tolower);
- if (value == "unknown" || value == "unsorted") {
- sortingOrder = unknown;
- }
- else if (value == "sorted") {
- sortingOrder = sorted;
- }
- else if (value == "queryname") {
- sortingOrder =queryname;
- }
- else if (value == "coordinate") {
- sortingOrder = coordinate;
- }
- else {
- std::cout << "Invalid sorting order " << kvPairs[i].value << " at line " << lineNumber;
- }
- }
- }
-}
diff --git a/libcpp/pbdata/sam/SAMHeader.hpp b/libcpp/pbdata/sam/SAMHeader.hpp
deleted file mode 100644
index 0a862a3..0000000
--- a/libcpp/pbdata/sam/SAMHeader.hpp
+++ /dev/null
@@ -1,18 +0,0 @@
-#ifndef _BLASR_SAM_HEADER_HPP_
-#define _BLASR_SAM_HEADER_HPP_
-
-#include <string>
-
-#include "sam/SAMKeywordValuePair.hpp"
-
-class SAMHeader {
- public:
- string formatVersion;
- enum SortingOrder {unknown, sorted , queryname, coordinate};
- SortingOrder sortingOrder;
-
- void StoreValues(std::vector<SAMKeywordValuePair> &kvPairs, int lineNumber = 0);
-};
-
-
-#endif
diff --git a/libcpp/pbdata/sam/SAMKeywordValuePair.cpp b/libcpp/pbdata/sam/SAMKeywordValuePair.cpp
deleted file mode 100644
index c034228..0000000
--- a/libcpp/pbdata/sam/SAMKeywordValuePair.cpp
+++ /dev/null
@@ -1,51 +0,0 @@
-#include "SAMKeywordValuePair.hpp"
-
-
-bool SplitSAMKeyValuePair(std::string &kvPair, std::string &key, std::string &value) {
- int sepIndex = kvPair.find_first_of(":");
- if (sepIndex == kvPair.npos) {
- return false;
- }
- else {
- key = kvPair.substr(0, sepIndex);
- value = kvPair.substr(sepIndex+1);
- return true;
- }
-}
-
-bool SplitSAMTypedKeyValuePair(std::string kvPair, std::string &key,
- std::string &kvType, std::string &value) {
- std::vector<std::string> strValues;
- ParseSeparatedList(kvPair, strValues, ':', 3);
- if (strValues.size() != 3) {
- return false;
- }
- else {
- key = strValues[0];
- kvType = strValues[1];
- value = strValues[2];
- return true;
- }
-}
-
-bool TypedKeywordValuePair::Separate(std::string &kvPair, std::string &kvKey,
- std::string &kvType, std::string &kvValue) {
- if (SplitSAMTypedKeyValuePair(kvPair, kvKey, kvType, kvValue) == false) {
- return false;
- }
- return true;
-}
-
-void KeywordValueStringsToPairs(std::vector<std::string> &kvStrings, std::vector<SAMKeywordValuePair> &kvPairs) {
-
- kvPairs.resize(kvStrings.size());
-
- if (kvStrings.size() == 0) {
- return;
- }
-
- int i;
- for (i = 0; i < kvStrings.size(); i++ ) {
- SplitSAMKeyValuePair(kvStrings[i], kvPairs[i].key, kvPairs[i].value);
- }
-}
diff --git a/libcpp/pbdata/sam/SAMKeywordValuePair.hpp b/libcpp/pbdata/sam/SAMKeywordValuePair.hpp
deleted file mode 100644
index b4610f8..0000000
--- a/libcpp/pbdata/sam/SAMKeywordValuePair.hpp
+++ /dev/null
@@ -1,50 +0,0 @@
-#ifndef _BLASR_SAM_KVPAIR_HPP_
-#define _BLASR_SAM_KVPAIR_HPP_
-
-#include <stdlib.h>
-
-#include <string>
-#include <iostream>
-#include <vector>
-
-#include "StringUtils.hpp"
-
-
-class SAMKeywordValuePair {
- public:
- std::string key;
- std::string value;
-};
-
-bool SplitSAMKeyValuePair(std::string &kvPair, std::string &key, std::string &value);
-
-bool SplitSAMTypedKeyValuePair(std::string kvPair, std::string &key,
- std::string &kvType, std::string &value);
-
-template<typename T>
-void StoreValue(std::string &valueStr, T &value);
-
-void KeywordValueStringsToPairs(std::vector<std::string> &kvStrings,
- std::vector<SAMKeywordValuePair> &kvPairs);
-
-class TypedKeywordValuePair {
- public:
- static bool Separate(std::string &kvPair, std::string &kvKey,
- std::string &kvType, std::string &kvValue);
-};
-
-
-template<typename T_Value>
-class KeywordValuePair {
- public:
-
- static bool Parse(std::string &kvPair,
- const char *key, T_Value &result);
-
- static bool Store(std::string &valueStr, T_Value &value);
-
-};
-
-#include "SAMKeywordValuePairImpl.hpp"
-
-#endif
diff --git a/libcpp/pbdata/sam/SAMKeywordValuePairImpl.hpp b/libcpp/pbdata/sam/SAMKeywordValuePairImpl.hpp
deleted file mode 100644
index 624acc5..0000000
--- a/libcpp/pbdata/sam/SAMKeywordValuePairImpl.hpp
+++ /dev/null
@@ -1,32 +0,0 @@
-template<typename T>
-void StoreValue(std::string &valueStr, T &value) {
- std::stringstream strm(valueStr);
- if (!(strm >> value)) {
- std::cout <<"Error parsing " << valueStr << std::endl;
- exit(1);
- }
-}
-
-template<typename T_Value>
-bool KeywordValuePair<T_Value>::Parse(std::string &kvPair,
- const char *key, T_Value &result) {
- std::string kvKey, kvValue;
- SplitSAMKeyValuePair(kvPair, kvKey, kvValue);
- if (kvKey != key) {
- return false;
- }
- else {
- std::stringstream strm(kvValue);
- if ( ! (kvValue >> result) ) {
- return false;
- }
- else {
- return true;
- }
- }
-}
-
-template<typename T_Value>
-bool KeywordValuePair<T_Value>::Store(std::string &valueStr, T_Value &value) {
- return (std::stringstream(valueStr) >> value);
-}
diff --git a/libcpp/pbdata/sam/SAMReader.hpp b/libcpp/pbdata/sam/SAMReader.hpp
deleted file mode 100644
index 16688d8..0000000
--- a/libcpp/pbdata/sam/SAMReader.hpp
+++ /dev/null
@@ -1,61 +0,0 @@
-#ifndef _BLASR_SAM_READER_HPP_
-#define _BLASR_SAM_READER_HPP_
-
-#include "sam/SAMKeywordValuePair.hpp"
-#include "sam/ReadGroup.hpp"
-#include "sam/ReferenceSequence.hpp"
-
-#include "sam/AlignmentSet.hpp"
-#include "StringUtils.hpp"
-#include "utils.hpp"
-
-template<typename T_ReferenceSequence, typename T_ReadGroup, typename T_SAMAlignment>
-class SAMReader {
- public:
- int lineNumber;
- std::ifstream samFile;
- std::istream *samFilePtr;
- bool Initialize(std::string samFileName);
-
- void Close();
-
- enum LineType {Blank, HSHeader, HSSequence, HSReadGroup, HSProgram, HSComment, Alignment, Error};
-
- void GetLine(std::istream &in, std::string &line);
-
- bool LineTypeIsHeader(LineType lineType);
-
- bool PeekLineIsHeader(std::istream &in);
-
- LineType GetLineType(std::string &line);
-
- void StoreKVPairs(std::string line, std::vector<SAMKeywordValuePair> &kvPairs);
-
- int StoreHeader(std::vector<SAMKeywordValuePair> &kvPairs,
- AlignmentSet<T_ReferenceSequence, T_ReadGroup, T_SAMAlignment> &alignments);
-
- void StoreReferenceSequence(std::vector<SAMKeywordValuePair> &kvPairs,
- AlignmentSet<T_ReferenceSequence, T_ReadGroup, T_SAMAlignment> &alignments);
-
- void StoreReadGroup(std::vector<SAMKeywordValuePair> &kvPairs,
- AlignmentSet<T_ReferenceSequence, T_ReadGroup, T_SAMAlignment> &alignments);
-
- void StoreAlignment(std::string & line,
- AlignmentSet<T_ReferenceSequence, T_ReadGroup, T_SAMAlignment> &alignments);
-
- // Not implemented
- void StoreProgram(std::vector<SAMKeywordValuePair> &kvPairs,
- AlignmentSet<T_ReferenceSequence, T_ReadGroup, T_SAMAlignment> &alignments ) {}
-
- void Read(std::string samFileName, AlignmentSet<T_ReferenceSequence, T_ReadGroup, T_SAMAlignment> &alignments);
-
- std::vector<std::string> ReadHeader(AlignmentSet<T_ReferenceSequence, T_ReadGroup, T_SAMAlignment> &alignments);
-
- void Read(AlignmentSet<T_ReferenceSequence, T_ReadGroup, T_SAMAlignment> &alignments);
-
- bool GetNextAlignment(SAMAlignment &alignment);
-};
-
-#include "SAMReaderImpl.hpp"
-
-#endif
diff --git a/libcpp/pbdata/sam/SAMReaderImpl.hpp b/libcpp/pbdata/sam/SAMReaderImpl.hpp
deleted file mode 100644
index b92ffc1..0000000
--- a/libcpp/pbdata/sam/SAMReaderImpl.hpp
+++ /dev/null
@@ -1,197 +0,0 @@
-#ifndef _BLASR_SAM_READER_IMPL_HPP_
-#define _BLASR_SAM_READER_IMPL_HPP_
-#include <iostream>
-#include "SAMReader.hpp"
-
-template<typename T_ReferenceSequence, typename T_ReadGroup, typename T_SAMAlignment>
-bool SAMReader<T_ReferenceSequence, T_ReadGroup, T_SAMAlignment>::Initialize(std::string samFileName) {
- if(samFileName != "stdin") {
- CrucialOpen(samFileName, samFile, std::ios::in);
- samFilePtr = &samFile;
- } else {
- samFilePtr = &std::cin;
- }
-}
-
-template<typename T_ReferenceSequence, typename T_ReadGroup, typename T_SAMAlignment>
-void SAMReader<T_ReferenceSequence, T_ReadGroup, T_SAMAlignment>::Close() {
- if(samFile.is_open()) {
- samFile.close();
- }
-}
-
-template<typename T_ReferenceSequence, typename T_ReadGroup, typename T_SAMAlignment>
-void SAMReader<T_ReferenceSequence, T_ReadGroup, T_SAMAlignment>::GetLine(std::istream &in, std::string &line) {
- getline(in, line);
-}
-
-template<typename T_ReferenceSequence, typename T_ReadGroup, typename T_SAMAlignment>
-bool SAMReader<T_ReferenceSequence, T_ReadGroup, T_SAMAlignment>::LineTypeIsHeader(LineType lineType) {
- return (lineType == HSHeader or
- lineType == HSSequence or
- lineType == HSReadGroup or
- lineType == HSProgram or
- lineType == HSComment);
-}
-
-template<typename T_ReferenceSequence, typename T_ReadGroup, typename T_SAMAlignment>
-bool SAMReader<T_ReferenceSequence, T_ReadGroup, T_SAMAlignment>::PeekLineIsHeader(std::istream &in) {
- if (in and in.peek() == '@') {
- return true;
- }
- else {
- return false;
- }
-}
-
-template<typename T_ReferenceSequence, typename T_ReadGroup, typename T_SAMAlignment>
-typename SAMReader<T_ReferenceSequence, T_ReadGroup, T_SAMAlignment>::LineType
-SAMReader<T_ReferenceSequence, T_ReadGroup, T_SAMAlignment>::GetLineType(std::string &line) {
- if (line.length() == 0) {
- return Blank;
- }
- else if (line[0] == '@') {
- std::stringstream strm(line);
- std::string tag;
- strm >> tag;
- if (tag == "@HD") { return HSHeader; }
- else if (tag == "@SQ") { return HSSequence; }
- else if (tag == "@RG") { return HSReadGroup; }
- else if (tag == "@PG") { return HSProgram; }
- else if (tag == "@CO") { return HSComment; }
- else { return Error; }
- }
- else {
- return Alignment;
- }
-}
-
-template<typename T_ReferenceSequence, typename T_ReadGroup, typename T_SAMAlignment>
-void SAMReader<T_ReferenceSequence, T_ReadGroup, T_SAMAlignment>::StoreKVPairs(std::string line,
- std::vector<SAMKeywordValuePair> &kvPairs) {
- //
- // Split on tab delineated line.
- //
- std::vector<std::string> kvPairStrings;
- Splice(line, "\t", kvPairStrings);
- KeywordValueStringsToPairs(kvPairStrings, kvPairs);
-}
-
-template<typename T_ReferenceSequence, typename T_ReadGroup, typename T_SAMAlignment>
-int SAMReader<T_ReferenceSequence, T_ReadGroup, T_SAMAlignment>::StoreHeader(std::vector<SAMKeywordValuePair> &kvPairs,
- AlignmentSet<T_ReferenceSequence, T_ReadGroup, T_SAMAlignment> &alignments) {
- alignments.header.StoreValues(kvPairs, lineNumber);
-}
-
-template<typename T_ReferenceSequence, typename T_ReadGroup, typename T_SAMAlignment>
-void SAMReader<T_ReferenceSequence, T_ReadGroup, T_SAMAlignment>::StoreReferenceSequence(std::vector<SAMKeywordValuePair> &kvPairs,
- AlignmentSet<T_ReferenceSequence, T_ReadGroup, T_SAMAlignment> &alignments) {
- alignments.references.push_back(T_ReferenceSequence());
- int lastRefIndex = alignments.references.size() - 1;
- alignments.references[lastRefIndex].StoreValues(kvPairs, lineNumber);
-}
-
-template<typename T_ReferenceSequence, typename T_ReadGroup, typename T_SAMAlignment>
-void SAMReader<T_ReferenceSequence, T_ReadGroup, T_SAMAlignment>::StoreReadGroup(std::vector<SAMKeywordValuePair> &kvPairs,
- AlignmentSet<T_ReferenceSequence, T_ReadGroup, T_SAMAlignment> &alignments) {
- alignments.readGroups.push_back(T_ReadGroup());
- int lastReadGroupIndex = alignments.readGroups.size() - 1;
- alignments.readGroups[lastReadGroupIndex].StoreValues(kvPairs, lineNumber);
-}
-
-template<typename T_ReferenceSequence, typename T_ReadGroup, typename T_SAMAlignment>
-void SAMReader<T_ReferenceSequence, T_ReadGroup, T_SAMAlignment>::StoreAlignment(std::string & line,
- AlignmentSet<T_ReferenceSequence, T_ReadGroup, T_SAMAlignment> &alignments) {
- alignments.alignments.push_back(T_SAMAlignment());
- int lastAlignmentIndex = alignments.alignments.size() - 1;
- alignments.alignments[lastAlignmentIndex].StoreValues(line, lineNumber);
-}
-
-template<typename T_ReferenceSequence, typename T_ReadGroup, typename T_SAMAlignment>
-void SAMReader<T_ReferenceSequence, T_ReadGroup, T_SAMAlignment>::Read(std::string samFileName, AlignmentSet<T_ReferenceSequence, T_ReadGroup, T_SAMAlignment> &alignments) {
- Initialize(samFileName);
- Read(alignments);
-}
-
-template<typename T_ReferenceSequence, typename T_ReadGroup, typename T_SAMAlignment>
-std::vector<std::string> SAMReader<T_ReferenceSequence, T_ReadGroup, T_SAMAlignment>::ReadHeader(AlignmentSet<T_ReferenceSequence, T_ReadGroup, T_SAMAlignment> &alignments) {
- std::vector<std::string> allHeaders;
- std::string line;
- LineType lineType;
- lineNumber = 0;
- while (*samFilePtr and PeekLineIsHeader(*samFilePtr)) {
- getline(*samFilePtr, line);
- lineType = GetLineType(line);
- if (LineTypeIsHeader(lineType)) {
- allHeaders.push_back(line);
- std::stringstream strm(line);
- std::string tag;
- strm >> tag;
- std::string remainder;
- getline(strm, remainder);
- std::vector<SAMKeywordValuePair> kvPairs;
- StoreKVPairs(remainder, kvPairs);
- if (lineType == HSHeader) {
- StoreHeader(kvPairs, alignments);
- }
- else if (lineType == HSSequence) {
- StoreReferenceSequence(kvPairs, alignments);
- }
- else if (lineType == HSReadGroup) {
- StoreReadGroup(kvPairs, alignments);
- }
- else if (lineType == HSProgram) {
- StoreProgram(kvPairs, alignments);
- }
- else if (lineType == HSComment) {
- // do nothing with comments for now.
- }
- }
- ++lineNumber;
- }
- return allHeaders;
-}
-
-template<typename T_ReferenceSequence, typename T_ReadGroup, typename T_SAMAlignment>
-void SAMReader<T_ReferenceSequence, T_ReadGroup, T_SAMAlignment>::Read(AlignmentSet<T_ReferenceSequence, T_ReadGroup, T_SAMAlignment> &alignments) {
- std::string line;
- LineType lineType;
- lineNumber = 0;
- ReadHeader(alignments);
- while (getline(*samFilePtr, line)) {
- lineType = GetLineType(line);
- if (LineTypeIsHeader(lineType)) {
- std::cout << "ERROR! Header line found outside of the header at " << lineNumber << std::endl;
- exit(1);
- }
- else if (lineType == Alignment) {
- StoreAlignment(line, alignments);
- }
- else {
- std::cout << "Error, line type unknown at " << lineNumber << std::endl;
- std::cout << line << std::endl;
- exit(1);
- }
- ++lineNumber;
- }
-}
-
-template<typename T_ReferenceSequence, typename T_ReadGroup, typename T_SAMAlignment>
-bool SAMReader<T_ReferenceSequence, T_ReadGroup, T_SAMAlignment>::GetNextAlignment(SAMAlignment &alignment) {
- if (*samFilePtr) {
- std::string line;
- if (getline(*samFilePtr, line)) {
- alignment.StoreValues(line, lineNumber);
- ++lineNumber;
- return true;
- }
- else {
- return false;
- }
- }
- else {
- return false;
- }
-}
-
-#endif
diff --git a/libcpp/pbdata/utils.hpp b/libcpp/pbdata/utils.hpp
deleted file mode 100644
index 9686cb5..0000000
--- a/libcpp/pbdata/utils.hpp
+++ /dev/null
@@ -1,20 +0,0 @@
-#ifndef _BLASR_UTILS_HPP_
-#define _BLASR_UTILS_HPP_
-#include <cstdlib>
-#include <string>
-#include <iostream>
-#include <fstream>
-
-template<typename t_file>
-void CrucialOpen(std::string &fileName, t_file &file,
- std::ios_base::openmode mode=(std::ios_base::openmode)0 );
-
-template<typename T_Int>
-T_Int CeilOfFraction(T_Int num, T_Int denom);
-
-template<typename T>
-T* ProtectedNew(unsigned long size);
-
-#include "utilsImpl.hpp"
-
-#endif // _BLASR_UTILS_HPP_
diff --git a/libcpp/pbdata/utils/BitUtils.cpp b/libcpp/pbdata/utils/BitUtils.cpp
deleted file mode 100644
index 0bc4bf3..0000000
--- a/libcpp/pbdata/utils/BitUtils.cpp
+++ /dev/null
@@ -1,99 +0,0 @@
-#include "BitUtils.hpp"
-
-int32_t CountBits(uint32_t v) {
- /*
- * Attribute Sean Anderson for this method.
- * The page: http://graphics.stanford.edu/~seander/bithacks.html
- * contains this code.
- */
- return std::bitset<sizeof(uint32_t)*8>(v).count();
-/*
- unsigned long long c;
- c = ((v & 0xfff) * 0x1001001001001ULL & 0x84210842108421ULL) % 0x1f;
- c += (((v & 0xfff000) >> 12) * 0x1001001001001ULL & 0x84210842108421ULL) %
- 0x1f;
- c += ((v >> 24) * 0x1001001001001ULL & 0x84210842108421ULL) % 0x1f;
- return c;*/
-}
-
-
-int GetSetBitPosition64(uint64_t v) {
- unsigned int s; // Output: Resulting position of bit with rank r [1-64]
- uint64_t a, b, c, d; // Intermediate temporaries for bit count.
- unsigned int t; // Bit count temporary.
-
- unsigned int r=1;
- // Do a normal parallel bit count for a 64-bit integer,
- // but store all intermediate steps.
- // a = (v & 0x5555...) + ((v >> 1) & 0x5555...);
- a = v - ((v >> 1) & ~0UL/3);
- // b = (a & 0x3333...) + ((a >> 2) & 0x3333...);
- b = (a & ~0UL/5) + ((a >> 2) & ~0UL/5);
- // c = (b & 0x0f0f...) + ((b >> 4) & 0x0f0f...);
- c = (b + (b >> 4)) & ~0UL/0x11;
- // d = (c & 0x00ff...) + ((c >> 8) & 0x00ff...);
- d = (c + (c >> 8)) & ~0UL/0x101;
- t = (d >> 32) + (d >> 48);
- // Now do branchless select!
- s = 64;
- // if (r > t) {s -= 32; r -= t;}
- s -= ((t - r) & 256) >> 3; r -= (t & ((t - r) >> 8));
- t = (d >> (s - 16)) & 0xff;
- // if (r > t) {s -= 16; r -= t;}
- s -= ((t - r) & 256) >> 4; r -= (t & ((t - r) >> 8));
- t = (c >> (s - 8)) & 0xf;
- // if (r > t) {s -= 8; r -= t;}
- s -= ((t - r) & 256) >> 5; r -= (t & ((t - r) >> 8));
- t = (b >> (s - 4)) & 0xf;
- // if (r > t) {s -= 4; r -= t;}
- s -= ((t - r) & 256) >> 6; r -= (t & ((t - r) >> 8));
- t = (a >> (s - 2)) & 0x3;
- // if (r > t) {s -= 2; r -= t;}
- s -= ((t - r) & 256) >> 7; r -= (t & ((t - r) >> 8));
- t = (v >> (s - 1)) & 0x1;
- // if (r > t) s--;
- s -= ((t - r) & 256) >> 8;
- // s = 64 - s;
- s = s - 1;
- return s;
-}
-
-unsigned int GetSetBitPosition32(UInt v) {
- unsigned int r; // Input: bit's desired rank [1-64].
- unsigned int s; // Output: Resulting position of bit with rank r [1-64]
- uint32_t a, b, c, d; // Intermediate temporaries for bit count.
- unsigned int t; // Bit count temporary.
- r = 1;
- // Do a normal parallel bit count for a 64-bit integer,
- // but store all intermediate steps.
- // a = (v & 0x5555...) + ((v >> 1) & 0x5555...);
- a = v - ((v >> 1) & ~0U/3);
- // b = (a & 0x3333...) + ((a >> 2) & 0x3333...);
- b = (a & ~0U/5) + ((a >> 2) & ~0U/5);
- // c = (b & 0x0f0f...) + ((b >> 4) & 0x0f0f...);
- c = (b + (b >> 4)) & ~0U/0x11;
- // d = (c & 0x00ff...) + ((c >> 8) & 0x00ff...);
- d = (c + (c >> 8)) & ~0U/0x101;
- t = (d >> 16) + (d >> 24);
-
-
- // Now do branchless select!
- s = 32;
- // if (r > t) {s -= 16; r -= t;}
- s -= ((t - r) & 256) >> 4; r -= (t & ((t - r) >> 8));
- t = (c >> (s - 8)) & 0xf;
- // if (r > t) {s -= 8; r -= t;}
- s -= ((t - r) & 256) >> 5; r -= (t & ((t - r) >> 8));
- t = (b >> (s - 4)) & 0xf;
- // if (r > t) {s -= 4; r -= t;}
- s -= ((t - r) & 256) >> 6; r -= (t & ((t - r) >> 8));
- t = (a >> (s - 2)) & 0x3;
- // if (r > t) {s -= 2; r -= t;}
- s -= ((t - r) & 256) >> 7; r -= (t & ((t - r) >> 8));
- t = (v >> (s - 1)) & 0x1;
- // if (r > t) s--;
- s -= ((t - r) & 256) >> 8;
- // s = 32 - s;
- s = s - 1;
- return s;
-}
diff --git a/libcpp/pbdata/utils/BitUtils.hpp b/libcpp/pbdata/utils/BitUtils.hpp
deleted file mode 100644
index 3914b7c..0000000
--- a/libcpp/pbdata/utils/BitUtils.hpp
+++ /dev/null
@@ -1,14 +0,0 @@
-#ifndef _BLASR_BIT_UTILS_HPP_
-#define _BLASR_BIT_UTILS_HPP_
-
-#include <stdint.h>
-#include <bitset>
-#include "Types.h"
-
-int32_t CountBits(uint32_t v);
-
-int GetSetBitPosition64(uint64_t v);
-
-unsigned int GetSetBitPosition32(UInt v);
-
-#endif // _BLASR_BIT_UTILS_HPP_
diff --git a/libcpp/pbdata/utils/SMRTReadUtils.cpp b/libcpp/pbdata/utils/SMRTReadUtils.cpp
deleted file mode 100644
index b2430b0..0000000
--- a/libcpp/pbdata/utils/SMRTReadUtils.cpp
+++ /dev/null
@@ -1,45 +0,0 @@
-
-#include "SMRTReadUtils.hpp"
-
-void GetSMRTReadCoordinates(FASTQSequence &seq, int &x, int &y) {
- std::string str(seq.title, seq.titleLength);
- std::vector<std::string> titleTokens;
- Splice(str, "_", titleTokens);
- int i;
- x = y = -1;
- int cmp;
- for (i = 0; i < titleTokens.size(); i++ ) {
- if (titleTokens[i].size() > 1 && titleTokens[i][0] == 'x') {
- x = atoi(&titleTokens[i].c_str()[1]);
- }
- if (titleTokens[i].size() > 1 && titleTokens[i][0] == 'y') {
- y = atoi(&titleTokens[i].c_str()[1]);
- }
- }
- assert("Could not parse a title to find an x coordinate" != 0 or x != -1);
- assert("Could not parse a title to find a y coordiante" != 0 or y != -1);
-}
-
-void GetSpringfieldHoleNumberFromTitle(FASTQSequence &seq, unsigned int &holeNumber) {
- std::vector<std::string> titleTokens;
- Splice(seq.title, "/", titleTokens);
- if (titleTokens.size() < 2) {
- return;
- }
- holeNumber = atoi(titleTokens[1].c_str());
-}
-
-bool ParsePBIReadName(std::string &readName, std::string &movieName, int &holeNumber) {
- std::vector<std::string> tokens;
- ParseSeparatedList(readName, tokens, '/');
- if (tokens.size() < 2) {
- movieName = "";
- holeNumber = 0;
- return false;
- }
- else {
- movieName = tokens[0];
- holeNumber = atoi(tokens[1].c_str());
- return true;
- }
-}
diff --git a/libcpp/pbdata/utils/SMRTReadUtils.hpp b/libcpp/pbdata/utils/SMRTReadUtils.hpp
deleted file mode 100644
index bbf0d9c..0000000
--- a/libcpp/pbdata/utils/SMRTReadUtils.hpp
+++ /dev/null
@@ -1,18 +0,0 @@
-#ifndef _BLASR_SMRT_READ_UTILS_HPP_
-#define _BLASR_SMRT_READ_UTILS_HPP_
-
-#include <stdlib.h>
-
-#include "FASTQSequence.hpp"
-#include "StringUtils.hpp"
-
-void GetSMRTReadCoordinates(FASTQSequence &seq, int &x, int &y);
-
-void GetSpringfieldHoleNumberFromTitle(FASTQSequence &seq,
- unsigned int &holeNumber);
-
-// Parse a PBIRead name of format movie/holeNumber/s_e, or /movie/holeNumber
-// and get movieName, holeNumber.
-bool ParsePBIReadName(std::string &readName, std::string &movieName, int &holeNumber);
-
-#endif
diff --git a/libcpp/pbdata/utils/SMRTTitle.cpp b/libcpp/pbdata/utils/SMRTTitle.cpp
deleted file mode 100644
index d1c3262..0000000
--- a/libcpp/pbdata/utils/SMRTTitle.cpp
+++ /dev/null
@@ -1,52 +0,0 @@
-#include "utils/SMRTTitle.hpp"
-
-/// Parse a Pacbio read name, it is a SMRTTitle, get movieName,
-/// holeNumber, start and end, set isSMRTTitle to be true.
-/// Otherwise, set isSMRTTitle to be false.
-/// Two types of smrtTitles are supported:
-/// movie/zmw/start_end --> start = start, end = end
-/// movie/zmw/start_end/start2_end2 --> start = start+start2, end = start+end2
-/// \param[in]: readName, a PacBio read name string.
-SMRTTitle::SMRTTitle(const std::string & readName) {
- isSMRTTitle = false;
- movieName = "";
- holeNumber = 0;
- start = end = 0;
-
- std::vector<std::string> values;
- ParseSeparatedList(readName, values, '/');
-
- int numValues = values.size();
- if (numValues == 3 or numValues == 4) {
- movieName = values[0];
- holeNumber = static_cast<UInt>(atoi(values[1].c_str()));
- std::vector<std::string> offsets;
- ParseSeparatedList(values[2], offsets, '_');
- if (offsets.size() == 2) {
- start = static_cast<DNALength>(atoi(offsets[0].c_str()));
- end = static_cast<DNALength>(atoi(offsets[1].c_str()));
- if (numValues == 3) {
- isSMRTTitle = true;
- } else if (numValues == 4) {
- offsets.clear();
- ParseSeparatedList(values[3], offsets, '_');
- if (offsets.size() == 2) {
- end = static_cast<DNALength>(start + atoi(offsets[1].c_str()));
- start = static_cast<DNALength>(start + atoi(offsets[0].c_str()));
- isSMRTTitle = true;
- }
- }
- }
- }
-}
-
-std::string SMRTTitle::ToString() {
- if (not isSMRTTitle) {
- return "";
- } else {
- std::stringstream ss;
- ss << movieName << "/" << holeNumber << "/" << start << "_" << end;
- return ss.str();
- }
-}
-
diff --git a/libcpp/pbdata/utils/SMRTTitle.hpp b/libcpp/pbdata/utils/SMRTTitle.hpp
deleted file mode 100644
index 33b108b..0000000
--- a/libcpp/pbdata/utils/SMRTTitle.hpp
+++ /dev/null
@@ -1,24 +0,0 @@
-#ifndef _BLASR_SMRT_TITLE_HPP_
-#define _BLASR_SMRT_TITLE_HPP_
-#include <string>
-#include <vector>
-#include <sstream>
-#include "Types.h"
-#include "StringUtils.hpp"
-
-class SMRTTitle {
-public:
- std::string movieName;
- UInt holeNumber;
- DNALength start;
- DNALength end;
- // if input name is a smrt title.
- bool isSMRTTitle;
-
- SMRTTitle(const std::string & name);
-
- /// \returns smrt title movie/zmw/s_e, if input read is a smrt title;
- /// otherwise, return an empty string.
- std::string ToString();
-};
-#endif
diff --git a/libcpp/pbdata/utilsImpl.hpp b/libcpp/pbdata/utilsImpl.hpp
deleted file mode 100644
index ee899cd..0000000
--- a/libcpp/pbdata/utilsImpl.hpp
+++ /dev/null
@@ -1,32 +0,0 @@
-#ifndef _BLASR_UTIL_IMPL_HPP_
-#define _BLASR_UTIL_IMPL_HPP_
-
-template<typename t_file>
-void CrucialOpen(std::string &fileName, t_file &file, std::ios_base::openmode mode) {
- if (mode==0)
- file.open(fileName.c_str());
- else
- file.open(fileName.c_str(), mode);
-
- if (!file.good()) {
- std::cout << "Could not open " << fileName << std::endl;
- exit(1);
- }
-}
-template<typename T_Int>
-T_Int CeilOfFraction(T_Int num, T_Int denom) {
- return num / denom + ((num % denom) && 1);
-}
-
-template<typename T>
-T* ProtectedNew(unsigned long size) {
- T* ptr;
- ptr = new T[size];
- if (ptr == NULL) {
- std::cout << "ERROR, allocating " << size * sizeof(T) << " bytes.";
- exit(1);
- }
- return ptr;
-}
-
-#endif
diff --git a/libcpp/rules.mk b/libcpp/rules.mk
deleted file mode 100644
index c836d78..0000000
--- a/libcpp/rules.mk
+++ /dev/null
@@ -1,17 +0,0 @@
-ARFLAGS := rc
-CXX_SHAREDFLAGS := -fPIC
-LD_SHAREDFLAGS := -shared -fPIC
-CPPFLAGS += $(patsubst %,-I%,${INCLUDES})
-
-
-%.a:
- ${AR} $(ARFLAGS) $@ $^
-
-%.so:
- ${CXX} ${LD_SHAREDFLAGS} ${LDFLAGS} -o $@ $^
-
-%.o: %.cpp
- $(CXX) $(CXXOPTS) $(CXXFLAGS) $(LEGACY) $(CPPFLAGS) -MF"$(@:%.o=%.d)" -MT"$(@:%.o=%.o) $(@:%.o=%.d)" -c $< -o $@
-
-%.shared.o: %.cpp
- $(CXX) $(CXXOPTS) $(CXXFLAGS) $(LEGACY) $(CPPFLAGS) $(CXX_SHAREDFLAGS) -MF"$(@:%.o=%.d)" -MT"$(@:%.o=%.o) $(@:%.o=%.d)" -c $< -o $@
diff --git a/libcpp/simple.mk b/libcpp/simple.mk
deleted file mode 100644
index e725a6e..0000000
--- a/libcpp/simple.mk
+++ /dev/null
@@ -1,16 +0,0 @@
-SHELL = bash
-G_BUILDOS_CMD := bash -c 'set -e; set -o pipefail; id=$$(lsb_release -si | tr "[:upper:]" "[:lower:]"); rel=$$(lsb_release -sr); case $$id in ubuntu) printf "$$id-%04d\n" $${rel/./};; centos) echo "$$id-$${rel%%.*}";; *) echo "$$id-$$rel";; esac' 2>/dev/null
-OS_STRING ?= $(shell $(G_BUILDOS_CMD))
-
-# magic for non-verbose builds
-V ?= 0
-
-CXX_0 = @echo " CXX $@"; $(CXX)
-CXX_1 = $(CXX)
-CXX_pp = $(CXX_$(V))
-
-AR_0 = @echo " AR $@"; $(AR)
-AR_1 = $(AR)
-AR_pp = $(AR_$(V))
-
-ARFLAGS := rc
diff --git a/libcpp/unittest/.gitignore b/libcpp/unittest/.gitignore
deleted file mode 100644
index 26ca380..0000000
--- a/libcpp/unittest/.gitignore
+++ /dev/null
@@ -1 +0,0 @@
-/test-runner
diff --git a/libcpp/unittest/Makefile b/libcpp/unittest/Makefile
deleted file mode 100644
index fe48ef7..0000000
--- a/libcpp/unittest/Makefile
+++ /dev/null
@@ -1,151 +0,0 @@
-SHELL=bash
-
-V := 0
-V@ := @
-ifeq ($(V),$(filter $(V),1))
- # Enable verbose mode if V=1 or V= specified on command ine
- V@ :=
-endif
-
-MKDIR := mkdir
-
-null :=
-space := $(null) $(null)
-
-
-
-OUTDIR := _output
-
-GTEST_SRCDIR := __UNSET__
-
-LIBBLASR_INCLUDE := __UNSET__
-LIBPBIHDF_INCLUDE := __UNSET__
-LIBPBDATA_INCLUDE := __UNSET__
-PBBAM_INCLUDE := __UNSET__
-HTSLIB_INCLUDE := __UNSET__
-HDF5_INCLUDE := __UNSET__
-BOOST_INCLUDE := __UNSET__
-GTEST_INCLUDE := __UNSET__
-
-LIBBLASR_LIB := __UNSET__
-LIBPBIHDF_LIB := __UNSET__
-LIBPBDATA_LIB := __UNSET__
-PBBAM_LIB := __UNSET__
-HTSLIB_LIB := __UNSET__
-HDF5_LIB := __UNSET__
-ZLIB_LIB := __UNSET__
-
-
-
-broken_test_sources := \
- alignment/files/ReaderAgglomerate_gtest.cpp \
- alignment/format/SAMHeaderPrinter_gtest.cpp \
- alignment/format/SAMPrinter_gtest.cpp \
- alignment/utils/FileUtils_gtest.cpp \
- $(null)
-
-
-gtest_sources := $(GTEST_SRCDIR)/gtest/gtest-all.cc \
- $(GTEST_SRCDIR)/gtest/gtest_main.cc \
- $(null)
-
-test_sources := $(wildcard pbdata/*.cpp) \
- $(wildcard pbdata/utils/*.cpp) \
- $(wildcard pbdata/metagenome/*.cpp) \
- $(wildcard pbdata/saf/*.cpp) \
- $(wildcard pbdata/reads/*.cpp) \
- $(wildcard pbdata/qvs/*.cpp) \
- \
- $(wildcard hdf/*.cpp) \
- \
- $(wildcard alignment/*.cpp) \
- $(wildcard alignment/utils/*.cpp) \
- $(wildcard alignment/datastructures/alignment/*.cpp) \
- $(wildcard alignment/files/*.cpp) \
- $(wildcard alignment/format/*.cpp) \
- $(null)
-
-# Remove broken tests from the test_sources list
-test_sources := $(filter-out $(broken_test_sources),$(test_sources))
-
-
-sources := $(gtest_sources) $(test_sources)
-objects := $(patsubst %.cc,$(OUTDIR)/%.o,$(filter %.cc,$(sources))) \
- $(patsubst %.cpp,$(OUTDIR)/%.o,$(filter %.cpp,$(sources))) \
- $(null)
-depfiles := $(objects:%.o=%.d)
-
-
-includes := \
- -I. \
- -I$(GTEST_INCLUDE) \
- -I$(LIBBLASR_INCLUDE) \
- -I$(LIBPBIHDF_INCLUDE) \
- -I$(LIBPBDATA_INCLUDE) \
- -I$(PBBAM_INCLUDE) \
- -I$(HTSLIB_INCLUDE) \
- -I$(HDF5_INCLUDE) \
- -I$(BOOST_INCLUDE) \
- $(null)
-
-libs := \
- $(LIBBLASR_LIB) \
- $(LIBPBIHDF_LIB) \
- $(LIBPBDATA_LIB) \
- $(PBBAM_LIB) \
- $(HTSLIB_LIB) \
- $(HDF5_LIB) \
- $(HDF5_CPP_LIB) \
- $(ZLIB_LIB) \
- $(null)
-
-
-sys_ldflags := -lpthread -ldl -lrt
-
-
-cxxopts := -std=c++11 -Wno-div-by-zero
-cxxflags := -O3
-ldflags := $(libs) $(sys_ldflags)
-
-
-
-CPPFLAGS := $(includes) $(EXTRA_CPPFLAGS)
-CXXFLAGS := $(cxxflags) $(cxxopts) $(EXTRA_CXXFLAGS)
-LDLIBS := $(ldflags) $(EXTRA_LDLIBS)
-
-OUTPUT_OPTION = -o $@
-COMPILE.cpp = $(CXX) $(CXXFLAGS) $(CPPFLAGS) $(TARGET_ARCH) -c
-COMPILE.cc = $(COMPILE.cpp)
-LINK.o = $(CXX) $(LDFLAGS) $(TARGET_ARCH)
-
-
-all: test-runner
-
-test-runner: $(objects)
- $(V@)$(LINK.o) $^ $(LDLIBS) $(OUTPUT_OPTION)
-
-gtest: test-runner
- $(V@)LD_LIBRARY_PATH=$(subst $(space),:,$(strip $(dir $(libs)))) ./$< --gtest_output=xml:$(OUTDIR)/xml/all.xml
-
-# Build objects
-$(OUTDIR)/%.o: %.cpp
- @echo " CXX $@"
- $(V@)$(COMPILE.cpp) $(OUTPUT_OPTION) $<
-
-$(OUTDIR)/%.o: %.cc
- @echo " CXX $@"
- $(V@)$(COMPILE.cc) $(OUTPUT_OPTION) $<
-
-# Make all directories of object files 'order-only' dependencies of all objects
-# This will make all the output directories we need before building any objects
-$(objects): | $(dir $(objects))
-
-# Create any output directories
-$(OUTDIR)/%/:
- $(V@)$(MKDIR) -p "$@"
-
-
-clean:
- $(V@)$(RM) -r $(OUTDIR)
-
--include ($DEPS)
diff --git a/libcpp/unittest/alignment/Makefile b/libcpp/unittest/alignment/Makefile
deleted file mode 100644
index 154ab5e..0000000
--- a/libcpp/unittest/alignment/Makefile
+++ /dev/null
@@ -1,35 +0,0 @@
-include ../../rules.mk
-include ../defines.mk
-
-SOURCES = $(wildcard *.cpp) \
- $(wildcard utils/*.cpp) \
- $(wildcard datastructures/alignment/*.cpp) \
- $(wildcard files/*.cpp) \
- $(wildcard format/*.cpp)
-
-ifneq ($(origin nopbbam), undefined)
- SOURCES := $(filter-out format/SAMHeaderPrinter_gtest.cpp, $(SOURCES))
-endif
-
-OBJECTS = $(SOURCES:.cpp=.o)
-
-EXE := test-runner
-
-all debug profile: $(EXE)
-
-libblasr_gtest.a: $(OBJECTS)
- $(AR) $(ARFLAGS)c $@ $^
-
-$(EXE): $(OBJECTS)
- $(CXX) $(CXXOPTS) $(CXXFLAGS) $^ $(GTEST_SRC) -o $@ -I$(GTEST_ROOT) $(LIBDIRS) $(LDFLAGS)
-
-$(OBJECTS): %.o: %.cpp
- $(CXX) $(CXXOPTS) $(CXXFLAGS) -c $< -o $@ $(INCDIRS)
-
-gtest: $(EXE)
- ./$< --gtest_output=xml:../xml/alignment.xml
-
-clean:
- @find . -type f -name \*.o -delete
- @find . -type f -name \*.d -delete
- @rm -f libblasr_gtest.a $(EXE) ../xml/alignment.xml
diff --git a/libcpp/unittest/alignment/datastructures/alignment/AlignmentMap_gtest.cpp b/libcpp/unittest/alignment/datastructures/alignment/AlignmentMap_gtest.cpp
deleted file mode 100644
index 52bdb2b..0000000
--- a/libcpp/unittest/alignment/datastructures/alignment/AlignmentMap_gtest.cpp
+++ /dev/null
@@ -1,63 +0,0 @@
-/*
- * =====================================================================================
- *
- * Filename: AlignmentMap_gtest.cpp
- *
- * Description: Test alignment/datastructures/alignment/AlignmentMap.hpp
- *
- * Version: 1.0
- * Created: 11/29/2012 01:47:50 PM
- * Revision: 08/20/2014
- * Compiler: gcc
- *
- * Author: Yuan Li (yli), yli at pacificbiosciences.com
- * Company: Pacific Biosciences
- *
- * =====================================================================================
- */
-
-#include <climits>
-#include <iostream>
-#include <fstream>
-#include "datastructures/alignment/AlignmentMap.hpp"
-#include "gtest/gtest.h"
-
-using namespace std;
-// Test
-// void CreateSequenceToAlignmentMap(const string & alignedSequence,
-// vector<int> & baseToAlignmentMap);
-TEST(AlignmentMap, CreateSequenceToAlignmentMap) {
- const string & alignedSequence1 = "ATCTGAG-AAA-";
- const int size1 = 10;
- int map1[size1] = {0, 1, 2, 3, 4,5, 6, 8, 9, 10};
-
- const string & alignedSequence2 = "--ATCTGAG----AAA----";
- const int size2 = 10;
- int map2[size2] = {2,3,4,5,6,7,8,13,14,15};
-
- const string & alignedSequence3 = "-------";
- const int size3 = 0;
-
- vector <int> resMap1;
- CreateSequenceToAlignmentMap(alignedSequence1, resMap1);
- EXPECT_EQ(size1, resMap1.size());
- for (int i = 0; i < size1; i++) {
- // cout << resMap1[i] << ", ";
- EXPECT_EQ(map1[i], resMap1[i]);
- }
- // cout << endl;
-
- vector <int> resMap2;
- CreateSequenceToAlignmentMap(alignedSequence2, resMap2);
- EXPECT_EQ(size2, resMap2.size());
- for (int i = 0; i < size2; i++) {
- // cout << resMap1[i] << ", ";
- EXPECT_EQ(map2[i], resMap2[i]);
- }
- // cout << endl;
-
- vector <int> resMap3;
- CreateSequenceToAlignmentMap(alignedSequence3, resMap3);
- EXPECT_EQ(size3, resMap3.size());
-
-}
diff --git a/libcpp/unittest/alignment/datastructures/alignment/CmpIndexedStringTable_gtest.cpp b/libcpp/unittest/alignment/datastructures/alignment/CmpIndexedStringTable_gtest.cpp
deleted file mode 100644
index 7080876..0000000
--- a/libcpp/unittest/alignment/datastructures/alignment/CmpIndexedStringTable_gtest.cpp
+++ /dev/null
@@ -1,143 +0,0 @@
-/*
- * =====================================================================================
- *
- * Filename: CmpIndexedStringTable_gtest.cpp
- *
- * Description: Test alignment/datastructures/alignment/CmpIndexedStringTable.h
- *
- * Version: 1.0
- * Created: 11/29/2012 01:50:24 PM
- * Revision: none
- * Compiler: gcc
- *
- * Author: Yuan Li (yli), yli at pacificbiosciences.com
- * Company: Pacific Biosciences
- *
- * =====================================================================================
- */
-#include "gtest/gtest.h"
-#include "datastructures/alignment/CmpIndexedStringTable.h"
-
-int ids[5] = {1, 2, 3, 30, 5};
-string names[5] = {"n1", "n2", "n3", "n30", "n5"};
-class CmpIndexedStringTableTest : public ::testing::Test {
-public:
- //Be careful, SetUp() not Setup()
- virtual void SetUp() {
- for(int i = 0; i < 5; i++) {
- cmpIndexedStringTableTest.ids.push_back(ids[i]);
- cmpIndexedStringTableTest.names.push_back(names[i]);
- }
- cmpIndexedStringTableTest.StoreArrayIndexMap();
-
- }
-
- virtual void TearDown() {
-
- }
-
- CmpIndexedStringTable cmpIndexedStringTableTest;
-};
-
-
-//
-// Test resize(int size)
-//
-TEST_F (CmpIndexedStringTableTest, resize) {
- cmpIndexedStringTableTest.resize(10);
-
- EXPECT_EQ(cmpIndexedStringTableTest.names.size(), 10);
- EXPECT_EQ(cmpIndexedStringTableTest.ids.size(), 10);
-}
-
-//
-// Test StoreArrayIndexMap()
-//
-TEST_F (CmpIndexedStringTableTest, StoreArrayIndexMap) {
- for(int i = 0; i < cmpIndexedStringTableTest.ids.size(); i++) {
- EXPECT_EQ(cmpIndexedStringTableTest.idToArrayIndex.find(cmpIndexedStringTableTest.ids[i])->second, i);
- }
- EXPECT_EQ(cmpIndexedStringTableTest.idToArrayIndex.find(1 )->second, 0);
- EXPECT_EQ(cmpIndexedStringTableTest.idToArrayIndex.find(2 )->second, 1);
- EXPECT_EQ(cmpIndexedStringTableTest.idToArrayIndex.find(3 )->second, 2);
- EXPECT_EQ(cmpIndexedStringTableTest.idToArrayIndex.find(30)->second, 3);
- EXPECT_EQ(cmpIndexedStringTableTest.idToArrayIndex.find(5 )->second, 4);
-}
-
-//
-// Test GetIndexOfId(int id, int & index)
-//
-TEST_F (CmpIndexedStringTableTest, GetIndexOfId) {
- int index = -1;
- int i = 0;
- for(i = 0; i < cmpIndexedStringTableTest.ids.size(); i++) {
- cmpIndexedStringTableTest.GetIndexOfId(ids[i], index);
- EXPECT_EQ(index, i);
- }
- i = 1;
- cmpIndexedStringTableTest.GetIndexOfId(i, index);
- EXPECT_EQ(index, 0);
-
- i = 2;
- cmpIndexedStringTableTest.GetIndexOfId(i, index);
- EXPECT_EQ(index, 1);
-
- i = 3;
- cmpIndexedStringTableTest.GetIndexOfId(i, index);
- EXPECT_EQ(index, 2);
-
- i = 5;
- cmpIndexedStringTableTest.GetIndexOfId(i, index);
- EXPECT_EQ(index, 4);
-
- i = 30;
- cmpIndexedStringTableTest.GetIndexOfId(i, index);
- EXPECT_EQ(index, 3);
-}
-
-//
-// Test GetNameAtIndex(int index, string & name)
-//
-TEST_F (CmpIndexedStringTableTest, GetNameAtIndex) {
- // "Warning: the terminology of CmpIndexedStringTable.GetNameAtIndex
- // is confusing"
-
- int index;
- string name;
- bool found;
-
- index = 1;
- found = cmpIndexedStringTableTest.GetNameAtIndex(index, name);
- EXPECT_EQ(name, "n1");
- EXPECT_TRUE(found);
-
-
- index = 2;
- found = cmpIndexedStringTableTest.GetNameAtIndex(index, name);
- EXPECT_EQ(name, "n2");
- EXPECT_TRUE(found);
-
-
- index = 3;
- found = cmpIndexedStringTableTest.GetNameAtIndex(index, name);
- EXPECT_EQ(name, "n3");
- EXPECT_TRUE(found);
-
- index = 30;
- found = cmpIndexedStringTableTest.GetNameAtIndex(index, name);
- EXPECT_EQ(name, "n30");
- EXPECT_TRUE(found);
-
- index = 5;
- found = cmpIndexedStringTableTest.GetNameAtIndex(index, name);
- EXPECT_EQ(name, "n5");
- EXPECT_TRUE(found);
-
- //
- //test getting name at an out-of-boundary index
- //
- index = 100;
- found = cmpIndexedStringTableTest.GetNameAtIndex(index, name);
- EXPECT_FALSE(found);
-}
-
diff --git a/libcpp/unittest/alignment/files/CCSIterator_gtest.cpp b/libcpp/unittest/alignment/files/CCSIterator_gtest.cpp
deleted file mode 100644
index eba2a24..0000000
--- a/libcpp/unittest/alignment/files/CCSIterator_gtest.cpp
+++ /dev/null
@@ -1,66 +0,0 @@
-/*
- * =====================================================================================
- *
- * Filename: CCSIterator_gtest.cpp
- *
- * Description: Test alignment/files/CCSIterator.hpp
- *
- * Version: 1.0
- * Created: 11/29/2012 04:51:02 PM
- * Revision: 08/20/2014
- * Compiler: gcc
- *
- * Author: Yuan Li (yli), yli at pacificbiosciences.com
- * Company: Pacific Biosciences
- *
- * =====================================================================================
- */
-
-
-#include "gtest/gtest.h"
-#include "files/CCSIterator.hpp"
-#include "reads/RegionTable.hpp"
-#include "HDFRegionTableReader.hpp"
-#include "pbdata/testdata.h"
-
-using namespace std;
-
-class CCSIteratorTestFixture: public testing::Test {
-public:
- CCSIteratorTestFixture() {
- }
-
- void SetUp() {
- fileName = baxFile2;
- reader = new HDFRegionTableReader();
- ccs = new CCSSequence();
- rgn = new RegionTable();
-
- int rev = reader->Initialize(fileName);
- EXPECT_TRUE(rev);
- reader->ReadTable(*rgn);
- reader->Close();
-
- rgn->SortTableByHoleNumber();
- }
-
- void TearDown() {
- if (reader) delete reader;
- if (ccs) delete ccs;
- if (rgn) delete rgn;
- }
-
- ~CCSIteratorTestFixture() {
- }
-
- string fileName;
- HDFRegionTableReader * reader;
- CCSSequence * ccs;
- RegionTable * rgn;
- CCSIterator it;
-};
-
-
-TEST_F(CCSIteratorTestFixture, Initialize) {
-
-}
diff --git a/libcpp/unittest/alignment/files/FragmentCCSIterator_gtest.cpp b/libcpp/unittest/alignment/files/FragmentCCSIterator_gtest.cpp
deleted file mode 100644
index e1b2d0c..0000000
--- a/libcpp/unittest/alignment/files/FragmentCCSIterator_gtest.cpp
+++ /dev/null
@@ -1,104 +0,0 @@
-/*
- * =====================================================================================
- *
- * Filename: FragmentCCSIterator_gtest.cpp
- *
- * Description: Test alignment/files/FragmentCCSIterator.hpp
- *
- * Version: 1.0
- * Created: 11/29/2012 04:51:29 PM
- * Revision: 08/20/2014
- * Compiler: gcc
- *
- * Author: Yuan Li (yli), yli at pacificbiosciences.com
- * Company: Pacific Biosciences
- *
- * =====================================================================================
- */
-
-#include <algorithm>
-#include <stdio.h>
-#include <string.h>
-#include "files/FragmentCCSIterator.hpp"
-#include "reads/RegionTable.hpp"
-#include "HDFRegionTableReader.hpp"
-#include "pbdata/testdata.h"
-#include <gtest/gtest.h>
-using namespace std;
-
-class FragmentCCSIteratorTestFixture: public testing::Test {
-public:
- FragmentCCSIteratorTestFixture() {
- }
-
- void SetUp() {
- fileName = baxFile1;
- reader = new HDFRegionTableReader();
- ccs = new CCSSequence();
- rgn = new RegionTable();
-
- int rev = reader->Initialize(fileName);
- EXPECT_TRUE(rev);
- reader->ReadTable(*rgn);
- reader->Close();
-
- rgn->SortTableByHoleNumber();
- }
-
- void TearDown() {
- if (reader) delete reader;
- if (ccs) delete ccs;
- if (rgn) delete rgn;
- }
-
- ~FragmentCCSIteratorTestFixture() {
- }
-
- string fileName;
- HDFRegionTableReader * reader;
- CCSSequence * ccs;
- RegionTable * rgn;
- FragmentCCSIterator it;
-};
-
-
-TEST_F(FragmentCCSIteratorTestFixture, Initialize) {
- // void Initialize(CCSSequence *_seqPtr, RegionTable *_regionTablePtr) {
- ccs->zmwData.holeNumber = 10;
- it.Initialize(ccs, rgn);
-
- int numPasses = it.GetNumPasses();
- EXPECT_EQ(numPasses, 7);
-/*
- * The region table of zmw 10 is:
- *
- (52,0): 10, 1, 0, 443, -1,
- (53,0): 10, 1, 487, 1168, -1,
- (54,0): 10, 1, 1213, 1907, -1,
- (55,0): 10, 1, 1956, 2619, -1,
- (56,0): 10, 1, 2668, 3423, -1,
- (57,0): 10, 1, 3474, 4205, -1,
- (58,0): 10, 1, 4256, 5949, -1,
- (59,0): 10, 1, 5997, 6161, -1,
- (60,0): 10, 0, 443, 487, 863,
- (61,0): 10, 0, 1168, 1213, 822,
- (62,0): 10, 0, 1907, 1956, 836,
- (63,0): 10, 0, 2619, 2668, 693,
- (64,0): 10, 0, 3423, 3474, 764,
- (65,0): 10, 0, 4205, 4256, 862,
- (66,0): 10, 0, 5949, 5997, 812,
- (67,0): 10, 2, 0, 4920, 788,
- *
- */
- int exp_directions[7] = {0, 1, 0, 1, 0, 1, 0};
- int exp_starts[7] = {0, 487, 1213, 1956, 2668, 3474, 4256};
- int exp_ends[7] = {443, 1168, 1907, 2619, 3423, 4205, 4920};
-
- int passDirection, start, numBases;
- for(int i=0; i < numPasses; i++) {
- it.GetNext(passDirection, start, numBases);
- EXPECT_EQ(passDirection, exp_directions[i]);
- EXPECT_EQ(start, exp_starts[i]);
- EXPECT_EQ(start + numBases, exp_ends[i]);
- }
-}
diff --git a/libcpp/unittest/alignment/files/ReaderAgglomerate_gtest.cpp b/libcpp/unittest/alignment/files/ReaderAgglomerate_gtest.cpp
deleted file mode 100644
index f27eb16..0000000
--- a/libcpp/unittest/alignment/files/ReaderAgglomerate_gtest.cpp
+++ /dev/null
@@ -1,129 +0,0 @@
-/*
- * =====================================================================================
- *
- * Filename: ReaderAgglomerate_gtest.cpp
- *
- * Description: Test alignment/files/ReaderAgglomerate.hpp
- *
- * Version: 1.0
- * Created: 02/25/2015 04:51:29 PM
- * Compiler: gcc
- *
- * Author: Yuan Li (yli), yli at pacificbiosciences.com
- * Company: Pacific Biosciences
- *
- * =====================================================================================
- */
-
-#include <algorithm>
-#include <stdio.h>
-#include <string.h>
-#include "files/ReaderAgglomerate.hpp"
-#include "pbdata/testdata.h"
-#include <gtest/gtest.h>
-using namespace std;
-
-class ReaderAgglomerateTest: public testing::Test {
-public:
- void SetUp() {
- reader = new ReaderAgglomerate();
- }
-
- void TearDown() {
- if (reader) {
- delete reader;
- reader = NULL;
- }
- }
- ReaderAgglomerate * reader;
-};
-
-#define INIT_READER(INFILE) \
- fn = INFILE; \
- reader->SetReadFileName(fn); \
- EXPECT_EQ(reader->Initialize(), 1);
-
-TEST_F(ReaderAgglomerateTest, Initialize) {
- string fn;
- INIT_READER(fastaFile1)
- reader->Close();
-
- INIT_READER(baxFile1)
- reader->Close();
-
- INIT_READER(baxFile3)
- reader->Close();
-}
-
-
-#define SIMPLE(INFILE, SEQ) \
- INIT_READER(INFILE) \
- for(int i = 0; i < 10; i++) {\
- reader->GetNext(SEQ);\
- }\
- reader->Close();
-
-TEST_F(ReaderAgglomerateTest, Simple) {
- string fn;
-
- // Fasta
- FASTASequence fastaSeq;
- SIMPLE(fastaFile1, fastaSeq)
-
- // Bax
- SMRTSequence smrtSeq;
- SIMPLE(baxFile1, smrtSeq)
- SIMPLE(baxFile3, smrtSeq)
-}
-
-#define GET_MOVIE_NAME(INFILE) \
- INIT_READER(INFILE) \
- reader->GetMovieName(movieName); \
- reader->Close();
-
-TEST_F(ReaderAgglomerateTest, GetMovieName) {
- string fn;
- string movieName = "";
- // Fasta
- GET_MOVIE_NAME(fastaFile1)
- EXPECT_EQ(movieName, "/mnt/secondary-siv/testdata/BlasrTestData/utest/data/read.fasta");
-
- // Bax
- GET_MOVIE_NAME(baxFile1)
- EXPECT_EQ(movieName, "m130220_114643_42129_c100471902550000001823071906131347_s1_p0");
-
- GET_MOVIE_NAME(baxFile3)
- EXPECT_EQ(movieName, "m150223_190837_42175_c100735112550000001823160806051530_s1_p0");
-}
-
-#define GET_CHEMISTRY_TRIPLE(INFILE, A, B, C) \
- INIT_READER(INFILE) \
- bindingKit = sequencingKit = version; \
- reader->GetChemistryTriple(bindingKit, sequencingKit, version); \
- reader->Close(); \
- EXPECT_EQ(bindingKit, A); \
- EXPECT_EQ(sequencingKit, B); \
- EXPECT_EQ(version, C);
-
-TEST_F(ReaderAgglomerateTest, GetChemistryTriple) {
- string fn;
- string bindingKit, sequencingKit, version;
-
- GET_CHEMISTRY_TRIPLE(baxFile3, "100356300", "100356200", "2.3")
-}
-
-TEST_F(ReaderAgglomerateTest, ReadFromBam) {
- string fn (bamFile1);
- reader->SetReadFileName(fn);
- EXPECT_EQ(reader->Initialize(), 1);
-
- SMRTSequence seq;
- int ret, count=0;
- while (ret = reader->GetNext(seq) and ret != 0) {
- count++;
- }
-
- EXPECT_EQ(count, 116);
-
- reader->Close();
-}
diff --git a/libcpp/unittest/alignment/format/SAMHeaderPrinter_gtest.cpp b/libcpp/unittest/alignment/format/SAMHeaderPrinter_gtest.cpp
deleted file mode 100644
index 7547254..0000000
--- a/libcpp/unittest/alignment/format/SAMHeaderPrinter_gtest.cpp
+++ /dev/null
@@ -1,138 +0,0 @@
-/*
- * =====================================================================================
- *
- * Filename: SAMHeaderPrinter_gtest.cpp
- *
- * Description: Test alignment/format/SAMHeaderPrinter.hpp
- *
- * Version: 1.0
- * Created: 03/24/2015 04:51:29 PM
- * Compiler: gcc
- *
- * Author: Yuan Li (yli), yli at pacificbiosciences.com
- * Company: Pacific Biosciences
- *
- * =====================================================================================
- */
-
-#define private public
-#define protected public
-
-#include <algorithm>
-#include <stdio.h>
-#include <string.h>
-#include "FASTAReader.hpp"
-#include "format/SAMHeaderPrinter.hpp"
-#include "pbdata/testdata.h"
-#include <gtest/gtest.h>
-using namespace std;
-
-class SAMHeaderPrinterTest: public testing::Test {
-public:
- void SetUp() {
- samQVs.SetDefaultQV();
- so = "UNKNOWN";
- readType = ReadType::SUBREAD;
-
- int rand;
- string fastaFn(fastaFile1);
- reader.computeMD5 = true;
- EXPECT_TRUE(reader.Init(fastaFn));
- reader.ReadAllSequencesIntoOne(sequence, &seqdb);
- }
-
- void TearDown() {
- if (printer) {
- delete printer;
- printer = NULL;
- }
- }
-
- SAMHeaderPrinter * printer;
- SupplementalQVList samQVs;
- string so;
- ReadType::ReadTypeEnum readType;
- FASTAReader reader;
- FASTASequence sequence;
- SequenceIndexDatabase<FASTASequence> seqdb;
-};
-
-
-const string bax1ExpectedHeader =
-"PU:m130220_114643_42129_c100471902550000001823071906131347_s1_p0\tPL:PACBIO\tDS:READTYPE=SUBREAD;BINDINGKIT=;SEQUENCINGKIT=;BASECALLERVERSION=2.0;InsertionQV=iq;DeletionQV=dq;SubstitutionQV=sq;MergeQV=mq;DeletionTag=dt";
-
-const string bax3ExpectedHeader =
-"PU:m150223_190837_42175_c100735112550000001823160806051530_s1_p0\tPL:PACBIO\tDS:READTYPE=SUBREAD;BINDINGKIT=100356300;SEQUENCINGKIT=100356200;BASECALLERVERSION=2.3;InsertionQV=iq;DeletionQV=dq;SubstitutionQV=sq;MergeQV=mq;DeletionTag=dt";
-
-const string pls1ExpectedHeader =
-"PU:m121215_065521_richard_c100425710150000001823055001121371_s1_p0\tPL:PACBIO\tDS:READTYPE=SUBREAD;BINDINGKIT=;SEQUENCINGKIT=;BASECALLERVERSION=1.3;InsertionQV=iq;DeletionQV=dq;SubstitutionQV=sq;MergeQV=mq;DeletionTag=dt";
-
-TEST_F(SAMHeaderPrinterTest, BAX_ONE_MOVIE_IN) {
- // Read from two bax files of the same movie.
- EXPECT_EQ(readType, ReadType::ReadTypeEnum::SUBREAD);
- vector<string> readsFiles = {baxFile1, baxFile2};
- printer = new SAMHeaderPrinter(so, seqdb, readsFiles, readType, samQVs, "blasr", "1.3.2", "blasr a b c");
-
- EXPECT_EQ(printer->_hd.ToString().find("@HD\tVN:1.5\tSO:UNKNOWN\tpb:3.0b"), 0);
- EXPECT_EQ(printer->_sqs._groups.size(), 12);
- EXPECT_EQ(printer->_sqs._groups[0].ToString().find ("@SQ\tSN:read1\tLN:100\tM5:"), 0);
- EXPECT_EQ(printer->_sqs._groups[11].ToString().find ("@SQ\tSN:read2x\tLN:100\tM5:"), 0);
-
- // Expect exactly one read group
- EXPECT_EQ(printer->_rgs._groups.size(), 1);
- EXPECT_NE(printer->_rgs._groups[0].ToString().find(bax1ExpectedHeader), string::npos);
-
- EXPECT_EQ(printer->_pgs._groups.size(), 1);
- EXPECT_EQ(printer->_cos._groups.size(), 0);
-}
-
-TEST_F(SAMHeaderPrinterTest, BAX_MULTI_MOVIE_IN) {
- // Read subread from more than one movies
- vector<string> readsFiles = {baxFile1, baxFile2, baxFile3, plsFile1};
- printer = new SAMHeaderPrinter(so, seqdb, readsFiles, readType, samQVs, "blasr", "1.3.2", "blasr a b c");
-
- EXPECT_EQ(printer->_hd.ToString().find("@HD\tVN:1.5\tSO:UNKNOWN\tpb:3.0b"), 0);
- EXPECT_EQ(printer->_sqs._groups.size(), 12);
- EXPECT_EQ(printer->_sqs._groups[0].ToString().find ("@SQ\tSN:read1\tLN:100\tM5:"), 0);
- EXPECT_EQ(printer->_sqs._groups[11].ToString().find ("@SQ\tSN:read2x\tLN:100\tM5:"), 0);
-
- // Expect three read groups because baxFile1 and baxFile2 contains reads of the same movie.
- EXPECT_EQ(printer->_rgs._groups.size(), 3);
-
- EXPECT_NE(printer->_rgs._groups[0].ToString().find(bax1ExpectedHeader), string::npos);
- EXPECT_NE(printer->_rgs._groups[1].ToString().find(bax3ExpectedHeader), string::npos);
- EXPECT_NE(printer->_rgs._groups[2].ToString().find(pls1ExpectedHeader), string::npos);
-
- EXPECT_EQ(printer->_pgs._groups.size(), 1);
- EXPECT_EQ(printer->_cos._groups.size(), 0);
-}
-
-
-const string bam1ExpectedHeader =
-"@RG\tID:b89a4406\tPL:PACBIO\tDS:READTYPE=SUBREAD;DeletionQV=dq;DeletionTag=dt;InsertionQV=iq;MergeQV=mq;SubstitutionQV=sq;Ipd=ip;BINDINGKIT=100356300;SEQUENCINGKIT=100356200;BASECALLERVERSION=2.3.0.0.140018\tPU:m140905_042212_sidney_c100564852550000001823085912221377_s1_X0";
-const string bam2ExpectedHeader =
-"PL:PACBIO\tDS:READTYPE=SUBREAD;DeletionQV=dq;DeletionTag=dt;InsertionQV=iq;MergeQV=mq;SubstitutionQV=sq;Ipd=ip;BINDINGKIT=100236500;SEQUENCINGKIT=001558034;BASECALLERVERSION=2.3.0.1.142990\tPU:m150325_224749_42269_c100795290850000001823159309091522_s1_p0";
-
-TEST_F(SAMHeaderPrinterTest, ONE_BAM_IN) {
- // Read the same file twice in order to test uniqueness of @RG
- vector<string> readsFiles = {bamFile1, bamFile1};
- printer = new SAMHeaderPrinter(so, seqdb, readsFiles, readType, samQVs, "blasr", "1.3.2", "blasr a b c");
-
- EXPECT_EQ(printer->_rgs._groups.size(), 1);
- EXPECT_EQ(printer->_rgs._groups[0].ToString(), bam1ExpectedHeader);
-
- EXPECT_EQ(printer->_pgs._groups.size(), 3);
-}
-
-TEST_F(SAMHeaderPrinterTest, TWO_BAM_IN) {
- // Read multiple bam files
- vector<string> readsFiles = {bamFile1, bamFile2};
- printer = new SAMHeaderPrinter(so, seqdb, readsFiles, readType, samQVs, "blasr", "1.3.2", "blasr a b c");
-
- EXPECT_EQ(printer->_rgs._groups.size(), 2);
- EXPECT_NE(printer->_rgs._groups[0].ToString().find(bam1ExpectedHeader), string::npos);
- EXPECT_NE(printer->_rgs._groups[1].ToString().find(bam2ExpectedHeader), string::npos);
-
- EXPECT_EQ(printer->_pgs._groups.size(), 3);
-}
-
diff --git a/libcpp/unittest/alignment/format/SAMPrinter_gtest.cpp b/libcpp/unittest/alignment/format/SAMPrinter_gtest.cpp
deleted file mode 100644
index 63331b7..0000000
--- a/libcpp/unittest/alignment/format/SAMPrinter_gtest.cpp
+++ /dev/null
@@ -1,45 +0,0 @@
-/*
- * =====================================================================================
- *
- * Filename: SAMHeaderPrinter_gtest.cpp
- *
- * Description: Test alignment/format/SAMHeaderPrinter.hpp
- *
- * Version: 1.0
- * Created: 03/24/2015 04:51:29 PM
- * Compiler: gcc
- *
- * Author: Yuan Li (yli), yli at pacificbiosciences.com
- * Company: Pacific Biosciences
- *
- * =====================================================================================
- */
-
-#define private public
-#define protected public
-
-#include <algorithm>
-#include <stdio.h>
-#include <string.h>
-#include "format/SAMPrinter.hpp"
-#include <gtest/gtest.h>
-using namespace std;
-
-TEST(SAMPrinterTest, AddMatchBlockCigarOps) {
- DNASequence qSeq; qSeq.Copy("XXXXXAAAAAGGGGGCCCCC");
- DNASequence tSeq; tSeq.Copy( "AAAAANGGGGCCCCC");
- blasr::Block b;
- b.qPos = 5;
- b.tPos = 0;
- b.length=15;
- vector<int> opSize;
- vector<char> opChar;
-
- const vector<int> expOpSize = {5 , 1 , 9 };
- const vector<char> expOpChar = {'=', 'X', '='};
-
- AddMatchBlockCigarOps(qSeq, tSeq, b, opSize, opChar);
-
- EXPECT_EQ(opSize, expOpSize);
- EXPECT_EQ(opChar, expOpChar);
-}
diff --git a/libcpp/unittest/alignment/utils/FileUtils_gtest.cpp b/libcpp/unittest/alignment/utils/FileUtils_gtest.cpp
deleted file mode 100644
index 1b2ea3b..0000000
--- a/libcpp/unittest/alignment/utils/FileUtils_gtest.cpp
+++ /dev/null
@@ -1,54 +0,0 @@
-/*
- * =====================================================================================
- *
- * Filename: FileUtils_gtest.cpp
- *
- * Description: Test alignment/utils/FileUtils.hpp
- *
- * Version: 1.0
- * Created: 10/29/2012 05:20:43 PM
- * Revision: 08/20/2014
- * Compiler: gcc
- *
- * Author: Yuan Li (yli), yli at pacificbiosciences.com
- * Company: Pacific Biosciences
- *
- * =====================================================================================
- */
-
-#include "gtest/gtest.h"
-#include "utils/FileUtils.hpp"
-
-using namespace std;
-
-string nonexistfile = "/nonexistingdir/nonexistingfile";
-string readablefile = "/bin/ls";
-string writeablefile = "/tmp/writabletmpfile";
-string expected_errmsg = "^.+$";
-
-TEST(FILEUTILS, CriticalOpenRead) {
- ifstream ifs;
- EXPECT_EXIT(CriticalOpenRead(nonexistfile, ifs, std::ios::in),
- ::testing::ExitedWithCode(1), expected_errmsg);
- CriticalOpenRead(readablefile, ifs, std::ios::in);
-}
-
-TEST(FILEUTILS, OpenRead) {
- ifstream ifs;
- EXPECT_EQ( OpenRead(nonexistfile, ifs, std::ios::in), 0);
- EXPECT_EQ( OpenRead(readablefile, ifs, std::ios::in), 1);
-}
-
-
-TEST(FILEUTILS, CriticalOpenWrite) {
- ofstream ofs;
- EXPECT_EXIT( CriticalOpenWrite(nonexistfile, ofs, std::ios::out),
- ::testing::ExitedWithCode(1), expected_errmsg);
- CriticalOpenWrite(writeablefile, ofs, std::ios::out);
-}
-
-TEST(FILEUTILS, OpenWrite) {
- ofstream ofs;
- EXPECT_EQ(OpenWrite(nonexistfile, ofs, std::ios::out), 0);
- EXPECT_EQ(OpenWrite(writeablefile, ofs, std::ios::out), 1);
-}
diff --git a/libcpp/unittest/alignment/utils/RangeUtils_gtest.cpp b/libcpp/unittest/alignment/utils/RangeUtils_gtest.cpp
deleted file mode 100644
index 482e586..0000000
--- a/libcpp/unittest/alignment/utils/RangeUtils_gtest.cpp
+++ /dev/null
@@ -1,63 +0,0 @@
-/*
- * =====================================================================================
- *
- * Filename: RangeUtils_gtest.cpp
- *
- * Description: Test alignment/utils/RangeUtils.hpp
- *
- * Version: 1.0
- * Created: 05/2/2013 06:01:01 PM
- * Revision: 08/21/2014
- * Compiler: gcc
- *
- * Author: Yuan Li (yli), yli at pacificbiosciences.com
- * Company: Pacific Biosciences
- *
- * =====================================================================================
- */
-
-#include "gtest/gtest.h"
-#include "utils/RangeUtils.hpp"
-
-TEST(RangeTest, RangeConstructor) {
- Range r(1, 2);
- EXPECT_EQ(r.start, 1);
- EXPECT_EQ(r.end, 2);
-
- Range r2(1);
- EXPECT_EQ(r2.end, 1);
-}
-
-TEST(RangeTest, Ranges) {
- UInt queryInRange[11] = {1,2,3,4,10,11,12,13,14,15,20};
- UInt queryNotInRange[8] = {0, 16, 17, 18, 19, 30, 5, 100000};
-
- Ranges ranges1(string("1,2,3,4,10-15,20-20"));
-
- for (int i = 0; i < 11; i++) {
- EXPECT_TRUE(ranges1.contains(queryInRange[i]));
- }
-
- for (int i = 0; i < 8; i++) {
- EXPECT_FALSE(ranges1.contains(queryNotInRange[i]));
- }
-}
-
-TEST(RangeTest, SetRanges) {
- Ranges rs;
- rs.setRanges("199");
-
- EXPECT_TRUE(rs.contains(199));
- EXPECT_EQ(rs.size(), 1);
-}
-
-
-TEST(RangeTest, max) {
- Ranges rs("199");
- EXPECT_EQ(rs.max(), 199);
- Ranges rs1("1, 10000, 10-30, 4000-5000");
- EXPECT_EQ(rs1.max(), 10000);
-
- Ranges rs2("1, 1000, 10-30, 4000-5000, 633-877");
- EXPECT_EQ(rs2.max(), 5000);
-}
diff --git a/libcpp/unittest/alignment/utils/RegionUtils_gtest.cpp b/libcpp/unittest/alignment/utils/RegionUtils_gtest.cpp
deleted file mode 100644
index 2daaa86..0000000
--- a/libcpp/unittest/alignment/utils/RegionUtils_gtest.cpp
+++ /dev/null
@@ -1,236 +0,0 @@
-/*
- * =====================================================================================
- *
- * Filename: RegionUtils_gtest.cpp
- *
- * Description: Test alignment/utils/RegionUtils.hpp
- *
- * Version: 1.0
- * Created: 11/29/2012 05:11:56 PM
- * Revision: none
- * Compiler: gcc
- *
- * Author: Yuan Li (yli), yli at pacificbiosciences.com
- * Company: Pacific Biosciences
- *
- * =====================================================================================
- */
-
-
-#include "gtest/gtest.h"
-#include "utils/RegionUtils.hpp"
-#include "reads/RegionTable.hpp"
-#include "HDFRegionTableReader.hpp"
-#include "pbdata/testdata.h"
-
-class RegionUtilTestFixture: public testing::Test {
-public:
- RegionUtilTestFixture() {
- fileName = baxFile1;
- reader = new HDFRegionTableReader();
- int rev = reader->Initialize(fileName);
- EXPECT_TRUE(rev);
- reader->ReadTable(regionTable);
- reader->Close();
- }
-
- void SetUp() {
- /* The region table for hole number 14798 is as follows.
- * type start end score
- * 1 0 712 -1
- * 1 760 2040 -1
- * 1 2098 3452 -1
- * 0 712 760 937
- * 0 2040 2098 741
- * 2 0 3424 819
- * where type 1 = insertion, 0 = adapter, 2 = HQRegion
- * */
- hqStart = 0;
- hqEnd = 3424;
- hqScore = 819;
- holeNumber = 14798;
-
- int srs[29][2] = {{95, 353},
- {404, 955},
- {998, 1243},
- {1289, 1529},
- {1576, 1824},
- {1869, 2132},
- {2178, 2444},
- {2486, 2727},
- {2767, 3004},
- {3047, 3286},
- {3329, 3537},
- {3583, 3818},
- {3862, 4096},
- {4139, 4404},
- {4447, 4673},
- {4717, 4956},
- {5004, 5228},
- {5275, 5508},
- {5552, 5790},
- {5835, 6072},
- {6113, 6338},
- {6389, 6604},
- {6647, 7145},
- {7189, 7421},
- {7468, 7693},
- {7733, 7951},
- {7989, 8197},
- {8243, 8482},
- {8522, 9244}};
-
- int rgn[59][5] = {{9, 1, 95, 353, -1},
- {9, 1, 404, 955, -1},
- {9, 1, 998, 1243, -1},
- {9, 1, 1289, 1529, -1},
- {9, 1, 1576, 1824, -1},
- {9, 1, 1869, 2132, -1},
- {9, 1, 2178, 2444, -1},
- {9, 1, 2486, 2727, -1},
- {9, 1, 2767, 3004, -1},
- {9, 1, 3047, 3286, -1},
- {9, 1, 3329, 3537, -1},
- {9, 1, 3583, 3818, -1},
- {9, 1, 3862, 4096, -1},
- {9, 1, 4139, 4404, -1},
- {9, 1, 4447, 4673, -1},
- {9, 1, 4717, 4956, -1},
- {9, 1, 5004, 5228, -1},
- {9, 1, 5275, 5508, -1},
- {9, 1, 5552, 5790, -1},
- {9, 1, 5835, 6072, -1},
- {9, 1, 6113, 6338, -1},
- {9, 1, 6389, 6604, -1},
- {9, 1, 6647, 7145, -1},
- {9, 1, 7189, 7421, -1},
- {9, 1, 7468, 7693, -1},
- {9, 1, 7733, 7951, -1},
- {9, 1, 7989, 8197, -1},
- {9, 1, 8243, 8482, -1},
- {9, 1, 8522, 9244, -1},
- {9, 0, 41, 95, 722},
- {9, 0, 353, 404, 784},
- {9, 0, 955, 998, 697},
- {9, 0, 1243, 1289, 804},
- {9, 0, 1529, 1576, 744},
- {9, 0, 1824, 1869, 844},
- {9, 0, 2132, 2178, 847},
- {9, 0, 2444, 2486, 666},
- {9, 0, 2727, 2767, 824},
- {9, 0, 3004, 3047, 883},
- {9, 0, 3286, 3329, 860},
- {9, 0, 3537, 3583, 891},
- {9, 0, 3818, 3862, 795},
- {9, 0, 4096, 4139, 906},
- {9, 0, 4404, 4447, 906},
- {9, 0, 4673, 4717, 886},
- {9, 0, 4956, 5004, 708},
- {9, 0, 5228, 5275, 957},
- {9, 0, 5508, 5552, 886},
- {9, 0, 5790, 5835, 733},
- {9, 0, 6072, 6113, 804},
- {9, 0, 6338, 6389, 666},
- {9, 0, 6604, 6647, 813},
- {9, 0, 7145, 7189, 795},
- {9, 0, 7421, 7468, 829},
- {9, 0, 7693, 7733, 774},
- {9, 0, 7951, 7989, 657},
- {9, 0, 8197, 8243, 760},
- {9, 0, 8482, 8522, 675},
- {9, 2, 0, 9244, 834}};
-
- for (int i = 0; i < 29; i++) {
- subreadIntervals.push_back(ReadInterval(srs[i][0], srs[i][1]));
- }
-
- for (int i = 0; i < 59; i++) {
- adapterIntervals.push_back(ReadInterval(rgn[i][2], rgn[i][3], rgn[i][4]));
- }
- }
-
- void TearDown() {
- }
-
- ~RegionUtilTestFixture() {
- delete reader;
- }
-
- HDFRegionTableReader * reader;
- RegionTable regionTable;
- string fileName;
- int hqStart, hqEnd, hqScore, holeNumber;
-
- // Data for testing Get*FullSubreadIndex.
- vector<ReadInterval> subreadIntervals;
- vector<ReadInterval> adapterIntervals;
-};
-
-TEST_F(RegionUtilTestFixture, LookupHQRegion) {
- int start, end, score;
- bool rev = LookupHQRegion(holeNumber, regionTable, start, end, score);
- EXPECT_EQ(rev, true);
- EXPECT_EQ(start, hqStart);
- EXPECT_EQ(end, hqEnd);
- EXPECT_EQ(score, hqScore);
-}
-
-TEST_F(RegionUtilTestFixture, GetHighQulitySubreadsIntervals) {
- vector<ReadInterval> intervals;
- intervals.push_back(ReadInterval(0, 712));
- intervals.push_back(ReadInterval(760, 2040));
- intervals.push_back(ReadInterval(2098, 3452));
-
- vector<int> directions;
- directions.push_back(0);
- directions.push_back(1);
- directions.push_back(0);
-
- int indx = GetHighQualitySubreadsIntervals(intervals, directions, hqStart, hqEnd);
- EXPECT_EQ(intervals.size(), 3);
- EXPECT_EQ(indx, 2);
- int starts [3] = {0, 760, 2098};
- int ends [3] = {712, 2040, 3424};
- int ds [3] = {0, 1, 0};
- for(int i=0; i < 3; i++) {
- EXPECT_EQ(intervals[i].start, starts[i]);
- EXPECT_EQ(intervals[i].end , ends[i] );
- EXPECT_EQ(directions[i] , ds[i] );
- }
-
- indx = GetHighQualitySubreadsIntervals(intervals, directions, hqStart, hqEnd, 800);
- EXPECT_EQ(intervals.size(), 2);
- // The first interval and its direction has been removed as the length is less
- // than 800.
- for(int i=0; i < 2; i++) {
- EXPECT_EQ(intervals[i].start, starts[i+1]);
- EXPECT_EQ(intervals[i].end , ends[i+1] );
- }
-}
-
-TEST_F(RegionUtilTestFixture, GetFullPassSubreadIndices ) {
- vector<int> vi = GetFullPassSubreadIndices(subreadIntervals, adapterIntervals);
- // vi = 0, ..., 27
- EXPECT_EQ(vi.size(), 28);
- for(int i=0; i < 28; i++) {
- EXPECT_EQ(vi[i], i);
- }
-}
-
-TEST_F(RegionUtilTestFixture, GetMedianLengthFullSubreadIndex) {
- int idx = GetMedianLengthFullSubreadIndex(subreadIntervals, adapterIntervals);
- EXPECT_EQ(idx, 18); // Median length subread (5552, 5790)
-}
-
-TEST_F(RegionUtilTestFixture, GetLongestFullSubreadIndex) {
- int idx = GetLongestFullSubreadIndex(subreadIntervals, adapterIntervals);
- EXPECT_EQ(idx, 1);
- // The longest full pass subread (404, 955)
-}
-
-TEST_F(RegionUtilTestFixture, GetTypicalFullSubreadIndex) {
- int idx = GetTypicalFullSubreadIndex(subreadIntervals, adapterIntervals);
- EXPECT_EQ(idx, 22);
- // Typical = the second longest full pass subread (6647, 7145)
-}
-
diff --git a/libcpp/unittest/build.mk b/libcpp/unittest/build.mk
deleted file mode 100644
index a8dde8f..0000000
--- a/libcpp/unittest/build.mk
+++ /dev/null
@@ -1,27 +0,0 @@
-all:
-
-include ../rules.mk
-include defines.mk
-
-EXE := test-runner
-
-all: $(EXE)
-
-gtest: $(EXE)
- ./$< --gtest_output=xml:./xml/all.xml
-
-LIBS := alignment/libblasr_gtest.a \
- hdf/libpbihdf_gtest.a \
- pbdata/libpbdata_gtest.a
-
-$(EXE): $(LIBS)
- $(CXX) $(CXXOPTS) $(CXXFLAGS) $(GTEST_SRC) -Wl,$(LD_WHOLE_ARCHIVE) $^ -Wl,$(LD_NO_WHOLE_ARCHIVE) -o $@ -I$(GTEST_ROOT) $(LIBDIRS) $(LDFLAGS)
-
-$(LIBS):
- ${MAKE} -C $(dir $@) PBINCROOT=${PBINCROOT}/.. $(notdir $@)
-
-clean:
- @${MAKE} -C alignment clean
- @${MAKE} -C hdf clean
- @${MAKE} -C pbdata clean
- @${RM} -fr $(EXE) xml
diff --git a/libcpp/unittest/common.mk b/libcpp/unittest/common.mk
deleted file mode 100644
index 5337ea9..0000000
--- a/libcpp/unittest/common.mk
+++ /dev/null
@@ -1,64 +0,0 @@
-SHELL=bash
-
-.PHONY: all debug profile clean
-
-#
-# Definitions common to all make files for unit tests.
-# All paths are relative from inside the subdirectories, not this file
-#
-
-PBINCROOT ?= $(realpath ../..)
-PREBUILT ?= $(realpath ../../../../../prebuilt.out)
-THIRD_PARTY_PREFIX ?= ../../..
-
-include $(PBINCROOT)/common.mk
-
-# All Google Test headers. Usually you shouldn't change this.
-GTEST_ROOT := $(THIRD_PARTY)/gtest/fused-src
-GTEST_SRC := $(GTEST_ROOT)/gtest/gtest-all.cc \
- $(GTEST_ROOT)/gtest/gtest_main.cc
-
-# INCLUDE DIRS
-INCDIRS = -I$(PBINCROOT)/alignment \
- -I$(PBINCROOT)/hdf \
- -I$(PBINCROOT)/pbdata \
- -I$(PBINCROOT)/unittest \
- -I$(GTEST_ROOT) \
- -I$(HDF5_INC)
-
-# LIB DIRS
-LIBDIRS = -L$(PBINCROOT)/alignment \
- -L$(PBINCROOT)/hdf \
- -L$(PBINCROOT)/pbdata \
- -L$(HDF5_LIB)
-
-LDFLAGS1 := -lblasr -lpbihdf -lpbdata
-# The order of -l{lib} matters
-
-ifeq ($(origin nopbbam), undefined)
- INCDIRS += -I$(PBBAM)/include -I$(PBBAM)/third-party/htslib
- LIBDIRS += -L$(PBBAM)/lib -L$(PBBAM)/third-party/htslib
- LDFLAGS1 += -lpbbam
-# Use libhts.a built with pbbam
-ifneq ($(wildcard "$(PBBAM)/third-party/htslib/libhts.a"), "")
- LDFLAGS1 += $(PBBAM)/third-party/htslib/libhts.a
-else
- LDFLAGS1 += lhts
-endif
-endif
-
-ifneq ($(ZLIB_ROOT), notfound)
- INCDIRS += -I$(ZLIB_ROOT)/include
- LIBDIRS += -L$(ZLIB_ROOT)/lib
-endif
-
-ifneq ($(wildcard "$(HDF5_LIB)/libhdf5_cpp.a"),"")
- LDFLAGS := $(LDFLAGS1) $(HDF5_LIB)/libhdf5_cpp.a $(HDF5_LIB)/libhdf5.a -lpthread -lz -ldl
-else
- LDFLAGS := $(LDFLAGS1) -lhdf5_cpp -lhdf5 -lpthread -lz -ldl
-endif
-
-
-CXX := g++
-CXXOPTS := -std=c++11 -Wno-div-by-zero
-CXXFLAGS := -O3
diff --git a/libcpp/unittest/hdf/HDF2DArray_gtest.cpp b/libcpp/unittest/hdf/HDF2DArray_gtest.cpp
deleted file mode 100644
index 96b27b6..0000000
--- a/libcpp/unittest/hdf/HDF2DArray_gtest.cpp
+++ /dev/null
@@ -1,96 +0,0 @@
-/*
- * ==========================================================================
- *
- * Filename: HDF2DArray_gtest.cpp
- *
- * Description: Test hdf/HDF2DArray.hpp
- *
- * Version: 1.0
- * Created: 08/21/2013 07:00:49 PM
- * Revision: 08/20/2014
- * Compiler: gcc
- *
- * Author: Yuan Li (yli), yli at pacificbiosciences.com
- * Company: Pacific Biosciences
- *
- * ==========================================================================
- */
-#include <string>
-#include "H5Cpp.h"
-#include "HDFArray.hpp"
-#include "HDFGroup.hpp"
-#include "HDF2DArray.hpp"
-#include "reads/HoleXY.hpp"
-#include "pbdata/testdata.h"
-#include "gtest/gtest.h"
-
-using namespace std;
-using namespace H5;
-/*
-//Note ::testing::Test not ::testing::TEST
-//SetUp() and TearDown(), not Setup() and Teardown()
-class HDF2DArrayTest: public :: testing::Test {
-public:
- virtual void SetUp() {
- }
- virtual void TearDown() {
- }
- string x;
-};
-
-TEST_F(HDF2DArrayTest, x) {
- EXPECT_TRUE(true);
-}
-*/
-
-class HDF2DArrayTest : public ::testing::Test {
-public:
- virtual void SetUp() {
- fileName = baxFile2; // Defined in testdata.h
- try {
- FileAccPropList propList;
- pbihdfFile.openFile(fileName.c_str(), H5F_ACC_RDONLY, propList);
- } catch (Exception &e) {
- cout << "ERROR, could not open hdf file" << fileName
- << ", exiting." << endl;
- exit(1);
- }
-
- ASSERT_NE(rootGroup.Initialize(pbihdfFile, "/"), 0);
- ASSERT_NE(pulseDataGroup.Initialize(rootGroup, "PulseData"), 0);
- ASSERT_NE(baseCallsGroup.Initialize(pulseDataGroup, "BaseCalls"), 0);
- ASSERT_NE(zmwGroup.Initialize(baseCallsGroup, "ZMW"), 0);
- }
-
- virtual void TearDown() {
- rootGroup.Close();
- pulseDataGroup.Close();
- baseCallsGroup.Close();
- zmwGroup.Close();
- pbihdfFile.close();
- }
-
- string fileName;
- H5File pbihdfFile;
- HDFGroup rootGroup, pulseDataGroup, baseCallsGroup, zmwGroup;
-};
-
-//Test HDF2DArray, int16
-TEST_F(HDF2DArrayTest, int16) {
- HDF2DArray<int16_t> xyArray;
- xyArray.Initialize(zmwGroup, "HoleXY");
- vector<HoleXY> xys;
- xys.resize(10);
- for(int i = 0; i < 10; i++){
- xyArray.Read(i, i+1, xys[i].xy);
- ASSERT_EQ(xys[i].xy[0], 43);
- ASSERT_EQ(xys[i].xy[1], 44 + i);
- }
-
- int last = 54493;
-
- xyArray.Read(last, last+1, xys[0].xy);
- ASSERT_EQ(xys[0].xy[0], -43);
- ASSERT_EQ(xys[0].xy[1], -44);
- xyArray.Close();
-}
diff --git a/libcpp/unittest/hdf/HDFBasReader_gtest.cpp b/libcpp/unittest/hdf/HDFBasReader_gtest.cpp
deleted file mode 100644
index a196395..0000000
--- a/libcpp/unittest/hdf/HDFBasReader_gtest.cpp
+++ /dev/null
@@ -1,56 +0,0 @@
-/*
- * ============================================================================
- *
- * Filename: HDFBasReader_gtest.cpp
- *
- * Description: Test hdf/HDFBasReader.hpp
- *
- * Version: 1.0
- * Created: 08/23/2013 10:17:14 AM
- * Revision: 08/20/2014
- * Compiler: gcc
- *
- * Author: Yuan Li (yli), yli at pacificbiosciences.com
- * Company: Pacific Biosciences
- *
- * ============================================================================
- */
-
-#include "gtest/gtest.h"
-#include "HDFBasReader.hpp"
-#include "pbdata/testdata.h"
-
-using namespace std;
-using namespace H5;
-
-class HDFBasReaderTEST : public ::testing::Test {
-public:
- virtual void SetUp() {
- fileName = baxFile3;
- reader.InitializeDefaultIncludedFields();
- ASSERT_EQ(reader.Initialize(fileName), 1);
- }
- virtual void TearDown() {
- reader.Close();
- }
- string fileName;
- T_HDFBasReader<SMRTSequence> reader;
-};
-
-TEST_F(HDFBasReaderTEST, ReadBaseFromBaseCalls) {
- ASSERT_EQ(reader.GetMovieName(),
- "m150223_190837_42175_c100735112550000001823160806051530_s1_p0");
- SMRTSequence seq;
-
- for(int i=0; i < 1000; i++) {
- reader.GetNext(seq);
- }
-}
-
-TEST_F(HDFBasReaderTEST, GetChemistryTriple) {
- string bindingKit, sequencingKit, version;
- reader.GetChemistryTriple(bindingKit, sequencingKit, version);
- EXPECT_EQ(bindingKit, "100356300");
- EXPECT_EQ(sequencingKit, "100356200");
- EXPECT_EQ(version, "2.3");
-}
diff --git a/libcpp/unittest/hdf/HDFCCSReader_gtest.cpp b/libcpp/unittest/hdf/HDFCCSReader_gtest.cpp
deleted file mode 100644
index 1ff04c1..0000000
--- a/libcpp/unittest/hdf/HDFCCSReader_gtest.cpp
+++ /dev/null
@@ -1,68 +0,0 @@
-/*
- * ============================================================================
- *
- * Filename: HDFCCSReader_gtest.cpp
- *
- * Description: Test hdf/HDFCCSReader.hpp
- *
- * Version: 1.0
- * Created: 08/23/2013 10:17:14 AM
- * Revision: 08/20/2014
- * Compiler: gcc
- *
- * Author: Yuan Li (yli), yli at pacificbiosciences.com
- * Company: Pacific Biosciences
- *
- * ============================================================================
- */
-
-#include "HDFCCSReader.hpp"
-#include "CCSSequence.hpp"
-#include "gtest/gtest.h"
-#include "pbdata/testdata.h"
-
-using namespace std;
-using namespace H5;
-
-class HDFCCSReaderTEST : public ::testing::Test {
-public:
- virtual void SetUp() {
- }
- virtual void TearDown() {
- }
-};
-
-TEST_F(HDFCCSReaderTEST, ReadCCSFromBasH5) {
- string fileName = baxFile2;
- HDFCCSReader<CCSSequence> reader;
- reader.InitializeDefaultIncludedFields();
- ASSERT_EQ(reader.Initialize(fileName), 1);
- ASSERT_EQ(reader.GetMovieName(),
- "m130220_114643_42129_c100471902550000001823071906131347_s1_p0");
-
- CCSSequence seq;
- for(int i=0; i < 1000; i++) {
- reader.GetNext(seq);
- }
- reader.Close();
-}
-
-TEST_F(HDFCCSReaderTEST, ReadCCSFromCCSH5) {
- string fileName = ccsFile1;
- HDFCCSReader<CCSSequence> reader;
- reader.SetReadBasesFromCCS();
- reader.InitializeDefaultIncludedFields();
- ASSERT_EQ(reader.Initialize(fileName), 1);
- ASSERT_EQ(reader.GetMovieName(),
- "m130328_211423_ethan_c100499512550000001823070408081371_s1_p0");
-
- CCSSequence seq;
- for(int i=0; i < 1000; i++) {
- reader.GetNext(seq);
- }
-
- reader.Close();
-}
-
-
-
diff --git a/libcpp/unittest/hdf/HDFPlsReader_gtest.cpp b/libcpp/unittest/hdf/HDFPlsReader_gtest.cpp
deleted file mode 100644
index a4f63a2..0000000
--- a/libcpp/unittest/hdf/HDFPlsReader_gtest.cpp
+++ /dev/null
@@ -1,49 +0,0 @@
-/*
- * ============================================================================
- *
- * Filename: HDFPlsReader_gtest.cpp
- *
- * Description: Test hdf/HDFPlsReader.hpp
- *
- * Version: 1.0
- * Created: 08/23/2013 11:13:34 AM
- * Revision: 08/20/2014
- * Compiler: gcc
- *
- * Author: Yuan Li (yli), yli at pacificbiosciences.com
- * Company: Pacific Biosciences
- *
- * ============================================================================
- */
-
-#include "HDFPlsReader.hpp"
-#include "gtest/gtest.h"
-#include "pbdata/testdata.h"
-
-using namespace std;
-using namespace H5;
-
-class HDFPlsReaderTEST : public ::testing::Test {
-public:
- virtual void SetUp() {
- fileName = plsFile1;
- ASSERT_EQ(reader.Initialize(fileName), 1);
- }
- virtual void TearDown() {
- reader.Close();
- }
- string fileName;
- HDFPlsReader reader;
-};
-
-TEST_F(HDFPlsReaderTEST, ReadToPulseFile) {
- PulseFile pulseFile;
- reader.IncludeField("NumEvent");
- reader.IncludeField("StartFrame");
- reader.ReadPulseFileInit(pulseFile);
- reader.ReadPulseFile(pulseFile);
- ASSERT_EQ(pulseFile.platformId, 0);
- ASSERT_EQ(pulseFile.startFrame.size(), 197626964);
-}
-
-
diff --git a/libcpp/unittest/hdf/HDFScanDataReader_gtest.cpp b/libcpp/unittest/hdf/HDFScanDataReader_gtest.cpp
deleted file mode 100644
index 9beb6b1..0000000
--- a/libcpp/unittest/hdf/HDFScanDataReader_gtest.cpp
+++ /dev/null
@@ -1,52 +0,0 @@
-#include "gtest/gtest.h"
-#include "HDFScanDataReader.hpp"
-#include "pbdata/testdata.h"
-
-using namespace std;
-using namespace H5;
-
-class HDFScanDataReaderTEST : public ::testing::Test {
-public:
- virtual void SetUp() {
- fileName = scanDataFile1;
- try{
- hdfFile.openFile(fileName.c_str(), H5F_ACC_RDONLY);
- ASSERT_EQ(rootGroup.Initialize(hdfFile, "/"), 1);
- ASSERT_EQ(reader.Initialize(dynamic_cast<HDFGroup*>(&rootGroup)), 1);
- } catch(H5::Exception & e) {
- cerr << "Failed to open " << fileName << endl;
- ASSERT_FALSE(true);
- }
- }
-
- virtual void TearDown() {
- reader.Close();
- hdfFile.close();
- }
-
- string fileName;
- H5::H5File hdfFile;
- HDFGroup rootGroup;
- HDFScanDataReader reader;
-};
-
-TEST_F(HDFScanDataReaderTEST, ReadBindingKit) {
- string bindingKit;
- EXPECT_EQ(reader.ReadBindingKit(bindingKit), 1);
- EXPECT_EQ(bindingKit, "100356300");
-
- // Test if bindkingKit can be read multiple times.
- EXPECT_EQ(reader.ReadBindingKit(bindingKit), 1);
- EXPECT_EQ(bindingKit, "100356300");
-}
-
-TEST_F(HDFScanDataReaderTEST, ReadSequencingKit) {
- string sequencingKit;
- EXPECT_EQ(reader.ReadSequencingKit(sequencingKit), 1);
- EXPECT_EQ(sequencingKit, "100356200");
-
- // Test if sequencingKit can be read multiple times.
- EXPECT_EQ(reader.ReadSequencingKit(sequencingKit), 1);
- EXPECT_EQ(sequencingKit, "100356200");
-}
-
diff --git a/libcpp/unittest/hdf/HDFScanDataWriter_gtest.cpp b/libcpp/unittest/hdf/HDFScanDataWriter_gtest.cpp
deleted file mode 100644
index 15831ca..0000000
--- a/libcpp/unittest/hdf/HDFScanDataWriter_gtest.cpp
+++ /dev/null
@@ -1,36 +0,0 @@
-/*
- * ============================================================================
- *
- * Filename: HDFScanDataWriter_gtest.cpp
- *
- * Description: Test data/HDFScanDataWriter.hpp
- *
- * Version: 1.0
- * Created: 10/14/2013 03:04:00 PM
- * Revision: 08/20/2014
- * Compiler: gcc
- *
- * Author: Yuan Li (yli), yli at pacificbiosciences.com
- * Company: Pacific Biosciences
- *
- * ============================================================================
- */
-
-#include "gtest/gtest.h"
-#include "HDFScanDataWriter.hpp"
-#include "HDFFile.hpp"
-#include "reads/ScanData.hpp"
-
-TEST(HDFScanDataWriter, Write) {
- ScanData sd;
- sd.frameRate = 100;
-
- HDFFile outFile;
- outFile.Open("scandata.h5", H5F_ACC_TRUNC);
- HDFScanDataWriter writer(outFile);
- writer.Write(sd);
- writer.WriteMovieName("xyz");
- writer.WriteFrameRate(70);
- writer.Close();
- outFile.Close();
-}
diff --git a/libcpp/unittest/hdf/HDFUtils_gtest.cpp b/libcpp/unittest/hdf/HDFUtils_gtest.cpp
deleted file mode 100644
index 7fab6d7..0000000
--- a/libcpp/unittest/hdf/HDFUtils_gtest.cpp
+++ /dev/null
@@ -1,38 +0,0 @@
-/*
- * ============================================================================
- *
- * Filename: HDFUtils_gtest.cpp
- *
- * Description: Test hdf/HDFUtils.hpp
- *
- * Version: 1.0
- * Created: 11/04/2013 10:55:10 AM
- * Revision: none
- * Compiler: gcc
- *
- * Author: Yuan Li (yli), yli at pacificbiosciences.com
- * Company: Pacific Biosciences
- *
- * ============================================================================
- */
-
-#include "HDFUtils.hpp"
-#include "gtest/gtest.h"
-#include "pbdata/testdata.h"
-
-TEST(HDFUtils, Create) {
- EXPECT_EQ(GetH5MovieName(baxFile1),
- "m130220_114643_42129_c100471902550000001823071906131347_s1_p0");
-
- EXPECT_EQ(GetH5MovieName(baxFile2),
- "m130220_114643_42129_c100471902550000001823071906131347_s1_p0");
-
- EXPECT_EQ(GetH5MovieName(plsFile1),
- "m121215_065521_richard_c100425710150000001823055001121371_s1_p0");
-
- EXPECT_EQ(GetH5MovieName(ccsFile1),
- "m130328_211423_ethan_c100499512550000001823070408081371_s1_p0");
-
- EXPECT_EQ(GetH5MovieName(rgnFile1),
- "m130427_152935_42178_c100518602550000001823079209281316_s1_p0");
-}
diff --git a/libcpp/unittest/hdf/HDFZMWReader_gtest.cpp b/libcpp/unittest/hdf/HDFZMWReader_gtest.cpp
deleted file mode 100644
index 63b8f6d..0000000
--- a/libcpp/unittest/hdf/HDFZMWReader_gtest.cpp
+++ /dev/null
@@ -1,125 +0,0 @@
-/*
- * ==========================================================================
- *
- * Filename: HDFZMWReader_gtest.cpp
- *
- * Description: Test hdf/HDFZMWReader.hpp
- *
- * Version: 1.0
- * Created: 08/21/2013 07:00:49 PM
- * Revision: 08/20/2014
- * Compiler: gcc
- *
- * Author: Yuan Li (yli), yli at pacificbiosciences.com
- * Company: Pacific Biosciences
- *
- * ==========================================================================
- */
-#include "HDFZMWReader.hpp"
-#include "gtest/gtest.h"
-#include "pbdata/testdata.h"
-
-using namespace std;
-using namespace H5;
-
-class HDFZMWReaderTEST : public ::testing::Test {
-public:
- virtual void SetUp() {
- }
- virtual void TearDown() {
- }
-
- void Initialize(H5File & pbihdfFile, string fileName,
- string groupName, HDFGroup & callsGroup) {
- try {
- FileAccPropList propList;
- pbihdfFile.openFile(fileName.c_str(), H5F_ACC_RDONLY, propList);
- } catch (Exception &e) {
- cout << "ERROR, could not open hdf file" << fileName
- << ", exiting." << endl;
- exit(1);
- }
-
- ASSERT_NE(callsGroup.Initialize(pbihdfFile, groupName), 0);
-
- /*
- HDFGroup rootGroup, pulseDataGroup;
- if (rootGroup.Initialize(pbihdfFile, "/") == 0) {
- cout << "ERROR, could not open /" << endl;
- exit(1);
- }
-
- if (pulseDataGroup.Initialize(rootGroup, "PulseData") == 0){
- cout << "ERROR, could not open /PulseData" << endl;
- exit(1);
- }
-
- ASSERT_NE(callsGroup.Initialize(pulseDataGroup, "BaseCalls"), 0);
- */
- }
-
- void Close(H5File & pbihdfFile, HDFGroup & callsGroup) {
- pbihdfFile.close();
- callsGroup.Close();
- }
-
- void TestGetNext(HDFZMWReader & zmwReader) {
- int count = 0;
- ZMWGroupEntry entry;
- while(zmwReader.GetNext(entry)) {
- count ++;
- ASSERT_EQ(zmwReader.curZMW, count);
- }
- ASSERT_EQ(count, zmwReader.nZMWEntries);
- }
-};
-
-TEST_F(HDFZMWReaderTEST, ReadZMWFromBaseCalls) {
- HDFZMWReader zmwReader;
- string fileName = baxFile2;
- string groupName = "/PulseData/BaseCalls";
- H5File pbihdfFile;
- HDFGroup baseCallsGroup;
-
- Initialize(pbihdfFile, fileName, groupName, baseCallsGroup);
- ASSERT_NE(zmwReader.Initialize(&baseCallsGroup), 0);
-
- TestGetNext(zmwReader);
- zmwReader.Close();
- Close(pbihdfFile, baseCallsGroup);
-}
-
-TEST_F(HDFZMWReaderTEST, ReadZMWFromPulseCalls) {
- string fileName = plsFile1;
- H5File pbihdfFile;
- try {
- FileAccPropList propList;
- pbihdfFile.openFile(fileName.c_str(), H5F_ACC_RDONLY, propList);
- } catch (Exception &e) {
- cout << "ERROR, could not open hdf file" << fileName
- << ", exiting." << endl;
- exit(1);
- }
-
- HDFGroup pulseCallsGroup;
- ASSERT_NE(pulseCallsGroup.Initialize(pbihdfFile,"/PulseData/PulseCalls"), 0);
-
- HDFZMWReader zmwReader;
- ASSERT_NE(zmwReader.Initialize(&pulseCallsGroup), 0);
- TestGetNext(zmwReader);
- zmwReader.Close();
-
- // Switch to read from CCS ZMW.
- HDFGroup ccsGroup;
- ASSERT_NE(ccsGroup.Initialize(pbihdfFile, "/PulseData/ConsensusBaseCalls"), 0);
- ASSERT_NE(zmwReader.Initialize(&ccsGroup), 0);
- TestGetNext(zmwReader);
- zmwReader.Close();
-
- // Close
- ccsGroup.Close();
- pulseCallsGroup.Close();
- pbihdfFile.close();
-}
-
-
diff --git a/libcpp/unittest/hdf/Makefile b/libcpp/unittest/hdf/Makefile
deleted file mode 100644
index d942d8f..0000000
--- a/libcpp/unittest/hdf/Makefile
+++ /dev/null
@@ -1,26 +0,0 @@
-include ../../rules.mk
-include ../defines.mk
-
-SOURCES = $(wildcard *.cpp)
-OBJECTS = $(SOURCES:.cpp=.o)
-
-EXE := test-runner
-
-all debug profile: $(EXE)
-
-libpbihdf_gtest.a: $(OBJECTS)
- $(AR) $(ARFLAGS)c $@ $^
-
-$(EXE): $(OBJECTS)
- $(CXX) $(CXXOPTS) $(CXXFLAGS) $^ $(GTEST_SRC) -o $@ -I$(GTEST_ROOT) $(LIBDIRS) $(LDFLAGS)
-
-$(OBJECTS): %.o: %.cpp
- $(CXX) $(CXXOPTS) $(CXXFLAGS) -c $< -o $@ $(INCDIRS)
-
-gtest: $(EXE)
- ./$< --gtest_output=xml:../xml/hdf.xml
-
-clean:
- @find . -type f -name \*.o -delete
- @find . -type f -name \*.d -delete
- @rm -f libpbihdf_gtest.a $(EXE) ../xml/hdf.xml
diff --git a/libcpp/unittest/normal.Makefile b/libcpp/unittest/normal.Makefile
deleted file mode 100644
index 798365f..0000000
--- a/libcpp/unittest/normal.Makefile
+++ /dev/null
@@ -1,9 +0,0 @@
-export
-# Same as .EXPORT_ALL_VARIABLES
-
-all clean gtest: mkdefines
- ${MAKE} -f build.mk $@
-
-mkdefines:
- #./conf-nightly.py defines.mk
- cp normal.defines.mk defines.mk
diff --git a/libcpp/unittest/normal.defines.mk b/libcpp/unittest/normal.defines.mk
deleted file mode 100644
index a8264c4..0000000
--- a/libcpp/unittest/normal.defines.mk
+++ /dev/null
@@ -1,54 +0,0 @@
-PBINCROOT?=..
-#THIRD_PARTY_PREFIX ?= ../../..
-
-#include $(PBINCROOT)/common.mk
-
-
-HDF_HEADERS:=hdf5-1.8.12-headers
-HDF5:=/home/UNIXHOME/cdunn/repo/pb/smrtanalysis-client/smrtanalysis/prebuilt.out/hdf5/hdf5-1.8.12/ubuntu-1404
-HDF5_INC?=../hdf/${HDF_HEADERS}/src
-HDF5_LIB?=${HDF5}/lib
-INCLUDES+=-I${PBINCROOT}/hdf/${HDF_HEADERS}/src -I${PBINCROOT}/hdf/${HDF_HEADERS}/c++/src
-#INCLUDES+=-I../pbdata -I../hdf -I.
-
-#OS := $(shell uname)
-
-#ifeq ($(OS), Darwin)
-# LD_WHOLE_ARCHIVE := -all_load
-# LD_NO_WHOLE_ARCHIVE := -noall_load
-#else
-# LD_WHOLE_ARCHIVE := --whole-archive
-# LD_NO_WHOLE_ARCHIVE := --no-whole-archive
-#endif
-
-LD_WHOLE_ARCHIVE := --whole-archive
-LD_NO_WHOLE_ARCHIVE := --no-whole-archive
-
-# All Google Test headers. Usually you shouldn't change this.
-#GTEST_ROOT := $(THIRD_PARTY)/gtest/fused-src
-GTEST_ROOT:=/home/UNIXHOME/cdunn/repo/gh/blasr_libcpp/../pbdagcon/test/cpp/gtest-1.7.0/fused-src
-GTEST_SRC := $(GTEST_ROOT)/gtest/gtest-all.cc \
- $(GTEST_ROOT)/gtest/gtest_main.cc
-
-# INCLUDE DIRS
-INCDIRS = -I$(PBINCROOT)/alignment \
- -I$(PBINCROOT)/hdf \
- -I$(PBINCROOT)/pbdata \
- -I$(PBINCROOT)/unittest \
- -I$(GTEST_ROOT)
-INCDIRS+=${INCLUDES}
-
-# LIB DIRS
-LIBDIRS = -L$(PBINCROOT)/alignment \
- -L$(PBINCROOT)/hdf \
- -L$(PBINCROOT)/pbdata \
- -L$(HDF5_LIB)
-
-LDFLAGS1 := -lblasr -lpbihdf -lpbdata
-# The order of -l{lib} matters
-
-#LDFLAGS := $(LDFLAGS1) -lhdf5_cpp -lhdf5 -lpthread -lz -ldl
-LDFLAGS := $(LDFLAGS1) $(HDF5_LIB)/libhdf5_cpp.a $(HDF5_LIB)/libhdf5.a -lpthread -lz -ldl
-
-CXXOPTS := -std=c++11 -Wno-div-by-zero
-CXXFLAGS := -O3
diff --git a/libcpp/unittest/pbdata/CCSSequence_gtest.cpp b/libcpp/unittest/pbdata/CCSSequence_gtest.cpp
deleted file mode 100644
index 02e72cd..0000000
--- a/libcpp/unittest/pbdata/CCSSequence_gtest.cpp
+++ /dev/null
@@ -1,117 +0,0 @@
-/*
- * =====================================================================================
- *
- * Filename: CCSSequence_gtest.cpp
- *
- * Description: Test pbdata/CCSSequence.hpp
- *
- * Version: 1.0
- * Created: 10/29/2012 05:17:04 PM
- * Revision: none
- * Compiler: gcc
- *
- * Author: Yuan Li (yli), yli at pacificbiosciences.com
- * Company: Pacific Biosciences
- *
- * =====================================================================================
- */
-
-#include "gtest/gtest.h"
-#include "CCSSequence.hpp"
-
-using namespace std;
-
-Nucleotide sr0[] = "ATATGGGGATTAGGGGATA";
-Nucleotide sr1[] = "TAATCCCGTAATCCCGGTAT"; //rc = TAATCCCGTAATCCCGGTAT
-Nucleotide sr2[] = "ATAGGGGGATTAGGGGATTCA";
-Nucleotide adapter[] = "CCC";
-Nucleotide unrolled_seq[] = "ATATGGGGATTAGGGGATACCCTAATCCCGTAATCCCGGTATCCCATAGGGGGATTAGGGGATTCA";
-int sz0 = 19;
-int sz1 = 20;
-int sz2 = 21;
-int adaptersz = 3;
-int unrolledsz = sz0 + sz1 + sz2 + adaptersz * 2;
-const int numSubreads = 3;
-
-
-class CCSSequenceTest: public:: testing:: Test{
-public:
- void CreateSMRTSequence(SMRTSequence & smrt, Nucleotide* seq,
- int holeNumber, int start, int end) {
- int size = end - start;
- smrt.seq = new Nucleotide[size];
- memcpy(smrt.seq, seq, size*sizeof(Nucleotide));
- smrt.length = size;
- smrt.deleteOnExit = false;
-
- smrt.zmwData.holeNumber = holeNumber;
- smrt.subreadStart = start;
- smrt.subreadEnd = end;
-
- stringstream ss;
- }
-
- void SetUp() {
- //Create a vector of subreads.
- subreads.resize(numSubreads);
- int s = 0;
- CreateSMRTSequence(subreads[0], &sr0[0], 1, s, s + sz0);
- s += sz0 + adaptersz;
- CreateSMRTSequence(subreads[1], &sr1[0], 1, s, s + sz1);
- s += sz1 + adaptersz;
- CreateSMRTSequence(subreads[2], &sr2[0], 1, s, s + sz2);
-
- //Create ccs
- stringstream ss;
- subreads[0].Print(ss);
-
- CreateSMRTSequence(ccs.unrolledRead, &unrolled_seq[0], 1, 0, unrolledsz);
- ccs.numPasses = numSubreads;
- CreateSMRTSequence((SMRTSequence&)ccs, &sr0[0], 1, 0, sz0);
- ccs.numConsensusBases = sz0;
- ccs.passStartBase.resize(numSubreads);
- ccs.passNumBases.resize(numSubreads);
- ccs.passDirection.resize(numSubreads);
- s = 0;
- for(int i=0; i < ccs.numPasses; i++) {
- ccs.passStartBase[i] = subreads[i].subreadStart;
- ccs.passDirection[i] = (i%2==0)?(0):(1);
- ccs.passNumBases[i] = subreads[i].length;
- }
- }
-
- void TearDown() {
- ccs.Free();
- for(int i=0; i<numSubreads; i++) {
- subreads[i].Free();
- }
- }
-
- CCSSequence ccs;
- vector<SMRTSequence> subreads;
-};
-
-
-TEST_F(CCSSequenceTest, Print) {
- stringstream ss, ss1;
- ccs.Print(ss);
- ccs.unrolledRead.Print(ss1);
- ASSERT_EQ(ss.str(), (string(
- "SMRTSequence for zmw 1, [0, 19)\nATATGGGGATTAGGGGATA\n")));
- ASSERT_EQ(ss1.str(), (string(
- "SMRTSequence for zmw 1, [0, 66)\nATATGGGGATTAGGGGATACCCTAATCCCGTAATCCCGGTATCCCATAGG\nGGGATTAGGGGATTCA\n")));
-}
-
-TEST_F(CCSSequenceTest, Explode) {
- vector<SMRTSequence> exploded_subreads;
-
- ccs.Explode(exploded_subreads);
- for(int i = 0; i < numSubreads; i++){
- stringstream ss, ss1;
- subreads[i].PrintSeq(ss);
- exploded_subreads[i].PrintSeq(ss1);
- ASSERT_EQ(ss.str(), ss1.str());
- }
-}
-
-
diff --git a/libcpp/unittest/pbdata/ChangeListID_gtest.cpp b/libcpp/unittest/pbdata/ChangeListID_gtest.cpp
deleted file mode 100644
index 18cc8b6..0000000
--- a/libcpp/unittest/pbdata/ChangeListID_gtest.cpp
+++ /dev/null
@@ -1,34 +0,0 @@
-/*
- * =====================================================================================
- *
- * Filename: ChangeListID_gtest.cpp
- *
- * Description: Test pbdata/ChangeListID.hpp
- *
- * Version: 1.0
- * Created: 02/26/2015 06:01:01 PM
- * Revision: none
- * Compiler: gcc
- *
- * Author: Yuan Li (yli), yli at pacificbiosciences.com
- * Company: Pacific Biosciences
- *
- * =====================================================================================
- */
-
-#include "gtest/gtest.h"
-#include "ChangeListID.hpp"
-
-using namespace std;
-
-// Test ChangeListID.GetVersion().
-TEST(ChangeListID, GetVersion) {
- string str = "2.3.0.143354";
- ChangeListID change = ChangeListID(str);
- EXPECT_EQ(change.GetVersion(), "2.3");
-
- str = "";
- change = ChangeListID(str);
- EXPECT_EQ(change.GetVersion(), "");
-}
-
diff --git a/libcpp/unittest/pbdata/DNASequence_gtest.cpp b/libcpp/unittest/pbdata/DNASequence_gtest.cpp
deleted file mode 100644
index 6d16f01..0000000
--- a/libcpp/unittest/pbdata/DNASequence_gtest.cpp
+++ /dev/null
@@ -1,279 +0,0 @@
-/*
- * =====================================================================================
- *
- * Filename: DNASequence_gtest.cpp
- *
- * Description: Test DNASequence.hpp
- *
- * Version: 1.0
- * Created: 10/27/2012 09:42:13 AM
- * Revision: none
- * Compiler: gcc
- *
- * Author: Yuan Li (yli), yli at pacificbiosciences.com
- * Company: Pacific Biosciences
- *
- * =====================================================================================
- */
-
-#include "gtest/gtest.h"
-#include "DNASequence.hpp"
-#include <climits>
-#include <iostream>
-#include <fstream>
-using namespace std;
-
-//Note ::testing::Test not ::testing::TEST
-//SetUp() and TearDown(), not Setup() and Teardown()
-class DNASequenceTest : public ::testing::Test {
-public:
- DNASequence dnaOne;
-};
-
-//Test DNASequence constructor
-TEST_F(DNASequenceTest, Constructor) {
- DNASequence dnaSeq;
- EXPECT_TRUE(dnaSeq.seq == NULL);
- EXPECT_TRUE(dnaSeq.length == 0);
- EXPECT_TRUE(dnaSeq.size() == dnaSeq.length);
- EXPECT_TRUE(dnaSeq.bitsPerNuc == 8);
- EXPECT_FALSE(dnaSeq.deleteOnExit);
-
- Nucleotide HKITTY[] = "HELLO,KITTY!";
- dnaSeq.seq = HKITTY;
- dnaSeq.length = sizeof(HKITTY)/sizeof(Nucleotide) - 1;
-// dnaSeq.Print(cout);
- EXPECT_EQ(dnaSeq.size(), 12);
-
-
- DNALength thisLen = 12;
- Nucleotide * thisNuc = new Nucleotide [thisLen];
- memcpy(thisNuc, HKITTY, thisLen);
- DNASequence newDnaSeq;
- newDnaSeq.seq = thisNuc;
- newDnaSeq.length = thisLen;
-// newDnaSeq.Print(cout);
- EXPECT_EQ(memcmp(newDnaSeq.seq, dnaSeq.seq, thisLen), 0);
- EXPECT_EQ(newDnaSeq.length, thisLen);
- if (!thisNuc) delete thisNuc;
-
- DNASequence nnewDnaSeq;
- thisLen = 12;
- string atgc ("atgcatgcatgc");
- thisNuc = new Nucleotide [thisLen];
- for (int i = 0 ; i < thisLen; i++) {
- thisNuc[i] = atgc[i];
- }
- string ret;
- nnewDnaSeq.seq = thisNuc;
- nnewDnaSeq.length = thisLen;
- for (int i = 0 ; i < thisLen; i++) {
- ret += nnewDnaSeq.seq[i];
- }
- EXPECT_STREQ(ret.c_str(), atgc.c_str());
-}
-
-//Test DNASequence Append()
-TEST_F(DNASequenceTest, Append) {
- DNALength oneLen = 10;
- Nucleotide * one = new Nucleotide [oneLen];
-
- string As("AAAAAAAAAA");
- for (int i = 0; i < oneLen; i++) {
- one[i] = As[i];
- }
- //Can not memcpy a string to a DNASequence directly
- //such as memcpy(one, As.c_str(), oneLen), because
- //DNASequence.seq is of type unsigned char, not char
-
- DNALength twoLen = 20;
- Nucleotide * two = new Nucleotide [twoLen];
-
- string Gs("GGGGGGGGGGGGGGGGGGGG");
- for (int i = 0; i < twoLen; i++) {
- two[i] = Gs[i];
- }
- //memcpy(two, Gs.c_str(), twoLen);
-
- Nucleotide * three = new Nucleotide [oneLen + twoLen];
- memcpy(three, one, oneLen);
- memcpy(three+oneLen, two, twoLen);
-
- DNASequence dnaTwo;
- dnaOne.seq = one;
- dnaOne.length = oneLen;
- dnaOne.deleteOnExit = true;
- dnaTwo.seq = two;
- dnaTwo.length = twoLen;
-
- dnaOne.Append(dnaTwo, 0);
- EXPECT_EQ(dnaOne.length, oneLen + twoLen);
- EXPECT_EQ(memcmp(dnaOne.seq, three, dnaOne.length), 0);
-
- string AGs("AAAAAAAAAAGGGGGGGGGGGGGGGGGGGG");
- for (int i = 0; i < dnaOne.length; i++) {
- EXPECT_EQ(AGs[i], (char)dnaOne.seq[i]);
- }
-
- //if appendPos is positive, overwrite this sequence
- //from appendPos to the end
- AGs = "AAGGGGGGGGGGGGGGGGGGGG";
- DNALength appendPos = 2;
- dnaOne.Append(dnaTwo, appendPos);
- EXPECT_EQ(dnaOne.length, appendPos + twoLen);
- for (int i = 0; i < dnaOne.length; i++) {
- EXPECT_EQ(AGs[i], (char)dnaOne.seq[i]);
- }
-
- if(!one) delete one;
- if(!two) delete two;
- if(!three) delete three;
-}
-
-//Test DNASequence TakeOwnership
-TEST_F(DNASequenceTest, TakeOwnership) {
- DNALength oneLen = 10;
- Nucleotide * one = new Nucleotide [oneLen];
-
- dnaOne.seq = one;
- dnaOne.length = oneLen;
-
- DNASequence dnaTwo;
-
- //a bug may occur if deleteOneExit is true and
- //TakeOwnership() is called twice. In that case, both
- //dnaOne and dnaTwo will become wild pointers
- dnaTwo.deleteOnExit = true;
- dnaTwo.TakeOwnership(dnaOne);
-
- EXPECT_EQ(dnaTwo.length, dnaOne.length);
- EXPECT_EQ(dnaTwo.deleteOnExit, dnaOne.deleteOnExit);
- EXPECT_EQ(dnaTwo.seq, dnaOne.seq);
-
- if(!one) delete one;
-}
-
-//Test DNASequence ShallowCopy
-TEST_F(DNASequenceTest, ShallowCopy) {
- DNALength oneLen = 10;
- Nucleotide * one = new Nucleotide [oneLen];
-
- string As("AAAAAAAAAA");
- for (int i = 0; i < oneLen; i++) {
- one[i] = As[i];
- }
- dnaOne.seq = one;
- dnaOne.length = oneLen;
-
- DNASequence dnaTwo;
- dnaTwo.ShallowCopy(dnaOne);
-
- EXPECT_EQ(dnaTwo.length, dnaOne.length);
- EXPECT_EQ(dnaTwo.seq , dnaOne.seq);
- EXPECT_EQ(dnaTwo.deleteOnExit, dnaOne.deleteOnExit);
-}
-
-
-//Test DNASequence.Copy(const DNASequence rhs,
-// DNALength rhsPos,
-// DNALength rhsLength)
-TEST_F(DNASequenceTest, Copy) {
- DNALength oneLen = 10;
- Nucleotide * one = new Nucleotide [oneLen];
-
- string As("AGAAAAACAA");
- for (int i = 0; i < oneLen; i++) {
- one[i] = As[i];
- }
-
- dnaOne.seq = one;
- dnaOne.length = oneLen;
-
- DNASequence dnaTwo;
- dnaTwo.Copy(dnaOne);
-
- EXPECT_EQ(dnaTwo.length, dnaOne.length);
- EXPECT_NE(dnaTwo.seq , dnaOne.seq);
- EXPECT_TRUE(dnaTwo.deleteOnExit);
- EXPECT_EQ(memcmp(dnaTwo.seq, dnaOne.seq, dnaOne.length), 0);
-
- //if rhs.length is 0, return this *
- DNASequence dnaThree;
- dnaTwo.Copy(dnaThree);
- //dnaTwo remains unchanged
- EXPECT_EQ(dnaTwo.length, 0);
- EXPECT_NE(dnaTwo.seq, dnaOne.seq);
- EXPECT_TRUE(dnaTwo.deleteOnExit);
- EXPECT_TRUE(dnaTwo.seq == NULL);
-
- //if rhsPos is not 0 and rhsLength is 0
- dnaTwo.Copy(dnaOne, 2);
- EXPECT_EQ(dnaTwo.length, dnaOne.length - 2);
- EXPECT_TRUE(dnaTwo.deleteOnExit);
- EXPECT_EQ(memcmp(dnaTwo.seq, dnaOne.seq + 2, dnaTwo.length), 0);
-
-
- //if the subsequence to copy is out of bounds
- EXPECT_GT(200, dnaOne.length);
- //EXPECT_EXIT(dnaTwo.Copy(dnaOne, 200), ::testing::ExitedWithCode(1), "");
-
-
- //if both rhsPos and rhsLength are less than MAXINT,
- //but rhsPos+ rhsLength > MAXINT
- DNALength rhsPos = 3;
- DNALength rhsLength = UINT_MAX -1;
- EXPECT_TRUE(rhsPos < UINT_MAX && rhsLength < UINT_MAX);
- EXPECT_TRUE(rhsLength > dnaOne.length + 1);
- //EXPECT_EXIT(dnaTwo.Copy(dnaOne, rhsPos, rhsLength), ::testing::ExitedWithCode(1), "");
-
-
- //if rhsPos > rhs.length
- //EXPECT_EXIT(dnaTwo.Copy(dnaOne, dnaOne.length + 1), ::testing::ExitedWithCode(1), "")
- // << "Copy a subsequence which is out of bounds. This needs to be taken care of. See bug 21867.";
-
-}
-
-//Test DNASequence Allocate(DNALength)
-TEST_F(DNASequenceTest, Allocate) {
- dnaOne.Allocate(0);
- EXPECT_EQ(dnaOne.length, 0);
-
- DNASequence dnaTwo;
- dnaTwo.Allocate(100);
- EXPECT_EQ(dnaTwo.length, 100);
-}
-
-//Test DNASequence ReferenceSubstring(rhs, pos, substrLength)
-TEST_F(DNASequenceTest, ReferenceSubstring) {
- DNALength oneLen = 10;
- dnaOne.seq = new Nucleotide[oneLen];
- dnaOne.length = oneLen;
-
- DNASequence dnaTwo;
- dnaTwo.ReferenceSubstring(dnaOne);
-
- EXPECT_EQ(dnaOne.seq, dnaTwo.seq);
- EXPECT_EQ(dnaOne.length, dnaTwo.length);
- EXPECT_FALSE(dnaTwo.deleteOnExit);
-
-// EXPECT_DEATH_IF_SUPPORTED(dnaTwo.ReferenceSubstring(dnaOne, 100), "");
- delete dnaOne.seq;
-}
-/*
-TEST_F(DNASequenceTest, CopyFromString) {
- // Test Copy(const std::string &)
- string str = "ATGCGGGCCTCGCCG";
- dnaOne.Copy(str);
-
- for (int i = 0; i < str.size(); i++) {
- EXPECT_EQ(dnaOne.seq[i], str[i]);
- }
-
- // Test operator = (const std::string)
- DNASequence dnaTwo;
- dnaTwo = str;
- for (int i = 0; i < str.size(); i++) {
- EXPECT_EQ(dnaOne.seq[i], str[i]);
- }
-}
-*/
diff --git a/libcpp/unittest/pbdata/FASTAReader_gtest.cpp b/libcpp/unittest/pbdata/FASTAReader_gtest.cpp
deleted file mode 100644
index f8aa7de..0000000
--- a/libcpp/unittest/pbdata/FASTAReader_gtest.cpp
+++ /dev/null
@@ -1,65 +0,0 @@
-/*
- * =====================================================================================
- *
- * Filename: FASTAReader_gtest.cpp
- *
- * Description: Test common/FASTAReader.h
- *
- * Version: 1.0
- * Created: 10/29/2012 05:18:52 PM
- * Revision: none
- * Compiler: gcc
- *
- * Author: Yuan Li (yli), yli at pacificbiosciences.com
- * Company: Pacific Biosciences
- *
- * =====================================================================================
- */
-
-#include "gtest/gtest.h"
-#include "FASTAReader.hpp"
-#include "pbdata/testdata.h"
-
-class FASTAReaderTest:public::testing::Test{
-public:
- void SetUp() {
- string filename(fastaFile1);
- reader.Initialize(filename);
- }
-
- void TearDown() {
- reader.Close();
- seq.Free();
- }
-
- FASTAReader reader;
- FASTASequence seq;
-};
-
-TEST_F(FASTAReaderTest, GetNext) {
- reader.GetNext(seq);
- EXPECT_EQ(strcmp(seq.title, "read1"), 0);
- EXPECT_EQ(seq.length, 100);
- string expected_seq = string(
- "AAAAAGGGGGCCCCCACGGCAGCCAGATTTAAATTGAGGGCCCCCCCTTT"
- "GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG");
- EXPECT_EQ(strcmp((char*)seq.seq, expected_seq.c_str()), 0);
-
- reader.GetNext(seq);
- EXPECT_EQ(strcmp(seq.title, "read2"), 0);
- EXPECT_EQ(seq.length, 99);
-}
-
-TEST_F(FASTAReaderTest, ReadAllSequences) {
- vector<FASTASequence> seqs;
- reader.ReadAllSequences(seqs);
-
- EXPECT_EQ(seqs.size(), 12);
- EXPECT_EQ(strcmp(seqs[11].title, "read2x"), 0);
-
- string expected_seq = string(
- "AAAAAGGGGGCCCACGGCAGCCAGATTTAAATTGAGGGCAACCCCCCTTT"
- "GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG");
- EXPECT_EQ(strcmp((char*)seqs[11].seq, expected_seq.c_str()), 0);
-}
-
diff --git a/libcpp/unittest/pbdata/FASTASequence_gtest.cpp b/libcpp/unittest/pbdata/FASTASequence_gtest.cpp
deleted file mode 100644
index 4161e76..0000000
--- a/libcpp/unittest/pbdata/FASTASequence_gtest.cpp
+++ /dev/null
@@ -1,143 +0,0 @@
-/*
- * =====================================================================================
- *
- * Filename: FASTASequence_gtest.cpp
- *
- * Description: Test pbdata/FASTASequence.hpp
- *
- * Version: 1.0
- * Created: 10/29/2012 05:19:13 PM
- * Revision: none
- * Compiler: gcc
- *
- * Author: Yuan Li (yli), yli at pacificbiosciences.com
- * Company: Pacific Biosciences
- *
- * =====================================================================================
- */
-
-#include "FASTASequence.hpp"
-#include "gtest/gtest.h"
-#include <climits>
-#include <iostream>
-#include <fstream>
-
-
-using namespace std;
-
-class FASTASequenceTest : public ::testing::Test {
-public:
- virtual void SetUp() {
- }
-
- virtual void TearDown() {
- fastaOne.Free();
- fastaTwo.Free();
- fastaThree.Free();
- }
-
- FASTASequence fastaOne;
- FASTASequence fastaTwo;
- FASTASequence fastaThree;
-
- std::streambuf * sbuf;
- ofstream ofs;
-};
-
-
-//Test FASTASequence
-TEST_F(FASTASequenceTest, ALLFUNC) {
- // Test constructor
- EXPECT_TRUE(fastaOne.title == NULL);
- EXPECT_TRUE(fastaOne.titleLength == 0);
- EXPECT_TRUE(fastaOne.seq == NULL);
- EXPECT_TRUE(fastaOne.length == 0);
- EXPECT_FALSE(fastaOne.deleteOnExit);
- EXPECT_EQ(fastaOne.GetStorageSize(), 0);
-
- DNASequence dna;
- Nucleotide thisNuc[] = "ATGCATGCTC";
- dna.seq = thisNuc;
- dna.length = 10;
-
- int titleLength = 22;
- string title("fasta_seq_one comments");
- fastaOne.title = new char [titleLength];
- memcpy(fastaOne.title, title.c_str(), titleLength);
-
- fastaOne.titleLength = titleLength;
-
- EXPECT_EQ(fastaOne.GetName(), string("fasta_seq_one"));
- fastaOne.seq = thisNuc;
- fastaOne.length = 10;
-
- // use ShallowCopy carefully, since title may double free
- // fastaTwo.ShallowCopy(fastaOne);
- // EXPECT_EQ(fastaTwo.seq, fastaOne.seq);
- // EXPECT_EQ(fastaTwo.title, fastaOne.title);
-
-
- // Test AppendToTitle
- fastaOne.AppendToTitle(string("XXX"));
- EXPECT_EQ(fastaOne.titleLength, 26);
-
- string newTitle = "fasta_seq_one commentsXXX";
- EXPECT_STREQ(fastaOne.title, newTitle.c_str());
-
-
- // Test ReverseComplementSelf()
- fastaOne.ReverseComplementSelf();
- string rcSeq = "GAGCATGCAT";
- for (int i = 0; i < rcSeq.size(); i++) {
- EXPECT_EQ(fastaOne.seq[i], rcSeq[i]);
- }
-
- // Test operator =
- fastaTwo=fastaOne;
- EXPECT_NE(fastaOne.title, fastaTwo.title);
- EXPECT_EQ(fastaOne.titleLength, fastaTwo.titleLength);
- EXPECT_STREQ(fastaOne.title, fastaTwo.title);
- EXPECT_NE(fastaOne.seq, fastaTwo.seq);
- for (int i = 0; i < fastaOne.length; i++) {
- EXPECT_EQ(fastaOne.seq[i], fastaTwo.seq[i]);
- }
-
- // Test MakeRC(rhs&)
- fastaOne.MakeRC(fastaThree);
-
- // Test PrintSeq
- stringstream ss;
- fastaThree.PrintSeq(ss);
- string thisTitle, thisComment, thisSeq;
- ss >> thisTitle;
- ss >> thisComment;
- ss >> thisSeq;
-
- EXPECT_EQ(thisTitle, ">fasta_seq_one");
- EXPECT_EQ(thisComment, "commentsXXX");
- EXPECT_EQ(thisSeq, "ATGCATGCTC");
-}
-
-
-TEST_F(FASTASequenceTest, CopyFromString) {
- string name = "read_name";
- string seq = "ATGGGCGC";
- fastaOne.Copy(name, seq);
- EXPECT_EQ(fastaOne.title, name);
- EXPECT_EQ(fastaOne.length, seq.size());
- EXPECT_EQ(fastaOne.deleteOnExit, true);
- for(int i = 0; i < fastaOne.length; i++) {
- EXPECT_EQ(fastaOne.seq[i], seq[i]);
- }
-
- // Copy sequence from another string.
- string seq2 = "GGTTGTG";
- fastaOne.Copy(seq2);
- // Name not changed.
- EXPECT_EQ(fastaOne.title, name);
- EXPECT_EQ(fastaOne.length, seq2.size());
- EXPECT_EQ(fastaOne.deleteOnExit, true);
- for(int i = 0; i < fastaOne.length; i++) {
- EXPECT_EQ(fastaOne.seq[i], seq2[i]);
- }
-}
diff --git a/libcpp/unittest/pbdata/FASTQReader_gtest.cpp b/libcpp/unittest/pbdata/FASTQReader_gtest.cpp
deleted file mode 100644
index 2fbbaca..0000000
--- a/libcpp/unittest/pbdata/FASTQReader_gtest.cpp
+++ /dev/null
@@ -1,90 +0,0 @@
-/*
- * =====================================================================================
- *
- * Filename: FASTQReader_gtest.cpp
- *
- * Description: Test pbdata/FASTQReader.hpp
- *
- * Version: 1.0
- * Created: 10/29/2012 05:19:32 PM
- * Revision: none
- * Compiler: gcc
- *
- * Author: Yuan Li (yli), yli at pacificbiosciences.com
- * Company: Pacific Biosciences
- *
- * =====================================================================================
- */
-
-
-
-#include "gtest/gtest.h"
-#include "FASTQReader.hpp"
-#include "pbdata/testdata.h"
-
-const string movie =
- "m130328_211423_ethan_c100499512550000001823070408081371_s1_p0";
-const int numSeqs = 208;
-
-class FASTQReaderTest:public::testing::Test{
-public:
- void SetUp() {
- string filename(fastqFile1);
- reader.Initialize(filename);
- }
-
- void TearDown() {
- reader.Close();
- seq.Free();
- }
-
- FASTQReader reader;
- FASTQSequence seq;
-};
-
-TEST_F(FASTQReaderTest, GetNext) {
- reader.GetNext(seq);
- EXPECT_EQ(strcmp(seq.title, string(movie + "/8").c_str()), 0);
- EXPECT_EQ(seq.length, 752);
- string expected_seq = string(
- "AATAAAAAAAAAAGAAAGCTTCGAAGTGAGCGAATTACTCTCAGGCAACT"
- "GCGGGTGAAGCCAGAGCAGGCATGATGACACTGGGGAATTTACGCAAATT"
- "TTACCATTGAATTTACACATGCGATGTGCTGGAATGCGGAAGACGGAAAC"
- "GAAACCAGCAATACATCAAACGCCGCACCAGAGAAGAGATATTTGCGCCC"
- "TAAACTAGGTAAGGCGGTTGACTTGAACAGCAAATCAAACGTCAACGAGC"
- "AGCGTGAGTATATACAAGTTATCTCGGATGGAGAACGTATTCTAAATGTA"
- "AGCACGAATCCCGGAAGAGGAAACCAGTTTCTTGGTTTTTCGCCATCCTC"
- "GAAGACCTGTTACAAACCGCACTGGACCTGGAAAGTTTCTGCGCGTAATC"
- "GACAAGACTAGTAACTATCGACATCAACCATCGATTACGGGTTGGGTCAA"
- "TGGGTTCAGATGCAGGTGAGTATCCTTCATATGATAGTCTGACGCTGGCA"
- "TTCGCTCAAAGGAAGTAGACGGTTTTGTAAATAGAAACGCTTGTGAAAAG"
- "CTGAATTTCGCGTCGTCTTCCAGCGATGCAGAGCTGTAGTAGTTCAGATG"
- "ATGACCGTTACTCAAAGTGCCTGCAACGGCTCGGGGCGTGCGCGTCCTGT"
- "GGTGGCTGCTTTTGTTGCGCTGTTTGCAGTGTATGGTTGTCGGGTGATGT"
- "TGCCTGCAAACCCACAAAACCCCACACACACAACAGTTGGGTTGTTGATT"
- "GG");
- string expected_qual = string(
- "(,)'(')''++),.$\"+*$'--.-/+&.$-./$',-.&#'/,.,)-,--,");
-
- for(int i=0; i < seq.length; i++){
- EXPECT_EQ(seq.seq[i], expected_seq[i]);
- }
-
- for(int i=0; i < expected_qual.size(); i++){
- EXPECT_EQ(seq.qual[i] + FASTQSequence::charToQuality,
- expected_qual[i]);
- }
-
- reader.GetNext(seq);
- EXPECT_EQ(strcmp(seq.title, string(movie+"/9").c_str()), 0);
-
- // Continue to read
- for(int i=2; i < numSeqs; i++) {
- EXPECT_TRUE(reader.GetNext(seq));
- }
- EXPECT_EQ(strcmp(seq.title, string(movie+"/249").c_str()), 0);
-
- // Can not proceed.
- EXPECT_FALSE(reader.GetNext(seq));
-}
-
diff --git a/libcpp/unittest/pbdata/Makefile b/libcpp/unittest/pbdata/Makefile
deleted file mode 100644
index a6474af..0000000
--- a/libcpp/unittest/pbdata/Makefile
+++ /dev/null
@@ -1,31 +0,0 @@
-include ../../rules.mk
-include ../defines.mk
-
-SOURCES = $(wildcard *.cpp) \
- $(wildcard utils/*.cpp) \
- $(wildcard metagenome/*.cpp) \
- $(wildcard saf/*.cpp) \
- $(wildcard reads/*.cpp) \
- $(wildcard qvs/*.cpp)
-OBJECTS = $(SOURCES:.cpp=.o)
-
-EXE := test-runner
-
-all debug profile: $(EXE)
-
-libpbdata_gtest.a: $(OBJECTS)
- $(AR) $(ARFLAGS)c $@ $^
-
-$(EXE): $(OBJECTS)
- $(CXX) $(CXXOPTS) $(CXXFLAGS) $^ $(GTEST_SRC) -o $@ -I$(GTEST_ROOT) $(LIBDIRS) $(LDFLAGS)
-
-$(OBJECTS): %.o: %.cpp
- $(CXX) $(CXXOPTS) $(CXXFLAGS) -c $< -o $@ $(INCDIRS)
-
-gtest: $(EXE)
- ./$< --gtest_output=xml:../xml/pbdata.xml
-
-clean:
- @find . -type f -name \*.o -delete
- @find . -type f -name \*.d -delete
- @rm -f libpbdata_gtest.a $(EXE) ../xml/pbdata.xml
diff --git a/libcpp/unittest/pbdata/NucConversion_gtest.cpp b/libcpp/unittest/pbdata/NucConversion_gtest.cpp
deleted file mode 100644
index b1df999..0000000
--- a/libcpp/unittest/pbdata/NucConversion_gtest.cpp
+++ /dev/null
@@ -1,105 +0,0 @@
-/*
- * =====================================================================================
- *
- * Filename: NucConversion_gtest.cpp
- *
- * Description: Test pbdata/NucConversion.hpp
- *
- * Version: 1.0
- * Created: 08/19/2014 05:21:12 PM
- * Revision: none
- * Compiler: gcc
- *
- * Author: Yuan Li (yli), yli at pacificbiosciences.com
- * Company: Pacific Biosciences
- *
- * =====================================================================================
- */
-#include "gtest/gtest.h"
-#include "NucConversion.hpp"
-
-
-// ACGT = 0123
-TEST(NucConversion, ASCIITo2BIT) {
- EXPECT_EQ(TwoBit['A'], 0);
- EXPECT_EQ(TwoBit['a'], 0);
- EXPECT_EQ(TwoBit['C'], 1);
- EXPECT_EQ(TwoBit['c'], 1);
- EXPECT_EQ(TwoBit['G'], 2);
- EXPECT_EQ(TwoBit['g'], 2);
- EXPECT_EQ(TwoBit['T'], 3);
- EXPECT_EQ(TwoBit['t'], 3);
- EXPECT_EQ(TwoBit['N'], 255);
- EXPECT_EQ(TwoBit['x'], 255);
-}
-
-TEST(NucConversion, ASCIITo3BIT) {
- EXPECT_EQ(ThreeBit['A'], 0);
- EXPECT_EQ(ThreeBit['a'], 0);
- EXPECT_EQ(ThreeBit['C'], 1);
- EXPECT_EQ(ThreeBit['c'], 1);
- EXPECT_EQ(ThreeBit['G'], 2);
- EXPECT_EQ(ThreeBit['g'], 2);
- EXPECT_EQ(ThreeBit['T'], 3);
- EXPECT_EQ(ThreeBit['t'], 3);
-
- EXPECT_EQ(ThreeBit['U'], 4);
- EXPECT_EQ(ThreeBit['M'], 4);
- EXPECT_EQ(ThreeBit['R'], 4);
- EXPECT_EQ(ThreeBit['W'], 4);
- EXPECT_EQ(ThreeBit['S'], 4);
- EXPECT_EQ(ThreeBit['Y'], 4);
- EXPECT_EQ(ThreeBit['K'], 4);
- EXPECT_EQ(ThreeBit['V'], 4);
- EXPECT_EQ(ThreeBit['H'], 4);
- EXPECT_EQ(ThreeBit['D'], 4);
- EXPECT_EQ(ThreeBit['N'], 4);
-
- EXPECT_EQ(ThreeBit['$'], 5);
-
- EXPECT_EQ(ThreeBit['p'], 255);
- EXPECT_EQ(ThreeBit['q'], 255);
-}
-
-TEST(NucConversion, ISACTG) {
- EXPECT_TRUE(IsACTG['A']);
- EXPECT_TRUE(IsACTG['a']);
- EXPECT_TRUE(IsACTG['C']);
- EXPECT_TRUE(IsACTG['c']);
- EXPECT_TRUE(IsACTG['G']);
- EXPECT_TRUE(IsACTG['g']);
- EXPECT_TRUE(IsACTG['T']);
- EXPECT_TRUE(IsACTG['t']);
-
- EXPECT_FALSE(IsACTG['w']);
- EXPECT_FALSE(IsACTG['N']);
-}
-
-
-TEST(NucConversion, ThreeBitToASCII) {
- char alphabeta[] = {'A', 'C', 'G', 'T'};
- for(int i = 0; i < 4; i++) {
- EXPECT_EQ(alphabeta[i], ThreeBitToAscii[ThreeBit[alphabeta[i]]]);
- }
-}
-
-TEST(NucConversion, AllToUpper) {
- char alphabeta[] = {'A', 'C', 'G', 'T', 'a', 'c', 'g', 't'};
- for(int i = 0; i < 8; i++) {
- EXPECT_EQ(toupper(alphabeta[i]), AllToUpper[alphabeta[i]]);
- }
-}
-
-TEST(NucConversion, AllToLower) {
- char alphabeta[] = {'A', 'C', 'G', 'T', 'a', 'c', 'g', 't'};
- for(int i = 0; i < 8; i++) {
- EXPECT_EQ(tolower(alphabeta[i]), AllToLower[alphabeta[i]]);
- }
-}
-
-TEST(NucConversion, ReverseComplementNuc) {
- EXPECT_EQ(ReverseComplementNuc['A'], 'T');
- EXPECT_EQ(ReverseComplementNuc['T'], 'A');
- EXPECT_EQ(ReverseComplementNuc['G'], 'C');
- EXPECT_EQ(ReverseComplementNuc['C'], 'G');
-}
diff --git a/libcpp/unittest/pbdata/SMRTSequence_gtest.cpp b/libcpp/unittest/pbdata/SMRTSequence_gtest.cpp
deleted file mode 100644
index 43f40d9..0000000
--- a/libcpp/unittest/pbdata/SMRTSequence_gtest.cpp
+++ /dev/null
@@ -1,62 +0,0 @@
-/*
- * =====================================================================================
- *
- * Filename: SMRTSequenceSequence_gtest.cpp
- *
- * Description: Test pbdata/SMRTSequenceSequence.h
- *
- * Version: 1.0
- * Created: 10/29/2012 05:17:04 PM
- * Revision: 08/19/2014
- * Compiler: gcc
- *
- * Author: Yuan Li (yli), yli at pacificbiosciences.com
- * Company: Pacific Biosciences
- *
- * =====================================================================================
- */
-
-#include "gtest/gtest.h"
-#include "SMRTSequence.hpp"
-
-using namespace std;
-
-Nucleotide seqnt[] = "ATATGGGGATTAGGGGATA";
-const string seqst("ATATGGGGATTAGGGGATA");
-
-class SMRTSequenceTest: public:: testing:: Test{
-public:
- void SetUp() {
- smrt.seq = seqnt;
- int len = sizeof(seqnt) / sizeof(Nucleotide) - 1;
- smrt.length = len;
- smrt.zmwData.holeNumber = 1;
- smrt.subreadStart = 0;
- smrt.subreadEnd = 19;
- smrt.AllocateDeletionQVSpace(len);
- for(int i=0; i < 19; i ++) {
- smrt.deletionQV[i] = i;
- }
- }
- void TearDown() {
- smrt.Free();
- }
- SMRTSequence smrt;
-};
-
-
-TEST_F(SMRTSequenceTest, Print) {
- stringstream ss;
- smrt.Print(ss);
- ASSERT_EQ(ss.str(), (string("SMRTSequence for zmw 1, [0, 19)\n")
- + seqst + "\n"));
-}
-
-
-TEST_F(SMRTSequenceTest, GetDeletionQV) {
- for(int i = 0; i < smrt.length; i ++){
- ASSERT_EQ(smrt.GetDeletionQV(i), i);
- }
-}
-
-
diff --git a/libcpp/unittest/pbdata/ScanData_gtest.cpp b/libcpp/unittest/pbdata/ScanData_gtest.cpp
deleted file mode 100644
index 1a3bdbb..0000000
--- a/libcpp/unittest/pbdata/ScanData_gtest.cpp
+++ /dev/null
@@ -1,31 +0,0 @@
-/*
- * =====================================================================================
- *
- * Filename: ScanData_gtest.cpp
- *
- * Description: Test pbdata/reads/ScanData.hpp
- *
- * Version: 1.0
- * Created: 11/29/2012 03:55:46 PM
- * Revision: 08/20/2014
- * Compiler: gcc
- *
- * Author: Yuan Li (yli), yli at pacificbiosciences.com
- * Company: Pacific Biosciences
- *
- * =====================================================================================
- */
-
-#include "gtest/gtest.h"
-#include "reads/ScanData.hpp"
-
-TEST(ScanDataTest, GetMovieName) {
- ScanData sd;
- EXPECT_EQ(sd.platformId, NoPlatform);
- EXPECT_EQ(sd.frameRate, 0);
- EXPECT_EQ(sd.numFrames, 0);
- EXPECT_EQ(sd.movieName.size(), 0);
- EXPECT_EQ(sd.runCode.size(), 0);
- EXPECT_EQ(sd.whenStarted.size(), 0);
- EXPECT_EQ(sd.baseMap.size(), 0);
-}
diff --git a/libcpp/unittest/pbdata/SeqUtils_gtest.cpp b/libcpp/unittest/pbdata/SeqUtils_gtest.cpp
deleted file mode 100644
index e83c955..0000000
--- a/libcpp/unittest/pbdata/SeqUtils_gtest.cpp
+++ /dev/null
@@ -1,50 +0,0 @@
-/*
- * =====================================================================================
- *
- * Filename: SeqUtils_gtest.cpp
- *
- * Description: Test pbdata/SeqUtils.hpp, SeqUtils_Impl.hpp
- *
- * Version: 1.0
- * Created: 10/29/2012 05:21:58 PM
- * Updated: 08/18/2014 05:49:51 PM
- * Revision: none
- * Compiler: gcc
- *
- * Author: Yuan Li (yli), yli at pacificbiosciences.com
- * Company: Pacific Biosciences
- *
- * =====================================================================================
- */
-#include "gtest/gtest.h"
-#include "SeqUtils.hpp"
-
-TEST(SeqUtils, OnlyACTG){
- DNASequence seq;
- Nucleotide seqnt[] = "ATGC";
- seq.seq = seqnt;
- seq.length = 4;
- EXPECT_EQ(OnlyACTG(seq), 1);
-
- Nucleotide seqnt1[] = "ATXYZ";
- seq.seq = seqnt1;
- seq.length = 5;
- EXPECT_EQ(OnlyACTG(seq), 0);
-}
-
-TEST(SeqUtils, CountMasked){
- DNASequence seq;
- Nucleotide seqnt[] = "ATGCNNNNNNATGC";
- seq.seq = seqnt;
- seq.length = 14;
- EXPECT_EQ(CountMasked(seq), 6);
-}
-
-TEST(SeqUtils, CountNotMasked){
- DNASequence seq;
- Nucleotide seqnt[] = "ATGCNNNNNNATGC";
- seq.seq = seqnt;
- seq.length = 14;
- EXPECT_EQ(CountNotMasked(seq), 8);
-
-}
diff --git a/libcpp/unittest/pbdata/StringUtils_gtest.cpp b/libcpp/unittest/pbdata/StringUtils_gtest.cpp
deleted file mode 100644
index abd6622..0000000
--- a/libcpp/unittest/pbdata/StringUtils_gtest.cpp
+++ /dev/null
@@ -1,80 +0,0 @@
-/*
- * ==================================================================
- *
- * Filename: StringUtils_gtest.cpp
- *
- * Description: Test pbdata/StringUtils.hpp
- *
- * Version: 1.0
- * Created: 03/28/2015 03:54:55 PM
- * Compiler: gcc
- *
- * Author: Yuan Li (yli), yli at pacificbiosciences.com
- * Company: Pacific Biosciences
- *
- * ==================================================================
- */
-#include "gtest/gtest.h"
-#include "reads/ReadType.hpp"
-#include "StringUtils.hpp"
-
-using namespace std;
-
-
-TEST(StringUtilTest, MakeReadGroupId) {
-
- string movieName = "m140905_042212_sidney_c100564852550000001823085912221377_s1_X0";
- ReadType::ReadTypeEnum readType = ReadType::SUBREAD;
- string expectedReadGroupId = "b89a4406";
- EXPECT_EQ(MakeReadGroupId(movieName, readType), expectedReadGroupId);
-
- movieName = "movie32";
- readType = ReadType::CCS;
- expectedReadGroupId = "f5b4ffb6";
- EXPECT_EQ(MakeReadGroupId(movieName, readType), expectedReadGroupId);
-}
-
-TEST(StringUtilTest, Splice) {
- vector<string> tokens;
-
- Splice("movie/zmw/0_1", "/", tokens);
- vector<string> exp = {"movie", "zmw", "0_1"};
- EXPECT_EQ(tokens, exp);
-
- string test = "abc,ef,12,4";
- Splice(test, ",", tokens);
- exp = vector<string>{"abc", "ef", "12", "4"};
- EXPECT_EQ(tokens, exp);
-
- Splice(test, "ef,", tokens);
- exp = vector<string>{"abc,", "12,4"};
- EXPECT_EQ(tokens, exp);
-
- Splice("", ",", tokens);
- exp = vector<string>{""};
- EXPECT_EQ(tokens, exp);
-
- Splice(",", ",", tokens);
- exp = vector<string>{"", ""};
- EXPECT_EQ(tokens, exp);
-
- Splice(",abc,", ",", tokens);
- exp = vector<string>{"", "abc", ""};
- EXPECT_EQ(tokens, exp);
-
- Splice("abc,", ",", tokens);
- exp = vector<string>{"abc", ""};
- EXPECT_EQ(tokens, exp);
-
- Splice(",abc", ",", tokens);
- exp = vector<string>{"", "abc"};
- EXPECT_EQ(tokens, exp);
-
- Splice("abc", "abc", tokens);
- exp = vector<string>{"", ""};
- EXPECT_EQ(tokens, exp);
-
- Splice("a\tb\tc", "\t", tokens);
- exp = vector<string>{"a", "b", "c"};
- EXPECT_EQ(tokens, exp);
-}
diff --git a/libcpp/unittest/pbdata/VectorUtils_gtest.cpp b/libcpp/unittest/pbdata/VectorUtils_gtest.cpp
deleted file mode 100644
index 70d9463..0000000
--- a/libcpp/unittest/pbdata/VectorUtils_gtest.cpp
+++ /dev/null
@@ -1,38 +0,0 @@
-/*
- * =====================================================================================
- *
- * Filename: VectorUtils_gtest.cpp
- *
- * Description: Test pbdata/VectorUtils.hpp
- *
- * Version: 1.0
- * Created: 01/17/2013 06:01:01 PM
- * Revision: none
- * Compiler: gcc
- *
- * Author: Yuan Li (yli), yli at pacificbiosciences.com
- * Company: Pacific Biosciences
- *
- * =====================================================================================
- */
-
-#include "gtest/gtest.h"
-#include "VectorUtils.hpp"
-
-using namespace std;
-
-// Test ClearMemory(vector<T> vt)
-TEST(VectorUtils, ClearMemory) {
- vector<int> vi;
- vi.push_back(1);
-
- int size = 1000000;
- vi.reserve(size);
- EXPECT_EQ(vi.size(), 1);
- EXPECT_EQ(vi.capacity(), size);
-
- ClearMemory(vi);
- EXPECT_EQ(vi.size(), 0);
- EXPECT_EQ(vi.capacity(), 0);
-}
-
diff --git a/libcpp/unittest/pbdata/defs_gtest.cpp b/libcpp/unittest/pbdata/defs_gtest.cpp
deleted file mode 100644
index f81686b..0000000
--- a/libcpp/unittest/pbdata/defs_gtest.cpp
+++ /dev/null
@@ -1,44 +0,0 @@
-/*
- * =====================================================================================
- *
- * Filename: defs_gtest.cpp
- *
- * Description: Test pbdata/defs.h
- *
- * Version: 1.0
- * Created: 10/29/2012 05:17:49 PM
- * Revision: none
- * Compiler: gcc
- *
- * Author: Yuan Li (yli), yli at pacificbiosciences.com
- * Company: Pacific Biosciences
- *
- * =====================================================================================
- */
-
-#include "gtest/gtest.h"
-#include "defs.h"
-
-TEST(DefsTest, MIN) {
- EXPECT_EQ(MIN(1,10000), 1);
- EXPECT_EQ(MIN(-1,10000), -1);
- EXPECT_EQ(MIN(-1,-2), -2);
-}
-
-TEST(DefsTest, MAX) {
- EXPECT_EQ(MAX(1,10000), 10000);
- EXPECT_EQ(MAX(-1,10000), 10000);
- EXPECT_EQ(MAX(-1,-2), -1);
-}
-
-TEST(DefsTest, SWAP) {
- int x = 10;
- int y = 100;
- SWAP(x, y);
-
- EXPECT_EQ(x, 100);
- EXPECT_EQ(y, 10);
-}
-
-
-
diff --git a/libcpp/unittest/pbdata/metagenome/TitleTable_gtest.cpp b/libcpp/unittest/pbdata/metagenome/TitleTable_gtest.cpp
deleted file mode 100644
index e4132a7..0000000
--- a/libcpp/unittest/pbdata/metagenome/TitleTable_gtest.cpp
+++ /dev/null
@@ -1,32 +0,0 @@
-/*
- * =====================================================================================
- *
- * Filename: TitleTable_gtest.cpp
- *
- * Description: Test pbdata/metagenome/TitleTable.hpp
- *
- * Version: 1.0
- * Created: 11/29/2012 03:34:56 PM
- * Revision: none
- * Compiler: gcc
- *
- * Author: Yuan Li (yli), yli at pacificbiosciences.com
- * Company: Pacific Biosciences
- *
- * =====================================================================================
- */
-
-#include "gtest/gtest.h"
-#include "metagenome/TitleTable.hpp"
-#include "pbdata/testdata.h"
-
-TEST(TitleTable, Read) {
- TitleTable tt;
- string fn = titleTable1;
- tt.Read(fn);
- EXPECT_STREQ(tt.table[0], "ref1 description1");
- EXPECT_STREQ(tt.table[1], "ref2 description2");
- EXPECT_EQ(tt.tableLength, 2);
- tt.Free();
-}
-
diff --git a/libcpp/unittest/pbdata/qvs/QualityValueVector_gtest.cpp b/libcpp/unittest/pbdata/qvs/QualityValueVector_gtest.cpp
deleted file mode 100644
index 4119c93..0000000
--- a/libcpp/unittest/pbdata/qvs/QualityValueVector_gtest.cpp
+++ /dev/null
@@ -1,50 +0,0 @@
-/*
- * =====================================================================================
- *
- * Filename: QualityValueVector_gtest.cpp
- *
- * Description: Test pbdata/qvs/QualityValueVector.hpp
- *
- * Version: 1.0
- * Created: 03/28/2015 05:21:58 PM
- * Revision: none
- * Compiler: gcc
- *
- * Author: Yuan Li (yli), yli at pacificbiosciences.com
- * Company: Pacific Biosciences
- *
- * =====================================================================================
- */
-#include "gtest/gtest.h"
-#include "qvs/QualityValue.hpp"
-#include "qvs/QualityValueVector.hpp"
-
-using namespace std;
-
-const string qvstr = "!#$%0123:;ABab{|}~";
-vector<uint8_t> data = {0,2,3,4,15,16,17,18,25,26,32,33,64,65,90,91,92,93};
-
-TEST(QualityValueVectorTest, Copy){
- EXPECT_EQ(qvstr.size(), data.size());
-
- QualityValueVector<QualityValue> qual;
- EXPECT_TRUE(qual.Empty());
-
- // Copy qvs from a string
- qual.Copy(qvstr);
- EXPECT_FALSE(qual.Empty());
- for(size_t i = 0; i < qvstr.size(); i++) {
- EXPECT_EQ(static_cast<uint8_t>(qual.data[i]), data[i]);
- }
-}
-
-TEST(QualityValueVectorTest, ToString){
- QualityValueVector<QualityValue> qual;
- qual.Copy(qvstr);
-
- // Test ToString()
- EXPECT_EQ(qual.ToString(), qvstr);
-
- EXPECT_EQ(static_cast<size_t>(qual.Length()), qvstr.size());
-}
-
diff --git a/libcpp/unittest/pbdata/reads/ReadType_gtest.cpp b/libcpp/unittest/pbdata/reads/ReadType_gtest.cpp
deleted file mode 100644
index 50f6a54..0000000
--- a/libcpp/unittest/pbdata/reads/ReadType_gtest.cpp
+++ /dev/null
@@ -1,57 +0,0 @@
-/*
- * ==================================================================
- *
- * Filename: ReadType_gtest.cpp
- *
- * Description: Test pbdata/reads/ReadType.hpp
- *
- * Version: 1.0
- * Created: 11/29/2012 03:54:55 PM
- * Revision: 08/20/2014
- * Compiler: gcc
- *
- * Author: Yuan Li (yli), yli at pacificbiosciences.com
- * Company: Pacific Biosciences
- *
- * ==================================================================
- */
-#include "gtest/gtest.h"
-#include "reads/ReadType.hpp"
-
-using namespace std;
-
-string standard = "Standard";
-string ccs = "CCS";
-string rccs = "RCCS";
-string noreadtype = "standard";
-
-string subread = "SUBREAD";
-string polymerase = "POLYMERASE";
-string hqregion = "HQREGION";
-string scarp = "SCARP";
-string unknown = "UNKNOWN";
-
-TEST(ReadTypeTest, ParseReadType) {
- EXPECT_EQ(ReadType::ParseReadType(standard), ReadType::Standard);
- EXPECT_EQ(ReadType::ParseReadType(ccs), ReadType::CCS);
- EXPECT_EQ(ReadType::ParseReadType(rccs), ReadType::RCCS);
- EXPECT_EQ(ReadType::ParseReadType(noreadtype), ReadType::NoReadType);
-
- EXPECT_EQ(ReadType::ParseReadType(subread), ReadType::SUBREAD);
- EXPECT_EQ(ReadType::ParseReadType(hqregion), ReadType::HQREGION);
- EXPECT_EQ(ReadType::ParseReadType(polymerase), ReadType::POLYMERASE);
- EXPECT_EQ(ReadType::ParseReadType(unknown), ReadType::UNKNOWN);
-}
-
-
-TEST(ReadTypeTest, ToString) {
- EXPECT_EQ(ReadType::ToString(ReadType::Standard), standard);
- EXPECT_EQ(ReadType::ToString(ReadType::CCS), ccs);
- EXPECT_EQ(ReadType::ToString(ReadType::RCCS), rccs);
- EXPECT_EQ(ReadType::ToString(ReadType::NoReadType), "NoReadType");
-
- EXPECT_EQ(ReadType::ToString(ReadType::SUBREAD), subread);
- EXPECT_EQ(ReadType::ToString(ReadType::HQREGION), hqregion);
- EXPECT_EQ(ReadType::ToString(ReadType::POLYMERASE), polymerase);
- EXPECT_EQ(ReadType::ToString(ReadType::UNKNOWN), unknown);
-}
diff --git a/libcpp/unittest/pbdata/saf/AlnGroup_gtest.cpp b/libcpp/unittest/pbdata/saf/AlnGroup_gtest.cpp
deleted file mode 100644
index d0daed4..0000000
--- a/libcpp/unittest/pbdata/saf/AlnGroup_gtest.cpp
+++ /dev/null
@@ -1,44 +0,0 @@
-/*
- * =====================================================================================
- *
- * Filename: AlnGroup_gtest.cpp
- *
- * Description: Test pbdata/saf/AlnGroup.hpp
- *
- * Version: 1.0
- * Created: 11/29/2012 04:00:29 PM
- * Revision: none
- * Compiler: gcc
- *
- * Author: Yuan Li (yli), yli at pacificbiosciences.com
- * Company: Pacific Biosciences
- *
- * =====================================================================================
- */
-#include "gtest/gtest.h"
-#include "saf/AlnGroup.hpp"
-
-using namespace std;
-
-//Test AlnGroup.FindPath();
-TEST(AlnGroupTest, FindPath) {
- AlnGroup alnGroup;
- unsigned int ids[10] = {3, 4, 6, 1, 2, 8, 9, 12, 11, 7};
- string paths[10] = {"path1", "path2", "path3", "path4", "path5",
- "path6", "path7", "path8", "path9", "path10"};
- for(int i = 0; i < 10; i++) {
- alnGroup.id.push_back(ids[i]);
- alnGroup.path.push_back(paths[i]);
- }
-
- string val, val1;
- int ret = alnGroup.FindPath(3, val);
- EXPECT_EQ(val, paths[0]);
- EXPECT_EQ(ret, 1);
-
-
- ret = alnGroup.FindPath(100, val1);
- EXPECT_EQ(ret, 0);
- EXPECT_EQ(val1, "");
-
-}
diff --git a/libcpp/unittest/pbdata/saf/MovieInfo_gtest.cpp b/libcpp/unittest/pbdata/saf/MovieInfo_gtest.cpp
deleted file mode 100644
index 02a2642..0000000
--- a/libcpp/unittest/pbdata/saf/MovieInfo_gtest.cpp
+++ /dev/null
@@ -1,43 +0,0 @@
-/*
- * =====================================================================================
- *
- * Filename: MovieInfo_gtest.cpp
- *
- * Description: Test pbdata/saf/MovieInfo.hpp
- *
- * Version: 1.0
- * Created: 11/29/2012 04:01:21 PM
- * Revision: 08/20/2014
- * Compiler: gcc
- *
- * Author: Yuan Li (yli), yli at pacificbiosciences.com
- * Company: Pacific Biosciences
- *
- * =====================================================================================
- */
-
-#include "gtest/gtest.h"
-#include "Types.h"
-#include "saf/MovieInfo.hpp"
-
-// Test MovieInfo.FindMovie
-TEST(MovieInfoTest, FindMovie) {
- MovieInfo movieInfo;
- int ids[5] = {3, 5, 7, 4, 0} ;
- string names[5] = {"movieX", "movieY", "abc", "m000000000032102389170_s0", "m000000000032102389170_s"};
-
- for (int i = 0; i < 5; i++) {
- movieInfo.name.push_back(names[i]);
- movieInfo.id.push_back(ids[i]);
- }
-
- string nameVal, nameVal2;
- int ret = movieInfo.FindMovie(4, nameVal);
- EXPECT_EQ(nameVal, names[3]);
- EXPECT_EQ(ret, 1);
-
- ret = movieInfo.FindMovie(-1, nameVal);
- EXPECT_EQ(nameVal2, "");
- EXPECT_EQ(ret, 0);
-
-}
diff --git a/libcpp/unittest/pbdata/saf/RefInfo_gtest.cpp b/libcpp/unittest/pbdata/saf/RefInfo_gtest.cpp
deleted file mode 100644
index 0e25e99..0000000
--- a/libcpp/unittest/pbdata/saf/RefInfo_gtest.cpp
+++ /dev/null
@@ -1,45 +0,0 @@
-/*
- * =====================================================================================
- *
- * Filename: RefInfo_gtest.cpp
- *
- * Description: Test pbdata/saf/RefInfo.hpp
- *
- * Version: 1.0
- * Created: 11/29/2012 04:02:00 PM
- * Revision: 08/20/2014
- * Compiler: gcc
- *
- * Author: Yuan Li (yli), yli at pacificbiosciences.com
- * Company: Pacific Biosciences
- *
- * =====================================================================================
- */
-
-#include "gtest/gtest.h"
-#include "saf/RefInfo.hpp"
-
-using namespace std;
-
-TEST(RefInfoTEST, RefIdToIndex) {
- RefInfo ri;
-
- string names[] = {"ref1", "ref3 description", "ref4 chr1 1:100"};
- ri.fullName.insert(ri.fullName.begin(), names, names+3);
-
- int id[] = {10, 7, 5};
- //int lens [] = {400, 300, 100};
- ri.id.insert(ri.id.begin(), id, id+3);
-
- int index;
- EXPECT_TRUE(ri.RefIdToIndex(10, index));
- EXPECT_EQ(index, 0);
-
- EXPECT_TRUE(ri.RefIdToIndex(7, index));
- EXPECT_EQ(index, 1);
-
- EXPECT_TRUE(ri.RefIdToIndex(5, index));
- EXPECT_EQ(index, 2);
-}
-
-
diff --git a/libcpp/unittest/pbdata/testdata.h b/libcpp/unittest/pbdata/testdata.h
deleted file mode 100644
index ec208f4..0000000
--- a/libcpp/unittest/pbdata/testdata.h
+++ /dev/null
@@ -1,71 +0,0 @@
-/* * ============================================================================
- *
- * Filename: testdata.h
- *
- * Description: List files used in unit tests.
- *
- * Version: 1.0
- * Created: 08/22/2013 11:10:54 AM
- * Revision: none
- * Compiler: gcc
- *
- * Author: Yuan Li (yli), yli at pacificbiosciences.com
- * Company: Pacific Biosciences
- *
- * ============================================================================
- */
-#include <string>
-
-using namespace std;
-
-const string baxFile1 =
- ("/mnt/secondary-siv/testdata/BlasrTestData/ctest/data/"
- "testLoadPulses/Analysis_Results/"
- "m130302_011223_pd1_c000000092559900001500000112311511_s1_p0.1.bax.h5");
-
-const string baxFile2 =
- ("/mnt/secondary-siv/testdata/BlasrTestData/ctest/data/"
- "testLoadPulses/Analysis_Results/"
- "m130302_011223_pd1_c000000092559900001500000112311511_s1_p0.2.bax.h5");
-
-const string baxFile3 =
- ("/mnt/secondary-siv/testdata/BlasrTestData/utest/data/"
- "test_read_chemistry_triple/"
- "m150223_190837_42175_c100735112550000001823160806051530_s1_p0.1.bax.h5");
-
-const string plsFile1 =
- ("/mnt/secondary-siv/testdata/BlasrTestData/ctest/data/"
- "testLoadPulses/Analysis_Results/"
- "m121215_065521_richard_c100425710150000001823055001121371_s1_p0.pls.h5");
-
-const string ccsFile1 =
- ("/mnt/secondary-siv/testdata/BlasrTestData/utest/data/ccs_P4-C2/"
- "m130328_211423_ethan_c100499512550000001823070408081371_s1_p0.ccs.h5");
-
-const string fastaFile1 =
- ("/mnt/secondary-siv/testdata/BlasrTestData/utest/"
- "data/read.fasta");
-
-const string fastqFile1 =
- ("/mnt/secondary-siv/testdata/BlasrTestData/utest/data/ccs_P4-C2/"
- "m130328_211423_ethan_c100499512550000001823070408081371_s1_p0.fastq");
-
-const string titleTable1 =
- ("/mnt/secondary-siv/testdata/BlasrTestData/utest/"
- "data/titleTable1");
-
-const string rgnFile1 =
- ("/mnt/secondary-siv/testdata/BlasrTestData/utest/"
- "data/test_regionTable.rgn.h5");
-
-const string scanDataFile1 =
- ("/mnt/secondary-siv/testdata/BlasrTestData/utest/"
- "data/scandata.h5");
-
-const string bamFile1 =
- ("/mnt/secondary-siv/testdata/BlasrTestData/ctest/data/test_bam/"
- "m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.subreads.bam");
-
-const string bamFile2 =
- ("/mnt/secondary-siv/testdata/BlasrTestData/ctest/data/test_bam/"
- "m150325_224749_42269_c100795290850000001823159309091522_s1_p0.subreads.bam");
diff --git a/libcpp/unittest/pbdata/utils/SMRTTitle_gtest.cpp b/libcpp/unittest/pbdata/utils/SMRTTitle_gtest.cpp
deleted file mode 100644
index 5618258..0000000
--- a/libcpp/unittest/pbdata/utils/SMRTTitle_gtest.cpp
+++ /dev/null
@@ -1,28 +0,0 @@
-#include "gtest/gtest.h"
-#include "utils/SMRTTitle.hpp"
-
-
-TEST(SMRTTitleTest, test1) {
- SMRTTitle title("1");
- EXPECT_EQ(title.isSMRTTitle, false);
- EXPECT_EQ(title.ToString(), "");
-}
-
-TEST(SMRTTitleTest, test2) {
- SMRTTitle title("1/2");
- EXPECT_EQ(title.isSMRTTitle, false);
- EXPECT_EQ(title.ToString(), "");
-}
-
-TEST(SMRTTitleTest, test3) {
- SMRTTitle title("m/1/3_4");
- EXPECT_EQ(title.isSMRTTitle, true);
- EXPECT_EQ(title.ToString(), "m/1/3_4");
-}
-
-TEST(SMRTTitleTest, test4) {
- SMRTTitle title("m/1/10_20/3_7");
- EXPECT_EQ(title.isSMRTTitle, true);
- EXPECT_EQ(title.ToString(), "m/1/13_17");
-}
-
diff --git a/libcpp/unittest/pbdata/utils_gtest.cpp b/libcpp/unittest/pbdata/utils_gtest.cpp
deleted file mode 100644
index a2f6b77..0000000
--- a/libcpp/unittest/pbdata/utils_gtest.cpp
+++ /dev/null
@@ -1,37 +0,0 @@
-/*
- * =====================================================================================
- *
- * Filename: utils_gtest.cpp
- *
- * Description: Test pbdata/utils.hpp
- *
- * Version: 1.0
- * Created: 08/19/2014 05:22:58 PM
- * Revision: none
- * Compiler: gcc
- *
- * Author: Yuan Li (yli), yli at pacificbiosciences.com
- * Company: Pacific Biosciences
- *
- * =====================================================================================
- */
-
-#include "gtest/gtest.h"
-#include "utils.hpp"
-
-using namespace std;
-
-TEST(UTILS, CrucialOpen) {
- ifstream ifs;
- string filename = "/nonexistingdir/nonexistingfile";
- //Expected behavour: exit with a message.
- EXPECT_EXIT( CrucialOpen(filename, ifs, std::ios::in),
- ::testing::ExitedWithCode(1), "");
-}
-
-TEST(UTILS, CeilOfFraction) {
- EXPECT_EQ(CeilOfFraction<int>(7, 100), 1);
- EXPECT_EQ(CeilOfFraction<int>(100, 7), 15);
- EXPECT_EQ(CeilOfFraction<int>(100, 99), 2);
- EXPECT_EQ(CeilOfFraction<int>(100, 5), 20);
-}
diff --git a/GNUmakefile b/makefile
similarity index 56%
rename from GNUmakefile
rename to makefile
index 2c3dd91..aac7f2c 100644
--- a/GNUmakefile
+++ b/makefile
@@ -1,8 +1,13 @@
all:
-ROOT:=.
-include defines.mk
-include rules.mk
+SRCDIR:=$(dir $(realpath $(firstword $(MAKEFILE_LIST))))
+-include ${CURDIR}/defines.mk
+-include ${SRCDIR}/rules.mk
+foo:
+ echo $(realpath $(firstword $(MAKEFILE_LIST)))
+ echo $(firstword $(MAKEFILE_LIST))
+ echo $(MAKEFILE_LIST)
+ echo ${SRCDIR}
CXXFLAGS += -O3 -g
CXXOPTS += \
@@ -11,7 +16,7 @@ CXXOPTS += \
-MMD -MP -w -fpermissive
GCXXFLAGS := -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer
CXXFLAGS += ${CXXOPTS} ${GCXXFLAGS}
-#INC_DIRS:=${LIBBLASR_INCLUDE} ${LIBPBIHDF_INCLUDE} ${LIBPBDATA_INCLUDE} ${PBBAM_INCLUDE} ${HTSLIB_INCLUDE} ${HDF5_INCLUDE} ${ZLIB_INCLUDE}
+#INC_DIRS:=${LIBBLASR_INC} ${LIBPBIHDF_INC} ${LIBPBDATA_INC} ${PBBAM_INC} ${HTSLIB_INC} ${HDF5_INC} ${ZLIB_INC}
#LIB_DIRS:=${LIBBLASR_LIB} ${LIBPBIHDF_LIB} ${LIBPBDATA_LIB} ${PBBAM_LIB} ${HTSLIB_LIB} ${HDF5_LIB} ${ZLIB_LIB}
#LDLIBS := \
# ${LIBBLASR_LIBFLAGS} ${LIBPBIHDF_LIBFLAGS} ${LIBPBDATA_LIBFLAGS} \
@@ -20,13 +25,15 @@ CXXFLAGS += ${CXXOPTS} ${GCXXFLAGS}
# HDF5 needs -ldl, but mobs does not pass it in.
-SRCS := $(wildcard *.cpp)
+SRCS := Blasr.cpp
OBJS := ${SRCS:.cpp=.o}
DEPS := ${SRCS:.cpp=.d}
-LD_LIBRARY_PATH=${HDF5_LIB}:${LIBBLASR_LIB}:${LIBPBIHDF_LIB}:${LIBPBDATA_LIB}
+LD_LIBRARY_PATH:=${HDF5_LIB}:${LIBBLASR_LIB}:${LIBPBIHDF_LIB}:${LIBPBDATA_LIB}:${LD_LIBRARY_PATH}
export LD_LIBRARY_PATH
+# Note: On macosx, this would be DYLD_LIBRARY_PATH.
+vpath %.cpp ${SRCDIR}
init-submodule:
${MAKE} update-submodule
@@ -37,7 +44,7 @@ update-submodule:
build-submodule:
# DON'T use pbbam which is not on github.
- cd libcpp && NOPBBAM=true HDF5_LIB=${HDF5_LIB}/libhdf5.so HDF5_INCLUDE=${HDF5_INCLUDE} ./configure.py
+ cd libcpp && NOPBBAM=true HDF5_LIB=${HDF5_LIB} HDF5_INC=${HDF5_INC} ./configure.py
${MAKE} -C libcpp
submodule-clean:
@@ -55,25 +62,31 @@ makeutils:
makeextrautils:
${MAKE} -C extrautils
-CTESTS := $(wildcard ctest/*.t)
+CTESTS := \
+ctest/affineAlign.t ctest/bamOut.t ctest/ccsH5.t ctest/filtercriteria.t ctest/m0-5.t ctest/samNM.t \
+ctest/aggressiveIntervalCut.t ctest/bug25328.t ctest/concordant.t ctest/fofn.t ctest/multipart.t ctest/useccsallBestN1.t \
+ctest/alignScore.t ctest/bug25741.t ctest/ecoli.t ctest/hitpolicy.t ctest/noSplitSubreads.t ctest/useccsallLargeGenome.t\
+ctest/bamIn.t ctest/bug25766.t ctest/fastMaxInterval.t ctest/holeNumbers.t ctest/open_fail.t ctest/verbose.t
+
SLOW_CTESTS := ctest/bug25328.t ctest/useccsallLargeGenome.t
cramtests: blasr utils
cram -v --shell=/bin/bash ${CTESTS}
- make -C utils cramtests
+ ${MAKE} -C utils cramtests
cramfast: blasr utils
cram -v --shell=/bin/bash $(filter-out ${SLOW_CTESTS},${CTESTS})
- make -C utils cramfast
+ ${MAKE} -C utils cramfast
gtest: blasr
# This requires the submodule to be configured with gtest.
- make -C libcpp gtest
+ ${MAKE} -C libcpp gtest
check: gtest cramtests
cleanall: cleanlib clean
+# cleanlib is only for submodule users
cleanlib: libcpp/defines.mk
${MAKE} -C libcpp clean
diff --git a/p4.common.mk b/p4.common.mk
deleted file mode 100644
index c913f27..0000000
--- a/p4.common.mk
+++ /dev/null
@@ -1,147 +0,0 @@
-OS := $(shell uname)
-
-# Determine where is PBINCROOT, either from github or PacBio SMRTAnalysis package.
-PBINCROOT ?= $(realpath ../../lib/cpp/)
-PREBUILT ?= $(realpath ../../../prebuilt.out)
-THIRD_PARTY_PREFIX ?= $(realpath ..)
-
-SUBMK = $(PBINCROOT)/sub.mk
-FETCHTMP = p4.fetch.tmpmk
-FETCHMK = p4.fetch.mk
-
-include $(PBINCROOT)/common.mk
-
-LIBBLASR_INCLUDE := $(PBINCROOT)/alignment
-LIBPBIHDF_INCLUDE := $(PBINCROOT)/hdf
-LIBPBDATA_INCLUDE := $(PBINCROOT)/pbdata
-PBBAM_INCLUDE := $(PBBAM)/include
-HTSLIB_INCLUDE := $(PBBAM)/../htslib/htslib
-HDF5_INCLUDE := $(HDF5_INC)
-ZLIB_INCLUDE := $(ZLIB_ROOT)/include
-
-LIBBLASR_LIB := $(PBINCROOT)/alignment
-LIBPBIHDF_LIB := $(PBINCROOT)/hdf
-LIBPBDATA_LIB := $(PBINCROOT)/pbdata
-PBBAM_LIB := $(PBBAM)/lib
-HTSLIB_LIB := $(PBBAM)/../htslib
-HDF5_LIB := $(HDF5_LIB)
-ZLIB_LIB := $(ZLIB_ROOT)/lib
-
-HTSLIB_SO := $(HTSLIB_LIB)/libhts.so
-PBBAM_SO := $(PBBAM_LIB)/libpbbam.so
-
-HTSLIB_A := $(HTSLIB_LIB)/libhts.a
-PBBAM_A := $(PBBAM_LIB)/libpbbam.a
-
-LIBPBIHDF_CPP_LIBFLAG := -lhdf5_cpp
-LIBPBIHDF_LIBFLAG := -lhdf5
-
-LIBBLASR_LIBFLAGS := -lblasr
-LIBPBIHDF_LIBFLAGS := -lpbihdf
-LIBPBDATA_LIBFLAGS := -lpbdata
-PBBAM_LIBFLAGS := -lpbbam
-HTSLIB_LIBFLAGS := -lhts
-HDF5_LIBFLAGS := $(LIBHDF5_CPP_LIBFLAG) $(LIBHDF5_LIBFLAG)
-ZLIB_LIBFLAGS := -lz
-
-
-INCDIRS = -I$(LIBBLASR_INCLUDE) \
- -I$(LIBPBIHDF_INCLUDE) \
- -I$(LIBPBDATA_INCLUDE) \
- -I$(HDF5_INCLUDE)
-
-LIBDIRS = -L$(LIBBLASR_LIB) \
- -L$(LIBPBIHDF_LIB) \
- -L$(LIBPBDATA_LIB) \
- -L$(HDF5_LIB)
-
-ifneq ($(ZLIB_ROOT), notfound)
- # NOTE: The zlib include directory is not needed since we do not
- # refer to any zlib include files directly in the blasr source
- # code. But we do need to link to the zlib library (static
- # or shared), since htslib depends on it.
- # INCDIRS += -I$(ZLIB_INCLUDE)
- LIBDIRS += -L$(ZLIB_LIB)
-endif
-
-CXXOPTS := -std=c++0x -pedantic \
- -Wall -Wuninitialized -Wno-div-by-zero \
- -MMD -MP -w -fpermissive
-
-DEFAULTCXXFLAG := -O3
-DEBUGCXXFLAG := -g -ggdb -fno-inline
-PROFILECXXFLAG := -Os -pg
-GCXXFLAG := -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer
-
-LIBS := $(LIBBLASR_LIBFLAGS) $(LIBPBIHDF_LIBFLAGS) $(LIBPBDATA_LIBFLAGS)
-PBBAMLIBS := $(PBBAM_LIBFLAGS)
-ifneq ($(SHARED_LIB),)
- PBBAMLIBS += $(HTSLIB_LIBFLAGS)
-else
- ifneq ($(wildcard "$(HTSLIB_LIB)/libhts.a"),"")
- PBBAMLIBS += $(HTSLIB_LIB)/libhts.a
- else
- PBBAMLIBS += $(HTSLIB_LIBFLAGS)
- endif
-endif
-
-ifneq ($(SHARED_LIB),)
- LIBS += $(HDF5_LIBFLAGS)
-else
- ifneq ($(wildcard "$(HDF5_LIB)/libhdf5_cpp.a"),"")
- LIBS += $(HDF5_LIB)/libhdf5_cpp.a $(HDF5_LIB)/libhdf5.a
- else
- LIBS += $(HDF5_LIBFLAGS)
- endif
-endif
-
-ifeq ($(origin nopbbam), undefined)
- INCDIRS += -I$(PBBAM_INCLUDE) \
- -I$(HTSLIB_INCLUDE) \
- -I$(BOOST_INCLUDE)
-
-
- LIBDIRS += -L$(PBBAM_LIB) \
- -L$(HTSLIB_LIB)
-
- LIBS += $(PBBAMLIBS)
-endif
-
-LIBS += $(ZLIB_LIBFLAGS)
-LIBS += -lpthread
-
-# NOTE: libdl is not needed when we are linking with shared libraries, but
-# is is needed for static linking, since the hdf5 library depends on it
-ifeq ($(SHARED_LIB),)
- LIBS += -ldl
-endif
-
-ifneq ($(SHARED_LIB),)
- STATIC :=
-else
- ifneq ($(OS), Darwin)
- STATIC := -static
- else
- STATIC :=
- endif
-endif
-
-ifneq ($(OS), Darwin)
- LIBS += -lrt
-else
- LIBS += -lsz
-endif
-
-# -lhdf5, -lhdf5_cpp, -lz required for HDF5
-# -lpbbam -lhts for BAM
-# -lpthread for multi-threading
-# -lrt for clock_gettime
-# -ldl for dlopen dlclose
-
-GLIBS = -Wl --eh-frame-hdr -fno-builtin-malloc -L$(HOME)/lib -ltcmalloc -lunwind -lprofiler $(LIBS)
-
-PBLIB :=
-ifeq ($(NO_SUBMAKES),)
- PBLIB := pblib
-endif
-
diff --git a/p4.fetch.tmpmk b/p4.fetch.tmpmk
deleted file mode 100644
index c171051..0000000
--- a/p4.fetch.tmpmk
+++ /dev/null
@@ -1,10 +0,0 @@
-REMOTE:=git://github.com/${NAME}.git
-REPO_DIR=blasr_libcpp
-
-# in case curl/tar/rsync/head are not available in our jenkins build
-PATH:=${PATH}:/bin:/usr/bin
-export PATH
-
-all:
- @ls $(REPO_DIR) 1>/dev/null 2>/dev/null || git clone ${REMOTE} ${REPO_DIR}
-
diff --git a/p4.mk b/p4.mk
deleted file mode 100644
index 60941d6..0000000
--- a/p4.mk
+++ /dev/null
@@ -1,76 +0,0 @@
-SHELL=bash -e -E -vx
-
-.PHONY: all pblib makeutils gtest cramtests cramfast check clean wipe
-
-include p4.common.mk
-
-BLASR_LIBCPP := blasr_libcpp
-SRCS := $(wildcard *.cpp)
-OBJS := $(SRCS:.cpp=.o)
-DEPS := $(SRCS:.cpp=.d)
-EXE = blasr
-UTILS = utils
-
-all : CXXFLAGS ?= $(DEFAULTCXXFLAG)
-debug : CXXFLAGS ?= $(DEBUGCXXFLAG)
-profile : CXXFLAGS ?= $(PROFILECXXFLAG)
-g: CXXFLAGS += $(GCXXFLAG)
-g: LIBS = $(GLIBS)
-MAKE := make
-
-all debug profile g: $(EXE) makeutils
-
-$(EXE): $(SRCS) mkliba
- $(CXX) $(CXXOPTS) $(CXXFLAGS) $(INCDIRS) -MF"$(@:%=%.d)" $(STATIC) -o $@ $(SRCS) $(LIBDIRS) $(LIBS)
-
-makeutils: mkliba
- export CXXFLAGS="$(CXXFLAGS)" && make -C $(UTILS) $(MODE) -f p4.mk
-
-fetch: $(PBINCROOT)
- @echo Fetching $(BLASR_LIBCPP)
- @echo "SHELL=bash -evx" > $(FETCHMK) && grep "^REF:=" $(SUBMK) >> $(FETCHMK) && grep "^NAME:=" $(SUBMK) >> $(FETCHMK) && echo "REPO_DIR:=$(BLASR_LIBCPP)" >> $(FETCHMK) && cat $(FETCHTMP) >> $(FETCHMK)
- make -f $(FETCHMK)
-
-mkliba: fetch mkpbbama
- $(BLASR_LIBCPP)/configure.py BOOST_INCLUDE=$(BOOST_INCLUDE) HTSLIB_INCLUDE=$(HTSLIB_INCLUDE) PBBAM_INCLUDE=$(PBBAM_INCLUDE) HTSLIB_LIB=$(HTSLIB_LIB) PBBAM_LIB=$(PBBAM_LIB)
- export CXXFLAGS="$(CXXFLAGS)" && make -C $(BLASR_LIBCPP)/pbdata/ libpbdata.a
- export CXXFLAGS="$(CXXFLAGS)" && make -C $(BLASR_LIBCPP)/hdf/ libpbihdf.a
- export CXXFLAGS="$(CXXFLAGS)" && make -C $(BLASR_LIBCPP)/alignment/ libblasr.a
-
-mklibso: fetch mkpbbamso
- $(BLASR_LIBCPP)/configure.py SHARED_LIB=true BOOST_INCLUDE=$(BOOST_INCLUDE) HTSLIB_INCLUDE=$(HTSLIB_INCLUDE) PBBAM_INCLUDE=$(PBBAM_INCLUDE) HTSLIB_LIB=$(HTSLIB_SO) PBBAM_LIB=$(PBBAM_SO)
- export CXXFLAGS="$(CXXFLAGS)" && make -C $(BLASR_LIBCPP) all
-
-mkpbbama:
- ls $(PBBAM_A) 2>/dev/null 1>/dev/null || (cd $(PBBAM) && rm -f builda && mkdir builda && cd builda && cmake ../ && make)
-
-mkpbbamso:
- ls $(PBBAM_SO) 2>/dev/null 1>/dev/null || cd $(PBBAM) && rm -f buildso && mkdir -p buildso && cd buildso && cmake -DPacBioBAM_build_shared=ON ../ && make
-
-CTESTS := $(wildcard ctest/*.t)
-SLOW_CTESTS := ctest/bug25328.t ctest/useccsallLargeGenome.t
-
-cramtests: $(EXE) $(UTILS)
- cram -v --shell=/bin/bash $(CTESTS)
- export CXXFLAGS="$(CXXFLAGS)" && make -C $(UTILS) cramtests
-
-cramfast: $(EXE) $(UTILS)
- cram -v --shell=/bin/bash $(filter-out $(SLOW_CTESTS),$(CTESTS))
- export CXXFLAGS="$(CXXFLAGS)" && make -C $(UTILS) cramfast
-
-gtest: $(EXE)
- export CXXFLAGS="$(CXXFLAGS)" && make -C $(PBINCROOT) gtest
-
-check: gtest cramtests
-
-wipe: clean
- @echo WIPING OUT $(BLASR_LIBCPP)...
- @rm -rf $(BLASR_LIBCPP)
-
-clean:
- @rm -f $(EXE) $(OBJS) $(DEPS) blasr.d
- @make -C $(UTILS) -f p4.mk clean
- @make -C $(BLASR_LIBCPP) cleanall
- @rm -f $(FETCHMK)
-
--include $(DEPS)
diff --git a/rules.mk b/rules.mk
index 39c8309..c62d67a 100644
--- a/rules.mk
+++ b/rules.mk
@@ -1,11 +1,11 @@
INCDIRS := \
- ${LIBBLASR_INCLUDE} \
- ${LIBPBDATA_INCLUDE} \
- ${LIBPBIHDF_INCLUDE} \
- ${PBBAM_INCLUDE} \
- ${HDF5_INCLUDE} \
- ${HTSLIB_INCLUDE} \
- ${BOOST_INCLUDE}
+ ${LIBBLASR_INC} \
+ ${LIBPBDATA_INC} \
+ ${LIBPBIHDF_INC} \
+ ${PBBAM_INC} \
+ ${HDF5_INC} \
+ ${HTSLIB_INC} \
+ ${BOOST_INC}
LIBDIRS := \
${LIBBLASR_LIB} \
${LIBPBDATA_LIB} \
@@ -13,6 +13,7 @@ LIBDIRS := \
${PBBAM_LIB} \
${HDF5_LIB} \
${HTSLIB_LIB} \
+ ${GCC_LIB} \
${ZLIB_LIB}
LDLIBS+= \
${LIBPBIHDF_LIBFLAGS} \
@@ -23,6 +24,7 @@ LDLIBS+= \
${HDF5_LIBFLAGS} \
${HTSLIB_LIBFLAGS} \
${ZLIB_LIBFLAGS} \
+ ${RT_LIBFLAGS} \
${PTHREAD_LIBFLAGS} \
${DL_LIBFLAGS}
# We repeat LIBPBIHDF_LIBFLAGS because of a circular dependency. See #77.
diff --git a/travis.sh b/travis.sh
index 4e27de9..bc776a6 100755
--- a/travis.sh
+++ b/travis.sh
@@ -4,6 +4,6 @@
set -ex
# There is a bug without --shared. Working on it. See #77.
-./configure.py --shared --sub --no-pbbam HDF5_INCLUDE=${HDF5_INCLUDE} HDF5_LIB=${HDF5_LIB}
+./configure.py --shared --sub --no-pbbam HDF5_INC=${HDF5_INC} HDF5_LIB=${HDF5_LIB}
make -j4 init-submodule
make --debug=b -j4 all
diff --git a/utils/.gitignore b/utils/.gitignore
new file mode 100644
index 0000000..e088241
--- /dev/null
+++ b/utils/.gitignore
@@ -0,0 +1,8 @@
+/loadPulses
+/pls2fasta
+/samFilter
+/samtoh5
+/samtom4
+/sawriter
+/sdpMatcher
+/toAfg
diff --git a/utils/Makefile b/utils/Makefile
deleted file mode 100644
index 53f40fa..0000000
--- a/utils/Makefile
+++ /dev/null
@@ -1,64 +0,0 @@
-SHELL=/bin/bash -e -E
-
-.PHONY=all cramtests
-
-PBINCROOT ?= $(realpath ../../../lib/cpp/)
-PREBUILT ?= $(realpath ../../../../prebuilt.out)
-THIRD_PARTY_PREFIX := $(realpath ../..)
-
-include ../common.mk
-
-all : CXXFLAGS ?= $(DEFAULTCXXFLAG)
-
-debug : CXXFLAGS ?= $(DEBUGCXXFLAG)
-
-profile : CXXFLAGS ?= $(PROFILECXXFLAG)
-
-g: CXXFLAGS += $(GCXXFLAG)
-g: LIBS = $(GLIBS)
-
-EXE = loadPulses pls2fasta samtoh5 samtom4 samFilter toAfg sawriter sdpMatcher
-
-all debug profile g: $(EXE)
-
-loadPulses: LoadPulses.cpp $(PBLIB)
- $(CXX) $(CXXOPTS) $(CXXFLAGS) $(INCDIRS) -MF"$(@:%=%.d)" $(STATIC) -o $@ $< $(LIBDIRS) $(LIBS)
-
-pls2fasta: PulseToFasta.cpp $(PBLIB)
- $(CXX) $(CXXOPTS) $(CXXFLAGS) $(INCDIRS) -MF"$(@:%=%.d)" $(STATIC) -o $@ $< $(LIBDIRS) $(LIBS)
-
-samtoh5: SamToCmpH5.cpp $(PBLIB)
- $(CXX) $(CXXOPTS) $(CXXFLAGS) $(INCDIRS) -MF"$(@:%=%.d)" $(STATIC) -o $@ $< $(LIBDIRS) $(LIBS)
-
-samtom4: SamToM4.cpp $(PBLIB)
- $(CXX) $(CXXOPTS) $(CXXFLAGS) $(INCDIRS) -MF"$(@:%=%.d)" $(STATIC) -o $@ $< $(LIBDIRS) $(LIBS)
-
-samFilter: SamFilter.cpp $(PBLIB)
- $(CXX) $(CXXOPTS) $(CXXFLAGS) $(INCDIRS) -MF"$(@:%=%.d)" $(STATIC) -o $@ $< $(LIBDIRS) $(LIBS)
-
-toAfg: ToAfg.cpp $(PBLIB)
- $(CXX) $(CXXOPTS) $(CXXFLAGS) $(INCDIRS) -MF"$(@:%=%.d)" $(STATIC) -o $@ $< $(LIBDIRS) $(LIBS)
-
-sawriter: SAWriter.cpp $(PBLIB)
- $(CXX) $(CXXOPTS) $(CXXFLAGS) $(INCDIRS) -MF"$(@:%=%.d)" $(STATIC) -o $@ $< $(LIBDIRS) $(LIBS)
-
-sdpMatcher: SDPMatcher.cpp $(PBLIB)
- $(CXX) $(CXXOPTS) $(CXXFLAGS) $(INCDIRS) -MF"$(@:%=%.d)" $(STATIC) -o $@ $< $(LIBDIRS) $(LIBS)
-
-pblib: $(PBINCROOT)/Makefile
- make -C $(PBINCROOT)
-
-CTESTS := $(wildcard ctest/*.t)
-SLOW_CTESTS := ctest/loadPulses.t ctest/pls2fasta.t
-
-cramtests: $(EXE)
- cram -v --shell=/bin/bash $(CTESTS)
-
-cramfast: $(EXE)
- cram -v --shell=/bin/bash $(filter-out $(SLOW_CTESTS), $(CTESTS))
-
-clean:
- @rm -f $(EXE)
- @rm -f *.d *.o
-
--include $(DEPS)
diff --git a/utils/GNUmakefile b/utils/makefile
similarity index 56%
rename from utils/GNUmakefile
rename to utils/makefile
index 3413244..88a7310 100644
--- a/utils/GNUmakefile
+++ b/utils/makefile
@@ -1,8 +1,8 @@
.PHONY=all cramtests
-ROOT:=..
-include ${ROOT}/defines.mk
-include ${ROOT}/rules.mk
+SRCDIR:=$(dir $(realpath $(lastword $(MAKEFILE_LIST))))
+-include ${CURDIR}/../defines.mk
+include ${SRCDIR}/../rules.mk
CXXOPTS := -std=c++0x -pedantic \
-Wall -Wuninitialized -Wno-div-by-zero \
@@ -14,22 +14,26 @@ EXE = loadPulses pls2fasta samtoh5 samtom4 samFilter toAfg sawriter sdpMatcher
LD_LIBRARY_PATH=${HDF5_LIB}:${LIBBLASR_LIB}:${LIBPBIHDF_LIB}:${LIBPBDATA_LIB}
export LD_LIBRARY_PATH
+vpath %.cpp ${SRCDIR}
all: ${EXE}
${EXE}:
${CXX} -o $@ $< ${CXXFLAGS} ${CPPFLAGS} -MF"${@:%=%.d}" ${STATIC} ${LDFLAGS} ${LDLIBS}
-loadPulses: LoadPulses.cpp
-pls2fasta: PulseToFasta.cpp
-samtoh5: SamToCmpH5.cpp
-samtom4: SamToM4.cpp
-samFilter: SamFilter.cpp
-toAfg: ToAfg.cpp
-sawriter: SAWriter.cpp
-sdpMatcher: SDPMatcher.cpp
+loadPulses: LoadPulses.o
+pls2fasta: PulseToFasta.o
+samtoh5: SamToCmpH5.o
+samtom4: SamToM4.o
+samFilter: SamFilter.o
+toAfg: ToAfg.o
+sawriter: SAWriter.o
+sdpMatcher: SDPMatcher.o
+
+CTESTS := \
+ ctest/loadPulses_fast.t ctest/pls2fasta_fast.t ctest/samFilter.t ctest/samtom4.t ctest/sdpMatcher.t \
+ ctest/loadPulses.t ctest/pls2fasta.t ctest/samtoh5.t ctest/sawriter.t ctest/toAfg.t
-CTESTS := $(wildcard ctest/*.t)
SLOW_CTESTS := ctest/loadPulses.t ctest/pls2fasta.t
cramtests: ${EXE}
diff --git a/utils/p4.mk b/utils/p4.mk
deleted file mode 100644
index 34a5e6f..0000000
--- a/utils/p4.mk
+++ /dev/null
@@ -1,65 +0,0 @@
-# This p4.mk is only used to make
-# //depot/software/smrtanalysis/bioinformatics/tools/blasr
-# on PacBio internal p4 build.
-
-SHELL=/bin/bash -e -E
-
-.PHONY=all cramtests
-
-PBINCROOT ?= $(realpath ../../../lib/cpp/)
-PREBUILT ?= $(realpath ../../../../prebuilt.out)
-THIRD_PARTY_PREFIX := $(realpath ../..)
-
-include ../p4.common.mk
-
-all : CXXFLAGS ?= $(DEFAULTCXXFLAG)
-debug : CXXFLAGS ?= $(DEBUGCXXFLAG)
-profile : CXXFLAGS ?= $(PROFILECXXFLAG)
-g: CXXFLAGS += $(GCXXFLAG)
-g: LIBS = $(GLIBS)
-
-EXE = loadPulses pls2fasta samtoh5 samtom4 samFilter toAfg sawriter sdpMatcher
-
-all debug profile g: $(EXE)
-
-loadPulses: LoadPulses.cpp $(PBLIB)
- $(CXX) $(CXXOPTS) $(CXXFLAGS) $(INCDIRS) -MF"$(@:%=%.d)" $(STATIC) -o $@ $< $(LIBDIRS) $(LIBS)
-
-pls2fasta: PulseToFasta.cpp $(PBLIB)
- $(CXX) $(CXXOPTS) $(CXXFLAGS) $(INCDIRS) -MF"$(@:%=%.d)" $(STATIC) -o $@ $< $(LIBDIRS) $(LIBS)
-
-samtoh5: SamToCmpH5.cpp $(PBLIB)
- $(CXX) $(CXXOPTS) $(CXXFLAGS) $(INCDIRS) -MF"$(@:%=%.d)" $(STATIC) -o $@ $< $(LIBDIRS) $(LIBS)
-
-samtom4: SamToM4.cpp $(PBLIB)
- $(CXX) $(CXXOPTS) $(CXXFLAGS) $(INCDIRS) -MF"$(@:%=%.d)" $(STATIC) -o $@ $< $(LIBDIRS) $(LIBS)
-
-samFilter: SamFilter.cpp $(PBLIB)
- $(CXX) $(CXXOPTS) $(CXXFLAGS) $(INCDIRS) -MF"$(@:%=%.d)" $(STATIC) -o $@ $< $(LIBDIRS) $(LIBS)
-
-toAfg: ToAfg.cpp $(PBLIB)
- $(CXX) $(CXXOPTS) $(CXXFLAGS) $(INCDIRS) -MF"$(@:%=%.d)" $(STATIC) -o $@ $< $(LIBDIRS) $(LIBS)
-
-sawriter: SAWriter.cpp $(PBLIB)
- $(CXX) $(CXXOPTS) $(CXXFLAGS) $(INCDIRS) -MF"$(@:%=%.d)" $(STATIC) -o $@ $< $(LIBDIRS) $(LIBS)
-
-sdpMatcher: SDPMatcher.cpp $(PBLIB)
- $(CXX) $(CXXOPTS) $(CXXFLAGS) $(INCDIRS) -MF"$(@:%=%.d)" $(STATIC) -o $@ $< $(LIBDIRS) $(LIBS)
-
-pblib:
- make -C ../ -f p4.mk mkliba
-
-CTESTS := $(wildcard ctest/*.t)
-SLOW_CTESTS := ctest/loadPulses.t ctest/pls2fasta.t
-
-cramtests: $(EXE)
- cram -v --shell=/bin/bash $(CTESTS)
-
-cramfast: $(EXE)
- cram -v --shell=/bin/bash $(filter-out $(SLOW_CTESTS), $(CTESTS))
-
-clean:
- @rm -f $(EXE)
- @rm -f *.d *.o
-
--include $(DEPS)
diff --git a/yli.common.mk b/yli.common.mk
deleted file mode 100644
index f33276b..0000000
--- a/yli.common.mk
+++ /dev/null
@@ -1,94 +0,0 @@
-OS := $(shell uname)
-
-# Determine where is PBINCROOT, either from github or PacBio SMRTAnalysis package.
-PBINCROOT ?= $(realpath ../../lib/cpp/)
-PREBUILT ?= $(realpath ../../../prebuilt.out)
-THIRD_PARTY_PREFIX ?= $(realpath ..)
-
-include $(PBINCROOT)/common.mk
-
-LIBBLASR_INCLUDE := $(PBINCROOT)/alignment
-LIBPBIHDF_INCLUDE := $(PBINCROOT)/hdf
-LIBPBDATA_INCLUDE := $(PBINCROOT)/pbdata
-PBBAM_INCLUDE := $(PBBAM)/include
-HTSLIB_INCLUDE := $(PBBAM)/../htslib/htslib
-
-LIBBLASR_LIB := $(PBINCROOT)/alignment
-LIBPBIHDF_LIB := $(PBINCROOT)/hdf
-LIBPBDATA_LIB := $(PBINCROOT)/pbdata
-PBBAM_LIB := $(PBBAM)/lib
-HTSLIB_LIB := $(PBBAM)/../htslib
-
-INCDIRS = -I$(LIBBLASR_INCLUDE) \
- -I$(LIBPBIHDF_INCLUDE) \
- -I$(LIBPBDATA_INCLUDE) \
- -I$(HDF5_INC)
-
-LIBDIRS = -L$(LIBBLASR_LIB) \
- -L$(LIBPBIHDF_LIB) \
- -L$(LIBPBDATA_LIB) \
- -L$(HDF5_LIB)
-
-
-ifneq ($(ZLIB_ROOT), notfound)
- INCDIRS += -I$(ZLIB_ROOT)/include
- LIBDIRS += -L$(ZLIB_ROOT)/lib
-endif
-
-CXXOPTS := -std=c++0x -pedantic \
- -Wall -Wuninitialized -Wno-div-by-zero \
- -MMD -MP -w -fpermissive
-
-DEFAULTCXXFLAG := -O3
-DEBUGCXXFLAG := -g -ggdb -fno-inline
-PROFILECXXFLAG := -Os -pg
-GCXXFLAG := -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer
-
-LIBS := -lblasr -lpbihdf -lpbdata
-PBBAMLIBS := -lpbbam
-ifneq ($(wildcard "$(HTSLIB_LIB)/libhts.a"),"")
- PBBAMLIBS += $(HTSLIB_LIB)/libhts.a
-else
- PBBAMLIBS += -lhts
-endif
-
-ifneq ($(wildcard "$(HDF5_LIB)/libhdf5_cpp.a"),"")
- LIBS += $(HDF5_LIB)/libhdf5_cpp.a $(HDF5_LIB)/libhdf5.a
-else
- LIBS += -lhdf5_cpp -lhdf5
-endif
-
-ifeq ($(origin nopbbam), undefined)
- INCDIRS += -I$(PBBAM_INCLUDE) \
- -I$(HTSLIB_INCLUDE) \
- -I$(BOOST_INCLUDE)
-
- LIBDIRS += -L$(PBBAM_LIB) \
- -L$(HTSLIB_LIB)
-
- LIBS += $(PBBAMLIBS)
-endif
-
-LIBS += -lz -lpthread -ldl
-
-ifneq ($(OS), Darwin)
- LIBS += -lrt
- STATIC := -static
-else
- LIBS += -lsz
- STATIC :=
-endif
-
-# -lhdf5, -lhdf5_cpp, -lz required for HDF5
-# -lpbbam -lhts for BAM
-# -lpthread for multi-threading
-# -lrt for clock_gettime
-# -ldl for dlopen dlclose
-
-GLIBS = -Wl --eh-frame-hdr -fno-builtin-malloc -L$(HOME)/lib -ltcmalloc -lunwind -lprofiler $(LIBS)
-
-PBLIB :=
-ifeq ($(NO_SUBMAKES),)
- PBLIB := pblib
-endif
-
diff --git a/yli.makefile b/yli.makefile
deleted file mode 100644
index bc8af98..0000000
--- a/yli.makefile
+++ /dev/null
@@ -1,80 +0,0 @@
-SHELL=/bin/bash -e -E
-
-.PHONY: all pblib makeutils gtest cramtests cramfast check clean cleanall cleanlib
-
-nopbbam=true
-
-GIT_BLASR_LIBPATH = libcpp
-PB_BLASR_LIBPATH = ../../lib/cpp
-# Determine where is PBINCROOT, either from github or PacBio SMRTAnalysis package.
-PBINCROOT ?= $(shell cd $(GIT_BLASR_LIBPATH) 2>/dev/null && pwd || echo -n notfound)
-ifeq ($(PBINCROOT), notfound)
- PBINCROOT := $(shell cd $(PB_BLASR_LIBPATH) 2>/dev/null && pwd || echo -n notfound)
- ifeq ($(PBINCROOT), notfound)
- $(error please check your blasr lib exists.)
- endif
-endif
-
-# common.mk contains the configuration for this build setup
-GIT_COMMON_MK = blasr_git_common.mk
-ifneq ($(shell ls $(GIT_COMMON_MK) 2>/dev/null || echo -n notfound), notfound)
-include $(GIT_COMMON_MK)
-endif
-
-include yli.common.mk
-
-SRCS := $(wildcard *.cpp)
-OBJS := $(SRCS:.cpp=.o)
-DEPS := $(SRCS:.cpp=.d)
-EXE = blasr
-UTILS = utils
-
-all : CXXFLAGS ?= $(DEFAULTCXXFLAG)
-debug : CXXFLAGS ?= $(DEBUGCXXFLAG)
-profile : CXXFLAGS ?= $(PROFILECXXFLAG)
-g: CXXFLAGS += $(GCXXFLAG)
-g: LIBS = $(GLIBS)
-
-all: MODE =
-debug: MODE=debug
-profile: MODE = profile
-g: MODE = g
-
-all debug profile g: $(EXE) makeutils
-
-$(EXE): $(SRCS) $(PBLIB)
- $(CXX) $(CXXOPTS) $(CXXFLAGS) $(INCDIRS) -MF"$(@:%=%.d)" $(STATIC) -o $@ $(SRCS) $(LIBDIRS) $(LIBS)
-
-# DON'T use pbbam which is not on github.
-pblib: $(PBINCROOT)/configure.py $(PBINCROOT)/makefile
- cd $(PBINCROOT) && NOPBBAM=true ./configure.py && export PBINCROOT=$(PBINCROOT) && export nopbbam=true && make -f makefile
-
-makeutils:
- export PBINCROOT=$(PBINCROOT) && export nopbbam=true && export COMMON_NO_THIRD_PARTY_REQD=true && export HDF5_LIB=$(HDF5_LIB) && export HDF5_INC=$(HDF5_INC) && make -C $(UTILS) $(MODE)
-
-CTESTS := $(wildcard ctest/*.t)
-SLOW_CTESTS := ctest/bug25328.t ctest/useccsallLargeGenome.t
-
-cramtests: $(EXE) $(UTILS)
- cram -v --shell=/bin/bash $(CTESTS)
- make -C $(UTILS) cramtests
-
-cramfast: $(EXE) $(UTILS)
- cram -v --shell=/bin/bash $(filter-out $(SLOW_CTESTS),$(CTESTS))
- make -C $(UTILS) cramfast
-
-gtest: $(EXE)
- make -C $(PBINCROOT) gtest
-
-check: gtest cramtests
-
-cleanall: cleanlib clean
-
-cleanlib: $(PBINCROOT)/makefile
- @COMMON_NO_THIRD_PARTY_REQD=true make -C $(PBINCROOT) cleanall
-
-clean:
- @rm -f $(EXE) $(OBJS) $(DEPS) blasr.d
- @COMMON_NO_THIRD_PARTY_REQD=true PBINCROOT=$(PBINCROOT) make -C $(UTILS) clean
-
--include $(DEPS)
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/blasr.git
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