[med-svn] [blasr] 01/02: Imported Upstream version 0~20150724+git3ca7fe8
Afif Elghraoui
afif-guest at moszumanska.debian.org
Mon Jul 27 09:33:42 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 e00b029a9dec71c93f16861ad5cf18a5acef0b2b
Author: Afif Elghraoui <afif at ghraoui.name>
Date: Sun Jul 26 22:14:55 2015 -0700
Imported Upstream version 0~20150724+git3ca7fe8
---
.gitmodules | 3 +
Blasr.cpp | 4464 ++
GNUmakefile | 85 +
LICENSES.txt | 32 +
MANUAL.md | 84 +
Makefile | 59 +
MappingIPC.h | 105 +
MappingParameters.h | 681 +
MappingSemaphores.h | 45 +
README.md | 52 +
RegisterBlasrOptions.h | 529 +
RegisterFilterOptions.h | 53 +
blasr_git_common.mk | 15 +
blasr_gitp4.mk | 24 +
common.mk | 139 +
configure.py | 204 +
ctest/affineAlign.t | 17 +
ctest/aggressiveIntervalCut.t | 12 +
ctest/alignScore.t | 9 +
ctest/bamIn.t | 52 +
ctest/bamOut.t | 22 +
ctest/bug25328.t | 13 +
ctest/bug25741.t | 9 +
ctest/bug25766.t | 13 +
ctest/ccsH5.t | 11 +
ctest/concordant.t | 32 +
ctest/ecoli.t | 20 +
ctest/fastMaxInterval.t | 12 +
ctest/filtercriteria.t | 30 +
ctest/fofn.t | 18 +
ctest/hitpolicy.t | 86 +
ctest/holeNumbers.t | 12 +
ctest/m0-5.t | 33 +
ctest/multipart.t | 13 +
ctest/noSplitSubreads.t | 18 +
ctest/open_fail.t | 8 +
ctest/samNM.t | 13 +
ctest/setup.sh | 29 +
ctest/useccsallBestN1.t | 11 +
ctest/useccsallLargeGenome.t | 13 +
ctest/verbose.t | 9 +
extrautils/BasH5Simulator.cpp | 524 +
extrautils/BuildSequenceDB.cpp | 52 +
extrautils/BwtToSuffixArray.cpp | 33 +
extrautils/CCSH5ToBam.cpp | 135 +
extrautils/Evolve.cpp | 169 +
extrautils/ExciseRepeats.cpp | 69 +
extrautils/GNUmakefile | 45 +
extrautils/Makefile | 78 +
extrautils/PrintTupleCountTable.cpp | 65 +
extrautils/SALS.cpp | 40 +
extrautils/SAModify.cpp | 77 +
extrautils/SWMatcher.cpp | 180 +
extrautils/SimpleShredder.cpp | 159 +
extrautils/StoreQualityByContextFromCmpH5.cpp | 283 +
extrautils/SuffixArrayToBWT.cpp | 48 +
extrautils/ctest/alchemy.t | 20 +
extrautils/ctest/bwt2sa.t | 21 +
extrautils/ctest/ccsh5tobam.t | 10 +
extrautils/ctest/cmpH5StoreQualityByContext.t | 16 +
extrautils/ctest/printTupleCountTable.t | 20 +
extrautils/ctest/sa2bwt.t | 19 +
extrautils/ctest/sals.t | 18 +
extrautils/ctest/samodify.t | 19 +
extrautils/ctest/setup.sh | 15 +
extrautils/ctest/swmatcher.t | 20 +
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 +
p4.common.mk | 147 +
p4.fetch.tmpmk | 10 +
p4.mk | 76 +
rules.mk | 31 +
travis.sh | 9 +
utils/GNUmakefile | 43 +
utils/LoadPulses.cpp | 2643 ++
utils/Makefile | 64 +
utils/PulseToFasta.cpp | 334 +
utils/SAWriter.cpp | 231 +
utils/SDPMatcher.cpp | 166 +
utils/SamFilter.cpp | 544 +
utils/SamToCmpH5.cpp | 209 +
utils/SamToM4.cpp | 222 +
utils/ToAfg.cpp | 178 +
utils/ctest/loadPulses.t | 193 +
utils/ctest/loadPulses_fast.t | 41 +
utils/ctest/pls2fasta.t | 20 +
utils/ctest/pls2fasta_fast.t | 15 +
utils/ctest/samFilter.t | 95 +
utils/ctest/samtoh5.t | 141 +
utils/ctest/samtom4.t | 44 +
utils/ctest/sawriter.t | 30 +
utils/ctest/sdpMatcher.t | 24 +
utils/ctest/setup.sh | 14 +
utils/ctest/toAfg.t | 70 +
utils/p4.mk | 65 +
yli.common.mk | 94 +
yli.makefile | 80 +
573 files changed, 110051 insertions(+)
diff --git a/.gitmodules b/.gitmodules
new file mode 100644
index 0000000..0790993
--- /dev/null
+++ b/.gitmodules
@@ -0,0 +1,3 @@
+[submodule "libcpp"]
+ path = libcpp
+ url = git://github.com/PacificBiosciences/blasr_libcpp.git
diff --git a/Blasr.cpp b/Blasr.cpp
new file mode 100644
index 0000000..95aee11
--- /dev/null
+++ b/Blasr.cpp
@@ -0,0 +1,4464 @@
+#ifdef __linux__
+# include <mcheck.h>
+#endif
+#include <string>
+#include <iostream>
+#include <vector>
+#include <set>
+#include <sstream>
+#include <pthread.h>
+#include <stdlib.h>
+#include <time.h>
+#include <signal.h>
+#include <execinfo.h>
+
+#include "MappingIPC.h"
+#include "MappingSemaphores.h"
+#include "RegisterBlasrOptions.h"
+
+#include "CCSSequence.hpp"
+#include "SMRTSequence.hpp"
+#include "FASTASequence.hpp"
+#include "FASTAReader.hpp"
+#include "SeqUtils.hpp"
+#include "defs.h"
+#include "utils.hpp"
+
+#include "tuples/DNATuple.hpp"
+#include "tuples/HashedTupleList.hpp"
+#include "algorithms/compare/CompareStrings.hpp"
+#include "algorithms/alignment/AffineKBandAlign.hpp"
+#include "algorithms/alignment/GuidedAlign.hpp"
+#include "algorithms/alignment/AffineGuidedAlign.hpp"
+#include "algorithms/alignment/FullQVAlign.hpp"
+#include "algorithms/alignment/ExtendAlign.hpp"
+#include "algorithms/alignment/OneGapAlignment.hpp"
+#include "algorithms/alignment/AlignmentUtils.hpp"
+#include "algorithms/alignment/QualityValueScoreFunction.hpp"
+#include "algorithms/alignment/IDSScoreFunction.hpp"
+#include "algorithms/alignment/DistanceMatrixScoreFunction.hpp"
+#include "algorithms/alignment/StringToScoreMatrix.hpp"
+#include "algorithms/alignment/AlignmentFormats.hpp"
+#include "algorithms/anchoring/LISPValue.hpp"
+#include "algorithms/anchoring/LISPValueWeightor.hpp"
+#include "algorithms/anchoring/LISSizeWeightor.hpp"
+#include "algorithms/anchoring/LISQValueWeightor.hpp"
+#include "algorithms/anchoring/FindMaxInterval.hpp"
+#include "algorithms/anchoring/MapBySuffixArray.hpp"
+#include "datastructures/anchoring/ClusterList.hpp"
+#include "algorithms/anchoring/ClusterProbability.hpp"
+#include "algorithms/anchoring/BWTSearch.hpp"
+#include "metagenome/SequenceIndexDatabase.hpp"
+#include "metagenome/TitleTable.hpp"
+#include "suffixarray/SharedSuffixArray.hpp"
+#include "suffixarray/SuffixArrayTypes.hpp"
+#include "tuples/TupleCountTable.hpp"
+#include "datastructures/anchoring/WeightedInterval.hpp"
+#include "datastructures/anchoring/AnchorParameters.hpp"
+#include "datastructures/alignment/AlignmentCandidate.hpp"
+#include "datastructures/alignment/AlignmentContext.hpp"
+#include "MappingMetrics.hpp"
+#include "reads/ReadInterval.hpp"
+#include "utils/FileOfFileNames.hpp"
+#include "utils/RegionUtils.hpp"
+#include "utils/TimeUtils.hpp"
+#include "qvs/QualityTransform.hpp"
+#include "files/ReaderAgglomerate.hpp"
+#include "files/CCSIterator.hpp"
+#include "files/FragmentCCSIterator.hpp"
+#include "HDFRegionTableReader.hpp"
+#include "bwt/BWT.hpp"
+#include "PackedDNASequence.hpp"
+#include "CommandLineParser.hpp"
+#include "qvs/QualityValue.hpp"
+#include "statistics/VarianceAccumulator.hpp"
+#include "statistics/pdfs.hpp"
+#include "statistics/cdfs.hpp"
+#include "statistics/StatUtils.hpp"
+#include "statistics/LookupAnchorDistribution.hpp"
+#include "format/StickAlignmentPrinter.hpp"
+#include "format/SAMPrinter.hpp"
+#include "format/XMLPrinter.hpp"
+#include "format/CompareSequencesPrinter.hpp"
+#include "format/VulgarPrinter.hpp"
+#include "format/IntervalPrinter.hpp"
+#include "format/SummaryPrinter.hpp"
+#include "format/SAMHeaderPrinter.hpp"
+#include "format/BAMPrinter.hpp"
+
+#define MAX_PHRED_SCORE 254
+#define MAPQV_END_ALIGN_WIGGLE 5
+
+//#define USE_GOOGLE_PROFILER
+
+#ifdef USE_GOOGLE_PROFILER
+#include "gperftools/profiler.h"
+#endif
+
+#ifdef USE_PBBAM
+#include "pbbam/BamWriter.h"
+using namespace PacBio::BAM;
+#else
+#define BamWriter ostream
+#endif
+using namespace std;
+
+MappingSemaphores semaphores;
+
+/*
+ * Declare global structures that are shared between threads.
+ */
+
+ostream *outFilePtr = NULL;
+BamWriter * bamWriterPtr = NULL;
+//ofstream clOut, nsOut, mcOut;
+
+HDFRegionTableReader *regionTableReader = NULL;
+
+typedef SMRTSequence T_Sequence;
+typedef FASTASequence T_GenomeSequence;
+typedef DNASuffixArray T_SuffixArray;
+typedef DNATuple T_Tuple;
+
+typedef LISPValueWeightor<T_GenomeSequence, DNATuple, vector<ChainedMatchPos> > PValueWeightor;
+typedef LISSMatchFrequencyPValueWeightor<T_GenomeSequence, DNATuple, vector<ChainedMatchPos> > MultiplicityPValueWeightor;
+
+ReaderAgglomerate *reader = NULL;
+
+typedef MappingData<T_SuffixArray, T_GenomeSequence, T_Tuple> MappingIPC;
+
+class ClusterInformation {
+public:
+ int maxClusterSize;
+ float meanAnchorBasesPerRead;
+ float sdAnchorBasesPerRead;
+ int score;
+ float pctSimilarity;
+ int readLength;
+ float nStdDev ;
+ int numSignificant;
+ int numForward, numReverse;
+};
+
+
+class ReadAlignments {
+public:
+ /*
+ This class stores the alignments from a read. A read may be
+ aligned in several different modes:
+ 1. Fullread - Treat the read as a unit from start to end
+ 2. Subread - Align each subread independently
+ 3. CCSDeNovo - Only align the CCS sequence from a read
+ 4. CCSAllPass - Align the de novo ccs sequences and then the
+ subreads to where the denovo ccs aligned.
+ 5. CCSFullPass - Same as allpass, except using only complete
+ subreads.
+ 6. ZmwSubreads - Align subreads of each zmw to where the longest
+ subread of the zmw aligned to.
+
+ The alignments are a raggad array of n sequences; n is 1 for cases
+ 1 and 3, the number of subreads for cases 2 and 4, and the number
+ of full length passes for case 5.
+
+ A ReadAligments class must only have alignments for a single type
+ of read in it.
+
+ */
+
+ vector<vector<T_AlignmentCandidate*> > subreadAlignments;
+ vector<SMRTSequence> subreads;
+ AlignMode alignMode;
+ SMRTSequence read;
+ int GetNAlignedSeq() {
+ return subreadAlignments.size();
+ }
+
+ bool AllSubreadsHaveAlignments() {
+ int i, nAlignedSeq;
+ nAlignedSeq = subreadAlignments.size();
+ for (i = 0; i < nAlignedSeq; i++) {
+ if (subreadAlignments[i].size() == 0) {
+ return false;
+ }
+ }
+ return true;
+ }
+
+ void Clear() {
+ int i;
+ int nAlignedSeq;
+ for (i = 0, nAlignedSeq = subreadAlignments.size(); i < nAlignedSeq; i++) {
+ int nAlignments;
+ int a;
+ for (a = 0, nAlignments = subreadAlignments[i].size(); a < nAlignments; a++) {
+ delete subreadAlignments[i][a];
+ }
+ subreadAlignments[i].clear();
+ }
+
+ for (i = 0, nAlignedSeq = subreads.size(); i< nAlignedSeq; i++) {
+ subreads[i].Free();
+ }
+ subreadAlignments.clear();
+ read.Free();
+ }
+
+ void Resize(int nSeq) {
+ subreadAlignments.resize(nSeq);
+ subreads.resize(nSeq);
+ }
+
+ void CheckSeqIndex(int seqIndex) {
+ if ( seqIndex < 0 or seqIndex >= int(subreads.size()) ) {
+ cout << "ERROR, adding a sequence to an unallocated position."
+ << endl;
+ assert(0);
+ }
+ }
+
+ void SetSequence(int seqIndex, SMRTSequence &seq) {
+ CheckSeqIndex(seqIndex);
+ subreads[seqIndex] = seq;
+ }
+
+ void AddAlignmentForSeq(int seqIndex, T_AlignmentCandidate *alignmentPtr) {
+ CheckSeqIndex(seqIndex);
+ subreadAlignments[seqIndex].push_back(alignmentPtr);
+ }
+
+ void AddAlignmentsForSeq(int seqIndex, vector<T_AlignmentCandidate*> &seqAlignmentPtrs) {
+ CheckSeqIndex(seqIndex);
+ subreadAlignments[seqIndex].insert(subreadAlignments[seqIndex].end(), seqAlignmentPtrs.begin(), seqAlignmentPtrs.end());
+ }
+
+ // Copy all T_AlignmentCandidate objects (to which subreadAlignment[seqIndex]
+ // is pointing) to newly created objects, and then return pointers to the new
+ // objects.
+ vector<T_AlignmentCandidate*> CopySubreadAlignments(int seqIndex) {
+ vector<T_AlignmentCandidate*> ret;
+ for (int i=0; i<int(subreadAlignments[seqIndex].size()); i++) {
+ T_AlignmentCandidate * q = new T_AlignmentCandidate();
+ *q = *(subreadAlignments[seqIndex][i]);
+ ret.push_back(q);
+ }
+ return ret;
+ }
+
+ void Print(ostream &out=cout) {
+ out << "A ReadAlignments object with "
+ << subreadAlignments.size()
+ << " groups of subread alignments." << endl;
+ for (int i = 0; i < int(subreadAlignments.size()); i++) {
+ out << " subreadAlignment group [" << i << "/"
+ << subreadAlignments.size() << "] has "
+ << subreadAlignments[i].size() << " alignments." << endl;
+ for(int j = 0; j < int(subreadAlignments[i].size()); j++) {
+ out << " [" << i << "][" << j << "/"
+ << subreadAlignments[i].size() << "]" << endl;
+ subreadAlignments[i][j]->Print(out);
+ }
+ }
+ /* subreads may have been freed or not initialized when
+ * being printed.
+ for (int i = 0; i < subreads.size(); i++) {
+ out << " subread [" << i << "/" << subreads.size()
+ << "]: ";
+ subreads[i].Print(out);
+ } */
+ out << " read: ";
+ read.Print(out);
+ out << endl << endl;
+ }
+
+ ~ReadAlignments() {
+ read.Free();
+ }
+};
+
+string GetMajorVersion() {
+ return "2.0.0";
+}
+
+const string GetVersion(void) {
+ string perforceVersionString("$Change$");
+ string version = GetMajorVersion();
+ if (perforceVersionString.size() > 12) {
+ version.insert(version.size(), ".");
+ version.insert(version.size(), perforceVersionString, 9, perforceVersionString.size() - 11);
+ }
+ return version;
+}
+
+
+//
+// Define a list of buffers that are meant to grow to high-water
+// marks, and not shrink down past that. The memory is reused rather
+// than having multiple calls to new.
+//
+class MappingBuffers {
+public:
+ vector<int> hpInsScoreMat, insScoreMat;
+ vector<int> kbandScoreMat;
+ vector<Arrow> hpInsPathMat, insPathMat;
+ vector<Arrow> kbandPathMat;
+ vector<int> scoreMat;
+ vector<Arrow> pathMat;
+ vector<int> affineScoreMat;
+ vector<Arrow> affinePathMat;
+ vector<ChainedMatchPos> matchPosList;
+ vector<ChainedMatchPos> rcMatchPosList;
+ vector<BasicEndpoint<ChainedMatchPos> > globalChainEndpointBuffer;
+ vector<Fragment> sdpFragmentSet, sdpPrefixFragmentSet, sdpSuffixFragmentSet;
+ TupleList<PositionDNATuple> sdpCachedTargetTupleList;
+ TupleList<PositionDNATuple> sdpCachedTargetPrefixTupleList;
+ TupleList<PositionDNATuple> sdpCachedTargetSuffixTupleList;
+ std::vector<int> sdpCachedMaxFragmentChain;
+ vector<double> probMat;
+ vector<double> optPathProbMat;
+ vector<float> lnSubPValueMat;
+ vector<float> lnInsPValueMat;
+ vector<float> lnDelPValueMat;
+ vector<float> lnMatchPValueMat;
+ vector<int> clusterNumBases;
+ ClusterList clusterList;
+ ClusterList revStrandClusterList;
+
+ void Reset() {
+ vector<int>().swap(hpInsScoreMat);
+ vector<int>().swap(insScoreMat);
+ vector<int>().swap(kbandScoreMat);
+ vector<Arrow>().swap(hpInsPathMat);
+ vector<Arrow>().swap(insPathMat);
+ vector<Arrow>().swap(kbandPathMat);
+ vector<int>().swap(scoreMat);
+ vector<Arrow>().swap(pathMat);
+ vector<ChainedMatchPos>().swap(matchPosList);
+ vector<ChainedMatchPos>().swap(rcMatchPosList);
+ vector<BasicEndpoint<ChainedMatchPos> >().swap(globalChainEndpointBuffer);
+ vector<Fragment>().swap(sdpFragmentSet);
+ vector<Fragment>().swap(sdpPrefixFragmentSet);
+ vector<Fragment>().swap(sdpSuffixFragmentSet);
+ sdpCachedTargetTupleList.Reset();
+ sdpCachedTargetPrefixTupleList.Reset();
+ sdpCachedTargetSuffixTupleList.Reset();
+ vector<int>().swap(sdpCachedMaxFragmentChain);
+ vector<double>().swap(probMat);
+ vector<double>().swap(optPathProbMat);
+ vector<float>().swap(lnSubPValueMat);
+ vector<float>().swap(lnInsPValueMat);
+ vector<float>().swap(lnDelPValueMat);
+ vector<float>().swap(lnMatchPValueMat);
+ vector<int>().swap(clusterNumBases);
+ }
+};
+
+
+int CountZero(unsigned char *ptr, int length) {
+ int i;
+ int nZero = 0;
+ for (i = 0; i < length; i++) {
+ if (ptr[i] == 0) { ++nZero; }
+ }
+ return nZero;
+}
+
+
+bool ReadHasMeaningfulQualityValues(FASTQSequence &sequence) {
+ if (sequence.qual.Empty() == true) {
+ return 0;
+ }
+ else {
+ int numZero=0, numNonZero=0;
+ if (sequence.qual.data == NULL) {
+ return false;
+ }
+ numZero = CountZero(sequence.qual.data, sequence.length);
+ numNonZero = sequence.length - numZero;
+ int subNumZero = 0, subNonZero = 0;
+
+ if (sequence.substitutionQV.data == NULL) {
+ return false;
+ }
+ subNumZero = CountZero(sequence.substitutionQV.data, sequence.length);
+ subNonZero = sequence.length - subNumZero;
+
+ if (numZero < 0.5*numNonZero and subNumZero < 0.5 * subNonZero) {
+ return true;
+ }
+ else {
+ return false;
+ }
+ }
+}
+
+
+void StoreRankingStats( vector<T_AlignmentCandidate*> &alignments,
+ VarianceAccumulator<float> &accumPValue,
+ VarianceAccumulator<float> &accumWeight) {
+ int i;
+ for (i = 0; i < int(alignments.size()); i++) {
+ alignments[i]->pvalVariance = accumPValue.GetVariance();
+ alignments[i]->pvalNStdDev = accumPValue.GetNStdDev(alignments[i]->clusterScore);
+ alignments[i]->weightVariance = accumWeight.GetVariance();
+ alignments[i]->weightNStdDev = accumWeight.GetNStdDev(alignments[i]->clusterWeight);
+ }
+
+}
+
+
+
+template<typename T_TargetSequence, typename T_QuerySequence, typename TDBSequence>
+void AlignIntervals(T_TargetSequence &genome, T_QuerySequence &read, T_QuerySequence &rcRead,
+ WeightedIntervalSet &weightedIntervals,
+ int mutationCostMatrix[][5],
+ int ins, int del, int sdpTupleSize,
+ int useSeqDB, SequenceIndexDatabase<TDBSequence> &seqDB,
+ vector<T_AlignmentCandidate*> &alignments,
+ MappingParameters ¶ms,
+ MappingBuffers &mappingBuffers,
+ int procId=0) {
+
+ vector<T_QuerySequence*> forrev;
+ forrev.resize(2);
+ forrev[Forward] = &read;
+ forrev[Reverse] = &rcRead;
+
+ //
+ // Use an edit distance scoring function instead of IDS. Although
+ // the IDS should be more accurate, it is more slow, and it is more
+ // important at this stage to have faster alignments than accurate,
+ // since all alignments are rerun using GuidedAlignment later on.
+ //
+ DistanceMatrixScoreFunction<DNASequence, FASTQSequence> distScoreFn(SMRTDistanceMatrix, params.insertion, params.deletion);
+ DistanceMatrixScoreFunction<DNASequence, FASTQSequence> distScoreFn2(SMRTDistanceMatrix, ins, ins);
+
+ //
+ // Assume there is at least one interval.
+ //
+ if (weightedIntervals.size() == 0)
+ return;
+
+ WeightedIntervalSet::iterator intvIt = weightedIntervals.begin();
+ int alignmentIndex = 0;
+
+
+ do {
+
+ T_AlignmentCandidate *alignment = alignments[alignmentIndex];
+ alignment->clusterWeight= (*intvIt).size; // totalAnchorSize == size
+ alignment->clusterScore = (*intvIt).pValue;
+
+ //
+ // Advance references. Intervals are stored in reverse order, so
+ // go backwards in the list, and alignments are in forward order.
+ // That should probably be changed.
+ //
+ ++alignmentIndex;
+
+ //
+ // Try aligning the read to the genome.
+ //
+ DNALength matchIntervalStart, matchIntervalEnd;
+ matchIntervalStart = (*intvIt).start;
+ matchIntervalEnd = (*intvIt).end;
+
+ bool readOverlapsContigStart = false;
+ bool readOverlapsContigEnd = false;
+ int startOverlappedContigIndex = 0;
+ int endOverlappedContigIndex = 0;
+ if (params.verbosity > 0) {
+ cout << "aligning interval : " << read.length << " " << (*intvIt).start << " "
+ << (*intvIt).end << " " << (*intvIt).qStart << " " << (*intvIt).qEnd
+ << " " << matchIntervalStart << " to " << matchIntervalEnd << " "
+ << params.approximateMaxInsertionRate << " " << endl;
+ }
+ assert(matchIntervalEnd >= matchIntervalStart);
+
+ //
+ // If using a sequence database, check to make sure that the
+ // boundaries of the sequence windows do not overlap with
+ // the boundaries of the reads. If the beginning is before
+ // the boundary, move the beginning up to the start of the read.
+ // If the end is past the end boundary of the read, similarly move
+ // the window boundary to the end of the read boundary.
+
+ DNALength tAlignedContigStart = 0;
+ int seqDBIndex = 0;
+
+
+ //
+ // Stretch the alignment interval so that it is close to where
+ // the read actually starts.
+ //
+ DNALength subreadStart = read.subreadStart;
+ DNALength subreadEnd = read.subreadEnd;
+ if ((*intvIt).GetStrandIndex() == Reverse) {
+ subreadEnd = read.MakeRCCoordinate(read.subreadStart) + 1;
+ subreadStart = read.MakeRCCoordinate(read.subreadEnd-1);
+ }
+
+ DNALength lengthBeforeFirstMatch = ((*intvIt).qStart - subreadStart) * params.approximateMaxInsertionRate ;
+ DNALength lengthAfterLastMatch = (subreadEnd - (*intvIt).qEnd) * params.approximateMaxInsertionRate;
+ if (matchIntervalStart < lengthBeforeFirstMatch or params.doGlobalAlignment) {
+ matchIntervalStart = 0;
+ }
+ else {
+ matchIntervalStart -= lengthBeforeFirstMatch;
+ }
+
+ if (genome.length < matchIntervalEnd + lengthAfterLastMatch or params.doGlobalAlignment) {
+ matchIntervalEnd = genome.length;
+ }
+ else {
+ matchIntervalEnd += lengthAfterLastMatch;
+ }
+
+ DNALength intervalContigStartPos, intervalContigEndPos;
+ if (useSeqDB) {
+ //
+ // The sequence db index is the one where the actual match is
+ // contained. The matchIntervalStart might be before the sequence
+ // index boundary due to the extrapolation of alignment start by
+ // insertion rate. If this is the case, bump up the
+ // matchIntervalStart to be at the beginning of the boundary.
+ // Modify bounds similarly for the matchIntervalEnd and the end
+ // of a boundary.
+ //
+ seqDBIndex = seqDB.SearchForIndex((*intvIt).start);
+ intervalContigStartPos = seqDB.seqStartPos[seqDBIndex];
+ if (intervalContigStartPos > matchIntervalStart) {
+ matchIntervalStart = intervalContigStartPos;
+ }
+ intervalContigEndPos = seqDB.seqStartPos[seqDBIndex+1] - 1;
+ if (intervalContigEndPos < matchIntervalEnd) {
+ matchIntervalEnd = intervalContigEndPos;
+ }
+ alignment->tName = seqDB.GetSpaceDelimitedName(seqDBIndex);
+ alignment->tLength = intervalContigEndPos - intervalContigStartPos;
+ //
+ // When there are multiple sequences in the database, store the
+ // index of this sequence. This lets one compare the contigs
+ // that reads are mapped to, for instance.
+ //
+ alignment->tIndex = seqDBIndex;
+ }
+ else {
+ alignment->tLength = genome.length;
+ alignment->tName = genome.GetName();
+ intervalContigStartPos = 0;
+ intervalContigEndPos = genome.length;
+ //
+ // When there are multiple sequences in the database, store the
+ // index of this sequence. This lets one compare the contigs
+ // that reads are mapped to, for instance.
+ //
+ }
+ alignment->qName = read.title;
+ //
+ // Look to see if a read overhangs the beginning of a contig.
+ //
+ if (params.verbosity > 2) {
+ cout << "Check for prefix/suffix overlap on interval: " << (*intvIt).qStart << " ?> " << (*intvIt).start - intervalContigStartPos <<endl;
+ }
+ if ( (*intvIt).qStart > (*intvIt).start - intervalContigStartPos) {
+ readOverlapsContigStart = true;
+ startOverlappedContigIndex = seqDBIndex;
+ }
+
+ //
+ // Look to see if the read overhangs the end of a contig.
+ //
+ if (params.verbosity > 2) {
+ cout << "Check for suffix/prefix overlap on interval, read overhang: " << read.length - (*intvIt).qEnd << " ?> " << matchIntervalEnd - (*intvIt).end <<endl;
+ }
+ if (read.length - (*intvIt).qEnd > matchIntervalEnd - (*intvIt).end) {
+ if (params.verbosity > 2) {
+ cout << "read overlaps genome end." << endl;
+ }
+ readOverlapsContigEnd = true;
+ endOverlappedContigIndex = seqDBIndex;
+ }
+ int alignScore;
+ alignScore = 0;
+
+ alignment->tAlignedSeqPos = matchIntervalStart;
+ alignment->tAlignedSeqLength = matchIntervalEnd - matchIntervalStart;
+ if ((*intvIt).GetStrandIndex() == Forward) {
+ alignment->tAlignedSeq.Copy(genome, alignment->tAlignedSeqPos, alignment->tAlignedSeqLength);
+ alignment->tStrand = Forward;
+ }
+ else {
+ DNALength rcAlignedSeqPos = genome.MakeRCCoordinate(alignment->tAlignedSeqPos + alignment->tAlignedSeqLength - 1);
+ genome.CopyAsRC(alignment->tAlignedSeq, rcAlignedSeqPos, alignment->tAlignedSeqLength);
+ // Map forward coordinates into reverse complement.
+
+ intervalContigStartPos = genome.MakeRCCoordinate(intervalContigStartPos) + 1;
+ intervalContigEndPos = genome.MakeRCCoordinate(intervalContigEndPos - 1);
+ swap(intervalContigStartPos, intervalContigEndPos);
+ alignment->tAlignedSeqPos = rcAlignedSeqPos;
+ alignment->tStrand = Reverse;
+ }
+
+ // Configure the part of the query that is aligned. The entire
+ // query should always be aligned.
+ alignment->qAlignedSeqPos = 0;
+ alignment->qAlignedSeq.ReferenceSubstring(read);
+ alignment->qAlignedSeqLength = alignment->qAlignedSeq.length;
+ alignment->qLength = read.length;
+ alignment->qStrand = 0;
+
+ if (params.verbosity > 1) {
+ cout << "aligning read " << endl;
+ static_cast<DNASequence*>(&(alignment->qAlignedSeq))->PrintSeq(cout);
+ cout << endl << "aligning reference" << endl;
+ static_cast<DNASequence*>(&(alignment->tAlignedSeq))->PrintSeq(cout);
+ cout << endl;
+ }
+
+ //
+ // The type of alignment that is performed depends on the mode
+ // blasr is running in. If it is running in normal mode, local
+ // aligment is performed and guided by SDP alignment. When
+ // running in overlap mode, the alignments are forced to the ends
+ // of reads.
+ //
+
+ int intervalSize = 0;
+ int m;
+ //
+ // Check to see if the matches to the genome are sufficiently
+ // dense to allow them to be used instead of having to redo
+ // sdp alignment.
+ //
+
+ // First count how much of the read matches the genome exactly.
+ for (m = 0; m < intvIt->matches.size(); m++) { intervalSize += intvIt->matches[m].l;}
+
+ int subreadLength = forrev[(*intvIt).GetStrandIndex()]->subreadEnd - forrev[(*intvIt).GetStrandIndex()]->subreadStart;
+ if ((1.0*intervalSize) / subreadLength < params.sdpBypassThreshold and !params.emulateNucmer) {
+ //
+ // Not enough of the read maps to the genome, need to use
+ // sdp alignment to define the regions of the read that map.
+ //
+ if (params.refineBetweenAnchorsOnly) {
+
+ //
+ // Run SDP alignment only between the genomic anchors,
+ // including the genomic anchors as part of the alignment.
+ //
+ int m;
+
+ vector<ChainedMatchPos> *matches;
+ vector<ChainedMatchPos> rcMatches;
+ Alignment anchorsOnly;
+ DNASequence tAlignedSeq;
+ FASTQSequence qAlignedSeq;
+ //
+ // The strand bookkeeping is a bit confusing, so hopefully
+ // this will set things straight.
+ //
+ // If the alignment is forward strand, the coordinates of the
+ // blocks are relative to the forward read, starting at 0, not
+ // the subread start.
+ // If the alignment is reverse strand, the coordinates of the
+ // blocks are relative to the reverse strand, starting at the
+ // position of the subread on the reverse strand.
+ //
+ // The coordinates of the blocks in the genome are always
+ // relative to the forward strand on the genome, starting at
+ // 0.
+ //
+
+ //
+ // The first step to refining between anchors only is to make
+ // the anchors relative to the tAlignedSeq.
+
+ matches = (vector<ChainedMatchPos>*) &(*intvIt).matches;
+ tAlignedSeq = alignment->tAlignedSeq;
+ qAlignedSeq = alignment->qAlignedSeq;
+
+ if (alignment->tStrand == 0) {
+ for (m = 0; m < matches->size(); m++) {
+ (*matches)[m].t -= alignment->tAlignedSeqPos;
+ (*matches)[m].q -= alignment->qAlignedSeqPos;
+ }
+ }
+ else {
+ //
+ // Flip the entire alignment if it is on the reverse strand.
+ DNALength rcAlignedSeqPos = genome.MakeRCCoordinate(alignment->tAlignedSeqPos + alignment->tAlignedSeqLength - 1);
+ for (m = 0; m < matches->size(); m++) {
+ (*matches)[m].t -= rcAlignedSeqPos;
+ (*matches)[m].q -= alignment->qAlignedSeqPos;
+ }
+
+ alignment->tAlignedSeq.CopyAsRC(tAlignedSeq);
+ rcMatches.resize((*intvIt).matches.size());
+ //
+ // Make the reverse complement of the match list.
+ //
+
+ // 1. Reverse complement the coordinates.
+ for (m = 0; m < (*intvIt).matches.size(); m++) {
+ int revCompIndex = rcMatches.size() - m - 1;
+ rcMatches[revCompIndex].q = read.MakeRCCoordinate((*intvIt).matches[m].q + (*intvIt).matches[m].l - 1);
+ rcMatches[revCompIndex].t = tAlignedSeq.MakeRCCoordinate((*intvIt).matches[m].t + (*intvIt).matches[m].l - 1);
+ rcMatches[revCompIndex].l = (*intvIt).matches[m].l;
+ }
+ matches = &rcMatches;
+ }
+
+ /*
+ Uncomment to get a dot plot
+ ofstream matchFile;
+ matchFile.open("matches.txt");
+ matchFile << "q t l " << endl;
+ for (m = 0; matches->size() > 0 and m < matches->size() - 1; m++) {
+ matchFile << (*matches)[m].q << " " << (*matches)[m].t << " " << (*matches)[m].l << endl;
+ }
+ */
+ DNASequence tSubSeq;
+ FASTQSequence qSubSeq;
+ for (m = 0; matches->size() > 0 and m < matches->size() - 1; m++) {
+ Block block;
+ block.qPos = (*matches)[m].q;
+ block.tPos = (*matches)[m].t;
+ block.length = (*matches)[m].l;
+
+ //
+ // Find the lengths of the gaps between anchors.
+ //
+ int tGap, qGap;
+ tGap = (*matches)[m+1].t - ((*matches)[m].t + (*matches)[m].l);
+ qGap = (*matches)[m+1].q - ((*matches)[m].q + (*matches)[m].l);
+ float gapRatio = (1.0*tGap)/qGap;
+
+ if (tGap > 0 and qGap > 0) {
+ DNALength tPos, qPos;
+ tPos = block.tPos + block.length;
+ qPos = block.qPos + block.length;
+ tSubSeq.ReferenceSubstring(tAlignedSeq, tPos, tGap);
+ qSubSeq.ReferenceSubstring(alignment->qAlignedSeq, qPos, qGap);
+ Alignment alignmentInGap;
+ int alignScore;
+
+ /*
+ The following code is experimental code for trying to do
+ something like affine gap alignment in long gaps. It
+ would eventually be used in cDNA alignment to align
+ between exons, but for now is being tested here by using
+ it to align when there is a big gap between anchors.
+ */
+ if (params.separateGaps == true and
+ qSubSeq.length > 0 and tSubSeq.length > 0 and
+ ( (1.0*qSubSeq.length)/tSubSeq.length < 0.25 )) {
+ alignScore = OneGapAlign(qSubSeq, tSubSeq, distScoreFn, mappingBuffers, alignmentInGap);
+ }
+ else {
+ /*
+ This is the 'normal/default' way to align between
+ gaps. It is more well tested than OneGapAlign.
+ */
+ alignScore = SDPAlign(qSubSeq, tSubSeq, distScoreFn, params.sdpTupleSize,
+ params.sdpIns, params.sdpDel, params.indelRate*2,
+ alignmentInGap, mappingBuffers, Global,
+ params.detailedSDPAlignment,
+ params.extendFrontAlignment,
+ params.recurseOver,
+ params.fastSDP);
+ }
+
+ //
+ // Now, splice the fragment alignment into the current
+ // alignment.
+ //
+ if (alignmentInGap.blocks.size() > 0) {
+ int b;
+ //
+ // Configure this block to be relative to the beginning
+ // of the aligned substring.
+ //
+ for (b = 0; b < alignmentInGap.size(); b++) {
+ alignmentInGap.blocks[b].tPos += tPos + alignmentInGap.tPos;
+ alignmentInGap.blocks[b].qPos += qPos + alignmentInGap.qPos;
+ assert(alignmentInGap.blocks[b].tPos < alignment->tAlignedSeq.length);
+ assert(alignmentInGap.blocks[b].qPos < alignment->qAlignedSeq.length);
+ }
+ }
+ // Add the original block
+ alignment->blocks.push_back(block);
+ anchorsOnly.blocks.push_back(block);
+ // Add the blocks for the refined alignment
+ alignment->blocks.insert(alignment->blocks.end(),
+ alignmentInGap.blocks.begin(),
+ alignmentInGap.blocks.end());
+ }
+ }
+
+ // Add the last block
+ m = (*matches).size() - 1;
+ Block block;
+ block.qPos = (*matches)[m].q;
+ block.tPos = (*matches)[m].t;
+
+ assert(block.tPos <= alignment->tAlignedSeq.length);
+ assert(block.qPos <= alignment->qAlignedSeq.length);
+
+ block.length = (*matches)[m].l;
+ alignment->blocks.push_back(block);
+ anchorsOnly.blocks.push_back(block);
+
+ //
+ // By convention, blocks start at 0, and the
+ // alignment->tPos,qPos give the start of the alignment.
+ // Modify the block positions so that they are offset by 0.
+ alignment->tPos = alignment->blocks[0].tPos;
+ alignment->qPos = alignment->blocks[0].qPos;
+ int b;
+ int blocksSize = alignment->blocks.size();
+ for (b = 0; b < blocksSize ; b++) {
+ assert(alignment->tPos <= alignment->blocks[b].tPos);
+ assert(alignment->qPos <= alignment->blocks[b].qPos);
+ alignment->blocks[b].tPos -= alignment->tPos;
+ alignment->blocks[b].qPos -= alignment->qPos;
+ }
+ for (b = 0; b < anchorsOnly.blocks.size(); b++) {
+ anchorsOnly.blocks[b].tPos -= alignment->tPos;
+ anchorsOnly.blocks[b].qPos -= alignment->qPos;
+ }
+ anchorsOnly.tPos = alignment->tPos;
+ anchorsOnly.qPos = alignment->qPos;
+ ComputeAlignmentStats(*alignment, alignment->qAlignedSeq.seq, alignment->tAlignedSeq.seq,
+ distScoreFn);
+
+ tAlignedSeq.Free();
+ qAlignedSeq.Free();
+ tSubSeq.Free();
+ qSubSeq.Free();
+ }
+ else {
+ alignScore = SDPAlign(alignment->qAlignedSeq, alignment->tAlignedSeq, distScoreFn,
+ sdpTupleSize, params.sdpIns, params.sdpDel, params.indelRate*3,
+ *alignment, mappingBuffers,
+ Local,
+ params.detailedSDPAlignment,
+ params.extendFrontAlignment,
+ params.recurseOver,
+ params.fastSDP);
+ ComputeAlignmentStats(*alignment, alignment->qAlignedSeq.seq, alignment->tAlignedSeq.seq,
+ distScoreFn);
+ }
+ }
+ else {
+ //
+ // The anchors used to anchor the sequence are sufficient to extend the alignment.
+ //
+ int m;
+ for (m = 0; m < (*intvIt).matches.size(); m++ ){
+ Block block;
+ block.qPos = (*intvIt).matches[m].q - alignment->qAlignedSeqPos;
+ block.tPos = (*intvIt).matches[m].t - alignment->tAlignedSeqPos;
+ block.length = (*intvIt).matches[m].l;
+ alignment->blocks.push_back(block);
+ }
+ }
+
+ //
+ // The anchors/sdp alignments may leave portions of the read
+ // unaligned at the beginning and end. If the parameters
+ // specify extending alignments, try and align extra bases at
+ // the beginning and end of alignments.
+ if (params.extendAlignments) {
+
+ //
+ // Modify the alignment so that the start and end of the
+ // alignment strings are at the alignment boundaries.
+ //
+ // Since the query sequence is pointing at a subsequence of the
+ // read (and is always in the forward direction), just reference
+ // a new portion of the read.
+ alignment->qAlignedSeqPos = alignment->qAlignedSeqPos + alignment->qPos;
+ alignment->qAlignedSeqLength = alignment->QEnd();
+ alignment->qAlignedSeq.ReferenceSubstring(read, alignment->qAlignedSeqPos, alignment->qAlignedSeqLength );
+ alignment->qPos = 0;
+
+ //
+ // Since the target sequence may be on the forward or reverse
+ // strand, a copy of the subsequence is made, and the original
+ // sequence free'd.
+ //
+ DNASequence tSubseq;
+ alignment->tAlignedSeqPos = alignment->tAlignedSeqPos + alignment->tPos;
+ alignment->tAlignedSeqLength = alignment->TEnd();
+ tSubseq.Copy(alignment->tAlignedSeq, alignment->tPos, alignment->tAlignedSeqLength);
+ alignment->tPos = 0;
+
+ alignment->tAlignedSeq.Free();
+ alignment->tAlignedSeq.TakeOwnership(tSubseq);
+
+ DNALength maximumExtendLength = 500;
+
+ if (alignment->blocks.size() > 0 ) {
+ int lastAlignedBlock = alignment->blocks.size() - 1;
+ DNALength lastAlignedQPos = alignment->blocks[lastAlignedBlock].QEnd() + alignment->qPos + alignment->qAlignedSeqPos;
+ DNALength lastAlignedTPos = alignment->blocks[lastAlignedBlock].TEnd() + alignment->tPos + alignment->tAlignedSeqPos;
+ T_AlignmentCandidate extendedAlignmentForward, extendedAlignmentReverse;
+ int forwardScore, reverseScore;
+
+ SMRTSequence readSuffix;
+ DNALength readSuffixLength;
+ DNASequence genomeSuffix;
+ DNALength genomeSuffixLength;
+
+ SMRTSequence readPrefix;
+ DNALength readPrefixLength;
+ DNASequence genomePrefix;
+ DNALength genomePrefixLength;
+
+ //
+ // Align the entire end of the read if it is short enough.
+ //
+ readSuffixLength = min(read.length - lastAlignedQPos, maximumExtendLength);
+ if (readSuffixLength > 0) {
+ readSuffix.ReferenceSubstring(read, lastAlignedQPos, readSuffixLength);
+ }
+ else {
+ readSuffix.length = 0;
+ }
+
+ //
+ // Align The entire end of the genome up to the maximum extend length;
+ //
+ genomeSuffixLength = min(intervalContigEndPos - lastAlignedTPos, maximumExtendLength);
+ if (genomeSuffixLength > 0) {
+ if (alignment->tStrand == Forward) {
+ genomeSuffix.Copy(genome, lastAlignedTPos, genomeSuffixLength);
+ }
+ else {
+ static_cast<DNASequence*>(&genome)->CopyAsRC(genomeSuffix, lastAlignedTPos, genomeSuffixLength);
+ }
+ }
+ else {
+ genomeSuffix.length = 0;
+ }
+ forwardScore = 0;
+ if (readSuffix.length > 0 and genomeSuffix.length > 0) {
+ forwardScore = ExtendAlignmentForward(readSuffix, 0,
+ genomeSuffix, 0,
+ params.extendBandSize,
+ // Reuse buffers to speed up alignment
+ mappingBuffers.scoreMat,
+ mappingBuffers.pathMat,
+ // Do the alignment in the forward direction.
+ extendedAlignmentForward,
+ distScoreFn,
+ 1, // don't bother attempting
+ // to extend the alignment
+ // if one of the sequences
+ // is less than 1 base long
+ params.maxExtendDropoff);
+ }
+
+ if ( forwardScore < 0 ) {
+ //
+ // The extended alignment considers the whole genome, but
+ // should be modified to be starting at the end of where
+ // the original alignment left off.
+ //
+ if (params.verbosity > 0) {
+ cout << "forward extended an alignment of score " << alignment->score << " with score " << forwardScore << " by " << extendedAlignmentForward.blocks.size() << " blocks and length " << extendedAlignmentForward.blocks[extendedAlignmentForward.blocks.size()-1].qPos << endl;
+ }
+ extendedAlignmentForward.tAlignedSeqPos = lastAlignedTPos;
+
+ extendedAlignmentForward.qAlignedSeqPos = lastAlignedQPos;
+
+ genomeSuffix.length = extendedAlignmentForward.tPos + extendedAlignmentForward.TEnd();
+ alignment->tAlignedSeq.Append(genomeSuffix);
+ alignment->qAlignedSeq.length += extendedAlignmentForward.qPos + extendedAlignmentForward.QEnd();
+ assert(alignment->qAlignedSeq.length <= read.length);
+ alignment->AppendAlignment(extendedAlignmentForward);
+ }
+
+ DNALength firstAlignedQPos = alignment->qPos + alignment->qAlignedSeqPos;
+ DNALength firstAlignedTPos = alignment->tPos + alignment->tAlignedSeqPos;
+
+ readPrefixLength = min(firstAlignedQPos, maximumExtendLength);
+ if (readPrefixLength > 0) {
+ readPrefix.ReferenceSubstring(read, firstAlignedQPos-readPrefixLength, readPrefixLength);
+ }
+ else {
+ readPrefix.length = 0;
+ }
+
+ genomePrefixLength = min(firstAlignedTPos - intervalContigStartPos, maximumExtendLength);
+ if (genomePrefixLength > 0) {
+ if (alignment->tStrand == 0) {
+ genomePrefix.Copy(genome, firstAlignedTPos - genomePrefixLength, genomePrefixLength);
+ }
+ else {
+ static_cast<DNASequence*>(&genome)->MakeRC(genomePrefix, firstAlignedTPos - genomePrefixLength, genomePrefixLength);
+ }
+ }
+ reverseScore = 0;
+ if (readPrefix.length > 0 and genomePrefix.length > 0) {
+ reverseScore = ExtendAlignmentReverse(readPrefix, readPrefix.length-1,
+ genomePrefix, genomePrefixLength - 1,
+ params.extendBandSize, //k
+ mappingBuffers.scoreMat,
+ mappingBuffers.pathMat,
+ extendedAlignmentReverse,
+ distScoreFn,
+ 1, // don't bother attempting
+ // to extend the alignment
+ // if one of the sequences
+ // is less than 1 base long
+ params.maxExtendDropoff);
+ }
+
+ if (reverseScore < 0 ) {
+ //
+ // Make alignment->tPos relative to the beginning of the
+ // extended alignment so that when it is appended, the
+ // coordinates match correctly.
+ if (params.verbosity > 0) {
+ cout << "reverse extended an alignment of score " << alignment->score << " with score " << reverseScore << " by " << extendedAlignmentReverse.blocks.size() << " blocks and length " << extendedAlignmentReverse.blocks[extendedAlignmentReverse.blocks.size()-1].qPos << endl;
+ }
+ extendedAlignmentReverse.tAlignedSeqPos = firstAlignedTPos - genomePrefixLength;
+ extendedAlignmentReverse.qAlignedSeqPos = firstAlignedQPos - readPrefixLength;
+ extendedAlignmentReverse.AppendAlignment(*alignment);
+
+ genomePrefix.Append(alignment->tAlignedSeq, genomePrefix.length - alignment->tPos);
+ alignment->tAlignedSeq.Free();
+ alignment->tAlignedSeq.TakeOwnership(genomePrefix);
+
+ alignment->blocks = extendedAlignmentReverse.blocks;
+
+ alignment->tAlignedSeqPos = extendedAlignmentReverse.tAlignedSeqPos;
+ alignment->tPos = extendedAlignmentReverse.tPos;
+
+
+ alignment->qAlignedSeqPos = extendedAlignmentReverse.qAlignedSeqPos;
+ alignment->qAlignedSeq.length = readPrefix.length + alignment->qAlignedSeq.length;
+ alignment->qPos = extendedAlignmentReverse.qPos;
+ alignment->qAlignedSeq.seq = readPrefix.seq;
+ //
+ // Make sure the two ways of accounting for aligned sequence
+ // length are in sync. This needs to go.
+ //
+ if (alignment->blocks.size() > 0) {
+ int lastBlock = alignment->blocks.size() - 1;
+ alignment->qAlignedSeqLength = alignment->qAlignedSeq.length;
+ alignment->tAlignedSeqLength = alignment->tAlignedSeq.length;
+ }
+ else {
+ alignment->qAlignedSeqLength = alignment->qAlignedSeq.length = 0;
+ alignment->tAlignedSeqLength = alignment->tAlignedSeq.length = 0;
+ }
+ } // end of if (reverseScore < 0 )
+ readSuffix.Free();
+ readPrefix.Free();
+ genomePrefix.Free();
+ genomeSuffix.Free();
+ }
+ tSubseq.Free();
+ }
+
+ if (params.verbosity > 0) {
+ cout << "interval align score: " << alignScore << endl;
+ StickPrintAlignment(*alignment,
+ (DNASequence&) alignment->qAlignedSeq,
+ (DNASequence&) alignment->tAlignedSeq,
+ cout,
+ 0, alignment->tAlignedSeqPos);
+
+ }
+ ComputeAlignmentStats(*alignment,
+ alignment->qAlignedSeq.seq,
+ alignment->tAlignedSeq.seq,
+ distScoreFn2);
+ //SMRTDistanceMatrix, ins, del );
+
+
+ intvIt++;
+ } while (intvIt != weightedIntervals.end());
+}
+
+
+bool FirstContainsSecond(DNALength aStart, DNALength aEnd, DNALength bStart, DNALength bEnd) {
+ return ((bStart > aStart and bEnd <= aEnd) or
+ (bStart >= aStart and bEnd < aEnd));
+}
+
+template<typename T_Sequence>
+bool CheckForSufficientMatch(T_Sequence &read, vector<T_AlignmentCandidate*> &alignmentPtrs, MappingParameters ¶ms) {
+ if (alignmentPtrs.size() > 0 and alignmentPtrs[0]->score < params.maxScore) {
+ return true;
+ }
+ else {
+ return false;
+ }
+}
+
+void DeleteAlignments(vector<T_AlignmentCandidate*> &alignmentPtrs, int startIndex=0) {
+ int i;
+ for (i = startIndex; i < int(alignmentPtrs.size()); i++ ) {
+ delete alignmentPtrs[i];
+ }
+ alignmentPtrs.resize(0);
+}
+
+int RemoveLowQualitySDPAlignments(int readLength, vector<T_AlignmentCandidate*> &alignmentPtrs, MappingParameters ¶ms) {
+ // Just a hack. For now, assume there is at least 1 match per 50 bases.
+ int totalBasesMatched = 0;
+ int a;
+ for (a = 0; a < int(alignmentPtrs.size()); a++) {
+ int b;
+ for (b = 0; b < int(alignmentPtrs[a]->blocks.size()); b++) {
+ totalBasesMatched += alignmentPtrs[a]->blocks[b].length;
+ }
+ int expectedMatches = params.sdpTupleSize/50.0 * readLength;
+ if (totalBasesMatched < expectedMatches) {
+ delete alignmentPtrs[a];
+ alignmentPtrs[a] = NULL;
+ }
+ }
+ int packedAlignmentIndex = 0;
+ for (a = 0; a < int(alignmentPtrs.size()); a++) {
+ if (alignmentPtrs[a] != NULL) {
+ alignmentPtrs[packedAlignmentIndex] = alignmentPtrs[a];
+ packedAlignmentIndex++;
+ }
+ }
+ alignmentPtrs.resize(packedAlignmentIndex);
+ return packedAlignmentIndex;
+}
+
+
+template<typename T_Sequence>
+int RemoveLowQualityAlignments(T_Sequence &read, vector<T_AlignmentCandidate*> &alignmentPtrs, MappingParameters ¶ms) {
+ if (params.verbosity > 0) {
+ cout << "checking at least " << alignmentPtrs.size() << " alignments to see if they are accurate." << endl;
+ }
+ UInt i;
+ for (i = 0; i < MIN(params.nCandidates, alignmentPtrs.size()); i++) {
+ if (params.verbosity > 0) {
+ cout << "Quality check " << i << " " << alignmentPtrs[i]->score << endl;
+ }
+ if (alignmentPtrs[i]->blocks.size() == 0 or
+ alignmentPtrs[i]->score > params.maxScore) {
+ //
+ // Since the alignments are sorted according to alignment
+ // score, once one of the alignments is too low of a score,
+ // all remaining alignments are also too low, and should be
+ // removed as well. Do that all at once.
+ //
+ if (alignmentPtrs[i]->blocks.size() == 0 and params.verbosity > 0) {
+ cout << "Removing empty alignment " << alignmentPtrs[i]->qName << endl;
+ }
+ if (params.verbosity > 0) {
+ cout << alignmentPtrs[i]->qName << " alignment " << i << " is too low of a score." << alignmentPtrs[i]->score << endl;
+ }
+ int deletedIndex = i;
+ for (; deletedIndex < alignmentPtrs.size(); deletedIndex++) {
+ delete alignmentPtrs[deletedIndex];
+ alignmentPtrs[deletedIndex] = NULL;
+ }
+ alignmentPtrs.erase(i + alignmentPtrs.begin(), alignmentPtrs.end());
+ break;
+ }
+ else {
+ if (params.verbosity > 0) {
+ cout << "Keeping alignment " << i << " " << alignmentPtrs[i]->qPos << " " << alignmentPtrs[i]->qLength
+ << " " << alignmentPtrs[i]->tName << " " << alignmentPtrs[i]->tPos << " " << alignmentPtrs[i]->tLength
+ << " from score: " << alignmentPtrs[i]->score << endl;
+ }
+ }
+ }
+ return alignmentPtrs.size();
+}
+
+int RemoveOverlappingAlignments(vector<T_AlignmentCandidate*> &alignmentPtrs, MappingParameters ¶ms) {
+ vector<unsigned char> alignmentIsContained;
+ alignmentIsContained.resize(alignmentPtrs.size());
+ std::fill(alignmentIsContained.begin(), alignmentIsContained.end(), false);
+
+ int j;
+ int numContained = 0;
+ int curNotContained = 0;
+
+ if (alignmentPtrs.size() > 0) {
+ UInt i;
+ for (i = 0; i < alignmentPtrs.size()-1; i++ ){
+ T_AlignmentCandidate *aref = alignmentPtrs[i];
+ if (aref->pctSimilarity < params.minPctSimilarity) {
+ continue;
+ }
+ for (j = i + 1; j < int(alignmentPtrs.size()); j++ ){
+ //
+ // Make sure this alignment isn't already removed.
+ //
+ if (alignmentIsContained[j]) {
+ continue;
+ }
+
+ //
+ // Only check for containment if the two sequences are from the same contig.
+ //
+ if (alignmentPtrs[i]->tIndex != alignmentPtrs[j]->tIndex) {
+ continue;
+ }
+
+ //
+ // Check for an alignment that is fully overlapping another
+ // alignment.
+ if (aref->GenomicTBegin() <= alignmentPtrs[j]->GenomicTBegin() and
+ aref->GenomicTEnd() >= alignmentPtrs[j]->GenomicTEnd() and
+ alignmentPtrs[i]->tIndex == alignmentPtrs[j]->tIndex) {
+ //
+ // Alignment i is contained in j is only true if it has a worse score.
+ //
+ if (aref->score <= alignmentPtrs[j]->score) {
+ alignmentIsContained[j] = true;
+ }
+ if (params.verbosity >= 2) {
+ cout << "alignment " << i << " is contained in " << j << endl;
+ cout << aref->tAlignedSeqPos << " " << alignmentPtrs[j]->tAlignedSeqPos << " "
+ << aref->tAlignedSeqPos + aref->tAlignedSeqLength << " "
+ << alignmentPtrs[j]->tAlignedSeqPos + alignmentPtrs[j]->tAlignedSeqLength << endl;
+ }
+ }
+ else if (alignmentPtrs[j]->GenomicTBegin() <= aref->GenomicTBegin() and
+ alignmentPtrs[j]->GenomicTEnd() >= aref->GenomicTEnd() and
+ alignmentPtrs[i]->tIndex == alignmentPtrs[j]->tIndex) {
+ if (params.verbosity >= 2) {
+ cout << "ALIGNMENT " << j << " is contained in " << i << endl;
+ cout << alignmentPtrs[j]->tAlignedSeqPos << " " << aref->tAlignedSeqPos << " "
+ << alignmentPtrs[j]->tAlignedSeqPos + alignmentPtrs[j]->tAlignedSeqLength << " "
+ << aref->tAlignedSeqPos + aref->tAlignedSeqLength << endl;
+ }
+ if (alignmentPtrs[j]->score <= aref->score) {
+ alignmentIsContained[i] = true;
+ }
+ }
+ }
+ }
+ for (i = 0; i < alignmentPtrs.size(); i++) {
+ T_AlignmentCandidate *aref = alignmentPtrs[i];
+ if (alignmentIsContained[i]) {
+ delete alignmentPtrs[i];
+ alignmentPtrs[i] = NULL;
+ numContained++;
+ }
+ else {
+ alignmentPtrs[curNotContained] = aref;
+ ++curNotContained;
+ }
+ }
+ alignmentPtrs.resize(alignmentPtrs.size() - numContained);
+ }
+ return alignmentPtrs.size();
+}
+
+template<typename T_RefSequence, typename T_Sequence>
+void RefineAlignments(vector<T_Sequence*> &bothQueryStrands,
+ T_RefSequence &genome,
+ vector<T_AlignmentCandidate*> &alignmentPtrs, MappingParameters ¶ms, MappingBuffers &mappingBuffers) {
+
+
+ UInt i;
+ for (i = 0; i < alignmentPtrs.size(); i++ ) {
+ RefineAlignment(bothQueryStrands, genome, *alignmentPtrs[i], params, mappingBuffers);
+ }
+ //
+ // It's possible the alignment references change their order after running
+ // the local alignments. This is made into a parameter rather than resorting
+ // every time so that the performance gain by resorting may be measured.
+ //
+ if (params.sortRefinedAlignments) {
+ std::sort(alignmentPtrs.begin(), alignmentPtrs.end(), SortAlignmentPointersByScore());
+ }
+}
+
+
+template<typename T_RefSequence, typename T_Sequence>
+void PairwiseLocalAlign(T_Sequence &qSeq, T_RefSequence &tSeq,
+ int k,
+ MappingParameters ¶ms, T_AlignmentCandidate &alignment,
+ MappingBuffers &mappingBuffers,
+ AlignmentType alignType=Global) {
+ //
+ // Perform a pairwise alignment between qSeq and tSeq, but choose
+ // the pairwise alignment method based on the parameters. The
+ // options for pairwise alignment are:
+ // - Affine KBanded alignment: usually used for sequences with no
+ // quality information.
+ // - KBanded alignment: For sequences with quality information.
+ // Gaps are scored with quality values.
+ //
+ QualityValueScoreFunction<DNASequence, FASTQSequence> scoreFn;
+ scoreFn.del = params.indel;
+ scoreFn.ins = params.indel;
+
+ DistanceMatrixScoreFunction<DNASequence, FASTASequence> distScoreFn2(
+ SMRTDistanceMatrix, params.indel, params.indel);
+
+ IDSScoreFunction<DNASequence, FASTQSequence> idsScoreFn;
+ idsScoreFn.ins = params.insertion;
+ idsScoreFn.del = params.deletion;
+ idsScoreFn.substitutionPrior = params.substitutionPrior;
+ idsScoreFn.globalDeletionPrior = params.globalDeletionPrior;
+ idsScoreFn.InitializeScoreMatrix(SMRTDistanceMatrix);
+
+ int kbandScore;
+ int qvAwareScore;
+ if (params.ignoreQualities || qSeq.qual.Empty() || !ReadHasMeaningfulQualityValues(qSeq) ) {
+
+ kbandScore = AffineKBandAlign(qSeq, tSeq, SMRTDistanceMatrix,
+ params.indel+2, params.indel - 3, // homopolymer insertion open and extend
+ params.indel+2, params.indel - 1, // any insertion open and extend
+ params.indel, // deletion
+ k*1.2,
+ mappingBuffers.scoreMat, mappingBuffers.pathMat,
+ mappingBuffers.hpInsScoreMat, mappingBuffers.hpInsPathMat,
+ mappingBuffers.insScoreMat, mappingBuffers.insPathMat,
+ alignment, Global);
+
+ alignment.score = kbandScore;
+ if (params.verbosity >= 2) {
+ cout << "align score: " << kbandScore << endl;
+ }
+ }
+ else {
+
+
+ if (qSeq.insertionQV.Empty() == false) {
+ qvAwareScore = KBandAlign(qSeq, tSeq, SMRTDistanceMatrix,
+ params.indel+2, // ins
+ params.indel+2, // del
+ k,
+ mappingBuffers.scoreMat, mappingBuffers.pathMat,
+ alignment, idsScoreFn, alignType);
+ if (params.verbosity >= 2) {
+ cout << "ids score fn score: " << qvAwareScore << endl;
+ }
+ }
+ else {
+ qvAwareScore = KBandAlign(qSeq, tSeq, SMRTDistanceMatrix,
+ params.indel+2, // ins
+ params.indel+2, // del
+ k,
+ mappingBuffers.scoreMat, mappingBuffers.pathMat,
+ alignment, scoreFn, alignType);
+ if (params.verbosity >= 2) {
+ cout << "qv score fn score: " << qvAwareScore << endl;
+ }
+ }
+ alignment.sumQVScore = qvAwareScore;
+ alignment.score = qvAwareScore;
+ alignment.probScore = 0;
+ }
+ // Compute stats and assign a default alignment score using an edit distance.
+ ComputeAlignmentStats(alignment, qSeq.seq, tSeq.seq, distScoreFn2);
+
+ if (params.scoreType == 1) {
+ alignment.score = alignment.sumQVScore;
+ }
+
+}
+
+template<typename T_RefSequence, typename T_Sequence>
+void RefineAlignment(vector<T_Sequence*> &bothQueryStrands,
+ T_RefSequence &genome,
+ T_AlignmentCandidate &alignmentCandidate, MappingParameters ¶ms,
+ MappingBuffers &mappingBuffers) {
+
+
+ FASTQSequence qSeq;
+ DNASequence tSeq;
+ DistanceMatrixScoreFunction<DNASequence, FASTQSequence> distScoreFn(
+ SMRTDistanceMatrix, params.deletion, params.insertion);
+
+ DistanceMatrixScoreFunction<DNASequence, FASTQSequence> distScoreFn2(
+ SMRTDistanceMatrix, params.indel, params.indel);
+
+ QualityValueScoreFunction<DNASequence, FASTQSequence> scoreFn;
+ IDSScoreFunction<DNASequence, FASTQSequence> idsScoreFn;
+ idsScoreFn.InitializeScoreMatrix(SMRTDistanceMatrix);
+ scoreFn.del = params.indel;
+ scoreFn.ins = params.indel;
+ idsScoreFn.ins = params.insertion;
+ idsScoreFn.del = params.deletion;
+ idsScoreFn.affineExtend = params.affineExtend;
+ idsScoreFn.affineOpen = params.affineOpen;
+ idsScoreFn.substitutionPrior = params.substitutionPrior;
+ idsScoreFn.globalDeletionPrior = params.globalDeletionPrior;
+
+ if (params.doGlobalAlignment) {
+ SMRTSequence subread;
+ subread.ReferenceSubstring(*bothQueryStrands[0],
+ bothQueryStrands[0]->subreadStart,
+ (bothQueryStrands[0]->subreadEnd -
+ bothQueryStrands[0]->subreadStart));
+
+ int drift = ComputeDrift(alignmentCandidate);
+ T_AlignmentCandidate refinedAlignment;
+
+ KBandAlign(subread, alignmentCandidate.tAlignedSeq, SMRTDistanceMatrix,
+ params.insertion, params.deletion,
+ drift,
+ mappingBuffers.scoreMat, mappingBuffers.pathMat,
+ refinedAlignment, idsScoreFn, Global);
+ refinedAlignment.RemoveEndGaps();
+ ComputeAlignmentStats(refinedAlignment,
+ subread.seq,
+ alignmentCandidate.tAlignedSeq.seq,
+ distScoreFn2);
+ //idsScoreFn);
+
+ alignmentCandidate.blocks = refinedAlignment.blocks;
+ alignmentCandidate.gaps = refinedAlignment.gaps;
+ alignmentCandidate.tPos = refinedAlignment.tPos;
+ alignmentCandidate.qPos = refinedAlignment.qPos + bothQueryStrands[0]->subreadStart;
+ alignmentCandidate.score = refinedAlignment.score;
+ subread.Free();
+ }
+ else if (params.useGuidedAlign) {
+ T_AlignmentCandidate refinedAlignment;
+ int lastBlock = alignmentCandidate.blocks.size() - 1;
+
+
+ if (alignmentCandidate.blocks.size() > 0) {
+
+ /*
+ * Refine the alignment without expanding past the current
+ * boundaries of the sequences that are already aligned.
+ */
+
+ //
+ // NOTE** this only makes sense when
+ // alignmentCandidate.blocks[0].tPos == 0. Otherwise the length
+ // of the sequence is not correct.
+ //
+ tSeq.Copy(alignmentCandidate.tAlignedSeq,
+ alignmentCandidate.tPos,
+ (alignmentCandidate.blocks[lastBlock].tPos +
+ alignmentCandidate.blocks[lastBlock].length -
+ alignmentCandidate.blocks[0].tPos));
+
+ // qSeq.ReferenceSubstring(alignmentCandidate.qAlignedSeq,
+ qSeq.ReferenceSubstring(*bothQueryStrands[0],
+ alignmentCandidate.qAlignedSeqPos + alignmentCandidate.qPos,
+ (alignmentCandidate.blocks[lastBlock].qPos +
+ alignmentCandidate.blocks[lastBlock].length));
+
+
+ if (!params.ignoreQualities && ReadHasMeaningfulQualityValues(alignmentCandidate.qAlignedSeq)) {
+ if (params.affineAlign) {
+ AffineGuidedAlign(qSeq, tSeq, alignmentCandidate,
+ idsScoreFn, params.bandSize,
+ mappingBuffers,
+ refinedAlignment, Global, false);
+ }
+ else {
+ GuidedAlign(qSeq, tSeq, alignmentCandidate,
+ idsScoreFn, params.guidedAlignBandSize,
+ mappingBuffers,
+ refinedAlignment, Global, false);
+ }
+ }
+ else {
+ if (params.affineAlign) {
+ AffineGuidedAlign(qSeq, tSeq, alignmentCandidate,
+ distScoreFn, params.bandSize,
+ mappingBuffers,
+ refinedAlignment, Global, false);
+ }
+ else {
+ GuidedAlign(qSeq, tSeq, alignmentCandidate,
+ distScoreFn, params.guidedAlignBandSize,
+ mappingBuffers,
+ refinedAlignment, Global, false);
+ }
+ }
+ ComputeAlignmentStats(refinedAlignment,
+ qSeq.seq,
+ tSeq.seq,
+ distScoreFn2, params.affineAlign);
+ //
+ // Copy the refine alignment, which may be a subsequence of the
+ // alignmentCandidate into the alignment candidate.
+ //
+
+ // First copy the alignment block and gap (the description of
+ // the base by base alignment).
+
+ alignmentCandidate.blocks.clear();
+ alignmentCandidate.blocks = refinedAlignment.blocks;
+
+ alignmentCandidate.CopyStats(refinedAlignment);
+
+ alignmentCandidate.gaps = refinedAlignment.gaps;
+ alignmentCandidate.score = refinedAlignment.score;
+ alignmentCandidate.nCells = refinedAlignment.nCells;
+
+ // Next copy the information that describes what interval was
+ // aligned. Since the reference sequences of the alignment
+ // candidate have been modified, they are reassigned.
+ alignmentCandidate.tAlignedSeq.Free();
+ alignmentCandidate.tAlignedSeq.TakeOwnership(tSeq);
+ alignmentCandidate.ReassignQSequence(qSeq);
+ alignmentCandidate.tAlignedSeqPos += alignmentCandidate.tPos;
+ alignmentCandidate.qAlignedSeqPos += alignmentCandidate.qPos;
+
+ //
+ // tPos and qPos are the positions within the interval where the
+ // alignment begins. The refined alignment has adifferent tPos
+ // and qPos from the alignment candidate.
+ alignmentCandidate.tPos = refinedAlignment.tPos;
+ alignmentCandidate.qPos = refinedAlignment.qPos;
+
+ // The lengths of the newly aligned sequences may differ, update those.
+ alignmentCandidate.tAlignedSeqLength = tSeq.length;
+ alignmentCandidate.qAlignedSeqLength = qSeq.length;
+ }
+ }
+ else {
+
+
+ //
+ // This assumes an SDP alignment has been performed to create 'alignmentCandidate'.
+
+ //
+ // Recompute the alignment using a banded smith waterman to
+ // get rid of any spurious effects of usign the seeded gaps.
+ //
+
+ //
+ // The k-banded alignment is over a subsequence of the first
+ // (sparse dynamic programming, SDP) alignment. The SDP
+ // alignment is over a large window that may contain the
+ // candidate sequence. The k-band alignment is over a tighter
+ // region.
+
+ int drift = ComputeDrift(alignmentCandidate);
+
+ //
+ // Rescore the alignment with a banded alignment that has a
+ // better model of sequencing error.
+ //
+
+ if (alignmentCandidate.blocks.size() == 0 ){
+ alignmentCandidate.score = 0;
+ return;
+ }
+ int lastBlock = alignmentCandidate.blocks.size() - 1;
+
+ //
+ // Assign the sequences that are going to be realigned using
+ // banded alignment. The SDP alignment does not give that great
+ // of a score, but it does do a good job at finding a backbone
+ // alignment that closely defines the sequence that is aligned.
+ // Reassign the subsequences for alignment with a tight bound
+ // around the beginning and ending of each sequence, so that
+ // global banded alignment may be performed.
+ //
+
+ //
+ // This section needs to be cleaned up substantially. Right now it
+ // copies a substring from the ref to a temp, then from the temp
+ // back to the ref. It may be possible to just keep one pointer per
+ // read to the memory that was allocated, then allow the seq
+ // parameter to float around. The reason for all the copying is
+ // that in case there is a compressed version of the genome the
+ // seqences must be transformed before alignment.
+ //
+
+ if (alignmentCandidate.qIsSubstring) {
+ qSeq.ReferenceSubstring(*bothQueryStrands[0], // the original sequence
+ alignmentCandidate.qPos + alignmentCandidate.qAlignedSeqPos,
+ alignmentCandidate.blocks[lastBlock].qPos + alignmentCandidate.blocks[lastBlock].length);
+ }
+ else {
+ qSeq.ReferenceSubstring(alignmentCandidate.qAlignedSeq, // the subsequence that the alignment points to
+ alignmentCandidate.qPos + alignmentCandidate.qAlignedSeqPos,
+ alignmentCandidate.blocks[lastBlock].qPos + alignmentCandidate.blocks[lastBlock].length - alignmentCandidate.blocks[0].qPos);
+ }
+
+ tSeq.Copy(alignmentCandidate.tAlignedSeq, // the subsequence the alignment points to
+ alignmentCandidate.tPos, // ofset into the subsequence
+ alignmentCandidate.blocks[lastBlock].tPos + alignmentCandidate.blocks[lastBlock].length - alignmentCandidate.blocks[0].tPos);
+
+ T_AlignmentCandidate refinedAlignment;
+
+ //
+ // When the parameter bandSize is 0, set the alignment band size
+ // to the drift off the diagonal, plus a little more for wiggle
+ // room. When the parameteris nonzero, use that as a fixed band.
+ //
+ int k;
+ if (params.bandSize == 0) {
+ k = abs(drift) * 1.5;
+ }
+ else {
+ k = params.bandSize;
+ }
+ if (params.verbosity > 0) {
+ cout << "drift: " << drift << " qlen: " << alignmentCandidate.qAlignedSeq.length << " tlen: " << alignmentCandidate.tAlignedSeq.length << " k: " << k << endl;
+ cout << "aligning in " << k << " * " << alignmentCandidate.tAlignedSeq.length << " " << k * alignmentCandidate.tAlignedSeq.length << endl;
+ }
+ if (k < 10) {
+ k = 10;
+ }
+
+ alignmentCandidate.tAlignedSeqPos += alignmentCandidate.tPos;
+
+ VectorIndex lastSDPBlock = alignmentCandidate.blocks.size() - 1;
+
+ if (alignmentCandidate.blocks.size() > 0) {
+ DNALength prevLength = alignmentCandidate.tAlignedSeqLength -= alignmentCandidate.tPos;
+ alignmentCandidate.tAlignedSeqLength = (alignmentCandidate.blocks[lastSDPBlock].tPos
+ + alignmentCandidate.blocks[lastSDPBlock].length
+ - alignmentCandidate.blocks[0].tPos);
+ }
+ else {
+ alignmentCandidate.tAlignedSeqLength = 0;
+ }
+
+ alignmentCandidate.tPos = 0;
+ alignmentCandidate.qAlignedSeqPos += alignmentCandidate.qPos;
+
+ if (alignmentCandidate.blocks.size() > 0) {
+ DNALength prevLength = alignmentCandidate.qAlignedSeqLength -= alignmentCandidate.qPos;
+ alignmentCandidate.qAlignedSeqLength = (alignmentCandidate.blocks[lastSDPBlock].qPos
+ + alignmentCandidate.blocks[lastSDPBlock].length
+ - alignmentCandidate.blocks[0].qPos);
+ }
+ else {
+ alignmentCandidate.qAlignedSeqLength = 0;
+ }
+ alignmentCandidate.qPos = 0;
+
+ alignmentCandidate.blocks.clear();
+ alignmentCandidate.tAlignedSeq.Free();
+ alignmentCandidate.tAlignedSeq.TakeOwnership(tSeq);
+ alignmentCandidate.ReassignQSequence(qSeq);
+
+ if (params.verbosity >= 2) {
+ cout << "refining target: " << endl;
+ alignmentCandidate.tAlignedSeq.PrintSeq(cout);
+ cout << "refining query: " << endl;
+ static_cast<DNASequence*>(&alignmentCandidate.qAlignedSeq)->PrintSeq(cout);
+ cout << endl;
+ }
+ PairwiseLocalAlign(qSeq, tSeq, k, params, alignmentCandidate, mappingBuffers, Fit);
+ }
+}
+
+void AssignRefContigLocation(T_AlignmentCandidate &alignment, SequenceIndexDatabase<FASTQSequence> &seqdb, DNASequence &genome) {
+ //
+ // If the sequence database is used, the start position of
+ // the alignment is relative to the start of the chromosome,
+ // not the entire index. Subtract off the start position of
+ // the chromosome to get the true position.
+ //
+ DNALength forwardTPos;
+ int seqDBIndex;
+ if (alignment.tStrand == 0) {
+ forwardTPos = alignment.tAlignedSeqPos;
+ seqDBIndex = seqdb.SearchForIndex(forwardTPos);
+ alignment.tAlignedSeqPos -= seqdb.seqStartPos[seqDBIndex];
+ }
+ else {
+ //
+ // Flip coordinates into forward strand in order to find the boundaries
+ // of the contig, then reverse them in order to find offset.
+ //
+
+ // Find the reverse complement coordinate of the index of the last aligned base.
+ assert(alignment.tAlignedSeqLength > 0);
+ forwardTPos = genome.MakeRCCoordinate(alignment.tAlignedSeqPos + alignment.tAlignedSeqLength - 1);
+ seqDBIndex = seqdb.SearchForIndex(forwardTPos);
+
+
+ //
+ // Find the reverse comlement coordinate of the last base of this
+ // sequence. This would normally be the start of the next contig
+ // -1 to get the length, but since an 'N' is added between every
+ // pair of sequences, this is -2.
+ //
+ DNALength reverseTOffset;
+ reverseTOffset = genome.MakeRCCoordinate(seqdb.seqStartPos[seqDBIndex+1]-2);
+ alignment.tAlignedSeqPos -= reverseTOffset;
+ }
+}
+
+void AssignRefContigLocations(vector<T_AlignmentCandidate*> &alignmentPtrs, SequenceIndexDatabase<FASTQSequence> &seqdb, DNASequence &genome) {
+
+ UInt i;
+ for (i = 0; i < alignmentPtrs.size(); i++) {
+ T_AlignmentCandidate *aref = alignmentPtrs[i];
+ AssignRefContigLocation(*aref, seqdb, genome);
+ }
+}
+
+
+template<typename T_RefSequence>
+void AssignGenericRefContigName(vector<T_AlignmentCandidate*> &alignmentPtrs, T_RefSequence &genome) {
+ UInt i;
+ for (i = 0; i < alignmentPtrs.size(); i++) {
+ T_AlignmentCandidate *aref = alignmentPtrs[i];
+ aref->tName = genome.title;
+ }
+}
+
+
+template<typename T_Sequence, typename T_RefSequence, typename T_SuffixArray, typename T_TupleCountTable>
+void MapRead(T_Sequence &read, T_Sequence &readRC, T_RefSequence &genome,
+ T_SuffixArray &sarray,
+ BWT &bwt,
+ SeqBoundaryFtr<FASTQSequence> &seqBoundary,
+ T_TupleCountTable &ct,
+ SequenceIndexDatabase<FASTQSequence> &seqdb,
+ MappingParameters ¶ms,
+ MappingMetrics &metrics,
+ vector<T_AlignmentCandidate*> &alignmentPtrs,
+ MappingBuffers &mappingBuffers,
+ MappingIPC *mapData) {
+
+ bool matchFound;
+ WeightedIntervalSet topIntervals(params.nCandidates);
+ int numKeysMatched=0, rcNumKeysMatched=0;
+ int expand = params.minExpand;
+ metrics.clocks.total.Tick();
+ int nTotalCells = 0;
+ int forwardNumBasesMatched = 0, reverseNumBasesMatched = 0;
+ do {
+ matchFound = false;
+ mappingBuffers.matchPosList.clear();
+ mappingBuffers.rcMatchPosList.clear();
+ alignmentPtrs.clear();
+ topIntervals.clear();
+ params.anchorParameters.expand = expand;
+
+ metrics.clocks.mapToGenome.Tick();
+
+ if (params.useSuffixArray) {
+ params.anchorParameters.lcpBoundsOutPtr = mapData->lcpBoundsOutPtr;
+ numKeysMatched =
+ MapReadToGenome(genome, sarray, read, params.lookupTableLength, mappingBuffers.matchPosList,
+ params.anchorParameters);
+
+ //
+ // Only print values for the read in forward direction (and only
+ // the first read).
+ //
+ mapData->lcpBoundsOutPtr = NULL;
+ if (!params.forwardOnly) {
+ rcNumKeysMatched =
+ MapReadToGenome(genome, sarray, readRC, params.lookupTableLength, mappingBuffers.rcMatchPosList,
+ params.anchorParameters);
+ }
+ }
+ else if (params.useBwt){
+ numKeysMatched = MapReadToGenome(bwt, read, read.subreadStart, read.subreadEnd,
+ mappingBuffers.matchPosList, params.anchorParameters, forwardNumBasesMatched);
+ if (!params.forwardOnly) {
+ rcNumKeysMatched = MapReadToGenome(bwt, readRC, readRC.subreadStart, readRC.subreadEnd,
+ mappingBuffers.rcMatchPosList, params.anchorParameters, reverseNumBasesMatched);
+ }
+ }
+
+ //
+ // Look to see if only the anchors are printed.
+ if (params.anchorFileName != "") {
+ int i;
+ if (params.nProc > 1) {
+#ifdef __APPLE__
+ sem_wait(semaphores.writer);
+#else
+ sem_wait(&semaphores.writer);
+#endif
+ }
+ *mapData->anchorFilePtr << read.title << endl;
+ for (i = 0; i < mappingBuffers.matchPosList.size(); i++) {
+ *mapData->anchorFilePtr << mappingBuffers.matchPosList[i] << endl;
+ }
+ *mapData->anchorFilePtr << readRC.title << " (RC) " << endl;
+ for (i = 0; i < mappingBuffers.rcMatchPosList.size(); i++) {
+ *mapData->anchorFilePtr << mappingBuffers.rcMatchPosList[i] << endl;
+ }
+
+ if (params.nProc > 1) {
+#ifdef __APPLE__
+ sem_post(semaphores.writer);
+#else
+ sem_post(&semaphores.writer);
+#endif
+ }
+ }
+
+ metrics.totalAnchors += mappingBuffers.matchPosList.size() + mappingBuffers.rcMatchPosList.size();
+ metrics.clocks.mapToGenome.Tock();
+
+ metrics.clocks.sortMatchPosList.Tick();
+ SortMatchPosList(mappingBuffers.matchPosList);
+ SortMatchPosList(mappingBuffers.rcMatchPosList);
+ metrics.clocks.sortMatchPosList.Tock();
+
+ PValueWeightor lisPValue(read, genome, ct.tm, &ct);
+ MultiplicityPValueWeightor lisPValueByWeight(genome);
+
+ LISSumOfLogPWeightor<T_GenomeSequence,vector<ChainedMatchPos> > lisPValueByLogSum(genome);
+
+ LISSizeWeightor<vector<ChainedMatchPos> > lisWeightFn;
+
+ IntervalSearchParameters intervalSearchParameters;
+ intervalSearchParameters.globalChainType = params.globalChainType;
+ intervalSearchParameters.advanceHalf = params.advanceHalf;
+ intervalSearchParameters.warp = params.warp;
+ intervalSearchParameters.fastMaxInterval = params.fastMaxInterval;
+ intervalSearchParameters.aggressiveIntervalCut = params.aggressiveIntervalCut;
+ intervalSearchParameters.verbosity = params.verbosity;
+
+ //
+ // If specified, only align a band from the anchors.
+ //
+ DNALength squareRefLength = read.length * 1.25 + params.limsAlign;
+ if (params.limsAlign != 0) {
+ int fi;
+ for (fi = 0; fi < mappingBuffers.matchPosList.size(); fi++) {
+ if (mappingBuffers.matchPosList[fi].t >= squareRefLength) { break; }
+ }
+ if (fi < mappingBuffers.matchPosList.size()) {
+ mappingBuffers.matchPosList.resize(fi);
+ }
+ }
+
+ metrics.clocks.findMaxIncreasingInterval.Tick();
+
+ //
+ // For now say that something that has a 50% chance of happening
+ // by chance is too high of a p value. This is probably many times
+ // the size.
+ //
+ intervalSearchParameters.maxPValue = log(0.5);
+ intervalSearchParameters.aboveCategoryPValue = -300;
+ VarianceAccumulator<float> accumPValue;
+ VarianceAccumulator<float> accumWeight;
+ VarianceAccumulator<float> accumNBases;
+
+ mappingBuffers.clusterList.Clear();
+ mappingBuffers.revStrandClusterList.Clear();
+
+ //
+ // Remove anchors that are fully encompassed by longer ones. This
+ // speeds up limstemplate a lot.
+ //
+
+ RemoveOverlappingAnchors(mappingBuffers.matchPosList);
+ RemoveOverlappingAnchors(mappingBuffers.rcMatchPosList);
+
+ if (params.pValueType == 0) {
+ int original = mappingBuffers.matchPosList.size();
+
+ int numMerged = 0;
+ if (params.printDotPlots) {
+ ofstream dotPlotOut;
+ string dotPlotName = string(read.title) + ".anchors";
+ CrucialOpen(dotPlotName, dotPlotOut, std::ios::out);
+ int mp;
+ for (mp = 0; mp < mappingBuffers.matchPosList.size(); mp++ ){
+ dotPlotOut << mappingBuffers.matchPosList[mp].q << " " << mappingBuffers.matchPosList[mp].t << " " << mappingBuffers.matchPosList[mp].l << " " << endl;
+ }
+ dotPlotOut.close();
+ }
+ /*
+ This is an optimization that is being tested out that places a grid over the
+ area where there are anchors, and then finds an increasing maximally weighted
+ path through the grid. The weight of a cell in the grid is the sum of the
+ number of anchors in it. All other anchors are to be removed. This will likely
+ only work for LIMSTemplate sequences, or other sequences with little structural
+ variation.
+ FindBand(mappingBuffers.matchPosList,
+ refCopy, read, 100);
+ */
+ FindMaxIncreasingInterval(Forward,
+ mappingBuffers.matchPosList,
+ // allow for indels to stretch out the mapping of the read.
+ (DNALength) ((read.subreadEnd - read.subreadStart) * (1 + params.indelRate)), params.nCandidates,
+ seqBoundary,
+ lisPValue,//lisPValue2,
+ lisWeightFn,
+ topIntervals, genome, read, intervalSearchParameters,
+ &mappingBuffers.globalChainEndpointBuffer,
+ mappingBuffers.clusterList,
+ accumPValue, accumWeight, accumNBases, read.title);
+ // Uncomment when the version of the weight functor needs the sequence.
+
+ mappingBuffers.clusterList.ResetCoordinates();
+
+ FindMaxIncreasingInterval(Reverse, mappingBuffers.rcMatchPosList,
+ (DNALength) ((read.subreadEnd - read.subreadStart) * (1 + params.indelRate)), params.nCandidates,
+ seqBoundary,
+ lisPValue,//lisPValue2
+ lisWeightFn,
+ topIntervals, genome, readRC, intervalSearchParameters,
+ &mappingBuffers.globalChainEndpointBuffer,
+ mappingBuffers.revStrandClusterList,
+ accumPValue, accumWeight, accumNBases, read.title);
+ }
+ else if (params.pValueType == 1) {
+ FindMaxIncreasingInterval(Forward,
+ mappingBuffers.matchPosList,
+ // allow for indels to stretch out the mapping of the read.
+ (DNALength) ((read.subreadEnd - read.subreadStart) * (1 + params.indelRate)), params.nCandidates,
+ seqBoundary,
+ lisPValueByWeight, // different from pvaltype == 2 and 0
+ lisWeightFn,
+ topIntervals, genome, read, intervalSearchParameters,
+ &mappingBuffers.globalChainEndpointBuffer,
+ mappingBuffers.clusterList,
+ accumPValue, accumWeight, accumNBases,
+ read.title);
+
+
+ mappingBuffers.clusterList.ResetCoordinates();
+ FindMaxIncreasingInterval(Reverse, mappingBuffers.rcMatchPosList,
+ (DNALength) ((read.subreadEnd - read.subreadStart) * (1 + params.indelRate)), params.nCandidates,
+ seqBoundary,
+ lisPValueByWeight, // different from pvaltype == 2 and 0
+ lisWeightFn,
+ topIntervals, genome, readRC, intervalSearchParameters,
+ &mappingBuffers.globalChainEndpointBuffer,
+ mappingBuffers.revStrandClusterList,
+ accumPValue, accumWeight, accumNBases,
+ read.title);
+ }
+ else if (params.pValueType == 2) {
+ FindMaxIncreasingInterval(Forward,
+ mappingBuffers.matchPosList,
+ // allow for indels to stretch out the mapping of the read.
+ (DNALength) ((read.subreadEnd - read.subreadStart) * (1 + params.indelRate)), params.nCandidates,
+ seqBoundary,
+ lisPValueByLogSum, // different from pvaltype == 1 and 0
+ lisWeightFn,
+ topIntervals, genome, read, intervalSearchParameters,
+ &mappingBuffers.globalChainEndpointBuffer,
+ mappingBuffers.clusterList,
+ accumPValue, accumWeight, accumNBases,
+ read.title);
+
+ mappingBuffers.clusterList.ResetCoordinates();
+ FindMaxIncreasingInterval(Reverse, mappingBuffers.rcMatchPosList,
+ (DNALength) ((read.subreadEnd - read.subreadStart) * (1 + params.indelRate)), params.nCandidates,
+ seqBoundary,
+ lisPValueByLogSum, // different from pvaltype == 1 and 0
+ lisWeightFn,
+ topIntervals, genome, readRC, intervalSearchParameters,
+ &mappingBuffers.globalChainEndpointBuffer,
+ mappingBuffers.revStrandClusterList,
+ accumPValue, accumWeight, accumNBases,
+ read.title);
+ }
+
+ mappingBuffers.clusterList.numBases.insert(mappingBuffers.clusterList.numBases.end(),
+ mappingBuffers.revStrandClusterList.numBases.begin(),
+ mappingBuffers.revStrandClusterList.numBases.end());
+
+ mappingBuffers.clusterList.numAnchors.insert(mappingBuffers.clusterList.numAnchors.end(),
+ mappingBuffers.revStrandClusterList.numAnchors.begin(),
+ mappingBuffers.revStrandClusterList.numAnchors.end());
+
+ metrics.clocks.findMaxIncreasingInterval.Tock();
+
+ //
+ // Print verbose output.
+ //
+ WeightedIntervalSet::iterator topIntIt, topIntEnd;
+ topIntEnd = topIntervals.end();
+ if (params.verbosity > 0) {
+ int topintind = 0;
+ cout << " intv: index start end qstart qend seq_boundary_start seq_boundary_end pvalue " << endl;
+ for (topIntIt = topIntervals.begin();topIntIt != topIntEnd ; ++topIntIt) {
+ cout << " intv: " << topintind << " " << (*topIntIt).start << " "
+ << (*topIntIt).end << " "
+ << (*topIntIt).qStart << " " << (*topIntIt).qEnd << " "
+ << seqBoundary((*topIntIt).start) << " " << seqBoundary((*topIntIt).end) << " "
+ << (*topIntIt).pValue << endl;
+ if (params.verbosity > 2) {
+ int m;
+ for (m = 0; m < (*topIntIt).matches.size(); m++) {
+ cout << " (" << (*topIntIt).matches[m].q << ", " << (*topIntIt).matches[m].t << ", " << (*topIntIt).matches[m].l << ") ";
+ }
+ cout << endl;
+ }
+ ++topintind;
+ }
+ }
+
+ //
+ // Allocate candidate alignments on the stack. Each interval is aligned.
+ //
+ alignmentPtrs.resize(topIntervals.size());
+ UInt i;
+ for (i = 0; i < alignmentPtrs.size(); i++ ) {
+ alignmentPtrs[i] = new T_AlignmentCandidate;
+ }
+ metrics.clocks.alignIntervals.Tick();
+ AlignIntervals( genome, read, readRC,
+ topIntervals,
+ SMRTDistanceMatrix,
+ params.indel, params.indel,
+ params.sdpTupleSize,
+ params.useSeqDB, seqdb,
+ alignmentPtrs,
+ params,
+ mappingBuffers,
+ params.startRead );
+
+ /* cout << read.title << endl;
+ for (i = 0; i < alignmentPtrs.size(); i++) {
+ cout << alignmentPtrs[i]->clusterScore << " " << alignmentPtrs[i]->score << endl;
+ }
+ */
+ StoreRankingStats(alignmentPtrs, accumPValue, accumWeight);
+
+ std::sort(alignmentPtrs.begin(), alignmentPtrs.end(), SortAlignmentPointersByScore());
+ metrics.clocks.alignIntervals.Tock();
+
+ //
+ // Evalutate the matches that are found for 'good enough'.
+ //
+
+ matchFound = CheckForSufficientMatch(read, alignmentPtrs, params);
+
+ //
+ // When no proper alignments are found, the loop will resume.
+ // Delete all alignments because they are bad.
+ //
+ if (expand < params.maxExpand and matchFound == false) {
+ DeleteAlignments(alignmentPtrs, 0);
+ }
+
+ //
+ // Record some metrics that show how long this took to run per base.
+ //
+
+ if (alignmentPtrs.size() > 0) {
+ metrics.RecordNumAlignedBases(read.length);
+ metrics.RecordNumCells(alignmentPtrs[0]->nCells);
+ }
+
+ if (matchFound == true) {
+ metrics.totalAnchorsForMappedReads += mappingBuffers.matchPosList.size() + mappingBuffers.rcMatchPosList.size();
+ }
+ ++expand;
+ } while ( expand <= params.maxExpand and matchFound == false);
+ metrics.clocks.total.Tock();
+ UInt i;
+ int totalCells = 0;
+ for (i = 0; i< alignmentPtrs.size(); i++) {
+ totalCells += alignmentPtrs[i]->nCells;
+ }
+ metrics.clocks.AddCells(totalCells);
+ int totalBases = 0;
+ for (i = 0; i < alignmentPtrs.size(); i++) {
+ totalBases += alignmentPtrs[i]->qLength;
+ }
+ metrics.clocks.AddBases(totalBases);
+ //
+ // Some of the alignments are to spurious regions. Delete the
+ // references that have too small of a score.
+ //
+
+ int effectiveReadLength = 0;
+ for (i = 0; i< read.length; i++) {
+ if (read.seq[i] != 'N') effectiveReadLength++;
+ }
+ if (params.sdpFilterType == 0) {
+ RemoveLowQualityAlignments(read, alignmentPtrs, params);
+ }
+ else if (params.sdpFilterType == 1) {
+ RemoveLowQualitySDPAlignments(effectiveReadLength, alignmentPtrs, params);
+ }
+
+ //
+ // Now remove overlapping alignments.
+ //
+
+ vector<T_Sequence*> bothQueryStrands;
+ bothQueryStrands.resize(2);
+ bothQueryStrands[Forward] = &read;
+ bothQueryStrands[Reverse] = &readRC;
+
+
+ //
+ // Possibly use banded dynamic programming to refine the columns
+ // of an alignment and the alignment score.
+ //
+ if (params.refineAlignments) {
+ RefineAlignments(bothQueryStrands, genome, alignmentPtrs, params, mappingBuffers);
+ RemoveLowQualityAlignments(read,alignmentPtrs,params);
+ RemoveOverlappingAlignments(alignmentPtrs, params);
+ }
+
+ if (params.forPicard) {
+ int a;
+ for (a = 0; a < alignmentPtrs.size(); a++ ) {
+ alignmentPtrs[a]->OrderGapsByType();
+ }
+ }
+
+ //
+ // Look to see if the number of anchors found for this read match
+ // what is expected given the expected distribution of number of
+ // anchors.
+ //
+
+ if (alignmentPtrs.size() > 0) {
+ int clusterIndex;
+ //
+ // Compute some stats on the read. For now this is fixed but will
+ // be updated on the fly soon.
+ //
+ float meanAnchorBasesPerRead, sdAnchorBasesPerRead;
+ float meanAnchorsPerRead, sdAnchorsPerRead;
+
+ int lookupValue;
+ //
+ // If a very short anchor size was used, or very long min match
+ // size there may be no precomputed distributions for it.
+ // Handle this by bounding the min match by the smallest and
+ // largest values for which there are precomputed statistics.
+
+ int boundedMinWordMatchLength = min(max(params.minMatchLength, anchorMinKValues[0]), anchorMinKValues[1]);
+
+ //
+ // Do a similar bounding for match length and accuracy.
+ //
+ int boundedMatchLength = min(max((int) alignmentPtrs[0]->qAlignedSeq.length, anchorReadLengths[0]), anchorReadLengths[1]);
+ int boundedPctSimilarity = min(max((int)alignmentPtrs[0]->pctSimilarity, anchorReadAccuracies[0]), anchorReadAccuracies[1]);
+
+ lookupValue = LookupAnchorDistribution(boundedMatchLength, boundedMinWordMatchLength, boundedPctSimilarity,
+ meanAnchorsPerRead, sdAnchorsPerRead, meanAnchorBasesPerRead, sdAnchorBasesPerRead);
+
+ float minExpAnchors = meanAnchorsPerRead - sdAnchorsPerRead;
+ //
+ // The number of standard deviations is just trial and error.
+ float minExpAnchorBases = meanAnchorBasesPerRead - 2 * sdAnchorBasesPerRead;
+ if (lookupValue < 0 or minExpAnchorBases < 0) {
+ minExpAnchorBases = 0;
+ }
+ int numSignificantClusters = 0;
+ int totalSignificantClusterSize = 0;
+ int maxClusterSize = 0;
+ int maxClusterIndex = 0;
+ int numAlnAnchorBases, numAlnAnchors, scaledMaxClusterSize;
+ alignmentPtrs[0]->ComputeNumAnchors(boundedMinWordMatchLength, numAlnAnchors, numAlnAnchorBases);
+ int totalAnchorBases = 0;
+ if (numAlnAnchorBases > meanAnchorBasesPerRead + sdAnchorBasesPerRead) {
+ numSignificantClusters = 1;
+ }
+ else {
+ if (alignmentPtrs[0]->score < params.maxScore) {
+ for (clusterIndex = 0; clusterIndex < mappingBuffers.clusterList.numBases.size(); clusterIndex++) {
+ if (mappingBuffers.clusterList.numBases[clusterIndex] > maxClusterSize) {
+ maxClusterSize = mappingBuffers.clusterList.numBases[clusterIndex];
+ maxClusterIndex = clusterIndex;
+ }
+ }
+ int scaledExpectedClusterSize = maxClusterSize / ((float)numAlnAnchorBases) * minExpAnchorBases;
+ for (clusterIndex = 0; clusterIndex < mappingBuffers.clusterList.numBases.size(); clusterIndex++) {
+ bool isSignificant = false;
+ if (mappingBuffers.clusterList.numBases[clusterIndex] >= scaledExpectedClusterSize) {
+ // cout << mappingBuffers.clusterList.numBases[clusterIndex] << " " << scaledExpectedClusterSize << " " << meanAnchorBasesPerRead << " " << sdAnchorBasesPerRead << endl;
+ ++numSignificantClusters;
+ totalSignificantClusterSize += meanAnchorBasesPerRead;
+ isSignificant = true;
+ }
+ //
+ // The following output block is useful in debugging mapqv
+ // calculation. It should be uncommented and examined when
+ // mapqvs do not look correct.
+ //
+ totalAnchorBases += mappingBuffers.clusterList.numBases[clusterIndex];
+ }
+ }
+
+ if (lookupValue == 0) {
+ int scaledMaxClusterSize;
+ alignmentPtrs[0]->ComputeNumAnchors(params.minMatchLength, numAlnAnchors, numAlnAnchorBases);
+ scaledMaxClusterSize = ( ((float)numAlnAnchorBases )/ meanAnchorBasesPerRead) * maxClusterSize;
+ }
+ }
+
+ for (i = 0; i < alignmentPtrs.size(); i++) {
+ alignmentPtrs[i]->numSignificantClusters = numSignificantClusters;
+ }
+ if (mapData->clusterFilePtr != NULL and topIntervals.size() > 0 and alignmentPtrs.size() > 0) {
+ WeightedIntervalSet::iterator intvIt = topIntervals.begin();
+ if (params.nProc > 1) {
+#ifdef __APPLE__
+ sem_wait(semaphores.hitCluster);
+#else
+ sem_wait(&semaphores.hitCluster);
+#endif
+ }
+
+ *mapData->clusterFilePtr << (*intvIt).size << " " << (*intvIt).pValue << " " << (*intvIt).nAnchors << " "
+ << read.length << " " << alignmentPtrs[0]->score << " " << alignmentPtrs[0]->pctSimilarity << " "
+ << " " << minExpAnchors << " " << alignmentPtrs[0]->qAlignedSeq.length << endl;
+
+ if (params.nProc > 1) {
+#ifdef __APPLE__
+ sem_post(semaphores.hitCluster);
+#else
+ sem_post(&semaphores.hitCluster);
+#endif
+ }
+ }
+
+ }
+
+
+ //
+ // Assign the query name and strand for each alignment.
+ //
+
+ for (i = 0; i < alignmentPtrs.size(); i++) {
+ T_AlignmentCandidate *aref = alignmentPtrs[i];
+ // aref->qStrand = aref->readIndex;
+ if (aref->tStrand == 0) {
+ aref->qName = read.GetName();
+ }
+ else {
+ aref->qName = readRC.GetName();
+ }
+ }
+
+ AssignRefContigLocations(alignmentPtrs, seqdb, genome);
+}
+
+
+void SumMismatches(SMRTSequence &read,
+ T_AlignmentCandidate &alignment,
+ int mismatchScore,
+ int fullIntvStart, int fullIntvEnd,
+ int &sum) {
+ int alnStart, alnEnd;
+ alignment.GetQIntervalOnForwardStrand(alnStart, alnEnd);
+ int p;
+ sum = 0;
+ if (read.substitutionQV.Empty() == false) {
+ for (p = fullIntvStart; p < alnStart; p++) {
+ sum += read.substitutionQV[p];
+ }
+ for (p = alnEnd; p < fullIntvEnd; p++) {
+ sum += read.substitutionQV[p];
+ }
+ } else {
+ // bug 24363, compute mismatch score when QV is not available.
+ sum += mismatchScore * ((alnStart - fullIntvStart) + (fullIntvEnd - alnEnd));
+ }
+}
+
+int FindMaxLengthAlignment(vector<T_AlignmentCandidate*> alignmentPtrs,
+ int &maxLengthIndex) {
+ int i;
+ int maxLength = 0;
+ maxLengthIndex = -1;
+
+ for (i = 0; i < int(alignmentPtrs.size()); i++) {
+ int qStart, qEnd;
+ alignmentPtrs[i]->GetQInterval(qStart, qEnd);
+ if (qEnd - qStart > maxLength) {
+ maxLengthIndex = i;
+ maxLength = qEnd - qStart;
+ }
+ }
+ return (maxLength != -1);
+}
+
+bool AlignmentsOverlap(T_AlignmentCandidate &alnA, T_AlignmentCandidate &alnB, float minPercentOverlap) {
+ int alnAStart, alnAEnd, alnBStart, alnBEnd;
+ bool useForwardStrand=true;
+ alnA.GetQInterval(alnAStart, alnAEnd, useForwardStrand);
+ alnB.GetQInterval(alnBStart, alnBEnd, useForwardStrand);
+ // Look if one alignment encompasses the other
+ int ovp = 0;
+ if (alnAStart <= alnBStart and alnAEnd >= alnBEnd) {
+ return true;
+ }
+ else if (alnBStart <= alnAStart and alnBEnd >= alnAEnd) {
+ return true;
+ //ovp = alnAEnd - alnAStart;
+ }
+ else {
+ //
+ // Look to see if the alignments overlap
+ //
+
+ if (alnAEnd >= alnBStart and alnAEnd <= alnBEnd) {
+ ovp = alnAEnd - alnBStart;
+ }
+ else if (alnAStart >= alnBStart and alnAStart <= alnBEnd) {
+ ovp = alnBEnd - alnAStart;
+ }
+ }
+
+ // float ovpPercent = (2.0*ovp) / ((alnAEnd - alnAStart) + (alnBEnd - alnBStart));
+ float ovpPercent = 0;
+ if (alnAEnd - alnAStart > 0 and alnBEnd - alnBStart > 0) {
+ // overlap percentage: maximum overlap percent in A and B.
+ ovpPercent = max(float(ovp)/float(alnAEnd - alnAStart),
+ float(ovp)/float(alnBEnd - alnBStart));
+ }
+
+ // returns true when an overlap is found.
+ return (ovpPercent > minPercentOverlap);
+}
+
+
+void PartitionOverlappingAlignments(vector<T_AlignmentCandidate*> &alignmentPtrs,
+ vector<set<int> > &partitions,
+ float minOverlap) {
+ if (alignmentPtrs.size() == 0) {
+ partitions.clear();
+ return;
+ }
+
+ set<int>::iterator setIt, setEnd;
+ int i, p;
+ bool overlapFound = false;
+ for (i = 0; i < int(alignmentPtrs.size()); i++) {
+ overlapFound = false;
+ for (p = 0; p < int(partitions.size()) and overlapFound == false; p++) {
+ setEnd = partitions[p].end();
+ for (setIt = partitions[p].begin(); setIt != partitions[p].end() and overlapFound == false; ++setIt) {
+ if (AlignmentsOverlap(*alignmentPtrs[i], *alignmentPtrs[*setIt], minOverlap) or
+ ((alignmentPtrs[i]->QAlignStart() <= alignmentPtrs[*setIt]->QAlignStart()) and
+ (alignmentPtrs[i]->QAlignEnd() > alignmentPtrs[*setIt]->QAlignEnd()))) {
+ partitions[p].insert(i);
+ overlapFound = true;
+ }
+ }
+ }
+ //
+ // If this alignment does not overlap any other, create a
+ // partition with it as the first element.
+ //
+ if (overlapFound == false) {
+ partitions.push_back(set<int>());
+ partitions[partitions.size()-1].insert(i);
+ }
+ }
+}
+
+void ScaleMapQVByClusterSize(T_AlignmentCandidate &alignment, MappingParameters ¶ms) {
+ if (alignment.numSignificantClusters > int(params.nCandidates)) {
+ alignment.mapQV = Phred((1-InversePhred(alignment.mapQV))* ((float)params.nCandidates / alignment.numSignificantClusters));
+ }
+ else if (alignment.numSignificantClusters == 0) {
+ alignment.mapQV = 0;
+ }
+}
+
+void StoreMapQVs(SMRTSequence &read,
+ vector<T_AlignmentCandidate*> &alignmentPtrs,
+ MappingParameters ¶ms) {
+
+ //
+ // Only weight alignments for mapqv against eachother if they are overlapping.
+ //
+ int a;
+ vector<set<int> > partitions; // Each set contains alignments that overlap on the read.
+ DistanceMatrixScoreFunction<DNASequence, FASTQSequence> distScoreFn;
+ distScoreFn.del = params.deletion;
+ distScoreFn.ins = params.insertion;
+ // bug 24363, set affineOpen and affineExtend for distScoreFn
+ distScoreFn.affineOpen = params.affineOpen;
+ distScoreFn.affineExtend = params.affineExtend;
+ distScoreFn.InitializeScoreMatrix(SMRTLogProbMatrix);
+ IDSScoreFunction<DNASequence, FASTQSequence> idsScoreFn;
+ idsScoreFn.ins = params.insertion;
+ idsScoreFn.del = params.deletion;
+ idsScoreFn.affineExtend = params.affineExtend;
+ idsScoreFn.affineOpen = params.affineOpen;
+ idsScoreFn.substitutionPrior = params.substitutionPrior;
+ idsScoreFn.globalDeletionPrior = params.globalDeletionPrior;
+
+ //
+ // Rescore the alignment so that it uses probabilities.
+ //
+ for (a = 0; a < int(alignmentPtrs.size()); a++) {
+ if (params.ignoreQualities == false) {
+ // bug 24363, pass -affineAlign to compute correct alignment score.
+ alignmentPtrs[a]->probScore = -ComputeAlignmentScore(*alignmentPtrs[a],
+ alignmentPtrs[a]->qAlignedSeq,
+ alignmentPtrs[a]->tAlignedSeq,
+ idsScoreFn,
+ params.affineAlign) / 10.0;
+ }
+ else {
+ alignmentPtrs[a]->probScore = -ComputeAlignmentScore(*alignmentPtrs[a],
+ alignmentPtrs[a]->qAlignedSeq,
+ alignmentPtrs[a]->tAlignedSeq,
+ distScoreFn,
+ params.affineAlign) / 10.0;
+ }
+ }
+ PartitionOverlappingAlignments(alignmentPtrs, partitions, params.minFractionToBeConsideredOverlapping);
+
+ int p;
+ set<int>::iterator partIt, partEnd;
+
+ //
+ // For each partition, store where on the read it begins, and where
+ // it ends.
+ //
+ vector<int> partitionBeginPos, partitionEndPos;
+ partitionBeginPos.resize(partitions.size());
+ partitionEndPos.resize(partitions.size());
+ fill(partitionBeginPos.begin(), partitionBeginPos.end(), -1);
+ fill(partitionEndPos.begin(), partitionEndPos.end(), -1);
+ vector<char> assigned;
+ assigned.resize( alignmentPtrs.size());
+ fill(assigned.begin(), assigned.end(), false);
+
+ for (p = 0; p < int(partitions.size()); p++) {
+ partEnd = partitions[p].end();
+ int alnStart, alnEnd;
+
+ if (partitions[p].size() > 0) {
+ partIt = partitions[p].begin();
+ alignmentPtrs[*partIt]->GetQInterval(alnStart, alnEnd);
+ partitionBeginPos[p] = alnStart;
+ partitionEndPos[p] = alnEnd;
+ ++partIt;
+ partEnd = partitions[p].end();
+ for (; partIt != partEnd; ++partIt) {
+ // Comment out because all reads are now in the forward strand.
+ // alignmentPtrs[*partIt]->GetQInterval(alnStart, alnEnd, convertToForwardStrand);
+ alignmentPtrs[*partIt]->GetQInterval(alnStart, alnEnd);
+ if (alnEnd - alnStart > partitionEndPos[p] - partitionBeginPos[p]) {
+ partitionBeginPos[p] = alnStart;
+ partitionEndPos[p] = alnEnd;
+ }
+ }
+ }
+ }
+
+ //
+ // For each partition, determine the widest parts of the read that
+ // are aligned in the partition. All alignments will be extended to
+ // the end of the widest parts of the partition.
+ //
+ const static bool convertToForwardStrand = true;
+
+ UInt i;
+
+ //
+ // For now, just use the alignment score as the probability score.
+ // Although it is possible to use the full forward probability, for
+ // the most part it is pretty much the same as the Vitterbi
+ // probability, but it takes a lot longer to compute.
+ //
+
+ //
+ // Now estimate what the alignment scores would be if they were
+ // extended past the ends of their current alignment.
+ //
+
+ for (p = 0; p < int(partitions.size()); p++) {
+ partEnd = partitions[p].end();
+ int alnStart, alnEnd;
+ for (partIt = partitions[p].begin(); partitions[p].size() > 0 and partIt != partEnd; ++partIt) {
+ int mismatchSum = 0;
+ alignmentPtrs[*partIt]->GetQInterval(alnStart, alnEnd, convertToForwardStrand);
+ if (alnStart - partitionBeginPos[p] > MAPQV_END_ALIGN_WIGGLE or
+ partitionEndPos[p] - alnEnd > MAPQV_END_ALIGN_WIGGLE) {
+ // bug 24363, use updated SumMismatches to compute mismatch score when
+ // no QV is available.
+ SumMismatches(read, *alignmentPtrs[*partIt], 15,
+ partitionBeginPos[p], partitionEndPos[p], mismatchSum);
+ }
+ //
+ // Random sequence can be aligned with about 50% similarity due
+ // to optimization, so weight the qv sum
+ //
+ alignmentPtrs[*partIt]->probScore += -(mismatchSum) * 0.5;
+ }
+ }
+
+ //
+ // Determine mapqv by summing qvscores in partitions
+
+ float mapQVDenominator = 0;
+ for (p = 0; p < int(partitions.size()); p++) {
+ set<int>::iterator nextIt;
+ if (partitions[p].size() == 0) {
+ continue;
+ }
+ int index = *partitions[p].begin();
+
+ mapQVDenominator = alignmentPtrs[index]->probScore;
+
+ if (partitions[p].size() > 1) {
+ partIt = partitions[p].begin();
+ partEnd = partitions[p].end();
+ ++partIt;
+
+ for (; partIt != partEnd; ++partIt) {
+ index = *partIt;
+ mapQVDenominator = LogSumOfTwo(mapQVDenominator, alignmentPtrs[index]->probScore);
+ }
+ }
+
+
+ for (partIt = partitions[p].begin();
+ partIt != partitions[p].end(); ++partIt) {
+ //
+ // If only one alignment is found, assume maximum mapqv.
+ //
+ assigned[*partIt] = true;
+ if (partitions[p].size() == 1) {
+ alignmentPtrs[*partIt]->mapQV = MAX_PHRED_SCORE;
+ }
+
+ //
+ // Look for overflow.
+ //
+ else if (alignmentPtrs[*partIt]->probScore - mapQVDenominator < -20) {
+ alignmentPtrs[*partIt]->mapQV = 0;
+ }
+ else {
+ double log10 = log(10);
+ double sub = alignmentPtrs[*partIt]->probScore - mapQVDenominator;
+ double expo = exp(log10*sub);
+ double diff = 1.0 - expo;
+ int phredValue;
+
+ if (expo == 0) {
+ phredValue = 0;
+ }
+ else if (diff == 0) {
+ phredValue = MAX_PHRED_SCORE;
+ }
+ else {
+ phredValue = Phred(diff);
+ }
+ if (phredValue > MAX_PHRED_SCORE) {
+ phredValue = MAX_PHRED_SCORE;
+ }
+
+ alignmentPtrs[*partIt]->mapQV = phredValue;
+ assigned[*partIt]=true;
+ }
+
+ if (params.scaleMapQVByNumSignificantClusters) {
+ ScaleMapQVByClusterSize(*alignmentPtrs[*partIt], params);
+ }
+ }
+ }
+
+ for (i = 0; i < assigned.size(); i++) {
+ assert(assigned[i]);
+ }
+}
+
+//
+// The full read is not the subread, and does not have masked off characters.
+//
+void PrintAlignment(T_AlignmentCandidate &alignment, SMRTSequence &fullRead, MappingParameters ¶ms, AlignmentContext &alignmentContext, ostream &outFile, BamWriter * bamWriterPtr) {
+ /*
+ if (alignment.score > params.maxScore) {
+ if (params.verbosity > 0) {
+ cout << "Not using " << alignment.qAlignedSeqPos << " " << alignment.tAlignedSeqPos << " because score: " << alignment.score << " is too low (" << params.maxScore << ")" << endl;
+ }
+ return;
+ }
+ if (alignment.pctSimilarity < params.minPctSimilarity) {
+ if (params.verbosity > 0) {
+ cout << "Not using " << alignment.qAlignedSeqPos << " " << alignment.tAlignedSeqPos << " because identity: " << alignment.pctSimilarity << " is too low (" << params.minPctIdentity << ")" << endl;
+ }
+ return;
+ }
+ if (alignment.tAlignedSeq.length < params.minAlnLength) {
+ if (params.verbosity > 0) {
+ cout << "Not using " << alignment.qAlignedSeqPos << " " << alignment.tAlignedSeqPos << " because length: " << alignment.tAlignedSeq.length << " is too short (" << params.minAlnLength << ")" << endl;
+ }
+ return;
+ }*/
+
+ try {
+ int lastBlock = alignment.blocks.size() - 1;
+ if (params.printFormat == StickPrint) {
+ PrintAlignmentStats(alignment, outFile);
+ StickPrintAlignment(alignment,
+ (DNASequence&) alignment.qAlignedSeq,
+ (DNASequence&) alignment.tAlignedSeq,
+ outFile,
+ alignment.qAlignedSeqPos, alignment.tAlignedSeqPos);
+ }
+ else if (params.printFormat == SAM) {
+ SAMOutput::PrintAlignment(alignment, fullRead, outFile, alignmentContext, params.samQVList, params.clipping, params.cigarUseSeqMatch);
+ }
+ else if (params.printFormat == BAM) {
+#ifdef USE_PBBAM
+ BAMOutput::PrintAlignment(alignment, fullRead, *bamWriterPtr, alignmentContext, params.samQVList, params.clipping, params.cigarUseSeqMatch);
+#else
+ REQUIRE_PBBAM_ERROR();
+#endif
+ }
+ else if (params.printFormat == CompareXML) {
+ XMLOutput::Print(alignment,
+ (DNASequence&) alignment.qAlignedSeq, (DNASequence&) alignment.tAlignedSeq,
+ outFile,
+ alignment.qAlignedSeqPos, alignment.tAlignedSeqPos);
+ }
+ else if (params.printFormat == Vulgar) {
+ PrintAlignmentStats(alignment, outFile);
+ VulgarOutput::Print(alignment, outFile);
+ }
+ else if (params.printFormat == CompareSequencesParsable) {
+ CompareSequencesOutput::Print(alignment, alignment.qAlignedSeq, alignment.tAlignedSeq, outFile);
+ }
+ else if (params.printFormat == Interval) {
+ if (alignment.blocks.size() > 0) {
+ IntervalOutput::Print(alignment, outFile);
+ }
+ }
+ else if (params.printFormat == SummaryPrint) {
+ if (alignment.blocks.size() > 0) {
+ SummaryOutput::Print(alignment, outFile);
+ }
+ }
+ }
+ catch (ostream::failure f) {
+ cout << "ERROR writing to output file. The output drive may be full, or you " << endl;
+ cout << "may not have proper write permissions." << endl;
+ exit(1);
+ }
+}
+
+vector<T_AlignmentCandidate*>
+SelectAlignmentsToPrint(vector<T_AlignmentCandidate*> alignmentPtrs,
+ MappingParameters & params,
+ const int & associatedRandInt) {
+ if (params.placeRandomly) {assert(params.hitPolicy.IsRandombest());}
+
+ if (alignmentPtrs.size() == 0) {return vector<T_AlignmentCandidate*>({});}
+
+ std::sort(alignmentPtrs.begin(), alignmentPtrs.end(),
+ SortAlignmentPointersByScore());
+
+ // Apply filter criteria and hit policy.
+ // Shallow copy AlignmentCandidate pointers.
+ vector<T_AlignmentCandidate*> filtered;
+ for (auto ptr: alignmentPtrs) {
+ if (params.filterCriteria.Satisfy(ptr)) {
+ filtered.push_back(ptr);
+ if (filtered.size() == params.nBest) break;
+ }
+ }
+
+ return params.hitPolicy.Apply(filtered, false, associatedRandInt);
+}
+
+// Print all alignments in vector<T_AlignmentCandidate*> alignmentPtrs
+void PrintAlignments(vector<T_AlignmentCandidate*> alignmentPtrs,
+ SMRTSequence &read,
+ MappingParameters ¶ms, ostream &outFile,
+ AlignmentContext alignmentContext,
+ BamWriter * bamWriterPtr) {
+ if (params.nProc > 1) {
+#ifdef __APPLE__
+ sem_wait(semaphores.writer);
+#else
+ sem_wait(&semaphores.writer);
+#endif
+ }
+ for (int i = 0; i < int(alignmentPtrs.size()); i++) {
+ T_AlignmentCandidate *aref = alignmentPtrs[i];
+
+ if (aref->blocks.size() == 0) {
+
+ //
+ // If the SDP alignment finds nothing, there will be no
+ // blocks. This may happen if the sdp block size is larger
+ // than the anchor size found with the suffix array. When no
+ // blocks are found there is no alignment, so zero-out the
+ // score and continue.
+ //
+ aref->score = 0;
+ if (params.verbosity > 0) {
+ cout << "Zero blocks found for " << aref->qName << " " << aref->qAlignedSeqPos << " " << aref->tAlignedSeqPos << endl;
+ }
+ continue;
+ }
+
+ //
+ // Configure some of the alignment context before printing.
+ //
+ if (i > 0 and params.placeRandomly == false) {
+ alignmentContext.isPrimary = false;
+ }
+ else {
+ alignmentContext.isPrimary = true;
+ }
+
+ if (params.printSAM or params.printBAM) {
+ DistanceMatrixScoreFunction<DNASequence, FASTASequence> editdistScoreFn(EditDistanceMatrix, 1, 1);
+ T_AlignmentCandidate & alignment = *alignmentPtrs[i];
+ alignmentContext.editDist = ComputeAlignmentScore(alignment,
+ alignment.qAlignedSeq,
+ alignment.tAlignedSeq,
+ editdistScoreFn);
+ }
+
+ PrintAlignment(*alignmentPtrs[i], read, params, alignmentContext, outFile, bamWriterPtr);
+ }
+
+ if (params.nProc > 1) {
+#ifdef __APPLE__
+ sem_post(semaphores.writer);
+#else
+ sem_post(&semaphores.writer);
+#endif
+ }
+
+}
+
+template<typename T_Sequence>
+bool GetNextReadThroughSemaphore(ReaderAgglomerate &reader, MappingParameters ¶ms, T_Sequence &read, AlignmentContext &context, int & associatedRandInt) {
+ //
+ // Grab the value of the semaphore for debugging purposes.
+ //
+ // uncomment when needed
+ // int semvalue;
+ // if (params.nProc > 1) {
+ // sem_getvalue(&semaphores.reader, &semvalue);
+ // }
+
+ //
+ // Wait on a semaphore
+ if (params.nProc > 1) {
+#ifdef __APPLE__
+ sem_wait(semaphores.reader);
+#else
+ sem_wait(&semaphores.reader);
+#endif
+ }
+
+ bool returnValue = true;
+ //
+ // CCS Reads are read differently from other reads. Do static casting here
+ // of this.
+ //
+ if (reader.GetNext(read, associatedRandInt) == 0) {
+ returnValue = false;
+ }
+
+ //
+ // Set the read group id before releasing the semaphore, since other
+ // threads may change the reader object to a new read group before
+ // sending this alignment out to printing.
+ context.readGroupId = reader.readGroupId;
+
+ if (params.nProc > 1) {
+#ifdef __APPLE__
+ sem_post(semaphores.reader);
+#else
+ sem_post(&semaphores.reader);
+#endif
+ }
+ return returnValue;
+}
+
+void AssignMapQV(vector<T_AlignmentCandidate*> &alignmentPtrs) {
+ int i;
+ int mapQV = 1;
+ if (alignmentPtrs.size() > 1 and alignmentPtrs[0]->score == alignmentPtrs[1]->score) {
+ // the top two alignments have the same score, don't consider them as mapped.
+ mapQV = 0;
+ }
+
+ for (i = 0; i < int(alignmentPtrs.size()); i++) {
+ alignmentPtrs[i]->mapQV = mapQV;
+ }
+}
+
+void PrintAlignmentPtrs(vector <T_AlignmentCandidate*> & alignmentPtrs,
+ ostream & out = cout) {
+ for(int alignmentIndex = 0;
+ alignmentIndex < int(alignmentPtrs.size());
+ alignmentIndex++) {
+ out << "["<< alignmentIndex << "/"
+ << alignmentPtrs.size() << "]" << endl;
+ T_AlignmentCandidate *alignment = alignmentPtrs[alignmentIndex];
+ alignment->Print(out);
+ }
+ out << endl;
+}
+
+// Extend target aligned sequence of the input alignement to both ends
+// by flankSize bases. Update alignment->tAlignedSeqPos,
+// alignment->tAlignedSeqLength and alignment->tAlignedSeq.
+void FlankTAlignedSeq(T_AlignmentCandidate * alignment,
+ SequenceIndexDatabase<FASTQSequence> &seqdb,
+ DNASequence & genome,
+ int flankSize) {
+ assert(alignment != NULL and alignment->tIsSubstring);
+
+ UInt forwardTPos, newTAlignedSeqPos, newTAlignedSeqLen;
+ // New aligned start position relative to this chromosome, with
+ // the same direction as alignment->tStrand.
+ newTAlignedSeqPos = UInt((alignment->tAlignedSeqPos > UInt(flankSize))?
+ (alignment->tAlignedSeqPos - flankSize): 0);
+ newTAlignedSeqLen = min(alignment->tAlignedSeqPos + alignment->tAlignedSeqLength +
+ flankSize, alignment->tLength) - newTAlignedSeqPos;
+
+ if (alignment->tStrand ==0) {
+ forwardTPos = newTAlignedSeqPos;
+ } else {
+ forwardTPos = alignment->tLength - newTAlignedSeqPos - 1;
+ }
+
+ // Find where this chromosome is in the genome.
+ int seqIndex = seqdb.GetIndexOfSeqName(alignment->tName);
+ assert(seqIndex != -1);
+ UInt newGenomePos = seqdb.ChromosomePositionToGenome(seqIndex, forwardTPos);
+
+ if (alignment->tIsSubstring == false) {
+ alignment->tAlignedSeq.Free();
+ }
+ alignment->tAlignedSeqPos = newTAlignedSeqPos;
+ alignment->tAlignedSeqLength = newTAlignedSeqLen;
+ if (alignment->tStrand == 0) {
+ alignment->tAlignedSeq.ReferenceSubstring(genome, newGenomePos, newTAlignedSeqLen);
+ } else {
+ // Copy and then reverse complement.
+ genome.MakeRC(alignment->tAlignedSeq,
+ newGenomePos + 1 - alignment->tAlignedSeqLength,
+ alignment->tAlignedSeqLength);
+ alignment->tIsSubstring = false;
+ }
+}
+
+// Align a subread of a SMRT sequence to target sequence of an alignment.
+// Input:
+// subread - a subread of a SMRT sequence.
+// unrolledRead - the full SMRT sequence.
+// alignment - an alignment.
+// passDirection - whether or not the subread has the
+// same direction as query of the alignment.
+// 0 = true, 1 = false.
+// subreadInterval - [start, end) interval of the subread in the
+// SMRT read.
+// subreadIndex - index of the subread in allReadAlignments.
+// params - mapping paramters.
+// Output:
+// allReadAlignments - where the sequence and alignments of the
+// subread are saved.
+// threadOut - an out stream for debugging the current thread.
+void AlignSubreadToAlignmentTarget(ReadAlignments & allReadAlignments,
+ SMRTSequence & subread, SMRTSequence & unrolledRead,
+ T_AlignmentCandidate * alignment,
+ int passDirection, ReadInterval & subreadInterval,
+ int subreadIndex,
+ MappingParameters & params,
+ MappingBuffers & mappingBuffers,
+ ostream & threadOut) {
+ assert(passDirection == 0 or passDirection == 1);
+ //
+ // Determine where in the genome the subread has mapped.
+ //
+ DNASequence alignedForwardRefSequence, alignedReverseRefSequence;
+
+ if (alignment->tStrand == 0) {
+ // This needs to be changed -- copy copies RHS into LHS,
+ // CopyAsRC copies LHS into RHS
+ alignedForwardRefSequence.Copy(alignment->tAlignedSeq);
+ alignment->tAlignedSeq.CopyAsRC(alignedReverseRefSequence);
+ }
+ else {
+ alignment->tAlignedSeq.CopyAsRC(alignedForwardRefSequence);
+ alignedReverseRefSequence.Copy(alignment->tAlignedSeq);
+ }
+
+ IDSScoreFunction<DNASequence, FASTQSequence> idsScoreFn;
+ idsScoreFn.ins = params.insertion;
+ idsScoreFn.del = params.deletion;
+ idsScoreFn.InitializeScoreMatrix(SMRTDistanceMatrix);
+ idsScoreFn.globalDeletionPrior = params.globalDeletionPrior;
+ idsScoreFn.substitutionPrior = params.substitutionPrior;
+
+ DistanceMatrixScoreFunction<DNASequence, FASTQSequence> distScoreFn2(
+ SMRTDistanceMatrix, params.indel, params.indel);
+ //
+ // Determine the strand to align the subread to.
+ //
+ T_AlignmentCandidate exploded;
+ bool sameAlignmentPassDirection = (alignment->tStrand == passDirection);
+ bool computeProbIsFalse = false;
+ DNASequence & alignedRefSequence = (sameAlignmentPassDirection?
+ alignedForwardRefSequence:alignedReverseRefSequence);
+ //
+ // In the original code, parameters: bandSize=10, alignType=Global,
+ // sdpTupleSize=4 (instead of 12, Local and 6) were used when
+ // alignment & pass have different directions.
+ //
+ int explodedScore = GuidedAlign(subread, alignedRefSequence,
+ idsScoreFn, 12, params.sdpIns, params.sdpDel,
+ params.indelRate, mappingBuffers, exploded,
+ Local, computeProbIsFalse, 6);
+
+ if (params.verbosity >= 3) {
+ threadOut << "zmw " << unrolledRead.zmwData.holeNumber
+ << ", subreadIndex " << subreadIndex
+ << ", passDirection " << passDirection
+ << ", subreadInterval [" << subreadInterval.start
+ << ", " << subreadInterval.end << ")" << endl
+ << "StickPrintAlignment subread-reference alignment which has"
+ << " the " << (sameAlignmentPassDirection?"same":"different")
+ << " direction as the ccs-reference (or the "
+ << "longestSubread-reference) alignment. " << endl
+ << "subread: " << endl;
+ static_cast<DNASequence*>(&subread)->PrintSeq(threadOut);
+ threadOut << endl;
+ threadOut << "alignedRefSeq: " << endl;
+ static_cast<DNASequence*>(&alignedRefSequence)->PrintSeq(threadOut);
+ StickPrintAlignment(exploded, (DNASequence&) subread,
+ (DNASequence&) alignedRefSequence,
+ threadOut, exploded.qAlignedSeqPos,
+ exploded.tAlignedSeqPos);
+ }
+
+ if (exploded.blocks.size() > 0) {
+ DistanceMatrixScoreFunction<DNASequence, FASTQSequence> distScoreFn(
+ SMRTDistanceMatrix, params.indel, params.indel);
+ ComputeAlignmentStats(exploded, subread.seq,
+ alignedRefSequence.seq,
+ distScoreFn2);
+ //SMRTDistanceMatrix, params.indel, params.indel);
+ if (exploded.score <= params.maxScore) {
+ //
+ // The coordinates of the alignment should be
+ // relative to the reference sequence (the specified chromosome,
+ // not the whole genome).
+ //
+ exploded.qStrand = 0;
+ exploded.tStrand = sameAlignmentPassDirection?0:1;
+ exploded.qLength = unrolledRead.length;
+ exploded.tLength = alignment->tLength;
+ exploded.tAlignedSeq.Copy(alignedRefSequence);
+ exploded.tAlignedSeqPos = (passDirection == 0)?
+ (alignment->tAlignedSeqPos):
+ (exploded.tLength - alignment->tAlignedSeqPos
+ - alignment->tAlignedSeqLength);
+ exploded.tAlignedSeqLength = alignment->tAlignedSeqLength;
+
+ exploded.qAlignedSeq.ReferenceSubstring(subread);
+ exploded.qAlignedSeqPos = subreadInterval.start;
+ exploded.qAlignedSeqLength = subreadInterval.end - subreadInterval.start;
+ exploded.mapQV = alignment->mapQV;
+ exploded.tName = alignment->tName;
+ exploded.tIndex = alignment->tIndex;
+
+ stringstream namestrm;
+ namestrm << "/" << subreadInterval.start
+ << "_" << subreadInterval.end;
+ exploded.qName = string(unrolledRead.title) + namestrm.str();
+
+ //
+ // Don't call AssignRefContigLocation as the coordinates
+ // of the alignment is already relative to the chromosome coordiantes.
+ //
+ // Save this alignment for printing later.
+ //
+ T_AlignmentCandidate *alignmentPtr = new T_AlignmentCandidate;
+ *alignmentPtr = exploded;
+ allReadAlignments.AddAlignmentForSeq(subreadIndex, alignmentPtr);
+ } // End of exploded score <= maxScore.
+ if (params.verbosity >= 3) {
+ threadOut << "exploded score: " << exploded.score << endl
+ << "exploded alignment: "<< endl;
+ exploded.Print(threadOut);
+ threadOut << endl;
+ }
+ } // End of exploded.blocks.size() > 0.
+}
+
+
+// Given a SMRT sequence and a subread interval, make the subread.
+// Input:
+// smrtRead - a SMRT sequence
+// subreadInterval - a subread interval
+// params - mapping parameters
+// Output:
+// subreadSequence - the constructed subread
+void MakeSubreadOfInterval(SMRTSequence & subreadSequence,
+ SMRTSequence & smrtRead, ReadInterval & subreadInterval,
+ MappingParameters & params) {
+ //
+ // subreadMapType is a way of limiting the portion of the read
+ // that is aligned. The output is similar, but the
+ // computation is slightly different. The subreadMapType 0
+ // was written first, and just creates a hard mask over the
+ // regions that are not to be aligned. The subreadMapType is
+ // slightly more formal mode where a new read is pointed to
+ // the subread then aligned.
+ //
+ // subreadMapType of 0 is always used, however eventually it
+ // may be faster to go to 1, just 1 isn't tested thoroughly
+ // yet.
+ //
+ // Note, for proper SAM printing, subreadMaptype of 0 is needed.
+ //
+ int start = subreadInterval.start;
+ int end = subreadInterval.end;
+
+ assert(smrtRead.length >= subreadSequence.length);
+ if (params.subreadMapType == 0) {
+ smrtRead.MakeSubreadAsMasked(subreadSequence, start, end);
+ }
+ else if (params.subreadMapType == 1) {
+ smrtRead.MakeSubreadAsReference(subreadSequence, start, end);
+ }
+
+ if (!params.preserveReadTitle) {
+ smrtRead.SetSubreadTitle(subreadSequence,
+ subreadSequence.subreadStart,
+ subreadSequence.subreadEnd);
+ }
+ else {
+ subreadSequence.CopyTitle(smrtRead.title);
+ }
+ subreadSequence.zmwData = smrtRead.zmwData;
+}
+
+// Given a SMRT sequence and one of its subreads, make the
+// reverse complement of the subread in the coordinate of the
+// reverse complement sequence of the SMRT sequence.
+// Input:
+// smrtRead - a SMRT read
+// subreadSequence - a subread of smrtRead
+// Output:
+// subreadSequenceRC - the reverse complement of the subread
+// in the coordinate of the reverse
+// complement of the SMRT read.
+void MakeSubreadRC(SMRTSequence & subreadSequenceRC,
+ SMRTSequence & subreadSequence,
+ SMRTSequence & smrtRead) {
+ assert(smrtRead.length >= subreadSequence.length);
+ // Reverse complement sequence of the subread.
+ subreadSequence.MakeRC(subreadSequenceRC);
+ // Update start and end positions of subreadSequenceRC in the
+ // coordinate of reverse compelement sequence of the SMRT read.
+ subreadSequenceRC.subreadStart = smrtRead.length - subreadSequence.subreadEnd;
+ subreadSequenceRC.subreadEnd = smrtRead.length - subreadSequence.subreadStart;
+ subreadSequenceRC.zmwData = smrtRead.zmwData;
+}
+
+// Print all alignments for subreads in allReadAlignments.
+// Input:
+// allReadAlignments - contains a set of subreads, each of which
+// is associated with a group of alignments.
+// alignmentContext - an alignment context of each subread used
+// for printing in SAM format.
+// params - mapping parameters.
+// Output:
+// outFilePtr - where to print alignments for subreads.
+// unalignedFilePtr - where to print sequences for unaligned subreads.
+void PrintAllReadAlignments(ReadAlignments & allReadAlignments,
+ AlignmentContext & alignmentContext,
+ ostream & outFilePtr,
+ ostream & unalignedFilePtr,
+ MappingParameters & params,
+ BamWriter * bamWriterPtr) {
+ int subreadIndex;
+ int nAlignedSubreads = allReadAlignments.GetNAlignedSeq();
+
+ //
+ // Initialize the alignemnt context with information applicable to SAM output.
+ //
+ alignmentContext.alignMode = allReadAlignments.alignMode;
+ for (subreadIndex = 0; subreadIndex < nAlignedSubreads; subreadIndex++) {
+ if (allReadAlignments.subreadAlignments[subreadIndex].size() > 0) {
+ alignmentContext.numProperlyAlignedSubreads++;
+ }
+ }
+
+ if (alignmentContext.numProperlyAlignedSubreads == int(allReadAlignments.subreadAlignments.size())) {
+ alignmentContext.allSubreadsProperlyAligned = true;
+ }
+ alignmentContext.nSubreads = nAlignedSubreads;
+
+ for (subreadIndex = 0; subreadIndex < nAlignedSubreads; subreadIndex++) {
+ alignmentContext.subreadIndex = subreadIndex;
+ if (subreadIndex < nAlignedSubreads-1 and allReadAlignments.subreadAlignments[subreadIndex+1].size() > 0) {
+ alignmentContext.nextSubreadPos = allReadAlignments.subreadAlignments[subreadIndex+1][0]->QAlignStart();
+ alignmentContext.nextSubreadDir = allReadAlignments.subreadAlignments[subreadIndex+1][0]->qStrand;
+ alignmentContext.rNext = allReadAlignments.subreadAlignments[subreadIndex+1][0]->tName;
+ alignmentContext.hasNextSubreadPos = true;
+ } else {
+ alignmentContext.nextSubreadPos = 0;
+ alignmentContext.nextSubreadDir = 0;
+ alignmentContext.rNext = "";
+ alignmentContext.hasNextSubreadPos = false;
+ }
+
+ if (allReadAlignments.subreadAlignments[subreadIndex].size() > 0) {
+ PrintAlignments(allReadAlignments.subreadAlignments[subreadIndex],
+ allReadAlignments.subreads[subreadIndex], // the source read
+ // for these alignments
+ params, outFilePtr,//*mapData->outFilePtr,
+ alignmentContext,
+ bamWriterPtr);
+ } else {
+ //
+ // Print the unaligned sequences.
+ //
+ if (params.printUnaligned == true) {
+ if (params.nProc == 1) {
+ //allReadAlignments.subreads[subreadIndex].PrintSeq(*mapData->unalignedFilePtr);
+ allReadAlignments.subreads[subreadIndex].PrintSeq(unalignedFilePtr);
+ }
+ else {
+#ifdef __APPLE__
+ sem_wait(semaphores.unaligned);
+#else
+ sem_wait(&semaphores.unaligned);
+#endif
+ //allReadAlignments.subreads[subreadIndex].PrintSeq(*mapData->unalignedFilePtr);
+ allReadAlignments.subreads[subreadIndex].PrintSeq(unalignedFilePtr);
+#ifdef __APPLE__
+ sem_post(semaphores.unaligned);
+#else
+ sem_post(&semaphores.unaligned);
+#endif
+ } // End of nproc > 1.
+ } // End of printing unaligned sequences.
+ } // End of finding no alignments for the subread with subreadIndex.
+ } // End of printing and processing alignmentContext for each subread.
+}
+
+//template<typename T_SuffixArray, typename T_GenomeSequence, typename T_Tuple>
+void MapReads(MappingData<T_SuffixArray, T_GenomeSequence, T_Tuple> *mapData) {
+ //
+ // Step 1, initialize local pointers to map data
+ // for programming shorthand.
+ //
+ MappingParameters params = mapData->params;
+
+ DNASuffixArray sarray;
+ TupleCountTable<T_GenomeSequence, DNATuple> ct;
+ SequenceIndexDatabase<FASTQSequence> seqdb;
+ FASTQSequence fastaGenome;
+ T_GenomeSequence genome;
+ BWT *bwtPtr;
+
+ mapData->ShallowCopySuffixArray(sarray);
+ mapData->ShallowCopyReferenceSequence(genome);
+ mapData->ShallowCopySequenceIndexDatabase(seqdb);
+ mapData->ShallowCopyTupleCountTable(ct);
+
+ bwtPtr = mapData->bwtPtr;
+ SeqBoundaryFtr<FASTQSequence> seqBoundary(&seqdb);
+
+ VectorIndex i, j;
+ if (params.match != 0) {
+ }
+
+ int numAligned = 0;
+
+ SMRTSequence smrtRead, smrtReadRC;
+ SMRTSequence unrolledReadRC;
+ CCSSequence ccsRead;
+ RegionAnnotation annotation;
+ T_Sequence read;
+ int readIndex = -1;
+ int readsFileIndex;
+ bool readIsCCS = false;
+
+
+ // Print verbose logging to pid.threadid.log for each thread.
+ ofstream threadOut;
+ if (params.verbosity >= 3) {
+ stringstream ss;
+ ss << getpid() << "." << pthread_self();
+ string threadLogFileName = ss.str() + ".log";
+ threadOut.open(threadLogFileName.c_str(), ios::out|ios::app);
+ }
+
+ //
+ // Reuse the following buffers during alignment. Since these keep
+ // storage contiguous, hopefully this will decrease memory
+ // fragmentation.
+ //
+ MappingBuffers mappingBuffers;
+ while (true) {
+ //
+ // Scan the next read from input. This may either be a CCS read,
+ // or regular read (though this may be aligned in whole, or by
+ // subread).
+ //
+ AlignmentContext alignmentContext;
+ // Associate each sequence to read in with a determined random int.
+ int associatedRandInt = 0;
+ if (mapData->reader->GetFileType() == HDFCCS ||
+ mapData->reader->GetFileType() == HDFCCSONLY) {
+ if (GetNextReadThroughSemaphore(*mapData->reader, params, ccsRead, alignmentContext, associatedRandInt) == false) {
+ break;
+ }
+ else {
+ readIsCCS = true;
+ smrtRead.Copy(ccsRead);
+ ccsRead.SetQVScale(params.qvScaleType);
+ ++readIndex;
+ smrtRead.SetQVScale(params.qvScaleType);
+ }
+ assert(ccsRead.zmwData.holeNumber == smrtRead.zmwData.holeNumber and
+ ccsRead.zmwData.holeNumber == ccsRead.unrolledRead.zmwData.holeNumber);
+ } else {
+ if (GetNextReadThroughSemaphore(*mapData->reader, params, smrtRead, alignmentContext, associatedRandInt) == false) {
+ break;
+ }
+ else {
+ ++readIndex;
+ smrtRead.SetQVScale(params.qvScaleType);
+ }
+ }
+
+ //
+ // Only normal (non-CCS) reads should be masked. Since CCS reads store the raw read, that is masked.
+ //
+ bool readHasGoodRegion = true;
+ if (params.useRegionTable and params.useHQRegionTable) {
+ if (readIsCCS) {
+ readHasGoodRegion = MaskRead(ccsRead.unrolledRead, ccsRead.unrolledRead.zmwData, *mapData->regionTablePtr);
+ }
+ else {
+ readHasGoodRegion = MaskRead(smrtRead, smrtRead.zmwData, *mapData->regionTablePtr);
+ }
+ //
+ // Store the high quality start and end of this read for masking purposes when printing.
+ //
+ int hqStart, hqEnd;
+ int score;
+ LookupHQRegion(smrtRead.zmwData.holeNumber, *mapData->regionTablePtr, hqStart, hqEnd, score);
+ smrtRead.lowQualityPrefix = hqStart;
+ smrtRead.lowQualitySuffix = smrtRead.length - hqEnd;
+ smrtRead.highQualityRegionScore = score;
+ }
+ else {
+ smrtRead.lowQualityPrefix = 0;
+ smrtRead.lowQualitySuffix = 0;
+ }
+
+ //
+ // Give the opportunity to align a subset of reads.
+ //
+ if ((params.maxReadIndex >= 0 and
+ smrtRead.zmwData.holeNumber > UInt(params.maxReadIndex))) {
+ if (readIsCCS) {
+ ccsRead.Free();
+ }
+ smrtRead.Free();
+ break;
+ }
+
+ if (readHasGoodRegion == false or
+ (params.readIndex >= 0 and
+ smrtRead.zmwData.holeNumber != UInt(params.readIndex)) or
+ (params.holeNumberRangesStr.size() > 0 and
+ not params.holeNumberRanges.contains(smrtRead.zmwData.holeNumber))) {
+ //
+ // Nothing to do with this read. Skip aligning it entirely.
+ //
+ if (readIsCCS) {
+ ccsRead.Free();
+ }
+ smrtRead.Free();
+ // Stop processing once the specified read index is reached.
+ // Eventually this will change to just seek to readIndex, and
+ // just align one read anyway.
+ if ((params.readIndex >= 0 and
+ smrtRead.zmwData.holeNumber > UInt(params.readIndex)) or
+ (params.holeNumberRangesStr.size() > 0 and
+ smrtRead.zmwData.holeNumber > params.holeNumberRanges.max())){
+ break;
+ }
+ continue;
+ }
+
+
+ //
+ // Discard reads that are too small, or not labeled as having any
+ // useable/good sequence.
+ //
+ if (smrtRead.length < UInt(params.minReadLength) or readHasGoodRegion == false or
+ smrtRead.highQualityRegionScore < params.minRawSubreadScore or
+ (params.maxReadLength != 0 and
+ smrtRead.length > UInt(params.maxReadLength))) {
+ if (readIsCCS) {
+ ccsRead.Free();
+ }
+ smrtRead.Free();
+ continue;
+ }
+
+ if (smrtRead.qual.Empty() == false and smrtRead.GetAverageQuality() < params.minAvgQual) {
+ if (readIsCCS) {
+ ccsRead.Free();
+ }
+ smrtRead.Free();
+ continue;
+ }
+
+ if (params.verbosity > 1) {
+ cout << "aligning read: " << endl;
+ smrtRead.PrintSeq(cout);
+ }
+
+ smrtRead.MakeRC(smrtReadRC);
+
+ if (readIsCCS) {
+ ccsRead.unrolledRead.MakeRC(unrolledReadRC);
+ }
+
+ //
+ // When aligning subreads separately, iterate over each subread, and print the alignments for these.
+ //
+
+ ReadAlignments allReadAlignments;
+ allReadAlignments.read = smrtRead;
+
+ if (readIsCCS == false and params.mapSubreadsSeparately) {
+ // (not readIsCCS and not -noSplitSubreads)
+ vector<ReadInterval> subreadIntervals;
+ vector<int> subreadDirections;
+ vector<ReadInterval> adapterIntervals;
+ //
+ // Determine endpoints of this subread in the main read.
+ //
+ if (params.useRegionTable == false) {
+ //
+ // When there is no region table, the subread is the entire
+ // read.
+ //
+ ReadInterval wholeRead(0, smrtRead.length);
+ // The set of subread intervals is just the entire read.
+ subreadIntervals.push_back(wholeRead);
+ }
+ else {
+ //
+ // Grab the subread & adapter intervals from the entire region table to
+ // iterate over.
+ //
+ CollectSubreadIntervals(smrtRead, mapData->regionTablePtr, subreadIntervals, params.byAdapter);
+ CollectAdapterIntervals(smrtRead, mapData->regionTablePtr, adapterIntervals);
+ }
+
+ // The assumption is that neighboring subreads must have the opposite
+ // directions. So create directions for subread intervals with
+ // interleaved 0s and 1s.
+ CreateDirections(subreadDirections, subreadIntervals.size());
+
+ //
+ // Trim the boundaries of subread intervals so that only high quality
+ // regions are included in the intervals, not N's. Remove intervals
+ // and their corresponding dirctions, if they are shorter than the
+ // user specified minimum read length or do not intersect with hq
+ // region at all. Finally, return index of the (left-most) longest
+ // subread in the updated vector.
+ //
+ int longestSubreadIndex = GetHighQualitySubreadsIntervals(
+ subreadIntervals, // a vector of subread intervals.
+ subreadDirections, // a vector of subread directions.
+ smrtRead.lowQualityPrefix, // hq region start pos.
+ smrtRead.length - smrtRead.lowQualitySuffix, // hq end pos.
+ params.minSubreadLength); // minimum read length.
+
+ int bestSubreadIndex = longestSubreadIndex;
+ if (params.concordantTemplate == "longestsubread") {
+ // Use the (left-most) longest full-pass subread as
+ // template for concordant mapping
+ int longestFullSubreadIndex = GetLongestFullSubreadIndex(
+ subreadIntervals, adapterIntervals);
+ if (longestFullSubreadIndex >= 0) {
+ bestSubreadIndex = longestFullSubreadIndex;
+ }
+ } else if (params.concordantTemplate == "typicalsubread") {
+ // Use the 'typical' full-pass subread as template for
+ // concordant mapping.
+ int typicalFullSubreadIndex = GetTypicalFullSubreadIndex(
+ subreadIntervals, adapterIntervals);
+ if (typicalFullSubreadIndex >= 0) {
+ bestSubreadIndex = typicalFullSubreadIndex;
+ }
+ } else if (params.concordantTemplate == "mediansubread") {
+ // Use the 'median-length' full-pass subread as template for
+ // concordant mapping.
+ int medianFullSubreadIndex = GetMedianLengthFullSubreadIndex(
+ subreadIntervals, adapterIntervals);
+ if (medianFullSubreadIndex >= 0) {
+ bestSubreadIndex = medianFullSubreadIndex;
+ }
+ } else {
+ assert(false);
+ }
+
+ // Flop all directions if direction of the longest subread is 1.
+ if (bestSubreadIndex >= 0 and
+ bestSubreadIndex < int(subreadDirections.size()) and
+ subreadDirections[bestSubreadIndex] == 1) {
+ UpdateDirections(subreadDirections, true);
+ }
+
+ int startIndex = 0;
+ int endIndex = subreadIntervals.size();
+
+ if (params.concordant) {
+ // Only the longest subread will be aligned in the first round.
+ startIndex = max(startIndex, bestSubreadIndex);
+ endIndex = min(endIndex, bestSubreadIndex + 1);
+ }
+
+ //
+ // Make room for alignments.
+ //
+ allReadAlignments.Resize(subreadIntervals.size());
+ allReadAlignments.alignMode = Subread;
+
+ DNALength intvIndex;
+ for (intvIndex = startIndex; intvIndex < endIndex; intvIndex++) {
+ SMRTSequence subreadSequence, subreadSequenceRC;
+ MakeSubreadOfInterval(subreadSequence, smrtRead,
+ subreadIntervals[intvIndex], params);
+ MakeSubreadRC(subreadSequenceRC, subreadSequence, smrtRead);
+
+ //
+ // Store the sequence that is being mapped in case no hits are
+ // found, and missing sequences are printed.
+ //
+ allReadAlignments.SetSequence(intvIndex, subreadSequence);
+
+ vector<T_AlignmentCandidate*> alignmentPtrs;
+ mapData->metrics.numReads++;
+
+ assert(subreadSequence.zmwData.holeNumber == smrtRead.zmwData.holeNumber);
+
+ //
+ // Try default and fast parameters to map the read.
+ //
+ MapRead(subreadSequence, subreadSequenceRC,
+ genome, // possibly multi fasta file read into one sequence
+ sarray, *bwtPtr, // The suffix array, and the bwt-fm index structures
+ seqBoundary, // Boundaries of contigs in the
+ // genome, alignments do not span
+ // the ends of boundaries.
+ ct, // Count table to use word frequencies in the genome to weight matches.
+ seqdb, // Information about the names of
+ // chromosomes in the genome, and
+ // where their sequences are in the genome.
+ params, // A huge list of parameters for
+ // mapping, only compile/command
+ // line values set.
+ mapData->metrics, // Keep track of time/ hit counts,
+ // etc.. Not fully developed, but
+ // should be.
+ alignmentPtrs, // Where the results are stored.
+ mappingBuffers, // A class of buffers for structurs
+ // like dyanmic programming
+ // matrices, match lists, etc., that are not
+ // reallocated between calls to
+ // MapRead. They are cleared though.
+ mapData // Some values that are shared
+ // across threads.
+ );
+
+ //
+ // No alignments were found, sometimes parameters are
+ // specified to try really hard again to find an alignment.
+ // This sets some parameters that use a more sensitive search
+ // at the cost of time.
+ //
+
+ if ((alignmentPtrs.size() == 0 or alignmentPtrs[0]->pctSimilarity < 80) and params.doSensitiveSearch) {
+ MappingParameters sensitiveParams = params;
+ sensitiveParams.SetForSensitivity();
+ MapRead(subreadSequence, subreadSequenceRC, genome,
+ sarray, *bwtPtr,
+ seqBoundary, ct, seqdb,
+ sensitiveParams, mapData->metrics,
+ alignmentPtrs, mappingBuffers,
+ mapData);
+ }
+
+ //
+ // Store the mapping quality values.
+ //
+ if (alignmentPtrs.size() > 0 and
+ alignmentPtrs[0]->score < params.maxScore and
+ params.storeMapQV) {
+ StoreMapQVs(subreadSequence, alignmentPtrs, params);
+ }
+
+ //
+ // Select alignments for this subread.
+ //
+ vector<T_AlignmentCandidate*> selectedAlignmentPtrs =
+ SelectAlignmentsToPrint(alignmentPtrs, params,
+ associatedRandInt);
+ allReadAlignments.AddAlignmentsForSeq(intvIndex, selectedAlignmentPtrs);
+
+ //
+ // Move reference from subreadSequence, which will be freed at
+ // the end of this loop to the smrtRead, which exists for the
+ // duration of aligning all subread of the smrtRead.
+ //
+ if (params.subreadMapType == 0) {
+ int a;
+ for (a = 0; a < alignmentPtrs.size(); a++) {
+ if (alignmentPtrs[a]->qStrand == 0) {
+ alignmentPtrs[a]->qAlignedSeq.ReferenceSubstring(smrtRead,
+ alignmentPtrs[a]->qAlignedSeq.seq - subreadSequence.seq,
+ alignmentPtrs[a]->qAlignedSeqLength);
+ }
+ else {
+ alignmentPtrs[a]->qAlignedSeq.ReferenceSubstring(smrtReadRC,
+ alignmentPtrs[a]->qAlignedSeq.seq - subreadSequenceRC.seq,
+ alignmentPtrs[a]->qAlignedSeqLength);
+ }
+ }
+ }
+ subreadSequence.Free();
+ subreadSequenceRC.Free();
+ } // End of looping over subread intervals within [startIndex, endIndex).
+
+ if (params.verbosity >= 3)
+ allReadAlignments.Print(threadOut);
+
+ if (params.concordant) {
+ allReadAlignments.read = smrtRead;
+ allReadAlignments.alignMode = ZmwSubreads;
+
+ if (startIndex >= 0 &&
+ startIndex < int(allReadAlignments.subreadAlignments.size())) {
+ vector<T_AlignmentCandidate*> selectedAlignmentPtrs =
+ allReadAlignments.CopySubreadAlignments(startIndex);
+
+ for(int alignmentIndex = 0; alignmentIndex < int(selectedAlignmentPtrs.size());
+ alignmentIndex++) {
+ FlankTAlignedSeq(selectedAlignmentPtrs[alignmentIndex],
+ seqdb, genome, params.flankSize);
+ }
+
+ for (intvIndex = 0; intvIndex < subreadIntervals.size(); intvIndex++) {
+ if (intvIndex == startIndex) continue;
+ int passDirection = subreadDirections[intvIndex];
+ int passStartBase = subreadIntervals[intvIndex].start;
+ int passNumBases = subreadIntervals[intvIndex].end - passStartBase;
+ if (passNumBases <= params.minReadLength) {continue;}
+
+ mapData->metrics.numReads++;
+ SMRTSequence subread;
+ subread.ReferenceSubstring(smrtRead, passStartBase, passNumBases);
+ subread.CopyTitle(smrtRead.title);
+ // The unrolled alignment should be relative to the entire read.
+ if (params.clipping == SAMOutput::subread) {
+ SMRTSequence maskedSubread;
+ MakeSubreadOfInterval(maskedSubread, smrtRead,
+ subreadIntervals[intvIndex], params);
+ allReadAlignments.SetSequence(intvIndex, maskedSubread);
+ maskedSubread.Free();
+ } else {
+ allReadAlignments.SetSequence(intvIndex, smrtRead);
+ }
+
+ for (int alnIndex = 0; alnIndex < selectedAlignmentPtrs.size(); alnIndex++) {
+ T_AlignmentCandidate * alignment = selectedAlignmentPtrs[alnIndex];
+ if (alignment->score > params.maxScore) break;
+ AlignSubreadToAlignmentTarget(allReadAlignments,
+ subread,
+ smrtRead,
+ alignment,
+ passDirection,
+ subreadIntervals[intvIndex],
+ intvIndex,
+ params, mappingBuffers, threadOut);
+ if (params.concordantAlignBothDirections) {
+ AlignSubreadToAlignmentTarget(allReadAlignments,
+ subread,
+ smrtRead,
+ alignment,
+ ((passDirection==0)?1:0),
+ subreadIntervals[intvIndex],
+ intvIndex,
+ params, mappingBuffers, threadOut);
+ }
+ } // End of aligning this subread to each selected alignment.
+ subread.Free();
+ } // End of aligning each subread to where the template subread aligned to.
+ for(int alignmentIndex = 0; alignmentIndex < selectedAlignmentPtrs.size();
+ alignmentIndex++) {
+ if (selectedAlignmentPtrs[alignmentIndex])
+ delete selectedAlignmentPtrs[alignmentIndex];
+ }
+ } // End of if startIndex >= 0 and < subreadAlignments.size()
+ } // End of if params.concordant
+ } // End of if (readIsCCS == false and params.mapSubreadsSeparately).
+ else { // if (readIsCCS or (not readIsCCS and -noSplitSubreads) )
+ //
+ // The read must be mapped as a whole, even if it contains subreads.
+ //
+ vector<T_AlignmentCandidate*> alignmentPtrs;
+ mapData->metrics.numReads++;
+ smrtRead.subreadStart = 0; smrtRead.subreadEnd = smrtRead.length;
+ smrtReadRC.subreadStart = 0; smrtReadRC.subreadEnd = smrtRead.length;
+
+ MapRead(smrtRead, smrtReadRC,
+ genome, sarray, *bwtPtr, seqBoundary, ct, seqdb, params, mapData->metrics,
+ alignmentPtrs, mappingBuffers, mapData);
+
+ //
+ // Store the mapping quality values.
+ //
+ if (alignmentPtrs.size() > 0 and
+ alignmentPtrs[0]->score < params.maxScore and
+ params.storeMapQV) {
+ StoreMapQVs(smrtRead, alignmentPtrs, params);
+ }
+
+ //
+ // Select de novo ccs-reference alignments for subreads to align to.
+ //
+ vector<T_AlignmentCandidate*> selectedAlignmentPtrs =
+ SelectAlignmentsToPrint(alignmentPtrs, params, associatedRandInt);
+
+ //
+ // Just one sequence is aligned. There is one primary hit, and
+ // all other are secondary.
+ //
+
+ if (readIsCCS == false or params.useCcsOnly) {
+ // if -noSplitSubreads or -useccsdenovo.
+ //
+ // Record some information for proper SAM Annotation.
+ //
+ allReadAlignments.Resize(1);
+ allReadAlignments.AddAlignmentsForSeq(0, selectedAlignmentPtrs);
+ if (params.useCcsOnly) {
+ allReadAlignments.alignMode = CCSDeNovo;
+ }
+ else {
+ allReadAlignments.alignMode = Fullread;
+ }
+ allReadAlignments.SetSequence(0, smrtRead);
+ }
+ else if (readIsCCS) { // if -useccsall or -useccs
+ // Flank alignment candidates to both ends.
+ for(int alignmentIndex = 0; alignmentIndex < selectedAlignmentPtrs.size();
+ alignmentIndex++) {
+ FlankTAlignedSeq(selectedAlignmentPtrs[alignmentIndex],
+ seqdb, genome, params.flankSize);
+ }
+
+ //
+ // Align the ccs subread to where the denovo sequence mapped (explode).
+ //
+ SMRTSequence readRC;
+
+ CCSIterator ccsIterator;
+ FragmentCCSIterator fragmentCCSIterator;
+ CCSIterator *subreadIterator;
+
+ //
+ // Choose a different iterator over subreads depending on the
+ // alignment mode. When the mode is allpass, include the
+ // framgents that are not necessarily full pass.
+ //
+ if (params.useAllSubreadsInCcs) {
+ //
+ // Use all subreads even if they are not full pass
+ fragmentCCSIterator.Initialize(&ccsRead, mapData->regionTablePtr);
+ subreadIterator = &fragmentCCSIterator;
+ allReadAlignments.alignMode = CCSAllPass;
+ }
+ else {
+ // Use only full pass reads.
+ ccsIterator.Initialize(&ccsRead);
+ subreadIterator = &ccsIterator;
+ allReadAlignments.alignMode = CCSFullPass;
+ }
+
+ allReadAlignments.Resize(subreadIterator->GetNumPasses());
+
+ int passDirection, passStartBase, passNumBases;
+ SMRTSequence subread;
+
+ //
+ // The read was previously set to the smrtRead, which was the
+ // de novo ccs sequence. Since the alignments of exploded
+ // reads are reported, the unrolled read should be used as the
+ // reference when printing.
+ //
+ allReadAlignments.read = ccsRead.unrolledRead;
+ subreadIterator->Reset();
+ int subreadIndex;
+
+ //
+ // Realign all subreads to selected reference locations.
+ //
+ for (subreadIndex = 0; subreadIndex < subreadIterator->GetNumPasses(); subreadIndex++) {
+ int retval = subreadIterator->GetNext(passDirection, passStartBase, passNumBases);
+ assert(retval == 1);
+ if (passNumBases <= params.minReadLength) { continue; }
+
+ ReadInterval subreadInterval(passStartBase, passStartBase + passNumBases);
+
+ subread.ReferenceSubstring(ccsRead.unrolledRead, passStartBase, passNumBases-1);
+ subread.CopyTitle(ccsRead.title);
+ // The unrolled alignment should be relative to the entire read.
+ allReadAlignments.SetSequence(subreadIndex, ccsRead.unrolledRead);
+
+ int alignmentIndex;
+ //
+ // Align this subread to all the positions that the de novo
+ // sequence has aligned to.
+ //
+ for (alignmentIndex = 0; alignmentIndex < selectedAlignmentPtrs.size(); alignmentIndex++) {
+ T_AlignmentCandidate *alignment = selectedAlignmentPtrs[alignmentIndex];
+ if (alignment->score > params.maxScore) break;
+ AlignSubreadToAlignmentTarget(allReadAlignments,
+ subread, ccsRead.unrolledRead,
+ alignment,
+ passDirection,
+ subreadInterval,
+ subreadIndex,
+ params, mappingBuffers, threadOut);
+ } // End of aligning this subread to where the de novo ccs has aligned to.
+ subread.Free();
+ } // End of alignining all subreads to where the de novo ccs has aligned to.
+ } // End of if readIsCCS and !params.useCcsOnly
+
+ } // End of if not (readIsCCS == false and params.mapSubreadsSeparately)
+
+ PrintAllReadAlignments(allReadAlignments, alignmentContext,
+ *mapData->outFilePtr,
+ *mapData->unalignedFilePtr,
+ params,
+ bamWriterPtr);
+
+ allReadAlignments.Clear();
+ smrtReadRC.Free();
+ smrtRead.Free();
+
+ if (readIsCCS) {
+ ccsRead.Free();
+ unrolledReadRC.Free();
+ }
+ numAligned++;
+ if(numAligned % 100 == 0) {
+ mappingBuffers.Reset();
+ }
+ } // End of while (true).
+ smrtRead.Free();
+ smrtReadRC.Free();
+ unrolledReadRC.Free();
+ read.Free();
+ ccsRead.Free();
+
+ if (params.nProc > 1) {
+#ifdef __APPLE__
+ sem_wait(semaphores.reader);
+ sem_post(semaphores.reader);
+#else
+ sem_wait(&semaphores.reader);
+ sem_post(&semaphores.reader);
+#endif
+ }
+ if (params.nProc > 1) {
+ pthread_exit(NULL);
+ }
+ threadOut.close();
+}
+
+float ComputePMatch(float accuracy, int anchorLength) {
+ assert(anchorLength >= 0);
+ if (anchorLength == 0) {
+ return 0;
+ }
+ else {
+ return pow(accuracy,anchorLength);
+ }
+}
+
+//
+// Assume the number of mismatches in a row follow a geometric distribution.
+//
+void GeometricDistributionSummaryStats(float pSuccess,
+ float &mean, float &variance) {
+ mean = 1/pSuccess;
+ variance = (1-pSuccess)/ (pow(pSuccess,2));
+}
+
+int ComputeExpectedWaitingBases(float mean, float variance, float certainty) {
+ float nStdDev;
+ assert(FindQNorm(certainty, nStdDev) != false);
+ return mean + sqrt(variance) * nStdDev;
+}
+
+int main(int argc, char* argv[]) {
+ //
+ // Configure parameters for refining alignments.
+ //
+ MappingParameters params;
+ ReverseCompressIndex index;
+ pid_t parentPID;
+ pid_t *pids;
+
+ CommandLineParser clp;
+ clp.SetHelp(BlasrHelp(params));
+ clp.SetConciseHelp(BlasrConciseHelp());
+ clp.SetProgramSummary(BlasrSummaryHelp());
+ clp.SetProgramName("blasr");
+ clp.SetVersion(GetVersion());
+
+ // Register Blasr options.
+ RegisterBlasrOptions(clp, params);
+
+ // Parse command line args.
+ clp.ParseCommandLine(argc, argv, params.readsFileNames);
+
+ string commandLine;
+ clp.CommandLineToString(argc, argv, commandLine);
+
+ if (params.printVerboseHelp) {
+ cout << BlasrHelp(params) << endl;
+ exit(0); // Not a failure.
+ }
+ if (params.printDiscussion) {
+ cout << BlasrDiscussion();
+ exit(0); // Not a failure.
+ }
+ if (argc < 3) {
+ cout << BlasrConciseHelp();
+ exit(1); // A failure.
+ }
+
+ int a, b;
+ for (a = 0; a < 5; a++ ) {
+ for (b = 0; b < 5; b++ ){
+ if (a != b) {
+ SMRTDistanceMatrix[a][b] += params.mismatch;
+ }
+ else {
+ SMRTDistanceMatrix[a][b] += params.match;
+ }
+ }
+ }
+
+ if (params.scoreMatrixString != "") {
+ if (StringToScoreMatrix(params.scoreMatrixString, SMRTDistanceMatrix) == false) {
+ cout << "ERROR. The string " << endl
+ << params.scoreMatrixString << endl
+ << "is not a valid format. It should be a quoted, space separated string of " << endl
+ << "integer values. The matrix: " << endl
+ << " A C G T N" << endl
+ << " A 1 2 3 4 5" << endl
+ << " C 6 7 8 9 10" << endl
+ << " G 11 12 13 14 15" << endl
+ << " T 16 17 18 19 20" << endl
+ << " N 21 22 23 24 25" << endl
+ << " should be specified as \"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\"" << endl;
+ exit(1);
+ }
+ }
+
+ cerr << "[INFO] " << GetTimestamp() << " [blasr] started." << endl;
+ params.MakeSane();
+
+ //
+ // The random number generator is used for subsampling for debugging
+ // and testing consensus and selecting hits when hit policy is random
+ // or randombest.
+ //
+ if (params.useRandomSeed == true) {
+ InitializeRandomGenerator(params.randomSeed);
+ }
+ else {
+ InitializeRandomGeneratorWithTime();
+ }
+
+ //
+ // Various aspects of timing are stored here. However this isn't
+ // quite finished.
+ //
+ MappingMetrics metrics;
+
+ ofstream fullMetricsFile;
+ if (params.fullMetricsFileName != "") {
+ CrucialOpen(params.fullMetricsFileName, fullMetricsFile, std::ios::out);
+ metrics.SetStoreList();
+ }
+
+ //
+ // If reading a separate region table, there is a 1-1 correspondence
+ // between region table and bas file.
+ //
+ if (params.readSeparateRegionTable) {
+ if (FileOfFileNames::IsFOFN(params.regionTableFileName)) {
+ FileOfFileNames::FOFNToList(params.regionTableFileName, params.regionTableFileNames);
+ }
+ else {
+ params.regionTableFileNames.push_back(params.regionTableFileName);
+ }
+ }
+
+ if (params.regionTableFileNames.size() != 0 and
+ params.regionTableFileNames.size() != params.queryFileNames.size()) {
+ cout << "Error, there are not the same number of region table files as input files." << endl;
+ exit(1);
+ }
+
+ // If reading a separate ccs fofn, there is a 1-1 corresponence
+ // between ccs fofn and base file.
+ if (params.readSeparateCcsFofn) {
+ if (FileOfFileNames::IsFOFN(params.ccsFofnFileName)) {
+ FileOfFileNames::FOFNToList(params.ccsFofnFileName, params.ccsFofnFileNames);
+ }
+ else {
+ params.ccsFofnFileNames.push_back(params.ccsFofnFileName);
+ }
+ }
+ if (params.ccsFofnFileNames.size() != 0 and
+ params.ccsFofnFileNames.size() != params.queryFileNames.size()) {
+ cout << "Error, there are not the same number of ccs files as input files." << endl;
+ exit(1);
+ }
+
+ parentPID = getpid();
+
+ SequenceIndexDatabase<FASTASequence> seqdb;
+ SeqBoundaryFtr<FASTASequence> seqBoundary(&seqdb);
+
+ //
+ // Initialize the sequence index database if it used. If it is not
+ // specified, it is initialized by default when reading a multiFASTA
+ // file.
+ //
+ if (params.useSeqDB) {
+ ifstream seqdbin;
+ CrucialOpen(params.seqDBName, seqdbin);
+ seqdb.ReadDatabase(seqdbin);
+ }
+
+ //
+ // Make sure the reads file exists and can be opened before
+ // trying to read any of the larger data structures.
+ //
+
+
+ FASTASequence fastaGenome;
+ T_Sequence genome;
+ FASTAReader genomeReader;
+
+ //
+ // The genome is in normal FASTA, or condensed (lossy homopolymer->unipolymer)
+ // format. Both may be read in using a FASTA reader.
+ //
+ if (!genomeReader.Init(params.genomeFileName)) {
+ cout << "Could not open genome file " << params.genomeFileName << endl;
+ exit(1);
+ }
+
+ if (params.printSAM or params.printBAM) {
+ genomeReader.computeMD5 = true;
+ }
+ //
+ // If no sequence title database is supplied, initialize one when
+ // reading in the reference, and consider a seqdb to be present.
+ //
+ if (!params.useSeqDB) {
+ genomeReader.ReadAllSequencesIntoOne(fastaGenome, &seqdb);
+ params.useSeqDB = true;
+ }
+ else {
+ genomeReader.ReadAllSequencesIntoOne(fastaGenome);
+ }
+ genomeReader.Close();
+ //
+ // The genome may have extra spaces in the fasta name. Get rid of those.
+ //
+ VectorIndex t;
+ for (t = 0; t < fastaGenome.titleLength; t++ ){
+ if (fastaGenome.title[t] == ' ') {
+ fastaGenome.titleLength = t;
+ fastaGenome.title[t] = '\0';
+ break;
+ }
+ }
+
+ genome.seq = fastaGenome.seq;
+ genome.length = fastaGenome.length;
+ genome.title = fastaGenome.title;
+ genome.deleteOnExit = false;
+ genome.titleLength = fastaGenome.titleLength;
+ genome.ToUpper();
+
+ DNASuffixArray sarray;
+ TupleCountTable<T_GenomeSequence, DNATuple> ct;
+
+ int listTupleSize;
+
+ ofstream outFile;
+ outFile.exceptions(ostream::failbit);
+ ofstream unalignedOutFile;
+ BWT bwt;
+
+ if (params.useBwt) {
+ if (bwt.Read(params.bwtFileName) == 0) {
+ cout << "ERROR! Could not read the BWT file. " << params.bwtFileName << endl;
+ exit(1);
+ }
+ }
+ else {
+ if (!params.useSuffixArray) {
+ //
+ // There was no explicit specification of a suffix
+ // array on the command line, so build it on the fly here.
+ //
+ genome.ToThreeBit();
+ vector<int> alphabet;
+ sarray.InitThreeBitDNAAlphabet(alphabet);
+ sarray.LarssonBuildSuffixArray(genome.seq, genome.length, alphabet);
+ if (params.minMatchLength > 0) {
+ if (params.anchorParameters.useLookupTable == true) {
+ if (params.lookupTableLength > params.minMatchLength) {
+ params.lookupTableLength = params.minMatchLength;
+ }
+ sarray.BuildLookupTable(genome.seq, genome.length, params.lookupTableLength);
+ }
+ }
+ genome.ConvertThreeBitToAscii();
+ params.useSuffixArray = 1;
+ }
+ else if (params.useSuffixArray) {
+ if (sarray.Read(params.suffixArrayFileName)) {
+ if (params.minMatchLength != 0) {
+ params.listTupleSize = min(8, params.minMatchLength);
+ }
+ else {
+ params.listTupleSize = sarray.lookupPrefixLength;
+ }
+ if (params.minMatchLength < sarray.lookupPrefixLength) {
+ cerr << "WARNING. The value of -minMatch " << params.minMatchLength << " is less than the smallest searched length of " << sarray.lookupPrefixLength << ". Setting -minMatch to " << sarray.lookupPrefixLength << "." << endl;
+ params.minMatchLength = sarray.lookupPrefixLength;
+ }
+ }
+ else {
+ cout << "ERROR. " << params.suffixArrayFileName << " is not a valid suffix array. " << endl
+ << " Make sure it is generated with the latest version of sawriter." << endl;
+ exit(1);
+ }
+ }
+ }
+
+ if (params.minMatchLength < sarray.lookupPrefixLength) {
+ cerr << "WARNING. The value of -minMatch " << params.minMatchLength << " is less than the smallest searched length of " << sarray.lookupPrefixLength << ". Setting -minMatch to " << sarray.lookupPrefixLength << "." << endl;
+ params.minMatchLength = sarray.lookupPrefixLength;
+ }
+
+ //
+ // It is required to have a tuple count table
+ // for estimating the background frequencies
+ // for word matching.
+ // If one is specified on the command line, simply read
+ // it in. If not, this is operating under the mode
+ // that everything is computed from scratch.
+ //
+ long l;
+ TupleMetrics saLookupTupleMetrics;
+ if (params.useCountTable) {
+ ifstream ctIn;
+ CrucialOpen(params.countTableName, ctIn, std::ios::in | std::ios::binary);
+ ct.Read(ctIn);
+ saLookupTupleMetrics = ct.tm;
+
+ } else {
+ saLookupTupleMetrics.Initialize(params.lookupTableLength);
+ ct.InitCountTable(saLookupTupleMetrics);
+ ct.AddSequenceTupleCountsLR(genome);
+ }
+
+ TitleTable titleTable;
+ if (params.useTitleTable) {
+ ofstream titleTableOut;
+ CrucialOpen(params.titleTableName, titleTableOut);
+ //
+ // When using a sequence index database, the title table is simply copied
+ // from the sequencedb.
+ //
+ if (params.useSeqDB) {
+ titleTable.Copy(seqdb.names, seqdb.nSeqPos-1);
+ titleTable.ResetTableToIntegers(seqdb.names, seqdb.nameLengths, seqdb.nSeqPos-1);
+ }
+ else {
+ //
+ // No seqdb, so there is just one sequence. Still the user specified a title
+ // table, so just the first sequence in the fasta file should be used.
+ //
+ titleTable.Copy(&fastaGenome.title, 1);
+ titleTable.ResetTableToIntegers(&genome.title, &genome.titleLength, 1);
+ fastaGenome.titleLength = strlen(genome.title);
+ }
+ titleTable.Write(titleTableOut);
+ }
+ else {
+ if (params.useSeqDB) {
+ //
+ // When using a sequence index database, but not the titleTable,
+ // it is necessary to truncate the titles at the first space to
+ // be compatible with the way other alignment programs interpret
+ // fasta titles. When printing the title table, there is all
+ // sorts of extra storage space, so the full line is stored.
+ //
+ seqdb.SequenceTitleLinesToNames();
+ }
+ }
+
+ ostream *outFilePtr = &cout;
+ ofstream outFileStrm;
+ ofstream unalignedFile;
+ ostream *unalignedFilePtr = NULL;
+ ofstream metricsOut, lcpBoundsOut;
+ ofstream anchorFileStrm;
+ ofstream clusterOut, *clusterOutPtr;
+
+ if (params.anchorFileName != "") {
+ CrucialOpen(params.anchorFileName, anchorFileStrm, std::ios::out);
+ }
+
+ if (params.clusterFileName != "") {
+ CrucialOpen(params.clusterFileName, clusterOut, std::ios::out);
+ clusterOutPtr = &clusterOut;
+ clusterOut << "total_size p_value n_anchors read_length align_score read_accuracy anchor_probability min_exp_anchors seq_length" << endl;
+ }
+ else {
+ clusterOutPtr = NULL;
+ }
+
+ if (params.outFileName != "") {
+ if (not params.printBAM) {
+ CrucialOpen(params.outFileName, outFileStrm, std::ios::out);
+ outFilePtr = &outFileStrm;
+ } // otherwise, use bamWriter and initialize it later
+ }
+
+ if (params.printHeader) {
+ switch(params.printFormat) {
+ case(SummaryPrint):
+ SummaryOutput::PrintHeader(*outFilePtr);
+ break;
+ case(Interval):
+ IntervalOutput::PrintHeader(*outFilePtr);
+ break;
+ case(CompareSequencesParsable):
+ CompareSequencesOutput::PrintHeader(*outFilePtr);
+ break;
+ }
+ }
+
+ if (params.printUnaligned == true) {
+ CrucialOpen(params.unalignedFileName, unalignedFile, std::ios::out);
+ unalignedFilePtr = &unalignedFile;
+ }
+
+ if (params.metricsFileName != "") {
+ CrucialOpen(params.metricsFileName, metricsOut);
+ }
+
+ if (params.lcpBoundsFileName != "") {
+ CrucialOpen(params.lcpBoundsFileName, lcpBoundsOut);
+ // lcpBoundsOut << "pos depth width lnwidth" << endl;
+ }
+
+ //
+ // Configure the mapping database.
+ //
+
+ MappingData<T_SuffixArray, T_GenomeSequence, T_Tuple> *mapdb = new MappingData<T_SuffixArray, T_GenomeSequence, T_Tuple>[params.nProc];
+
+ int procIndex;
+ pthread_attr_t *threadAttr = new pthread_attr_t[params.nProc];
+ // MappingSemaphores semaphores;
+ //
+ // When there are multiple processes running along, sometimes there
+ // are semaphores to worry about.
+ //
+
+ if (params.nProc > 1) {
+ semaphores.InitializeAll();
+ }
+ for (procIndex = 0; procIndex < params.nProc; procIndex++ ){
+ pthread_attr_init(&threadAttr[procIndex]);
+ }
+
+ //
+ // Start the mapping jobs.
+ //
+ int readsFileIndex = 0;
+ if (params.subsample < 1) {
+ InitializeRandomGeneratorWithTime();
+ reader = new ReaderAgglomerate(params.subsample);
+ }
+ else {
+ reader = new ReaderAgglomerate(params.startRead, params.stride);
+ }
+ // In case the input is fasta, make all bases in upper case.
+ reader->SetToUpper();
+
+
+ regionTableReader = new HDFRegionTableReader;
+ RegionTable regionTable;
+ //
+ // Store lists of how long it took to map each read.
+ //
+ metrics.clocks.SetStoreList(true);
+ if (params.useCcs) {
+ reader->UseCCS();
+ }
+
+ string commandLineString; // Restore command.
+ clp.CommandLineToString(argc, argv, commandLineString);
+
+ if (params.printSAM or params.printBAM) {
+ string so = "UNKNOWN"; // sorting order;
+ string version = GetVersion(); //blasr version;
+ SAMHeaderPrinter shp(so, seqdb,
+ params.queryFileNames, params.queryReadType,
+ params.samQVList, "BLASR", version,
+ commandLineString);
+ string headerString = shp.ToString();// SAM/BAM header
+ if (params.printSAM) {
+ *outFilePtr << headerString;
+ } else if (params.printBAM) {
+#ifdef USE_PBBAM
+ BamHeader header = BamHeader(headerString);
+ // Both file name and SAMHeader are required in order to create a BamWriter.
+ bamWriterPtr = new BamWriter(params.outFileName, header);
+#else
+ REQUIRE_PBBAM_ERROR();
+#endif
+ }
+ }
+
+ for (readsFileIndex = 0; readsFileIndex < params.queryFileNames.size(); readsFileIndex++ ){
+ params.readsFileIndex = readsFileIndex;
+ //
+ // Configure the reader to use the correct read and region
+ // file names.
+ //
+ reader->SetReadFileName(params.queryFileNames[params.readsFileIndex]);
+
+ //
+ // Initialize using already set file names.
+ //
+ int initReturnValue = reader->Initialize();
+ if (initReturnValue <= 0) {
+ cerr << "WARNING! Could not open file " << params.queryFileNames[params.readsFileIndex] << endl;
+ continue;
+ }
+
+ // Check whether use ccs only.
+ if (reader->GetFileType() == HDFCCSONLY) {
+ params.useAllSubreadsInCcs = false;
+ params.useCcs = params.useCcsOnly = true;
+ }
+
+ string changeListIdString;
+ reader->hdfBasReader.GetChangeListID(changeListIdString);
+ ChangeListID changeListId(changeListIdString);
+ params.qvScaleType = DetermineQVScaleFromChangeListID(changeListId);
+ if (reader->FileHasZMWInformation() and params.useRegionTable) {
+ if (params.readSeparateRegionTable) {
+ if (regionTableReader->Initialize(params.regionTableFileNames[params.readsFileIndex]) == 0) {
+ cout << "ERROR! Could not read the region table " << params.regionTableFileNames[params.readsFileIndex] <<endl;
+ exit(1);
+ }
+ params.useRegionTable = true;
+ }
+ else {
+ if (reader->HasRegionTable()) {
+ if (regionTableReader->Initialize(params.queryFileNames[params.readsFileIndex]) == 0) {
+ cout << "ERROR! Could not read the region table " << params.queryFileNames[params.readsFileIndex] <<endl;
+ exit(1);
+ }
+ params.useRegionTable = true;
+ }
+ else {
+ params.useRegionTable = false;
+ }
+ }
+ }
+ else {
+ params.useRegionTable = false;
+ }
+
+ //
+ // Check to see if there is a region table. If there is a separate
+ // region table, use that (over the region table in the bas
+ // file). If there is a region table in the bas file, use that,
+ // without having to specify a region table on the command line.
+ //
+ if (params.useRegionTable) {
+ regionTable.Reset();
+ regionTableReader->ReadTable(regionTable);
+ regionTableReader->Close();
+ regionTable.SortTableByHoleNumber();
+ }
+
+ //
+ // Check to see if there is a separate ccs fofn. If there is a separate
+ // ccs fofn, use that over the one in the bas file.
+ //
+ //if (params.readSeparateCcsFofn and params.useCcs) {
+ // if (reader->SetCCS(params.ccsFofnFileNames[params.readsFileIndex]) == 0) {
+ // cout << "ERROR! Could not read the ccs file "
+ // << params.ccsFofnFileNames[params.readsFileIndex] << endl;
+ // exit(1);
+ // }
+ // }
+
+ if (reader->GetFileType() != HDFCCS and
+ reader->GetFileType() != HDFBase and
+ reader->GetFileType() != HDFPulse and
+ params.concordant) {
+ cerr << "WARNING! Option concordant is only enabled when "
+ << "input reads are in PacBio base h5 or pulse h5 format." << endl;
+ params.concordant = false;
+ }
+
+
+#ifdef USE_GOOGLE_PROFILER
+ char *profileFileName = getenv("CPUPROFILE");
+ if (profileFileName != NULL) {
+ ProfilerStart(profileFileName);
+ }
+ else {
+ ProfilerStart("google_profile.txt");
+ }
+#endif
+
+ assert (initReturnValue > 0);
+ if (params.nProc == 1) {
+ mapdb[0].Initialize(&sarray, &genome, &seqdb, &ct, &index, params, reader, ®ionTable,
+ outFilePtr, unalignedFilePtr, &anchorFileStrm, clusterOutPtr);
+ mapdb[0].bwtPtr = &bwt;
+ if (params.fullMetricsFileName != "") {
+ mapdb[0].metrics.SetStoreList(true);
+ }
+ if (params.lcpBoundsFileName != "") {
+ mapdb[0].lcpBoundsOutPtr = &lcpBoundsOut;
+ }
+ else {
+ mapdb[0].lcpBoundsOutPtr = NULL;
+ }
+
+ MapReads(&mapdb[0]);
+ metrics.Collect(mapdb[0].metrics);
+ }
+ else {
+ pthread_t *threads = new pthread_t[params.nProc];
+ for (procIndex = 0; procIndex < params.nProc; procIndex++ ){
+ //
+ // Initialize thread-specific parameters.
+ //
+
+ mapdb[procIndex].Initialize(&sarray, &genome, &seqdb, &ct, &index, params, reader, ®ionTable,
+ outFilePtr, unalignedFilePtr, &anchorFileStrm, clusterOutPtr);
+ mapdb[procIndex].bwtPtr = &bwt;
+ if (params.fullMetricsFileName != "") {
+ mapdb[procIndex].metrics.SetStoreList(true);
+ }
+ if (params.lcpBoundsFileName != "") {
+ mapdb[procIndex].lcpBoundsOutPtr = &lcpBoundsOut;
+ }
+ else {
+ mapdb[procIndex].lcpBoundsOutPtr = NULL;
+ }
+
+ if (params.outputByThread) {
+ ofstream *outPtr =new ofstream;
+ mapdb[procIndex].outFilePtr = outPtr;
+ stringstream outNameStream;
+ outNameStream << params.outFileName << "." << procIndex;
+ mapdb[procIndex].params.outFileName = outNameStream.str();
+ CrucialOpen(mapdb[procIndex].params.outFileName, *outPtr, std::ios::out);
+ }
+ pthread_create(&threads[procIndex], &threadAttr[procIndex], (void* (*)(void*))MapReads, &mapdb[procIndex]);
+ }
+ for (procIndex = 0; procIndex < params.nProc; procIndex++) {
+ pthread_join(threads[procIndex], NULL);
+ }
+ for (procIndex = 0; procIndex < params.nProc; procIndex++) {
+ metrics.Collect(mapdb[procIndex].metrics);
+ if (params.outputByThread) {
+ delete mapdb[procIndex].outFilePtr;
+ }
+ }
+ if (threads) {
+ delete threads;
+ threads = NULL;
+ }
+ }
+ reader->Close();
+ }
+
+ if (!reader) {delete reader; reader = NULL;}
+
+ fastaGenome.Free();
+#ifdef USE_GOOGLE_PROFILER
+ ProfilerStop();
+#endif
+
+ if (mapdb != NULL) {
+ delete[] mapdb;
+ }
+ if (threadAttr != NULL) {
+ delete[] threadAttr;
+ }
+ seqdb.FreeDatabase();
+ if (regionTableReader) {
+ delete regionTableReader;
+ }
+ if (params.metricsFileName != "") {
+ metrics.PrintSummary(metricsOut);
+ }
+ if (params.fullMetricsFileName != "") {
+ metrics.PrintFullList(fullMetricsFile);
+ }
+ if (params.outFileName != "") {
+ if (params.printBAM) {
+#ifdef USE_PBBAM
+ assert(bamWriterPtr);
+ try {
+ bamWriterPtr->TryFlush();
+ delete bamWriterPtr;
+ bamWriterPtr = NULL;
+ } catch (std::exception e) {
+ cout << "Error, could not flush bam records to bam file." << endl;
+ exit(1);
+ }
+#else
+ REQUIRE_PBBAM_ERROR();
+#endif
+ } else {
+ outFileStrm.close();
+ }
+ }
+ cerr << "[INFO] " << GetTimestamp() << " [blasr] ended." << endl;
+ return 0;
+}
diff --git a/GNUmakefile b/GNUmakefile
new file mode 100644
index 0000000..2c3dd91
--- /dev/null
+++ b/GNUmakefile
@@ -0,0 +1,85 @@
+all:
+
+ROOT:=.
+include defines.mk
+include rules.mk
+
+CXXFLAGS += -O3 -g
+CXXOPTS += \
+ -std=c++0x -pedantic \
+ -Wall -Wuninitialized -Wno-div-by-zero \
+ -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} ${ZLIB_INCLUDE}
+#LIB_DIRS:=${LIBBLASR_LIB} ${LIBPBIHDF_LIB} ${LIBPBDATA_LIB} ${PBBAM_LIB} ${HTSLIB_LIB} ${HDF5_LIB} ${ZLIB_LIB}
+#LDLIBS := \
+# ${LIBBLASR_LIBFLAGS} ${LIBPBIHDF_LIBFLAGS} ${LIBPBDATA_LIBFLAGS} \
+# ${PBBAM_LIBFLAGS} ${HTSLIB_LIBFLAGS} ${HDF5_LIBFLAGS} ${ZLIB_LIBFLAGS} \
+# -ldl -lpthread
+
+# HDF5 needs -ldl, but mobs does not pass it in.
+
+SRCS := $(wildcard *.cpp)
+OBJS := ${SRCS:.cpp=.o}
+DEPS := ${SRCS:.cpp=.d}
+
+LD_LIBRARY_PATH=${HDF5_LIB}:${LIBBLASR_LIB}:${LIBPBIHDF_LIB}:${LIBPBDATA_LIB}
+export LD_LIBRARY_PATH
+
+
+init-submodule:
+ ${MAKE} update-submodule
+ ${MAKE} build-submodule
+
+update-submodule:
+ git submodule update --init
+
+build-submodule:
+ # DON'T use pbbam which is not on github.
+ cd libcpp && NOPBBAM=true HDF5_LIB=${HDF5_LIB}/libhdf5.so HDF5_INCLUDE=${HDF5_INCLUDE} ./configure.py
+ ${MAKE} -C libcpp
+
+submodule-clean:
+ ${RM} -r libcpp
+
+# The rules above must be run separately.
+all: blasr makeutils
+#all: makeextrautils #This would require pbbam.
+blasr: ${OBJS}
+ ${CXX} -o $@ ${CXXFLAGS} ${CPPFLAGS} -MF"${@:%=%.d}" ${OBJS} ${LDFLAGS} ${LDLIBS}
+ @echo LD_LIBRARY_PATH=${LD_LIBRARY_PATH}
+
+makeutils:
+ ${MAKE} -C utils
+makeextrautils:
+ ${MAKE} -C extrautils
+
+CTESTS := $(wildcard ctest/*.t)
+SLOW_CTESTS := ctest/bug25328.t ctest/useccsallLargeGenome.t
+
+cramtests: blasr utils
+ cram -v --shell=/bin/bash ${CTESTS}
+ make -C utils cramtests
+
+cramfast: blasr utils
+ cram -v --shell=/bin/bash $(filter-out ${SLOW_CTESTS},${CTESTS})
+ make -C utils cramfast
+
+gtest: blasr
+ # This requires the submodule to be configured with gtest.
+ make -C libcpp gtest
+
+check: gtest cramtests
+
+cleanall: cleanlib clean
+
+cleanlib: libcpp/defines.mk
+ ${MAKE} -C libcpp clean
+
+clean:
+ ${RM} blasr ${OBJS} ${DEPS} blasr.d
+ ${MAKE} -C utils clean
+ ${MAKE} -C extrautils clean
+
+-include ${DEPS}
diff --git a/LICENSES.txt b/LICENSES.txt
new file mode 100644
index 0000000..5360bf2
--- /dev/null
+++ b/LICENSES.txt
@@ -0,0 +1,32 @@
+Copyright (c) 2011-2015, Pacific Biosciences of California, Inc.
+
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are
+met:
+
+* Redistributions of source code must retain the above copyright
+ notice, this list of conditions and the following disclaimer.
+
+* Redistributions in binary form must reproduce the above copyright
+ notice, this list of conditions and the following disclaimer in the
+ documentation and/or other materials provided with the distribution.
+
+* Neither the name of Pacific Biosciences nor the names of its
+ contributors may be used to endorse or promote products derived from
+ this software without specific prior written permission.
+
+NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
+GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
+BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
+WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
+MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS CONTRIBUTORS
+BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR
+BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE
+OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN
+IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
diff --git a/MANUAL.md b/MANUAL.md
new file mode 100644
index 0000000..92b96b0
--- /dev/null
+++ b/MANUAL.md
@@ -0,0 +1,84 @@
+##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
new file mode 100644
index 0000000..938351b
--- /dev/null
+++ b/Makefile
@@ -0,0 +1,59 @@
+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/MappingIPC.h b/MappingIPC.h
new file mode 100644
index 0000000..acd1789
--- /dev/null
+++ b/MappingIPC.h
@@ -0,0 +1,105 @@
+#ifndef MAPPING_IPC_H_
+#define MAPPING_IPC_H_
+
+#include <pthread.h>
+
+#include "MappingParameters.h"
+
+#include "FASTASequence.hpp"
+#include "FASTQSequence.hpp"
+#include "tuples/TupleList.hpp"
+#include "tuples/DNATuple.hpp"
+#include "tuples/CompressedDNATuple.hpp"
+#include "tuples/TupleCountTable.hpp"
+#include "files/ReaderAgglomerate.hpp"
+#include "MappingMetrics.hpp"
+#include "suffixarray/SuffixArrayTypes.hpp"
+#include "metagenome/SequenceIndexDatabase.hpp"
+#include "reads/RegionTable.hpp"
+#include "bwt/BWT.hpp"
+/*
+ * This structure contains pointers to all required data structures
+ * for mapping reads to a suffix array and evaluating the significance
+ * of the matches.
+ */
+
+template<typename T_SuffixArray, typename T_GenomeSequence, typename T_Tuple>
+class MappingData {
+public:
+ T_SuffixArray *suffixArrayPtr;
+ BWT *bwtPtr;
+ T_GenomeSequence *referenceSeqPtr;
+ SequenceIndexDatabase<FASTASequence> *seqDBPtr;
+ TupleCountTable<T_GenomeSequence, T_Tuple> *ctabPtr;
+ MappingParameters params;
+ MappingMetrics metrics;
+ RegionTable *regionTablePtr;
+ ReaderAgglomerate *reader;
+ ostream *outFilePtr;
+ ostream *unalignedFilePtr;
+ ostream *anchorFilePtr;
+ ostream *clusterFilePtr;
+ ostream *lcpBoundsOutPtr;
+
+ // Declare a semaphore for blocking on reading from the same hdhf file.
+
+ void ShallowCopySuffixArray(T_SuffixArray &dest) {
+ dest.index = suffixArrayPtr->index;
+ dest.length = suffixArrayPtr->length;
+ dest.target = suffixArrayPtr->target;
+ dest.startPosTable = suffixArrayPtr->startPosTable;
+ dest.endPosTable = suffixArrayPtr->endPosTable;
+ dest.lookupTableLength = suffixArrayPtr->lookupTableLength;
+ dest.lookupPrefixLength = suffixArrayPtr->lookupPrefixLength;
+ dest.tm = suffixArrayPtr->tm;
+ dest.deleteStructures = false;
+ // dest.useLCPTable = suffixArrayPtr->useLCPTable;
+ }
+
+ void ShallowCopySequenceIndexDatabase(SequenceIndexDatabase<FASTQSequence> &dest) {
+ dest.nSeqPos = seqDBPtr->nSeqPos;
+ dest.seqStartPos = seqDBPtr->seqStartPos;
+ dest.nameLengths = seqDBPtr->nameLengths;
+ dest.names = seqDBPtr->names;
+ dest.deleteStructures = false;
+ }
+
+ void ShallowCopyTupleCountTable( TupleCountTable<T_GenomeSequence, T_Tuple> &dest) {
+ dest.countTable = ctabPtr->countTable;
+ dest.countTableLength = ctabPtr->countTableLength;
+ dest.nTuples = ctabPtr->nTuples;
+ dest.tm = ctabPtr->tm;
+ dest.deleteStructures = false;
+ }
+
+ void ShallowCopyReferenceSequence(T_GenomeSequence &refSeq) {
+ refSeq.ShallowCopy(*referenceSeqPtr);
+ refSeq.deleteOnExit = false;
+ }
+
+ void Initialize(T_SuffixArray *saP, T_GenomeSequence *refP,
+ SequenceIndexDatabase<FASTASequence> *seqDBP,
+ TupleCountTable<T_GenomeSequence, T_Tuple> *ctabP,
+ ReverseCompressIndex *rciP,
+ MappingParameters ¶msP,
+ ReaderAgglomerate *readerP,
+ RegionTable *regionTableP,
+ ostream *outFileP,
+ ostream *unalignedFileP,
+ ostream *anchorFilePtrP,
+ ostream *clusterFilePtrP=NULL) {
+ suffixArrayPtr = saP;
+ referenceSeqPtr = refP;
+ seqDBPtr = seqDBP;
+ ctabPtr = ctabP;
+ regionTablePtr = regionTableP;
+ params = paramsP;
+ reader = readerP;
+ outFilePtr = outFileP;
+ unalignedFilePtr = unalignedFileP;
+ anchorFilePtr = anchorFilePtrP;
+ clusterFilePtr= clusterFilePtrP;
+ }
+};
+
+#endif
diff --git a/MappingParameters.h b/MappingParameters.h
new file mode 100644
index 0000000..1e67e96
--- /dev/null
+++ b/MappingParameters.h
@@ -0,0 +1,681 @@
+#ifndef MAPPING_PARAMETERS_H_
+#define MAPPING_PARAMETERS_H_
+
+#define REQUIRE_PBBAM_ERROR() \
+assert("blasr must be compiled with lib pbbam to perform IO on bam." == 0);
+
+#include <vector>
+
+#include "reads/ReadType.hpp"
+#include "utils/FileOfFileNames.hpp"
+#include "utils/RangeUtils.hpp"
+#include "tuples/TupleMetrics.hpp"
+#include "datastructures/anchoring/AnchorParameters.hpp"
+#include "qvs/QualityValue.hpp"
+#include "format/SAMPrinter.hpp"
+#include "algorithms/alignment/AlignmentFormats.hpp"
+#include "files/BaseSequenceIO.hpp"
+#include "datastructures/alignment/FilterCriteria.hpp"
+
+class MappingParameters {
+public:
+ //
+ // Parameters for global substitution, insertion, and deletion priors.
+ //
+ float minFractionToBeConsideredOverlapping;
+ float indelRate;
+ float minRatio;
+ int indel;
+ int idsIndel;
+ int sdpIndel;
+ int sdpIns, sdpDel;
+ int insertion;
+ int deletion;
+ int mismatch;
+ int sdpTupleSize;
+ int match;
+ int showAlign;
+ int refineAlign;
+ bool useScoreCutoff;
+ int maxScore;
+ int argi;
+ int nProc;
+ int globalChainType;
+ int readIndex;
+ SAMOutput::Clipping clipping;
+ string clippingString;
+ QVScale qvScaleType;
+ vector<string> readsFileNames; // = queryFileNames, genomeFileName
+ vector<string> queryFileNames;
+ string genomeFileName;
+ // Query file type: FASTA/FASTQ/HDF*/PBBAM,
+ // Note that mixed query file types is not allowed.
+ FileType queryFileType;
+ // Query read type, SUBREAD, CCS or UNKNOWN
+ // Note that mixed read types is not allowed.
+ ReadType::ReadTypeEnum queryReadType;
+ vector<string> regionTableFileNames;
+ vector<string> ccsFofnFileNames;
+ string tupleListName;
+ string posTableName;
+ string outFileName;
+ string suffixArrayFileName;
+ string bwtFileName;
+ string indexFileName;
+ string anchorFileName;
+ string clusterFileName;
+ VectorIndex nBest;
+ int printWindow;
+ int doCondense;
+ int do4BitComp;
+ int cutoff;
+ int useSuffixArray;
+ int useBwt;
+ int useReverseCompressIndex;
+ int useTupleList;
+ int useSeqDB;
+ string seqDBName;
+ int useCountTable;
+ string countTableName;
+ int minMatchLength;
+ int listTupleSize;
+ int printFormat;
+ int maxExpand, minExpand;
+ int startRead;
+ int stride;
+ int pValueType;
+ float subsample;
+ int sortRefinedAlignments;
+ int verbosity;
+ bool printSAM;
+ bool cigarUseSeqMatch;
+ bool printBAM;
+ bool storeMapQV;
+ bool useRandomSeed;
+ int randomSeed;
+ bool placeRandomly;
+ bool printHeader;
+ bool samplePaths;
+ bool warp, nowarp;
+ //bool usePrefixLookupTable;
+ bool doSensitiveSearch;
+ bool emulateNucmer;
+ bool refineBetweenAnchorsOnly;
+ bool byAdapter;
+ bool extendDenovoCCSSubreads;
+ TupleMetrics saTupleMetrics;
+ TupleMetrics sdpTupleMetrics;
+ int lookupTableLength;
+ //int branchQualityThreshold;
+ int qualityLowerCaseThreshold;
+ AnchorParameters anchorParameters;
+ int readsFileIndex;
+ //int numBranches;
+ bool storeMetrics;
+ bool ignoreQualities;
+ bool extendFrontAlignment;
+ bool extendAlignments;
+ int maxExtendDropoff;
+ int minReadLength;
+ int maxReadLength;
+ int minSubreadLength;
+ int minRawSubreadScore;
+ int minAvgQual;
+ bool overlap;
+ bool advanceHalf;
+ int advanceExactMatches;
+ float approximateMaxInsertionRate;
+ float minPctSimilarity; // [0, 100]
+ float minPctAccuracy; // [0, 100]
+ bool refineAlignments;
+ int nCandidates;
+ bool doGlobalAlignment;
+ string tempDirectory;
+ bool useTitleTable;
+ string titleTableName;
+ bool readSeparateRegionTable;
+ bool readSeparateCcsFofn;
+ string regionTableFileName;
+ string ccsFofnFileName;
+ //float averageMismatchScore;
+ bool mapSubreadsSeparately;
+ bool concordant;
+ int flankSize;
+ bool useRegionTable;
+ bool useHQRegionTable;
+ bool printUnaligned;
+ string unalignedFileName;
+ string metricsFileName;
+ string lcpBoundsFileName;
+ string fullMetricsFileName;
+ bool printSubreadTitle;
+ bool useCcs;
+ bool useAllSubreadsInCcs;
+ bool useCcsOnly;
+ bool detailedSDPAlignment, nouseDetailedSDPAlignment;
+ int chunkSize;
+ int subreadMapType;
+ int sdpFilterType;
+ bool useGuidedAlign;
+ int guidedAlignBandSize;
+ int bandSize;
+ int extendBandSize;
+ bool useQVScore;
+ int scoreType;
+ bool printVerboseHelp;
+ bool printDiscussion;
+ float sdpBypassThreshold;
+ bool computeAlignProbability;
+ float qvMatchWeight;
+ float qvMismatchWeight;
+ float qvInsWeight;
+ float qvDelWeight;
+ float readAccuracyPrior;
+ bool printVersion;
+ int substitutionPrior;
+ int globalDeletionPrior;
+ bool outputByThread;
+ int maxReadIndex;
+ int recurseOver;
+ bool forPicard;
+ bool separateGaps;
+ string scoreMatrixString;
+ bool printDotPlots;
+ bool preserveReadTitle;
+ bool forwardOnly;
+ bool printOnlyBest;
+ bool affineAlign;
+ int affineExtend;
+ int affineOpen;
+ bool scaleMapQVByNumSignificantClusters;
+ int limsAlign;
+ string holeNumberRangesStr;
+ Ranges holeNumberRanges;
+ int minAlnLength;
+ bool printSAMQV;
+ vector<string> samQV;
+ SupplementalQVList samQVList;
+ bool fastMaxInterval;
+ bool aggressiveIntervalCut;
+ bool fastSDP;
+ string concordantTemplate;
+ bool concordantAlignBothDirections;
+ FilterCriteria filterCriteria;
+ string hitPolicyStr;
+ HitPolicy hitPolicy;
+ bool enableHiddenPaths;
+
+ void Init() {
+ readIndex = -1;
+ maxReadIndex = -1;
+ qvMatchWeight = 1.0;
+ qvMismatchWeight = 1.0;
+ qvInsWeight = 1.0;
+ qvDelWeight = 1.0;
+ minFractionToBeConsideredOverlapping = 0.75;
+ minRatio = 0.25;
+ indelRate = 0.3;
+ indel = 5;
+ insertion = 4; // asymmetric indel parameters
+ deletion = 5;
+ idsIndel = 15;
+ sdpIndel = 5;
+ sdpIns = 5;
+ sdpDel = 10;
+ sdpTupleSize = 11;
+ match = 0;
+ mismatch = 0;
+ showAlign = 1;
+ refineAlign = 1;
+ useScoreCutoff = false;
+ maxScore = -200;
+ argi = 1;
+ nProc = 1;
+ readsFileNames.clear();
+ queryFileNames.clear();
+ genomeFileName = "";
+ queryReadType = ReadType::UNKNOWN;
+ queryFileType = FileType::None;
+ tupleListName = "";
+ posTableName = "";
+ suffixArrayFileName= "";
+ bwtFileName = "";
+ indexFileName = "";
+ anchorFileName = "";
+ outFileName = "";
+ nBest = 10;
+ nCandidates = 10;
+ printWindow = 0;
+ doCondense = 0;
+ do4BitComp = 0;
+ pValueType = 0;
+ cutoff = 0;
+ useSuffixArray = 0;
+ useBwt = 0;
+ useReverseCompressIndex = 0;
+ useTupleList = 0;
+ useSeqDB = 0;
+ seqDBName = "";
+ useCountTable = 0;
+ countTableName = "";
+ lookupTableLength = 8;
+ anchorParameters.minMatchLength = minMatchLength = 12;
+ printFormat = SummaryPrint;
+ maxExpand = 0;
+ minExpand = 0;
+ startRead = 0;
+ stride = 1;
+ subsample = 1.1;
+ listTupleSize = 6;
+ sortRefinedAlignments = 1;
+ anchorParameters.verbosity = verbosity = 0;
+ saTupleMetrics.Initialize(listTupleSize);
+ sdpTupleMetrics.Initialize(sdpTupleSize);
+ qualityLowerCaseThreshold = 0;
+ anchorParameters.branchQualityThreshold = 0;
+ readsFileIndex = 0;
+ printSAM = false;
+ printBAM = false;
+ useRandomSeed = false;
+ randomSeed = 0;
+ placeRandomly = false;
+ samplePaths = false;
+ nowarp = false;
+ storeMapQV = true;
+ warp = true;
+ extendDenovoCCSSubreads = false;
+ storeMetrics = false;
+ ignoreQualities = true;
+ extendFrontAlignment = false;
+ extendAlignments = false;
+ maxExtendDropoff = 10;
+ minReadLength = 50;
+ maxReadLength = 0; // means no max read length
+ minSubreadLength = 0;
+ minRawSubreadScore = -1; // raw subread score in region table should be in range [0, 1000].
+ minAvgQual = 0;
+ overlap = false;
+ advanceHalf = false;
+ refineAlignments = true;
+ anchorParameters.advanceExactMatches = advanceExactMatches = 0;
+ approximateMaxInsertionRate = 1.30;
+ minPctSimilarity = 0;
+ minPctAccuracy = 0;
+ doGlobalAlignment = false;
+ tempDirectory = "";
+ useTitleTable = false;
+ titleTableName = "";
+ readSeparateRegionTable = false;
+ readSeparateCcsFofn = false;
+ regionTableFileName = "";
+ ccsFofnFileName = "";
+ mapSubreadsSeparately=true;
+ concordant=false;
+ flankSize=40;
+ useRegionTable = true;
+ useHQRegionTable=true;
+ printUnaligned = false;
+ unalignedFileName = "";
+ globalChainType = 0;
+ metricsFileName = "";
+ fullMetricsFileName = "";
+ doSensitiveSearch = false;
+ emulateNucmer = false;
+ refineBetweenAnchorsOnly = false;
+ printSubreadTitle = true;
+ detailedSDPAlignment = true;
+ nouseDetailedSDPAlignment = false;
+ subreadMapType = 0;
+ useCcs = false;
+ useCcsOnly = false;
+ useAllSubreadsInCcs = false;
+ chunkSize = 10000000;
+ sdpFilterType = 0;
+ anchorParameters.stopMappingOnceUnique = true;
+ useGuidedAlign = true;
+ bandSize = 0;
+ extendBandSize = 10;
+ guidedAlignBandSize = 10;
+ useQVScore = false;
+ printVerboseHelp = false;
+ printDiscussion = false;
+ sdpBypassThreshold = 1000000.0;
+ scoreType = 0;
+ byAdapter = false;
+ qvScaleType = PHRED;
+ printHeader = false;
+ computeAlignProbability = false;
+ readAccuracyPrior = 0.85;
+ printVersion = false;
+ clipping = SAMOutput::none;
+ clippingString = "";
+ substitutionPrior = 20;
+ globalDeletionPrior = 13;
+ outputByThread = false;
+ recurseOver = 10000;
+ forPicard = false;
+ separateGaps = false;
+ scoreMatrixString = "";
+ printDotPlots = false;
+ preserveReadTitle = false;
+ forwardOnly = false;
+ printOnlyBest = false;
+ affineAlign = false;
+ affineExtend = 0;
+ affineOpen = 10;
+ scaleMapQVByNumSignificantClusters = false;
+ limsAlign = 0;
+ holeNumberRangesStr = "";
+ minAlnLength = 0;
+ printSAMQV = false;
+ cigarUseSeqMatch = false;
+ samQV.clear();
+ samQVList.clear();
+ fastMaxInterval = false;
+ aggressiveIntervalCut = false;
+ fastSDP = false;
+ concordantTemplate = "mediansubread"; // typicalsubread or longestsubread
+ concordantAlignBothDirections = false;
+
+ hitPolicyStr = "all";
+ ResetFilterAndHit();
+ enableHiddenPaths = false; //turn off hidden paths.
+ }
+
+ MappingParameters()
+ : filterCriteria(0, 0, 0, false, Score(0, ScoreSign::NEGATIVE))
+ , hitPolicy("all", ScoreSign::NEGATIVE)
+ {
+ Init();
+ }
+
+ void MakeSane() {
+ // Expand FOFN
+ FileOfFileNames::ExpandFileNameList(readsFileNames);
+
+ // Must have at least a query and a genome
+ if (readsFileNames.size() <= 1) {
+ cout << "Error, you must provide at least one reads file and a genome file." <<endl;
+ exit(1);
+ }
+
+ // Separate query reads files and a genome read file
+ // The last reads file is the genome
+ queryFileNames = readsFileNames;
+ queryFileNames.pop_back();
+ genomeFileName = readsFileNames.back();
+
+ // Check query file type.
+ BaseSequenceIO::DetermineFileTypeByExtension(queryFileNames[0], queryFileType);
+ for (size_t i = 1; i < queryFileNames.size(); i++) {
+ FileType fileType;
+ BaseSequenceIO::DetermineFileTypeByExtension(queryFileNames[i], fileType);
+ if (fileType != queryFileType) {
+ cout << "ERROR, mixed query file types is not allowed." << endl;
+ exit(1);
+ }
+ }
+
+#ifdef __APPLE__
+ nProc = 1;
+ cerr << "WARNING, multi-threading is not yet supported on Apple iOS." << endl;
+#endif
+
+ // -useQuality can not be used in combination with a fasta input
+ if (!ignoreQualities) {
+ if (queryFileType == Fasta) {
+ cout<<"ERROR, you can not use -useQuality option when any of the input reads files are in multi-fasta format."<<endl;
+ exit(1);
+ }
+ }
+
+ //
+ // Fix all logical incompatibilities with parameters.
+ //
+ if (nowarp) {
+ warp = false;
+ }
+
+ if (nCandidates < nBest) {
+ cerr << "Warning: resetting nCandidates to nBest " << nBest << endl;
+ nCandidates = nBest;
+ }
+
+ if (placeRandomly and hitPolicyStr != "randombest") {
+ cerr << "Warning: placeRepeatsRandomly is deprecated, resetting hit policy to randombest." << endl;
+ hitPolicyStr = "randombest";
+ }
+ if ((hitPolicyStr == "random" or hitPolicyStr == "randombest") and nBest == 1) {
+ cerr << "Warning: When attempting to select equivalently scoring reads at random " << endl
+ << "the bestn parameter should be greater than one." << endl;
+ }
+
+ if (concordant) {
+ if (useCcs) {
+ concordant = false;
+ } else {
+ useRegionTable = true;
+ useHQRegionTable = true;
+ }
+ if (concordantTemplate != "longestsubread" and concordantTemplate != "typicalsubread" and concordantTemplate != "mediansubread") {
+ cout << "ERROR, unsupported concordantTemplate: " << concordantTemplate << endl;
+ exit(1);
+ }
+ }
+
+ if (sdpFilterType > 1) {
+ cerr << "Warning: using new filter method for SDP alignments. The parameter is " << endl
+ << "either 0 or 1, but " << sdpFilterType << " was specified." << endl;
+ sdpFilterType = 1;
+ }
+ if (sdpFilterType == 0) {
+ detailedSDPAlignment = true;
+ nouseDetailedSDPAlignment = false;
+ }
+ if (detailedSDPAlignment == false) {
+ sdpFilterType = 1;
+ }
+ if (useGuidedAlign == true and bandSize == 0) {
+ bandSize = 16;
+ }
+ anchorParameters.minMatchLength = minMatchLength;
+ if (suffixArrayFileName != "") {
+ useSuffixArray = true;
+ }
+ if (bwtFileName != "") {
+ useBwt = true;
+ }
+ if (useBwt and useSuffixArray) {
+ cout << "ERROR, sa and bwt must be used independently." << endl;
+ exit(1);
+ }
+ if (countTableName != "") {
+ useCountTable = true;
+ }
+ if (metricsFileName != "" or fullMetricsFileName != "") {
+ storeMetrics = true;
+ }
+ if (useCcsOnly) {
+ useCcs = true;
+ }
+ if (useAllSubreadsInCcs == true) {
+ useCcs = true;
+ }
+ if (titleTableName != "") {
+ useTitleTable = true;
+ }
+ if (unalignedFileName != "") {
+ printUnaligned = true;
+ }
+ if (regionTableFileName != "") {
+ useRegionTable = true;
+ readSeparateRegionTable = true;
+ }
+ if (ccsFofnFileName != "") {
+ readSeparateCcsFofn = true;
+ }
+ if (nouseDetailedSDPAlignment == true) {
+ detailedSDPAlignment = false;
+ }
+ if (nouseDetailedSDPAlignment == false) {
+ detailedSDPAlignment = true;
+ }
+ if (anchorParameters.maxLCPLength != 0 and anchorParameters.maxLCPLength < anchorParameters.minMatchLength) {
+ cerr << "ERROR: maxLCPLength is less than minLCPLength, which will result in no hits." << endl;
+ }
+ if (subsample < 1 and stride > 1) {
+ cout << "ERROR, subsample and stride must be used independently." << endl;
+ exit(1);
+ }
+
+ if (subreadMapType < 0 or subreadMapType > 1) {
+ cout << "Error, subreadImplType must be 0 or 1" << endl;
+ exit(1);
+ }
+
+ if (emulateNucmer) {
+ SetEmulateNucmer();
+ }
+
+ if (randomSeed != 0) {
+ useRandomSeed = true;
+ }
+ if (printSAM) {
+ printFormat = SAM;
+ forPicard = true;
+ }
+ //
+ // Parse the clipping.
+ //
+ if (clippingString == "soft") {
+ clipping = SAMOutput::soft;
+ }
+ else if (clippingString == "hard") {
+ clipping = SAMOutput::hard;
+ }
+ else if (clippingString == "none") {
+ clipping = SAMOutput::none;
+ }
+ else if (clippingString == "subread") {
+ clipping = SAMOutput::subread;
+ }
+ else if (clippingString != "") {
+ cout << "ERROR, clipping should either be soft, hard, or none." << endl;
+ exit(1);
+ }
+
+ if (printBAM) {
+#ifndef USE_PBBAM
+ REQUIRE_PBBAM_ERROR();
+#else
+ cigarUseSeqMatch = true; // ALWAYS true for BAM
+ printFormat = BAM;
+ forPicard = true;
+ printSAM = false;
+ samQVList.SetDefaultQV();
+ printSAMQV = true;
+ if (clipping != SAMOutput::soft) {
+ // Only support two clipping methods: soft or subread.
+ clipping = SAMOutput::subread;
+ }
+ if (queryFileType != PBBAM and not enableHiddenPaths) {
+ // bax|fasta|fastq -> bam paths are turned off by default
+ cout << "ERROR, could not output alignments in BAM unless input reads are in PacBio BAM files." << endl;
+ exit(1);
+ }
+ if (outFileName == "") {
+ cout << "ERROR, BAM output file must be specified." << endl;
+ exit(1);
+ }
+ if (outputByThread) {
+ cout << "ERROR, could not output alignments by threads in BAM format." << endl;
+ exit(1);
+ }
+#endif
+ }
+
+ if (limsAlign != 0) {
+ mapSubreadsSeparately = false;
+ forwardOnly = true;
+ }
+
+ if (holeNumberRangesStr.size() > 0) {
+ if (not holeNumberRanges.setRanges(holeNumberRangesStr)) {
+ cout << "ERROR, could not parse hole number ranges: "
+ << holeNumberRangesStr << "." << endl;
+ exit(1);
+ }
+ }
+
+ if (printSAMQV) {
+ if (samQV.size() == 0) {
+ samQVList.SetDefaultQV();
+ }
+ else {
+ samQVList.UseQV(samQV);
+ }
+ }
+
+ if (minRawSubreadScore > 1000) {
+ cout << "ERROR, minimum raw subread score should be less than 1000." << endl;
+ exit(1);
+ }
+ if (minRawSubreadScore != -1 and byAdapter) {
+ cout << "ERROR, minRawSubreadScore and byAdapter should not be used together." << endl;
+ exit(1);
+ }
+ // Determine query read type
+ queryReadType = DetermineQueryReadType();
+ // Pass verbosity
+ anchorParameters.verbosity = verbosity;
+
+ // Set filter criteria and hit policy
+ ResetFilterAndHit();
+ }
+ void ResetFilterAndHit(void) {
+ filterCriteria = FilterCriteria(minAlnLength, minPctSimilarity,
+ minPctAccuracy, true,
+ Score(static_cast<float>(maxScore), ScoreSign::NEGATIVE));
+ hitPolicy = HitPolicy(hitPolicyStr, ScoreSign::NEGATIVE);
+ }
+
+ ReadType::ReadTypeEnum DetermineQueryReadType() {
+ if (useCcsOnly or queryFileType == HDFCCSONLY) {
+ return ReadType::CCS;
+ }
+ if (queryFileType == PBBAM) {
+ // Read type in BAM may be CCS, SUBREAD, HQREGION or POLYMERASE.
+ // Determine it later.
+ return ReadType::UNKNOWN;
+ }
+ if (mapSubreadsSeparately) {
+ return ReadType::SUBREAD;
+ } else {
+ if (useHQRegionTable) {
+ return ReadType::HQREGION;
+ } else {
+ return ReadType::POLYMERASE;
+ }
+ }
+ }
+
+ void SetEmulateNucmer() {
+ anchorParameters.stopMappingOnceUnique = true;
+ anchorParameters.advanceExactMatches = 30;
+ anchorParameters.maxAnchorsPerPosition = 1;
+ sdpBypassThreshold = 0.75;
+ sdpTupleSize = 15;
+ anchorParameters.minMatchLength = 30;
+ useGuidedAlign = true;
+ refineAlignments = false;
+ }
+
+ void SetForSensitivity() {
+ advanceExactMatches = 0;
+ anchorParameters.numBranches = 1;
+ anchorParameters.maxAnchorsPerPosition = 10000;
+ }
+};
+
+
+#endif
diff --git a/MappingSemaphores.h b/MappingSemaphores.h
new file mode 100644
index 0000000..d7524f6
--- /dev/null
+++ b/MappingSemaphores.h
@@ -0,0 +1,45 @@
+#ifndef ALIGNMENT_MAPPING_SEMAPHORE_H_
+#define ALIGNMENT_MAPPING_SEMAPHORE_H_
+#include <vector>
+#include <pthread.h>
+#include <semaphore.h>
+
+#ifndef __APPLE__
+class MappingSemaphores {
+ public:
+ sem_t reader;
+ sem_t writer;
+ sem_t unaligned;
+ sem_t hitCluster;
+ MappingSemaphores& operator=(MappingSemaphores &rhs) {
+ return *this;
+ }
+
+ void InitializeAll() {
+ sem_init(&reader, 0, 1);
+ sem_init(&writer, 0, 1);
+ sem_init(&unaligned, 0, 1);
+ sem_init(&hitCluster, 0, 1);
+ }
+};
+#else
+class MappingSemaphores {
+ public:
+ sem_t *reader;
+ sem_t *writer;
+ sem_t *unaligned;
+ sem_t *hitCluster;
+ MappingSemaphores& operator=(MappingSemaphores &rhs) {
+ return *this;
+ }
+
+ void InitializeAll() {
+ reader = sem_open("/reader", O_CREAT, 0644, 1);
+ writer = sem_open("/writer", O_CREAT, 0644, 1);
+ unaligned = sem_open("/unaligned", O_CREAT, 0644, 1);
+ hitCluster = sem_open("/hitCluster", O_CREAT, 0644, 1);
+ }
+};
+#endif
+
+#endif
diff --git a/README.md b/README.md
new file mode 100644
index 0000000..8bc8e40
--- /dev/null
+++ b/README.md
@@ -0,0 +1,52 @@
+# NEWS: refactored blasr has been put online. Please try it out!
+
+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/RegisterBlasrOptions.h b/RegisterBlasrOptions.h
new file mode 100644
index 0000000..e1f8fe6
--- /dev/null
+++ b/RegisterBlasrOptions.h
@@ -0,0 +1,529 @@
+/*
+ * ============================================================================
+ *
+ * Filename: RegisterOptions.hpp
+ *
+ * Description:
+ *
+ * Version: 1.0
+ * Created: 04/29/2015 04:48:26 PM
+ * Revision: none
+ * Compiler: gcc
+ *
+ * Author: Yuan Li (yli), yli at pacificbiosciences.com
+ * Company: Pacific Biosciences
+ *
+ * ============================================================================
+ */
+
+#include "libconfig.h"
+#include "CommandLineParser.hpp"
+#include "MappingParameters.h"
+#include "RegisterFilterOptions.h"
+#include <sstream>
+using namespace std;
+
+void RegisterBlasrOptions(CommandLineParser & clp, MappingParameters & params) {
+ int trashbinInt;
+ float trashbinFloat;
+ bool trashbinBool;
+ clp.RegisterStringOption("sa", ¶ms.suffixArrayFileName, "");
+ clp.RegisterStringOption("ctab", ¶ms.countTableName, "" );
+ clp.RegisterStringOption("regionTable", ¶ms.regionTableFileName, "");
+ clp.RegisterStringOption("ccsFofn", ¶ms.ccsFofnFileName, "");
+ clp.RegisterIntOption("bestn", (int*) ¶ms.nBest, "", CommandLineParser::PositiveInteger);
+ clp.RegisterIntOption("limsAlign", ¶ms.limsAlign, "", CommandLineParser::PositiveInteger);
+ clp.RegisterFlagOption("printOnlyBest", ¶ms.printOnlyBest, "");
+ clp.RegisterFlagOption("outputByThread", ¶ms.outputByThread, "");
+ clp.RegisterFlagOption("rbao", ¶ms.refineBetweenAnchorsOnly, "");
+ clp.RegisterFlagOption("allowAdjacentIndels", ¶ms.forPicard, "");
+ clp.RegisterFlagOption("onegap", ¶ms.separateGaps, "");
+ clp.RegisterFlagOption("allowAdjacentIndels", ¶ms.forPicard, "");
+ clp.RegisterFlagOption("placeRepeatsRandomly", ¶ms.placeRandomly, "");
+ clp.RegisterIntOption("randomSeed", ¶ms.randomSeed, "", CommandLineParser::Integer);
+ clp.RegisterFlagOption("extend", ¶ms.extendAlignments, "");
+ clp.RegisterIntOption("branchExpand", ¶ms.anchorParameters.branchExpand, "", CommandLineParser::NonNegativeInteger);
+ clp.RegisterIntOption("maxExtendDropoff", ¶ms.maxExtendDropoff, "", CommandLineParser::NonNegativeInteger);
+ clp.RegisterFlagOption("nucmer", ¶ms.emulateNucmer, "");
+ clp.RegisterIntOption("maxExpand", ¶ms.maxExpand, "", CommandLineParser::PositiveInteger);
+ clp.RegisterIntOption("minExpand", ¶ms.minExpand, "", CommandLineParser::NonNegativeInteger);
+ clp.RegisterStringOption("seqdb", ¶ms.seqDBName, "");
+ clp.RegisterStringOption("anchors", ¶ms.anchorFileName, "");
+ clp.RegisterStringOption("clusters", ¶ms.clusterFileName, "");
+ clp.RegisterFlagOption("samplePaths", (bool*) ¶ms.samplePaths, "");
+ clp.RegisterFlagOption("noStoreMapQV", ¶ms.storeMapQV, "");
+ clp.RegisterFlagOption("nowarp", (bool*) ¶ms.nowarp, "");
+ clp.RegisterFlagOption("noRefineAlign", (bool*) ¶ms.refineAlign, "");
+ clp.RegisterFlagOption("guidedAlign", (bool*)¶ms.useGuidedAlign, "");
+ clp.RegisterFlagOption("useGuidedAlign", (bool*)&trashbinBool, "");
+ clp.RegisterFlagOption("noUseGuidedAlign", (bool*)¶ms.useGuidedAlign, "");
+ clp.RegisterFlagOption("header", (bool*)¶ms.printHeader, "");
+ clp.RegisterIntOption("subreadImplType", ¶ms.subreadMapType, "", CommandLineParser::PositiveInteger);
+ clp.RegisterIntOption("bandSize", ¶ms.bandSize, "", CommandLineParser::PositiveInteger);
+ clp.RegisterIntOption("extendBandSize", ¶ms.extendBandSize, "", CommandLineParser::PositiveInteger);
+ clp.RegisterIntOption("guidedAlignBandSize", ¶ms.guidedAlignBandSize, "", CommandLineParser::PositiveInteger);
+ clp.RegisterIntOption("maxAnchorsPerPosition", ¶ms.anchorParameters.maxAnchorsPerPosition, "", CommandLineParser::PositiveInteger);
+ clp.RegisterIntOption("stopMappingOnceUnique", (int*) ¶ms.anchorParameters.stopMappingOnceUnique, "", CommandLineParser::NonNegativeInteger);
+ clp.RegisterStringOption("out", ¶ms.outFileName, "");
+ clp.RegisterIntOption("match", ¶ms.match, "", CommandLineParser::Integer);
+ clp.RegisterIntOption("mismatch", ¶ms.mismatch, "", CommandLineParser::Integer);
+ clp.RegisterIntOption("minMatch", ¶ms.minMatchLength, "", CommandLineParser::PositiveInteger);
+ clp.RegisterIntOption("maxMatch", ¶ms.anchorParameters.maxLCPLength, "", CommandLineParser::NonNegativeInteger);
+ clp.RegisterIntOption("maxLCPLength", ¶ms.anchorParameters.maxLCPLength, "", CommandLineParser::NonNegativeInteger);
+ clp.RegisterIntOption("indel", ¶ms.indel, "", CommandLineParser::Integer);
+ clp.RegisterIntOption("insertion", ¶ms.insertion, "", CommandLineParser::Integer);
+ clp.RegisterIntOption("deletion", ¶ms.deletion, "", CommandLineParser::Integer);
+ clp.RegisterIntOption("idsIndel", ¶ms.idsIndel, "", CommandLineParser::Integer);
+ clp.RegisterIntOption("sdpindel", ¶ms.sdpIndel, "", CommandLineParser::Integer);
+ clp.RegisterIntOption("sdpIns", ¶ms.sdpIns, "", CommandLineParser::Integer);
+ clp.RegisterIntOption("sdpDel", ¶ms.sdpDel, "", CommandLineParser::Integer);
+ clp.RegisterFloatOption("indelRate", ¶ms.indelRate, "", CommandLineParser::NonNegativeFloat);
+ clp.RegisterFloatOption("minRatio", ¶ms.minRatio, "", CommandLineParser::NonNegativeFloat);
+ clp.RegisterFloatOption("sdpbypass", ¶ms.sdpBypassThreshold, "", CommandLineParser::NonNegativeFloat);
+ clp.RegisterFloatOption("minFrac", &trashbinFloat, "", CommandLineParser::NonNegativeFloat);
+ clp.RegisterIntOption("maxScore", ¶ms.maxScore, "", CommandLineParser::Integer);
+ clp.RegisterStringOption("bwt", ¶ms.bwtFileName, "");
+ clp.RegisterIntOption("m", ¶ms.printFormat, "", CommandLineParser::NonNegativeInteger);
+ clp.RegisterFlagOption("sam", ¶ms.printSAM, "");
+#ifdef USE_PBBAM
+ clp.RegisterFlagOption("bam", ¶ms.printBAM, "");
+#endif
+ clp.RegisterStringOption("clipping", ¶ms.clippingString, "");
+ clp.RegisterIntOption("sdpTupleSize", ¶ms.sdpTupleSize, "", CommandLineParser::PositiveInteger);
+ clp.RegisterIntOption("pvaltype", ¶ms.pValueType, "", CommandLineParser::NonNegativeInteger);
+ clp.RegisterIntOption("start", ¶ms.startRead, "", CommandLineParser::NonNegativeInteger);
+ clp.RegisterIntOption("stride", ¶ms.stride, "", CommandLineParser::NonNegativeInteger);
+ clp.RegisterFloatOption("subsample", ¶ms.subsample, "", CommandLineParser::PositiveFloat);
+ clp.RegisterIntOption("nproc", ¶ms.nProc, "", CommandLineParser::PositiveInteger);
+ clp.RegisterFlagOption("sortRefinedAlignments",(bool*) ¶ms.sortRefinedAlignments, "");
+ clp.RegisterIntOption("quallc", ¶ms.qualityLowerCaseThreshold, "", CommandLineParser::Integer);
+ clp.RegisterFlagOption("v", (bool*) ¶ms.verbosity, "");
+ clp.RegisterIntOption("V", ¶ms.verbosity, "Specify a level of verbosity.", CommandLineParser::NonNegativeInteger);
+ clp.RegisterIntOption("contextAlignLength", ¶ms.anchorParameters.contextAlignLength, "", CommandLineParser::PositiveInteger);
+ clp.RegisterFlagOption("skipLookupTable", ¶ms.anchorParameters.useLookupTable, "");
+ clp.RegisterStringOption("metrics", ¶ms.metricsFileName, "");
+ clp.RegisterStringOption("lcpBounds", ¶ms.lcpBoundsFileName, "");
+ clp.RegisterStringOption("fullMetrics", ¶ms.fullMetricsFileName, "");
+ clp.RegisterIntOption("nbranch", ¶ms.anchorParameters.numBranches, "", CommandLineParser::NonNegativeInteger);
+ clp.RegisterFlagOption("divideByAdapter", ¶ms.byAdapter, "");
+ clp.RegisterFlagOption("useQuality", ¶ms.ignoreQualities, "");
+ clp.RegisterFlagOption("noFrontAlign", ¶ms.extendFrontAlignment, "");
+ clp.RegisterIntOption("minReadLength", ¶ms.minReadLength, "", CommandLineParser::NonNegativeInteger);
+ clp.RegisterIntOption("maxReadLength", ¶ms.maxReadLength, "", CommandLineParser::NonNegativeInteger);
+ clp.RegisterIntOption("minSubreadLength", ¶ms.minSubreadLength, "", CommandLineParser::NonNegativeInteger);
+ clp.RegisterIntOption("minRawSubreadScore", ¶ms.minRawSubreadScore, "", CommandLineParser::NonNegativeInteger);
+ clp.RegisterIntOption("minAvgQual", ¶ms.minAvgQual, "", CommandLineParser::Integer);
+ clp.RegisterFlagOption("advanceHalf", ¶ms.advanceHalf, "");
+ clp.RegisterIntOption("advanceExactMatches", ¶ms.anchorParameters.advanceExactMatches, "", CommandLineParser::NonNegativeInteger);
+ clp.RegisterFlagOption("useccs", ¶ms.useCcs, "");
+ clp.RegisterFlagOption("useccsdenovo", ¶ms.useCcsOnly, "");
+ clp.RegisterFlagOption("useccsall", ¶ms.useAllSubreadsInCcs, "");
+ clp.RegisterFlagOption("extendDenovoCCSSubreads", ¶ms.extendDenovoCCSSubreads, "");
+ clp.RegisterFlagOption("noRefineAlignments", ¶ms.refineAlignments, "");
+ clp.RegisterIntOption("nCandidates", ¶ms.nCandidates, "", CommandLineParser::NonNegativeInteger);
+ clp.RegisterFlagOption("useTemp", (bool*) ¶ms.tempDirectory, "");
+ clp.RegisterFlagOption("noSplitSubreads", ¶ms.mapSubreadsSeparately, "");
+ clp.RegisterFlagOption("concordant", ¶ms.concordant, "");
+ // When -concordant is turned on, blasr first selects a subread (e.g., the median length full-pass subread)
+ // of a zmw as template, maps the template subread to a reference, then infers directions of all other subreads
+ // of the same zmw based on direction of the template, and finally maps all other subreads to the same
+ // genomic coordinates as the template. When -concordantAlignBothDirections is turned on, blasr will align
+ // all other subreads both forwardly and backwardly, without infering their directions. This is a hidden
+ // diagnostic option only useful for analyzing movies which have lots of un-identified or missed adapters such
+ // that directions of subreads can not be inferred accurately.
+ clp.RegisterFlagOption("concordantAlignBothDirections", ¶ms.concordantAlignBothDirections, "");
+ clp.RegisterIntOption("flankSize", ¶ms.flankSize, "", CommandLineParser::NonNegativeInteger);
+ clp.RegisterIntOption("subreadMapType", ¶ms.subreadMapType, "", CommandLineParser::NonNegativeInteger);
+ clp.RegisterStringOption("titleTable", ¶ms.titleTableName, "");
+ clp.RegisterFlagOption("useSensitiveSearch", ¶ms.doSensitiveSearch, "");
+ clp.RegisterFlagOption("ignoreRegions", ¶ms.useRegionTable, "");
+ clp.RegisterFlagOption("ignoreHQRegions", ¶ms.useHQRegionTable, "");
+ clp.RegisterFlagOption("computeAlignProbability", ¶ms.computeAlignProbability, "");
+ clp.RegisterStringOption("unaligned", ¶ms.unalignedFileName, "");
+ clp.RegisterFlagOption("global", ¶ms.doGlobalAlignment, "");
+ clp.RegisterIntOption("globalChainType", ¶ms.globalChainType, "", CommandLineParser::NonNegativeInteger);
+ clp.RegisterFlagOption("noPrintSubreadTitle", (bool*) ¶ms.printSubreadTitle, "");
+ clp.RegisterIntOption("saLookupTableLength", ¶ms.lookupTableLength, "", CommandLineParser::PositiveInteger);
+ clp.RegisterFlagOption("useDetailedSDP", ¶ms.detailedSDPAlignment, "");
+ clp.RegisterFlagOption("nouseDetailedSDP", &trashbinBool, "");
+ clp.RegisterIntOption("sdpFilterType", ¶ms.sdpFilterType, "", CommandLineParser::NonNegativeInteger);
+ clp.RegisterIntOption("scoreType", ¶ms.scoreType, "", CommandLineParser::NonNegativeInteger);
+ clp.RegisterFlagOption("h", ¶ms.printVerboseHelp, "");
+ clp.RegisterFlagOption("help", ¶ms.printDiscussion, "");
+ clp.RegisterFloatOption("accuracyPrior", ¶ms.readAccuracyPrior, "", CommandLineParser::NonNegativeFloat);
+ clp.RegisterIntOption("readIndex", ¶ms.readIndex, "", CommandLineParser::NonNegativeInteger);
+ // holeNumberRangesStr is a string of comma-delimited hole number ranges, such as '1,2,3,10-15'.
+ // Blasr only analyzes reads whose hole numbers are in the specified hole number ranges.
+ clp.RegisterStringOption("holeNumbers", ¶ms.holeNumberRangesStr, "");
+ clp.RegisterIntOption("maxReadIndex", ¶ms.maxReadIndex, "", CommandLineParser::NonNegativeInteger);
+ clp.RegisterIntOption("substitutionPrior", ¶ms.substitutionPrior, "", CommandLineParser::NonNegativeInteger);
+ clp.RegisterIntOption("deletionPrior", ¶ms.globalDeletionPrior, "", CommandLineParser::NonNegativeInteger);
+ clp.RegisterIntOption("recurseOver", ¶ms.recurseOver, "", CommandLineParser::NonNegativeInteger);
+ clp.RegisterStringOption("scoreMatrix", ¶ms.scoreMatrixString, "");
+ clp.RegisterFlagOption("printDotPlots", ¶ms.printDotPlots, "");
+ clp.RegisterFlagOption("preserveReadTitle", ¶ms.preserveReadTitle,"");
+ clp.RegisterFlagOption("forwardOnly", ¶ms.forwardOnly,"");
+ clp.RegisterFlagOption("affineAlign", ¶ms.affineAlign, "");
+ clp.RegisterIntOption("affineOpen", ¶ms.affineOpen, "", CommandLineParser::NonNegativeInteger);
+ clp.RegisterIntOption("affineExtend", ¶ms.affineExtend, "", CommandLineParser::NonNegativeInteger);
+ clp.RegisterFlagOption("scaleMapQVByNClusters", ¶ms.scaleMapQVByNumSignificantClusters, "", false);
+ clp.RegisterFlagOption("printSAMQV", ¶ms.printSAMQV, "", false);
+ clp.RegisterFlagOption("cigarUseSeqMatch", ¶ms.cigarUseSeqMatch, "");
+ clp.RegisterStringListOption("samQV", ¶ms.samQV, "");
+ clp.RegisterFlagOption("fastMaxInterval", ¶ms.fastMaxInterval, "", false);
+ clp.RegisterFlagOption("aggressiveIntervalCut", ¶ms.aggressiveIntervalCut, "", false);
+ clp.RegisterFlagOption("fastSDP", ¶ms.fastSDP, "", false);
+ clp.RegisterStringOption("concordantTemplate", ¶ms.concordantTemplate, "typicalsubread");
+
+ RegisterFilterOptions(clp, params.minAlnLength, params.minPctSimilarity, params.minPctAccuracy,
+ params.hitPolicyStr, trashbinBool=true, trashbinInt, params.maxScore);
+}
+
+const string BlasrHelp(MappingParameters & params) {
+ stringstream helpStream;
+ helpStream << " Options for blasr " << endl
+ << " Basic usage: 'blasr reads.{bam|fasta|bax.h5|fofn} genome.fasta [-options] " << endl
+ << " option\tDescription (default_value)." << endl << endl
+ << " Input Files." << endl
+ << " reads.bam is a PacBio BAM file of reads." << endl
+ << " This is the preferred input to blasr because rich quality" << endl
+ << " value (insertion,deletion, and substitution quality values) information is " << endl
+ << " maintained. The extra quality information improves variant detection and mapping"<<endl
+ << " speed." << endl
+ << " reads.fasta is a multi-fasta file of reads. While any fasta file is valid input, " << endl
+ << " reads.bax.h5|reads.plx.h5 is the old DEPRECATED output format of SMRT reads." << endl
+ << " input.fofn File of file names accepted." << endl << endl
+ << " -sa suffixArrayFile"<< endl
+ << " Use the suffix array 'sa' for detecting matches" << endl
+ << " between the reads and the reference. The suffix" << endl
+ << " array has been prepared by the sawriter program." << endl << endl
+ << " -ctab tab "<<endl
+ << " A table of tuple counts used to estimate match significance. This is " << endl
+ << " by the program 'printTupleCountTable'. While it is quick to generate on " << endl
+ << " the fly, if there are many invocations of blasr, it is useful to"<<endl
+ << " precompute the ctab." <<endl << endl
+ << " -regionTable table (DEPRECATED)" << endl
+ << " Read in a read-region table in HDF format for masking portions of reads." << endl
+ << " This may be a single table if there is just one input file, " << endl
+ << " or a fofn. When a region table is specified, any region table inside " << endl
+ << " the reads.plx.h5 or reads.bax.h5 files are ignored."<< endl
+ << endl
+ << "(DEPRECATED) Options for modifying reads." << endl
+ << " There is ancilliary information about substrings of reads " << endl
+ << " that is stored in a 'region table' for each read file. Because " << endl
+ << " HDF is used, the region table may be part of the .bax.h5 or .plx.h5 file," << endl
+ << " or a separate file. A contiguously read substring from the template " << endl
+ << " is a subread, and any read may contain multiple subreads. The boundaries " << endl
+ << " of the subreads may be inferred from the region table either directly or " <<endl
+ << " by definition of adapter boundaries. Typically region tables also" << endl
+ << " contain information for the location of the high and low quality regions of"<<endl
+ << " reads. Reads produced by spurrious reads from empty ZMWs have a high"<<endl
+ << " quality start coordinate equal to high quality end, making no usable read." <<endl
+ << " -useccs " << endl
+ << " Align the circular consensus sequence (ccs), then report alignments" << endl
+ << " of the ccs subreads to the window that the ccs was mapped to. Only " << endl
+ << " alignments of the subreads are reported." << endl
+ << " -useccsall"<<endl
+ << " Similar to -useccs, except all subreads are aligned, rather than just" << endl
+ << " the subreads used to call the ccs. This will include reads that only"<<endl
+ << " cover part of the template." << endl
+ << " -useccsdenovo" << endl
+ << " Align the circular consensus, and report only the alignment of the ccs"<<endl
+ << " sequence." << endl
+ << " -noSplitSubreads (false)" <<endl
+ << " Do not split subreads at adapters. This is typically only " << endl
+ << " useful when the genome in an unrolled version of a known template, and " << endl
+ << " contains template-adapter-reverse_template sequence." << endl
+ << " -ignoreRegions(false)" << endl
+ << " Ignore any information in the region table." << endl
+ << " -ignoreHQRegions (false)Ignore any hq regions in the region table." << endl
+ << endl
+ << " Alignments To Report." << endl
+ << " -bestn n (10)" <<endl
+ << " Report the top 'n' alignments." << endl
+ << " -hitPolicy" << endl
+ << " " << params.hitPolicy.Help(string(15, ' ')) << endl
+ << " -placeRepeatsRandomly (false)" << endl
+ << " DEPRECATED! If true, equivalent to -hitPolicy randombest." << endl
+ << " -randomSeed (0)" << endl
+ << " Seed for random number generator. By default (0), use current time as seed. " << endl
+ << " -noSortRefinedAlignments (false) " << endl
+ << " Once candidate alignments are generated and scored via sparse dynamic "<< endl
+ << " programming, they are rescored using local alignment that accounts " << endl
+ << " for different error profiles." <<endl
+ << " Resorting based on the local alignment may change the order the hits are returned." << endl
+ << " -allowAdjacentIndels " << endl
+ << " When specified, adjacent insertion or deletions are allowed. Otherwise, adjacent " << endl
+ << " insertion and deletions are merged into one operation. Using quality values " << endl
+ << " to guide pairwise alignments may dictate that the higher probability alignment "<<endl
+ << " contains adjacent insertions or deletions. Current tools such as GATK do not permit" << endl
+ << " this and so they are not reported by default." << endl << endl
+ << " Output Formats and Files" << endl
+ << " -out out (terminal) " << endl
+ << " Write output to 'out'." << endl
+#ifdef USE_PBBAM
+ << " -bam Write output in PacBio BAM format. This is the preferred output format." << endl
+ << " Input query reads must be in PacBio BAM format." << endl
+#endif
+ << " -sam Write output in SAM format." << endl
+ << " -m t " << endl
+ << " If not printing SAM, modify the output of the alignment." << endl
+ << " t=" << StickPrint << " Print blast like output with |'s connecting matched nucleotides." << endl
+ << " " << SummaryPrint << " Print only a summary: score and pos." << endl
+ << " " << CompareXML << " Print in Compare.xml format." << endl
+ << " " << Vulgar << " Print in vulgar format (DEPRECATED)." << endl
+ << " " << Interval << " Print a longer tabular version of the alignment." << endl
+ << " " << CompareSequencesParsable << " Print in a machine-parsable format that is read by compareSequences.py." << endl
+ << " -header" <<endl
+ << " Print a header as the first line of the output file describing the contents of each column."<<endl
+ << " -titleTable tab (NULL) " << endl
+ << " Construct a table of reference sequence titles. The reference sequences are " << endl
+ << " enumerated by row, 0,1,... The reference index is printed in alignment results" << endl
+ << " rather than the full reference name. This makes output concise, particularly when" << endl
+ << " very verbose titles exist in reference names."<< endl
+ << " -unaligned file" << endl
+ << " Output reads that are not aligned to 'file'" << endl
+ << " -clipping [none|hard|subread|soft] (none)" << endl
+ << " Use no/hard/subread/soft clipping, ONLY for SAM/BAM output."<< endl
+ << " -printSAMQV (false)" << endl
+ << " Print quality values to SAM output." << endl
+ << " -cigarUseSeqMatch (false)" << endl
+ << " CIGAR strings in SAM/BAM output use '=' and 'X' to represent sequence match and mismatch instead of 'M'." << endl << endl
+ << " Options for anchoring alignment regions. This will have the greatest effect on speed and sensitivity." << endl
+ << " -minMatch m (12) " << endl
+ << " Minimum seed length. Higher minMatch will speed up alignment, " << endl
+ << " but decrease sensitivity." << endl
+// << " -maxExpand M (1)" << endl
+// << " Perform no more than M iterations of searches through the suffix " << endl
+// << " array for matches. At each iteration, all matches of length LCPi-M" << endl
+// << " are found, where LCPi is the length of the longest common prefix " << endl
+// << " between the string at i and anywhere in the genome."<<endl
+// << " The number of matches grows as M increases, and can become very large with M > 3." << endl
+ << " -maxMatch l (inf)" << endl
+ << " Stop mapping a read to the genome when the lcp length reaches l. " << endl
+ << " This is useful when the query is part of the reference, for example when " <<endl
+ << " constructing pairwise alignments for de novo assembly."<<endl
+ << " -maxLCPLength l (inf)" << endl
+ << " The same as -maxMatch." << endl
+ << " -maxAnchorsPerPosition m (10000) " << endl
+ << " Do not add anchors from a position if it matches to more than 'm' locations in the target." << endl
+// << " -advanceHalf (false) " << endl
+// << " A trick for speeding up alignments at the cost of sensitivity. If " << endl
+// << " a cluster of anchors of size n, (a1,...,an) is found, normally anchors " << endl
+// << " (a2,...an) of size n-1 is also clustered to make sure a1 did not decrease the " << endl
+// << " cluster score. When advanceHalf is specified, clustering begins at a_(n/2)."<<endl<< endl
+ << " -advanceExactMatches E (0)" << endl
+ << " Another trick for speeding up alignments with match - E fewer anchors. Rather than" << endl
+ << " finding anchors between the read and the genome at every position in the read, " <<endl
+ << " when an anchor is found at position i in a read of length L, the next position " << endl
+ << " in a read to find an anchor is at i+L-E." << endl
+ << " Use this when alignining already assembled contigs." << endl
+ << " -nCandidates n (10)" << endl
+ << " Keep up to 'n' candidates for the best alignment. A large value of n will slow mapping" << endl
+ << " because the slower dynamic programming steps are applied to more clusters of anchors" <<endl
+ << " which can be a rate limiting step when reads are very long."<<endl
+ << " -concordant(false)" << endl
+ << " Map all subreads of a zmw (hole) to where the longest full pass subread of the zmw " << endl
+ << " aligned to. This requires to use the region table and hq regions." << endl
+ << " This option only works when reads are in base or pulse h5 format." << endl
+ << " -concordantTemplate(mediansubread)" << endl
+ << " Select a full pass subread of a zmw as template for concordant mapping." << endl
+ << " longestsubread - use the longest full pass subread" << endl
+ << " mediansubread - use the median length full pass subread" << endl
+ << " typicalsubread - use the second longest full pass subread if length of" << endl
+ << " the longest full pass subread is an outlier" << endl
+ << " -fastMaxInterval(false)" << endl
+ << " Fast search maximum increasing intervals as alignment candidates. The search " << endl
+ << " is not as exhaustive as the default, but is much faster." << endl
+ << " -aggressiveIntervalCut(false)" << endl
+ << " Agreesively filter out non-promising alignment candidates, if there " << endl
+ << " exists at least one promising candidate. If this option is turned on, " << endl
+ << " Blasr is likely to ignore short alignments of ALU elements." << endl
+ << " -fastSDP(false)" << endl
+ << " Use a fast heuristic algorithm to speed up sparse dynamic programming." << endl
+ << endl
+ << " Options for Refining Hits." << endl
+// << " -indelRate i (0.30)" << endl
+// << " The approximate maximum rate to allow drifting from the diagonal." <<endl << endl
+ << " -sdpTupleSize K (11)" << endl
+ << " Use matches of length K to speed dynamic programming alignments. This controls" <<endl
+ << " accuracy of assigning gaps in pairwise alignments once a mapping has been found,"<<endl
+ << " rather than mapping sensitivity itself."<<endl
+ << " -scoreMatrix \"score matrix string\" " << endl
+ << " Specify an alternative score matrix for scoring fasta reads. The matrix is " << endl
+ << " in the format " << endl
+ << " ACGTN" << endl
+ << " A abcde" << endl
+ << " C fghij" << endl
+ << " G klmno" << endl
+ << " T pqrst" << endl
+ << " N uvwxy" << " . The values a...y should be input as a quoted space separated " << endl
+ << " string: \"a b c ... y\". Lower scores are better, so matches should be less " << endl
+ << " than mismatches e.g. a,g,m,s = -5 (match), mismatch = 6. " << endl
+ << " -affineOpen value (10) " << endl
+ << " Set the penalty for opening an affine alignment." << endl
+ << " -affineExtend a (0)" << endl
+ << " Change affine (extension) gap penalty. Lower value allows more gaps." << endl << endl
+ << " Options for overlap/dynamic programming alignments and pairwise overlap for de novo assembly. " << endl
+ << " -useQuality (false)" << endl
+ << " Use substitution/insertion/deletion/merge quality values to score gap and " << endl
+ << " mismatch penalties in pairwise alignments. Because the insertion and deletion" << endl
+ << " rates are much higher than substitution, this will make many alignments " <<endl
+ << " favor an insertion/deletion over a substitution. Naive consensus calling methods "<<endl
+ << " will then often miss substitution polymorphisms. This option should be " << endl
+ << " used when calling consensus using the Quiver method. Furthermore, when " << endl
+ << " not using quality values to score alignments, there will be a lower consensus " << endl
+ << " accuracy in homolymer regions." << endl
+ << " -affineAlign (false)" << endl
+ << " Refine alignment using affine guided align." << endl << endl
+ << " Options for filtering reads and alignments" << endl
+ << " -minReadLength l(50)" << endl
+ << " Skip reads that have a full length less than l. Subreads may be shorter." << endl
+ << " -minSubreadLength l(0)" << endl
+ << " Do not align subreads of length less than l." << endl
+ << " -minRawSubreadScore m(0)" << endl
+ << " Do not align subreads whose quality score in region table is less than m (quality scores should be in range [0, 1000])." << endl
+ << " -maxScore m(-200)" << endl //params.filterCriteria.scoreCutoff
+ << " Maximum score to output (high is bad, negative good)." << endl
+ << " -minAlnLength" << endl
+ << " " << params.filterCriteria.MinAlnLengthHelp() << endl
+ << " -minPctSimilarity" << endl
+ << " " << params.filterCriteria.MinPctSimilarityHelp() << endl
+ << " -minPctAccuracy" << endl
+ << " " << params.filterCriteria.MinPctAccuracyHelp() << endl << endl
+ << " Options for parallel alignment." << endl
+ << " -nproc N (1)" << endl
+ << " Align using N processes. All large data structures such as the suffix array and " << endl
+ << " tuple count table are shared."<<endl
+ << " -start S (0)" << endl
+ << " Index of the first read to begin aligning. This is useful when multiple instances " << endl
+ << " are running on the same data, for example when on a multi-rack cluster."<<endl
+ << " -stride S (1)" << endl
+ << " Align one read every 'S' reads." << endl << endl
+ << " Options for subsampling reads." << endl
+ << " -subsample (0)" << endl
+ << " Proportion of reads to randomly subsample (expressed as a decimal) and align." << endl
+ << " -holeNumbers LIST " << endl
+ << " When specified, only align reads whose ZMW hole numbers are in LIST." << endl
+ << " LIST is a comma-delimited string of ranges, such as '1,2,3,10-13'." << endl
+ << " This option only works when reads are in bam, bax.h5 or plx.h5 format." << endl
+ << endl
+// << " Options for dynamic programming alignments. " << endl << endl
+// << " -ignoreQuality" << endl
+// << " Ignore quality values when computing alignments (they still may be used." << endl
+// << " when mapping)." << endl << endl
+// << " -v Print some verbose information." << endl
+// << " -V 2 Make verbosity more verbose. Probably only useful for development." << endl
+ << " -h Print this help file." << endl << endl
+ << "To cite BLASR, please use: Chaisson M.J., and Tesler G., Mapping " << endl
+ << "single molecule sequencing reads using Basic Local Alignment with " << endl
+ << "Successive Refinement (BLASR): Theory and Application, BMC " << endl
+ << "Bioinformatics 2012, 13:238." << endl
+ << "Please report any bugs to "
+ << "'https://github.com/PacificBiosciences/blasr/issues'." << endl << endl;
+ return helpStream.str();
+}
+
+const string BlasrConciseHelp(void) {
+ stringstream ss;
+ ss << "blasr - a program to map reads to a genome" << endl
+ << " usage: blasr reads genome " << endl
+ << " Run with -h for a list of commands " << endl
+ << " -help for verbose discussion of how to run blasr." << endl;
+ return ss.str();
+}
+
+const string BlasrSummaryHelp(void) {
+ stringstream ss;
+ ss << " Basic usage: 'blasr reads.{bam|fasta|bax.h5|fofn} genome.fasta [-options] " << endl
+ << " [option]\tDescription (default_value)." << endl << endl
+ << " Input Files." << endl
+ << " reads.bam is the NEW native output format for SMRT reads."
+ "This is the preferred input to blasr because rich quality"
+ "value (insertion,deletion, and substitution quality values) information is "
+ "maintained. The extra quality information improves variant detection and mapping"<<
+ "speed." << endl
+ << " reads.fasta is a multi-fasta file of reads. While any fasta file is valid input, "
+ "it is preferable to use bax.h5 or plx.h5 files because they contain "
+ "more rich quality value information." << endl
+ << " reads.bax.h5|reads.plx.h5 is the OLD (DEPRECATED) output format of "
+ "SMRT reads. " << endl
+ << " reads.fofn File of file names accepted."
+ << endl << endl;
+ return ss.str();
+}
+
+const string BlasrDiscussion(void) {
+ stringstream ss;
+ ss << "NAME" << endl
+ << " blasr - Map SMRT Sequences to a reference genome."<< endl << endl
+ << "SYNOPSIS" << endl
+ << " blasr reads.bam genome.fasta -bam -out out.bam" << endl << endl
+ << " blasr reads.fasta genome.fasta " << endl << endl
+ << " blasr reads.fasta genome.fasta -sa genome.fasta.sa" << endl << endl
+ << " blasr reads.bax.h5 genome.fasta [-sa genome.fasta.sa] " << endl << endl
+ << " blasr reads.bax.h5 genome.fasta -sa genome.fasta.sa -maxScore -100 -minMatch 15 ... " << endl << endl
+ << " blasr reads.bax.h5 genome.fasta -sa genome.fasta.sa -nproc 24 -out alignment.out ... " << endl << endl
+ << "DESCRIPTION " << endl
+ << " blasr is a read mapping program that maps reads to positions " << endl
+ << " in a genome by clustering short exact matches between the read and" << endl
+ << " the genome, and scoring clusters using alignment. The matches are" << endl
+ << " generated by searching all suffixes of a read against the genome" << endl
+ << " using a suffix array. Global chaining methods are used to score " << endl
+ << " clusters of matches." << endl << endl
+ << " The only required inputs to blasr are a file of reads and a" << endl
+ << " reference genome. It is exremely useful to have read filtering" << endl
+ << " information, and mapping runtime may decrease substantially when a" << endl
+ << " precomputed suffix array index on the reference sequence is" << endl
+ << " specified." << endl
+ << " " << endl
+ << " Although reads may be input in FASTA format, the recommended input is" << endl
+ << " PacBio BAM files because these contain qualtiy value" << endl
+ << " information that is used in the alignment and produces higher quality" << endl
+ << " variant detection." << endl
+ << " Although alignments can be output in various formats, the recommended " << endl
+ << " output format is PacBio BAM." << endl
+ << " Support to bax.h5 and plx.h5 files will be DEPRECATED." << endl
+ << " Support to region tables for h5 files will be DEPRECATED." << endl
+ //<< " Read filtering information is contained in the .bax.h5 input files as" << endl
+ //<< " well as generated by other post-processing programs with analysis of" << endl
+ //<< " pulse files and read in from a separate .region.h5 file. The current" << endl
+ //<< " set of filters that are applied to reads are high quality region" << endl
+ //<< " filtering, and adapter filtering. Regions outside high-quality" << endl
+ //<< " regions are ignored in mapping. Reads that contain regions annotated" << endl
+ //<< " as adapter are split into non-adapter (template) regions, and mapped" << endl
+ //<< " separately." << endl
+ << " " << endl
+ << " When suffix array index of a genome is not specified, the suffix array is" << endl
+ << " built before producing alignment. This may be prohibitively slow" << endl
+ << " when the genome is large (e.g. Human). It is best to precompute the" << endl
+ << " suffix array of a genome using the program sawriter, and then specify" << endl
+ << " the suffix array on the command line using -sa genome.fa.sa." << endl
+ << " " << endl
+ << " The optional parameters are roughly divided into three categories:" << endl
+ << " control over anchoring, alignment scoring, and output. " << endl
+ << " " << endl
+ << " The default anchoring parameters are optimal for small genomes and" << endl
+ << " samples with up to 5% divergence from the reference genome. The main" << endl
+ << " parameter governing speed and sensitivity is the -minMatch parameter." << endl
+ << " For human genome alignments, a value of 11 or higher is recommended. " << endl
+ << " Several methods may be used to speed up alignments, at the expense of" << endl
+ << " possibly decreasing sensitivity. " << endl
+ << " " << endl
+// << " If the genome is highly repetitive or divergent from the read" << endl
+// << " sequences, the value of -maxExpand should be increased. This option" << endl
+// << " controls how much the search for anchors is expanded past a simple" << endl
+// << " greedy search. A value for -maxExpand of 1 is sufficent for" << endl
+// << " non-repetitive genomes, and values of -maxExpand greater than 5 are" << endl
+// << " not recommended." << endl
+// << " " << endl
+ << " Regions that are too repetitive may be ignored during mapping by" << endl
+ << " limiting the number of positions a read maps to with the" << endl
+ << " -maxAnchorsPerPosition option. Values between 500 and 1000 are effective" << endl
+ << " in the human genome." << endl
+ << " " << endl
+ << " For small genomes such as bacterial genomes or BACs, the default parameters " << endl
+ << " are sufficient for maximal sensitivity and good speed." << endl
+ << endl << endl;
+ return ss.str();
+}
diff --git a/RegisterFilterOptions.h b/RegisterFilterOptions.h
new file mode 100644
index 0000000..de422db
--- /dev/null
+++ b/RegisterFilterOptions.h
@@ -0,0 +1,53 @@
+#include "libconfig.h"
+#include "CommandLineParser.hpp"
+#include "datastructures/alignment/FilterCriteria.hpp"
+#include <sstream>
+using namespace std;
+
+/// Register options for filtering alignments.
+void RegisterFilterOptions(CommandLineParser & clp, int & minAlnLength,
+ float & minPctSimilarity, float & minPctAccuracy,
+ string & hitPolicyStr, bool & useScoreCutoff,
+ int & scoreSignInt, int & scoreCutoff) {
+ ScoreSign ss = static_cast<ScoreSign>(scoreSignInt);
+ Score sc(static_cast<float>(scoreCutoff), ss);
+ FilterCriteria fc(static_cast<DNALength>(minAlnLength),
+ minPctSimilarity, minPctAccuracy,
+ useScoreCutoff, sc);
+
+ HitPolicy hp("randombest", ScoreSign::NEGATIVE);
+
+ clp.RegisterIntOption("minAlnLength", &minAlnLength,
+ fc.MinAlnLengthHelp(),
+ CommandLineParser::PositiveInteger);
+ clp.RegisterIntOption("minAlignLength", &minAlnLength,
+ "Alias of -minAlnLength",
+ CommandLineParser::PositiveInteger);
+ clp.RegisterIntOption("minLength", &minAlnLength,
+ "Alias of -minAlnLength",
+ CommandLineParser::PositiveInteger);
+
+ clp.RegisterFloatOption("minPctSimilarity", &minPctSimilarity,
+ fc.MinPctSimilarityHelp(),
+ CommandLineParser::PositiveFloat);
+ clp.RegisterFloatOption("minPctIdentity", &minPctSimilarity,
+ "Alias of -minPctSimilarity",
+ CommandLineParser::PositiveFloat);
+
+ clp.RegisterFloatOption("minPctAccuracy", &minPctAccuracy,
+ fc.MinPctAccuracyHelp(),
+ CommandLineParser::PositiveFloat);
+ clp.RegisterFloatOption("minAccuracy", &minPctAccuracy,
+ "Alias of -minPctAccuracy",
+ CommandLineParser::PositiveFloat);
+
+ clp.RegisterStringOption("hitPolicy", &hitPolicyStr, hp.Help());
+
+ clp.RegisterIntOption("scoreSign", &scoreSignInt,
+ fc.ScoreSignHelp(),
+ CommandLineParser::Integer);
+
+ clp.RegisterIntOption("scoreCutoff", &scoreCutoff,
+ fc.ScoreCutoffHelp(),
+ CommandLineParser::Integer);
+}
diff --git a/blasr_git_common.mk b/blasr_git_common.mk
new file mode 100644
index 0000000..5834a55
--- /dev/null
+++ b/blasr_git_common.mk
@@ -0,0 +1,15 @@
+# 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
new file mode 100644
index 0000000..0b05708
--- /dev/null
+++ b/blasr_gitp4.mk
@@ -0,0 +1,24 @@
+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
new file mode 100644
index 0000000..9f2723c
--- /dev/null
+++ b/common.mk
@@ -0,0 +1,139 @@
+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
new file mode 100755
index 0000000..126c362
--- /dev/null
+++ b/configure.py
@@ -0,0 +1,204 @@
+#!/usr/bin/env python
+"""Configure the build.
+
+- Create defines.mk
+"""
+import commands
+import contextlib
+import optparse
+import os
+import sys
+
+#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 = '${ROOT}'
+
+def log(msg):
+ sys.stderr.write(msg)
+ sys.stderr.write('\n')
+
+def shell(cmd):
+ log(cmd)
+ status, output = commands.getstatusoutput(cmd)
+ if status:
+ raise Exception('%d <- %r' %(status, cmd))
+ return output
+
+def system(cmd):
+ log(cmd)
+ status = os.system(cmd)
+ if status:
+ raise Exception('%d <- %r' %(status, cmd))
+ return
+
+ at contextlib.contextmanager
+def cd(nwd):
+ cwd = os.getcwd()
+ log('cd %r -> %r' %(cwd, nwd))
+ os.chdir(nwd)
+ yield
+ os.chdir(cwd)
+ log('cd %r <- %r' %(cwd, nwd))
+
+def update_content(fn, content):
+ current_content = open(fn).read() if os.path.exists(fn) else None
+ if content != current_content:
+ log('writing to %r' %fn)
+ log('"""\n' + content + '"""')
+ open(fn, 'w').write(content)
+
+def get_OS_STRING():
+ G_BUILDOS_CMD = """bash -c 'set -e; set -o pipefail; id=$(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 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)
+ 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',
+ 'ZLIB_LIB', 'ZLIB_LIBFLAGS',
+ 'PTHREAD_LIBFLAGS',
+ 'DL_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):
+ content1 = compose_defines_pacbio(envin)
+ if shared:
+ content1 += 'LDLIBS+=-lrt\n'
+ else:
+ content1 += 'LDFLAGS+=-static\n'
+ content1 += 'SUB_CONF_FLAGS+=--shared\n'
+ update(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_LIB': os.path.join(subdir, 'pbdata'),
+ 'LIBBLASR_LIB': os.path.join(subdir, 'alignment'),
+ #'LIBPBIHDF_LIB': '' if nopbbam else os.path.join(subdir, 'hdf'),
+ }
+ for k in defaults:
+ if k not in env:
+ env[k] = defaults[k]
+
+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_LIB': os.path.join(ROOT, 'libcpp', 'alignment'),
+ 'LIBPBDATA_LIB': os.path.join(ROOT, 'libcpp', 'pbdata'),
+ 'LIBPBIHDF_LIB': os.path.join(ROOT, 'libcpp', 'hdf'),
+ 'LIBBLASR_LIBFLAGS': '-lblasr',
+ 'LIBPBDATA_LIBFLAGS': '-lpbdata',
+ 'LIBPBIHDF_LIBFLAGS': '-lpbihdf',
+ 'HDF5_LIBFLAGS': '-lhdf5_cpp -lhdf5',
+ 'ZLIB_LIBFLAGS': '-lz',
+ 'PTHREAD_LIBFLAGS': '-lpthread',
+ 'DL_LIBFLAGS': '-ldl', # neeeded by HDF5 always
+ 'SHELL': 'bash -xe',
+ }
+ #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
+ }
+ if not nopbbam:
+ defaults.update(pbbam_defaults)
+ for k in defaults:
+ if k not in env:
+ env[k] = defaults[k]
+
+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 parse_args(args):
+ parser = optparse.OptionParser()
+ parser.add_option('--no-pbbam', action='store_true',
+ help='Avoid compiling anything which would need pbbam.')
+ parser.add_option('--submodules', action='store_true',
+ 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.')
+ return parser.parse_args(list(args))
+
+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)
+ envin = get_make_style_env(os.environ, makevars)
+ 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)
+
+
+if __name__=="__main__":
+ main(*sys.argv)
diff --git a/ctest/affineAlign.t b/ctest/affineAlign.t
new file mode 100644
index 0000000..caec49d
--- /dev/null
+++ b/ctest/affineAlign.t
@@ -0,0 +1,17 @@
+Set up
+ $ . $TESTDIR/setup.sh
+
+Test affineAlign
+ $ rm -rf $OUTDIR/affineAlign.m0
+ $ $EXEC $DATDIR/affineAlign.fofn $DATDIR/substr_with_ins.fasta -m 0 -out $OUTDIR/affineAlign.m0 -affineAlign -readIndex 493 -insertion 100 -deletion 100
+ [INFO]* (glob)
+ [INFO]* (glob)
+ $ diff $OUTDIR/affineAlign.m0 $STDDIR/affineAlign_2014_06_10.m0
+
+ $ rm -rf $OUTDIR/ecoli_affine.m0
+ $ $EXEC $DATDIR/ecoli_affine.fasta $DATDIR/ecoli_reference.fasta -m 0 -out $OUTDIR/ecoli_affine.m0 -affineAlign -insertion 100 -deletion 100
+ [INFO]* (glob)
+ [INFO]* (glob)
+ $ diff $OUTDIR/ecoli_affine.m0 $STDDIR/ecoli_affine_2014_06_10.m0
+
+# Note that MapQV for -affineAlign has been fixed in 2014 04 18, bug 24363
diff --git a/ctest/aggressiveIntervalCut.t b/ctest/aggressiveIntervalCut.t
new file mode 100644
index 0000000..571e8fe
--- /dev/null
+++ b/ctest/aggressiveIntervalCut.t
@@ -0,0 +1,12 @@
+Set up
+ $ . $TESTDIR/setup.sh
+
+Test -aggressiveIntervalCut.
+ $ rm -f $TMP1
+ $ BASFILE=/mnt/data3/vol53/2450598/0001/Analysis_Results/m130812_185809_42141_c100533960310000001823079711101380_s1_p0.bas.h5
+ $ REFFA=/mnt/secondary/Smrtpipe/repository/Ecoli_BL21_O26/sequence/Ecoli_BL21_O26.fasta
+ $ $EXEC $BASFILE $REFFA -holeNumbers 1-100 -out $TMP1 -aggressiveIntervalCut
+ [INFO] * [blasr] started. (glob)
+ [INFO] * [blasr] ended. (glob)
+ $ echo $?
+ 0
diff --git a/ctest/alignScore.t b/ctest/alignScore.t
new file mode 100644
index 0000000..492f92e
--- /dev/null
+++ b/ctest/alignScore.t
@@ -0,0 +1,9 @@
+Set up
+ $ . $TESTDIR/setup.sh
+
+Test alignment score
+ $ rm -rf $OUTDIR/testscore.m0
+ $ $EXEC $DATDIR/read.fasta $DATDIR/ref.fasta -minReadLength 1 -m 0 -out $OUTDIR/testscore.m0
+ [INFO]* (glob)
+ [INFO]* (glob)
+ $ diff $OUTDIR/testscore.m0 $STDDIR/testscore.m0
diff --git a/ctest/bamIn.t b/ctest/bamIn.t
new file mode 100644
index 0000000..d518c35
--- /dev/null
+++ b/ctest/bamIn.t
@@ -0,0 +1,52 @@
+Set up
+ $ . $TESTDIR/setup.sh
+
+Test using bam as input
+ $ $EXEC $DATDIR/test_bam/tiny_bam.fofn $DATDIR/lambda_ref.fasta -m 4 -out $OUTDIR/tiny_bam_in.m4
+ [INFO]* (glob)
+ [INFO]* (glob)
+
+Check whether blasr produces identical results taking fasta sequences of the bam as input
+ $ $EXEC $DATDIR/test_bam/tiny_fasta.fofn $DATDIR/lambda_ref.fasta -m 4 -out $OUTDIR/tiny_fasta_in.m4
+ [INFO]* (glob)
+ [INFO]* (glob)
+ $ diff $OUTDIR/tiny_bam_in.m4 $OUTDIR/tiny_fasta_in.m4
+
+Test bam in, sam out
+ $ $EXEC $DATDIR/test_bam/tiny_bam.fofn $DATDIR/lambda_ref.fasta -sam -out $OUTDIR/tiny_bam_in.sam -printSAMQV -clipping subread -cigarUseSeqMatch
+ [INFO]* (glob)
+ [INFO]* (glob)
+
+Test bam in, bam out
+ $ $EXEC $DATDIR/test_bam/tiny_bam.fofn $DATDIR/lambda_ref.fasta -bam -out $OUTDIR/tiny_bam_in.bam -clipping subread
+ [INFO]* (glob)
+ [INFO]* (glob)
+
+Check whether sam out and bam out have identical alignments, not checking qvs
+ $ $SAMTOOLS view -h $OUTDIR/tiny_bam_in.bam -o $OUTDIR/tiny_bam_in.bam.sam
+ $ cut -f 2-11 $OUTDIR/tiny_bam_in.bam.sam |sed -n '6,$p' > $TMP1.aln
+ $ cut -f 2-11 $OUTDIR/tiny_bam_in.sam |sed -n '6,$p' > $TMP2.aln
+ $ diff $TMP1.aln $TMP2.aln
+
+Check whether sam out and bam out have identical read groups @RG
+ $ awk '/^@RG/' $OUTDIR/tiny_bam_in.bam.sam > $TMP1.rg
+ $ awk '/^@RG/' $OUTDIR/tiny_bam_in.sam > $TMP2.rg
+ $ diff $TMP1.rg $TMP2.rg
+
+Compare iq produced with stdout
+ $ sed -n '6,$p' $OUTDIR/tiny_bam_in.bam.sam | awk '{gsub(/\t/,"\n");}1' | awk '/^iq:Z:/' > $TMP1.iq
+ $ sed -n '6,$p' $STDDIR/$UPDATEDATE/tiny_bam_in.bam.sam | awk '{gsub(/\t/,"\n");}1' | awk '/^iq:Z:/' > $TMP2.iq
+ $ diff $TMP1.iq $TMP2.iq
+
+TODO:Check whether sam out and bam out have identical insertion qvs
+Currently QVs in bam are in 'native' orientation, and QVs in sam are in 'genomic' orientation. This needs to be fixed.
+$ sed -n '6,$p' $OUTDIR/tiny_bam_in.sam | awk '{gsub(/\t/,"\n");}1' | awk '/^iq:Z:/' > $TMP2.iq
+
+Test with multiple nproc
+ $ $EXEC $DATDIR/test_bam/two_bam.fofn $DATDIR/lambda_ref.fasta -bam -nproc 15 -out $OUTDIR/two_bam_in.bam
+ [INFO]* (glob)
+ [INFO]* (glob)
+ $ $SAMTOOLS view -h $OUTDIR/two_bam_in.bam -o $OUTDIR/two_bam_in.bam.sam
+
+TODO: test -concordant, when pbbam API to query over ZMWs is available.
+TODO: test bam with ccs reads
diff --git a/ctest/bamOut.t b/ctest/bamOut.t
new file mode 100644
index 0000000..a15b811
--- /dev/null
+++ b/ctest/bamOut.t
@@ -0,0 +1,22 @@
+Set up
+ $ . $TESTDIR/setup.sh
+
+Test generating bam output
+
+Input is bam, clipping=soft and subread should produce identical results
+ $ $EXEC $DATDIR/test_bam/tiny_bam.fofn $DATDIR/lambda_ref.fasta -bam -out $OUTDIR/tiny_bam_in_soft.bam -clipping soft
+ [INFO]* (glob)
+ [INFO]* (glob)
+
+ $ $EXEC $DATDIR/test_bam/tiny_bam.fofn $DATDIR/lambda_ref.fasta -bam -out $OUTDIR/tiny_bam_in_subread.bam -clipping subread
+ [INFO]* (glob)
+ [INFO]* (glob)
+
+ $ $SAMTOOLS view $OUTDIR/tiny_bam_in_soft.bam | sed -n '6,$p' > $TMP1.bam_in_soft
+ $ $SAMTOOLS view $OUTDIR/tiny_bam_in_subread.bam | sed -n '6,$p' > $TMP2.bam_in_subread
+ $ diff $TMP1.bam_in_soft $TMP2.bam_in_subread
+
+Test if bam cigar strings are correct
+ $ head -2 $TMP1.bam_in_soft |cut -f 6
+ 25=1I28=1I41=1I5=1D6=1X12=1I15=1I2=1I16=1D10=1I11=1I74=1D12=1D7=3I4=1I6=1D1=2D14=1D16=1I8=1D4=1D5=1D20=1I3=1I10=1I37=1I13=1I25=1I15=1I7=1I11=1I3=2I1=1I16=1I6=1I8=1I11=1X1=1I5=1I56=1I17=
+ 28=1D7=1I1=1I9=2I12=1I3=1D13=1I15=1I2=1X49=1I19=1I14=1I5=1D17=1D20=1D86=1I21=1I9=1I24=1I6=1I1=1I2=1D11=1D4=1D3=1D31=1D6=1I6=1I9=1I57=2I24=1I26=1I8=1I43=1S
diff --git a/ctest/bug25328.t b/ctest/bug25328.t
new file mode 100644
index 0000000..2127433
--- /dev/null
+++ b/ctest/bug25328.t
@@ -0,0 +1,13 @@
+Set up
+ $ . $TESTDIR/setup.sh
+
+bug_25328, unrolled resequencing test
+ $ INFA=$DATDIR/bug_25328_zmw_38131.fasta
+ $ REF=$DATDIR/All4mers_circular_72x_l50256.fasta
+ $ OUTFA=$OUTDIR/bug_25328.m4
+ $ $EXEC $INFA $REF -bestn 1 -nCandidates 1 -forwardOnly -maxMatch 14 -m 4 -out $OUTFA
+ [INFO]* (glob)
+ [INFO]* (glob)
+
+ $ awk '$7-$6 >= 15000' $OUTFA |wc -l
+ 1
diff --git a/ctest/bug25741.t b/ctest/bug25741.t
new file mode 100644
index 0000000..d29829a
--- /dev/null
+++ b/ctest/bug25741.t
@@ -0,0 +1,9 @@
+Set up
+ $ . $TESTDIR/setup.sh
+
+bug_25741, if input bas.h5 does not contain mergeQV, blasr with -printSAMQV, -nproc>1 should not write garbage 'mq' values to output.
+ $ $EXEC $DATDIR/bas_wo_mergeQV.fofn $DATDIR/lambda_ref.fasta -printSAMQV -sam -clipping subread -out $OUTDIR/out_printSAMQV.sam -nproc 12
+ [INFO]* (glob)
+ [INFO]* (glob)
+ $ grep 'mq' $OUTDIR/out_printSAMQV.sam |wc -l
+ 1
diff --git a/ctest/bug25766.t b/ctest/bug25766.t
new file mode 100644
index 0000000..eaf9e06
--- /dev/null
+++ b/ctest/bug25766.t
@@ -0,0 +1,13 @@
+Set up
+ $ . $TESTDIR/setup.sh
+
+bug_25766, added an option -minRawSubreadScore
+ $ BASFILE=$DATDIR/lambda_bax.fofn
+ $ REF=$DATDIR/lambda_ref.fasta
+ $ $EXEC $BASFILE $REF -out $TMP1 -minRawSubreadScore 700 -nproc 18
+ [INFO]* (glob)
+ [INFO]* (glob)
+ $ echo $?
+ 0
+ $ sort $TMP1 > $TMP2
+ $ diff $TMP2 $STDDIR/bug_25766.m4
diff --git a/ctest/ccsH5.t b/ctest/ccsH5.t
new file mode 100644
index 0000000..b3e0477
--- /dev/null
+++ b/ctest/ccsH5.t
@@ -0,0 +1,11 @@
+Set up
+ $ . $TESTDIR/setup.sh
+
+Test using *.ccs.h5 as input
+# The results should be exactly the same as
+# blasr $DATDIR/ccsasinput_bas.fofn $DATDIR/ccsasinput.fasta -m 4 -out tmp.m4 -useccsdenovo
+ $ rm -rf $OUTDIR/ccsasinput.m4
+ $ $EXEC $DATDIR/ccsasinput.fofn $DATDIR/ccsasinput.fasta -m 4 -out $OUTDIR/ccsasinput.m4
+ [INFO]* (glob)
+ [INFO]* (glob)
+ $ diff $OUTDIR/ccsasinput.m4 $STDDIR/ccsasinput_2014_06_10.m4
diff --git a/ctest/concordant.t b/ctest/concordant.t
new file mode 100644
index 0000000..129c9fa
--- /dev/null
+++ b/ctest/concordant.t
@@ -0,0 +1,32 @@
+Set up
+ $ . $TESTDIR/setup.sh
+
+Test -concordant
+ $ rm -rf $OUTDIR/concordant_subset.sam
+ $ $EXEC $DATDIR/ecoli_lp.fofn $DATDIR/ecoli_reference.fasta -concordant -sam -out $OUTDIR/concordant_subset.sam -nproc 12 -holeNumbers 1-10000 -sa $DATDIR/ecoli_reference.sa
+ [INFO]* (glob)
+ [INFO]* (glob)
+ $ sed -n 6,110864p $OUTDIR/concordant_subset.sam > $OUTDIR/tmp1
+ $ sort $OUTDIR/tmp1 > $OUTDIR/tmp11
+ $ sed -n 6,110864p $STDDIR/$UPDATEDATE/concordant_subset.sam > $OUTDIR/tmp2
+ $ sort $OUTDIR/tmp2 > $OUTDIR/tmp22
+ $ diff $OUTDIR/tmp11 $OUTDIR/tmp22
+ $ rm -rf $OUTDIR/tmp1 $OUTDIR/tmp2 $OUTDIR/tmp11 $OUTDIR/tmp22
+#2014_05_28 --> changelist 135254, use MAX_BAND_SIZE to contrain GuidedAlign
+#2014_08_21 --> changelist 138516, added YS, YE, ZM tags.
+#2014_08_28 --> changelist 139176, update SAM MD5
+#2014_09_12 --> changelist 140410, changed the default value of '-concordantTemplate' from 'longestsubread' to 'typicalsubread'
+#2014_09_17 --> changelist 140573, changed SDPFragment LessThan to make sure blasr compiled with gcc 4.4 and 4.8 can produce identical results.
+#2014_10_16 --> changelist 141378, changed the default value of '-concordantTemplate' from 'typicalsubread' to 'mediansubread'
+#2015_03_01 --> changelist 146599, reads from the same movie should have unique readGroupId
+#2015_03_28 --> changelist 148101, 148080 updated read group id, 148100 updated TLEN
+#2015_04_09 --> changelist 148796, updated read group id
+#2015_04_25 --> changelist 149721, update CIGAR string, replace M with X=.
+
+Test -concordant FMR1 case (the 'typical subread' is selected as template for concordant mapping)
+ $ FOFN=$DATDIR/FMR1_concordant.fofn
+ $ REF=$DATDIR/FMR1_130CGG.fasta
+ $ $EXEC $FOFN $REF -concordant -out $OUTDIR/FMR1_zmw_37927.m4 -m 4 -holeNumbers 37927
+ [INFO]* (glob)
+ [INFO]* (glob)
+ $ diff $OUTDIR/FMR1_zmw_37927.m4 $STDDIR/FMR1_zmw_37927.m4
diff --git a/ctest/ecoli.t b/ctest/ecoli.t
new file mode 100644
index 0000000..c6291a2
--- /dev/null
+++ b/ctest/ecoli.t
@@ -0,0 +1,20 @@
+Set up
+ $ . $TESTDIR/setup.sh
+
+Test blasr on ecoli.
+Test blasr with -sam
+
+# The following job takes a very long time to finish, let us use a subset of reads instead
+#See $STDOUT/ecoli_v1.4.sam for 1.4 output.
+# $STDOUT/ecoli_2014_03_28.sam for bug before mapQV for affineAlign/align without QV is fixed.
+ $ rm -rf $OUTDIR/ecoli_subset.sam
+ $ $EXEC $DATDIR/ecoli_subset.fasta $DATDIR/ecoli_reference.fasta -sam -out $OUTDIR/ecoli_subset.sam -nproc 15
+ [INFO]* (glob)
+ [INFO]* (glob)
+
+ $ sed -n '5,$ p' $OUTDIR/ecoli_subset.sam | sort | cut -f 1-11 > $TMP1
+ $ sed -n '5,$ p' $STDDIR/$UPDATEDATE/ecoli_subset.sam | sort | cut -f 1-11 > $TMP2
+ $ diff $TMP1 $TMP2
+ $ rm $TMP1 $TMP2
+# 2015_03_08 --> changelist 148101, 148080 updated read group id; 148100 updated TLEN
+# 2015_04_09 --> changelist 148796, updated read group id
diff --git a/ctest/fastMaxInterval.t b/ctest/fastMaxInterval.t
new file mode 100644
index 0000000..323fab1
--- /dev/null
+++ b/ctest/fastMaxInterval.t
@@ -0,0 +1,12 @@
+Set up
+ $ . $TESTDIR/setup.sh
+
+Test -fastMaxInterval.
+ $ rm -f $TMP1
+ $ BASFILE=/mnt/data3/vol53/2450598/0001/Analysis_Results/m130812_185809_42141_c100533960310000001823079711101380_s1_p0.bas.h5
+ $ REFFA=/mnt/secondary/Smrtpipe/repository/Ecoli_BL21_O26/sequence/Ecoli_BL21_O26.fasta
+ $ $EXEC $BASFILE $REFFA -holeNumbers 1-100 -out $TMP1 -fastMaxInterval
+ [INFO] * [blasr] started. (glob)
+ [INFO] * [blasr] ended. (glob)
+ $ echo $?
+ 0
diff --git a/ctest/filtercriteria.t b/ctest/filtercriteria.t
new file mode 100644
index 0000000..9634e9e
--- /dev/null
+++ b/ctest/filtercriteria.t
@@ -0,0 +1,30 @@
+Set up
+ $ . $TESTDIR/setup.sh
+
+ $ NAME=test_filtercriteria
+ $ DATDIR=$DATDIR/$NAME
+ $ OUTDIR=$OUTDIR/$NAME
+ $ STDDIR=$STDDIR/$NAME
+ $ mkdir -p $OUTDIR
+
+Test -minPctSimilarity
+ $ I=$DATDIR/tiny_bam.fofn
+ $ R=$DATDIR/lambdaNEB.fa
+ $ O=$OUTDIR/min_pct_similarity_90.m4
+
+ $ $EXEC $I $R -out $O -m 4 -minPctSimilarity 90
+ [INFO]* (glob)
+ [INFO]* (glob)
+ $ echo $?
+ 0
+ $ awk '$4 < 90 {print}' $O |wc -l |cut -f 1 -d ' '
+ 0
+
+ $ O=$OUTDIR/min_aln_len_1000.m4
+ $ $EXEC $I $R -out $O -m 4 -minAlnLength 1000
+ [INFO]* (glob)
+ [INFO]* (glob)
+ $ echo $?
+ 0
+ $ wc -l $O |cut -f 1 -d ' '
+ 12
diff --git a/ctest/fofn.t b/ctest/fofn.t
new file mode 100644
index 0000000..348b6f7
--- /dev/null
+++ b/ctest/fofn.t
@@ -0,0 +1,18 @@
+Set up
+ $ . $TESTDIR/setup.sh
+
+Test blasr with *.fofn input
+# $ rm -rf $OUTDIR/lambda_bax.m4
+# $ $EXEC $DATDIR/lambda_bax.fofn $DATDIR/lambda_ref.fasta -m 4 -out lambda_bax_tmp.m4 -nproc 15 -minMatch 14
+# [INFO]* (glob)
+# [INFO]* (glob)
+# $ sort lambda_bax_tmp.m4 > $OUTDIR/lambda_bax.m4
+# $ diff $OUTDIR/lambda_bax.m4 $STDDIR/lambda_bax.m4
+# This test takes a long time, use a subset instad.
+
+ $ rm -rf $OUTDIR/lambda_bax_subset.m4
+ $ $EXEC $DATDIR/lambda_bax.fofn $DATDIR/lambda_ref.fasta -m 4 -out $OUTDIR/lambda_bax_tmp_subset.m4 -nproc 15 -minMatch 14 -holeNumbers 1-1000 -sa $DATDIR/lambda_ref.sa
+ [INFO]* (glob)
+ [INFO]* (glob)
+ $ sort $OUTDIR/lambda_bax_tmp_subset.m4 > $OUTDIR/lambda_bax_subset.m4
+ $ diff $OUTDIR/lambda_bax_subset.m4 $STDDIR/lambda_bax_subset.m4
diff --git a/ctest/hitpolicy.t b/ctest/hitpolicy.t
new file mode 100644
index 0000000..062a4ae
--- /dev/null
+++ b/ctest/hitpolicy.t
@@ -0,0 +1,86 @@
+Set up
+ $ . $TESTDIR/setup.sh
+
+ $ NAME=test_hitpolicy
+ $ DATDIR=$DATDIR/$NAME
+ $ OUTDIR=$OUTDIR/$NAME
+ $ STDDIR=$STDDIR/$NAME
+ $ mkdir -p $OUTDIR
+
+ $ I=$DATDIR/tiny_bam.fofn
+ $ R=$DATDIR/test_hitpolicy_target.fa
+ $ O=$OUTDIR/hitpolicy_all.m4
+ $ X=$STDDIR/hitpolicy_all.m4
+
+Test hitpolicy all
+ $ $EXEC $I $R -out $O -m 4 -hitPolicy all
+ [INFO]* (glob)
+ [INFO]* (glob)
+ $ echo $?
+ 0
+ $ wc -l $O | cut -f 1 -d ' '
+ 683
+
+Test hitpolicy allbest
+ $ O=$OUTDIR/hitpolicy_allbest.m4
+ $ X=$STDDIR/hitpolicy_allbest.m4
+ $ $EXEC $I $R -out $O -m 4 -hitPolicy allbest && sort $O > $TMP1 && mv $TMP1 $O
+ [INFO]* (glob)
+ [INFO]* (glob)
+ $ echo $?
+ 0
+ $ sort $O > $TMP1 && mv $TMP1 $O
+ $ diff $O $X && echo $?
+ 0
+
+Test hitpolicy random
+ $ O=$OUTDIR/hitpolicy_random.m4
+ $ X=$STDDIR/hitpolicy_random.m4
+ $ $EXEC $I $R -out $O -m 4 -hitPolicy random -randomSeed 1
+ [INFO]* (glob)
+ [INFO]* (glob)
+ $ sort $O > $TMP1 && mv $TMP1 $O
+ $ diff $O $X && echo $?
+ 0
+
+Test hitpolicy randombest bam inputs, nproc > 1, fixed seed
+ $ O=$OUTDIR/hitpolicy_randombest_bam_in.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)
+ $ sort $O > $TMP1 && mv $TMP1 $O
+ $ diff $O $X && echo $?
+ 0
+
+Test hitpolicy randombest bax inputs, nproc > 1, fixed seed
+ $ I=$DATDIR/tiny_bax.fofn
+ $ O=$OUTDIR/hitpolicy_randombest_bax_in.m4
+ $ X=$STDDIR/hitpolicy_randombest_bax_in.m4
+ $ $EXEC $I $R -out $O -m 4 -hitPolicy randombest -randomSeed 1 -nproc 10
+ [INFO]* (glob)
+ [INFO]* (glob)
+ $ sort $O > $TMP1 && mv $TMP1 $O
+ $ diff $O $X && echo $?
+ 0
+
+Test hitpolicy randombest fasta inputs, nproc > 1, fixed seed
+ $ I=$DATDIR/tiny_fasta.fofn
+ $ O=$OUTDIR/hitpolicy_randombest_fasta_in.m4
+ $ X=$STDDIR/hitpolicy_randombest_fasta_in.m4
+ $ $EXEC $I $R -out $O -m 4 -hitPolicy randombest -randomSeed 1 -nproc 10
+ [INFO]* (glob)
+ [INFO]* (glob)
+ $ sort $O > $TMP1 && mv $TMP1 $O
+ $ diff $O $X && echo $?
+ 0
+
+Test hitpolicy leftmost
+ $ O=$OUTDIR/hitpolicy_leftmost.m4
+ $ X=$STDDIR/hitpolicy_leftmost.m4
+ $ $EXEC $I $R -out $O -m 4 -hitPolicy leftmost -nproc 10
+ [INFO]* (glob)
+ [INFO]* (glob)
+ $ # target is lambda x 6, leftmost -> only map to the very first x.
+ $ awk '$10 > 48502 {print}' $O |wc -l
+ 0
diff --git a/ctest/holeNumbers.t b/ctest/holeNumbers.t
new file mode 100644
index 0000000..427f31a
--- /dev/null
+++ b/ctest/holeNumbers.t
@@ -0,0 +1,12 @@
+Set up
+ $ . $TESTDIR/setup.sh
+
+Test -holeNumbers
+ $ rm -f $OUTDIR/holeNumbers.m4
+ $ $EXEC $DATDIR/lambda_bax.fofn $DATDIR/lambda_ref.fasta -m 4 -out $OUTDIR/holeNumbers.m4 -holeNumbers 14798,55000-55100 -nproc 8
+ [INFO]* (glob)
+ [INFO]* (glob)
+ $ sort $OUTDIR/holeNumbers.m4 > $TMP1
+ $ sort $STDDIR/holeNumbers_2014_05_29.m4 > $TMP2
+ $ diff $TMP1 $TMP2
+ $ rm $TMP1 $TMP2
diff --git a/ctest/m0-5.t b/ctest/m0-5.t
new file mode 100644
index 0000000..84182b3
--- /dev/null
+++ b/ctest/m0-5.t
@@ -0,0 +1,33 @@
+Set up
+ $ . $TESTDIR/setup.sh
+
+Test blasr with -m 0 ~ 5
+ $ rm -rf $OUTDIR/read.m0
+ $ $EXEC $DATDIR/read.fasta $DATDIR/ref.fasta -m 0 -out $OUTDIR/read.m0
+ [INFO]* (glob)
+ [INFO]* (glob)
+ $ diff $OUTDIR/read.m0 $STDDIR/read.m0
+
+ $ rm -rf $OUTDIR/read.m1
+ $ $EXEC $DATDIR/read.fasta $DATDIR/ref.fasta -m 1 -out $OUTDIR/read.m1
+ [INFO]* (glob)
+ [INFO]* (glob)
+ $ diff $OUTDIR/read.m1 $STDDIR/read_2014_05_29.m1
+
+ $ rm -rf $OUTDIR/read.m2
+ $ $EXEC $DATDIR/read.fasta $DATDIR/ref.fasta -m 2 -out $OUTDIR/read.m2
+ [INFO]* (glob)
+ [INFO]* (glob)
+ $ diff $OUTDIR/read.m2 $STDDIR/read.m2
+
+ $ rm -rf $OUTDIR/read.m3
+ $ $EXEC $DATDIR/read.fasta $DATDIR/ref.fasta -m 3 -out $OUTDIR/read.m3
+ [INFO]* (glob)
+ [INFO]* (glob)
+ $ diff $OUTDIR/read.m3 $STDDIR/read.m3
+
+ $ rm -rf $OUTDIR/read.m4
+ $ $EXEC $DATDIR/read.fasta $DATDIR/ref.fasta -m 4 -out $OUTDIR/read.m4
+ [INFO]* (glob)
+ [INFO]* (glob)
+ $ diff $OUTDIR/read.m4 $STDDIR/read.m4
diff --git a/ctest/multipart.t b/ctest/multipart.t
new file mode 100644
index 0000000..2cf6e81
--- /dev/null
+++ b/ctest/multipart.t
@@ -0,0 +1,13 @@
+Set up
+ $ . $TESTDIR/setup.sh
+
+Test input.fofn containing a new bas.h5 file. Note that the new bas.h5 file does not
+contain any /PulseData, instead contains /MultiPart/Parts.
+ $ rm -f $TMP1
+ $ BASFILE=/mnt/data3/vol53/2450598/0001/Analysis_Results/m130812_185809_42141_c100533960310000001823079711101380_s1_p0.bas.h5
+ $ REFFA=/mnt/secondary/Smrtpipe/repository/Ecoli_BL21_O26/sequence/Ecoli_BL21_O26.fasta
+ $ $EXEC $BASFILE $REFFA -holeNumbers 1-100 -out $TMP1
+ [INFO] * [blasr] started. (glob)
+ [INFO] * [blasr] ended. (glob)
+ $ echo $?
+ 0
diff --git a/ctest/noSplitSubreads.t b/ctest/noSplitSubreads.t
new file mode 100644
index 0000000..3667cbd
--- /dev/null
+++ b/ctest/noSplitSubreads.t
@@ -0,0 +1,18 @@
+Set up
+ $ . $TESTDIR/setup.sh
+
+Test blasr with -noSplitSubreads
+# $ rm -rf $OUTDIR/lambda_bax_noSplitSubreads.m4
+# $ $EXEC $DATDIR/lambda_bax.fofn $DATDIR/lambda_ref.fasta -noSplitSubreads -m 4 -out lambda_bax_noSplitSubreads_tmp.m4 -nproc 15
+# [INFO]* (glob)
+# [INFO]* (glob)
+# $ sort lambda_bax_noSplitSubreads_tmp.m4 > $OUTDIR/lambda_bax_noSplitSubreads.m4
+# $ diff $OUTDIR/lambda_bax_noSplitSubreads.m4 $STDDIR/lambda_bax_noSplitSubreads.m4
+# This test takes a long time, use a subset instad.
+
+ $ rm -rf $OUTDIR/lambda_bax_noSplitSubreads_subset.m4
+ $ $EXEC $DATDIR/lambda_bax.fofn $DATDIR/lambda_ref.fasta -noSplitSubreads -m 4 -out $OUTDIR/lambda_bax_noSplitSubreads_tmp_subset.m4 -nproc 15 -holeNumbers 1-1000 -sa $DATDIR/lambda_ref.sa
+ [INFO]* (glob)
+ [INFO]* (glob)
+ $ sort $OUTDIR/lambda_bax_noSplitSubreads_tmp_subset.m4 > $OUTDIR/lambda_bax_noSplitSubreads_subset.m4
+ $ diff $OUTDIR/lambda_bax_noSplitSubreads_subset.m4 $STDDIR/lambda_bax_noSplitSubreads_subset.m4
diff --git a/ctest/open_fail.t b/ctest/open_fail.t
new file mode 100644
index 0000000..ac7369f
--- /dev/null
+++ b/ctest/open_fail.t
@@ -0,0 +1,8 @@
+Set up
+ $ . $TESTDIR/setup.sh
+
+If fail to open an bax/bas.h5 file because of unable to initialize required dataset, give an warning.
+ $ $EXEC $DATDIR/open_fail_no_dyset.fofn $DATDIR/lambda_ref.fasta -m 4
+ [INFO]* (glob)
+ Could not open /mnt/secondary-siv/testdata/BlasrTestData/ctest/data/open_fail_no_dyset.fofn
+ [1]
diff --git a/ctest/samNM.t b/ctest/samNM.t
new file mode 100644
index 0000000..93ae89c
--- /dev/null
+++ b/ctest/samNM.t
@@ -0,0 +1,13 @@
+Set up
+ $ . $TESTDIR/setup.sh
+
+Test Sam out nm tag
+ $ rm -rf $OUTDIR/read.sam
+ $ $EXEC $DATDIR/read.fasta $DATDIR/ref.fasta -sam -out $OUTDIR/read.sam
+ [INFO]* (glob)
+ [INFO]* (glob)
+ $ tail -n+5 $OUTDIR/read.sam |cut -f 21
+ NM:i:2
+ NM:i:3
+ NM:i:2
+ NM:i:4
diff --git a/ctest/setup.sh b/ctest/setup.sh
new file mode 100755
index 0000000..8d44dc2
--- /dev/null
+++ b/ctest/setup.sh
@@ -0,0 +1,29 @@
+# Set up directories
+CURDIR=$TESTDIR
+REMOTEDIR=/mnt/secondary-siv/testdata/BlasrTestData/ctest
+DATDIR=$REMOTEDIR/data
+OUTDIR=$CURDIR/out
+STDDIR=$REMOTEDIR/stdout
+
+# Set up the executable: blasr.
+EXEC=$TESTDIR/../blasr
+
+# Define tmporary files
+TMP1=$OUTDIR/$$.tmp.out
+TMP2=$OUTDIR/$$.tmp.stdout
+
+# Make OUTDIR
+mkdir -p $OUTDIR
+
+#FIXME: make samtools independent of absolute build path.
+SAMTOOLS=/mnt/secondary/Smrtpipe/builds/Internal_Mainline_Nightly_LastSuccessfulBuild/analysis/bin/samtools
+
+#Update date
+UPDATEDATE=2015_04_27
+
+# 2014_08_21 --> change 138516: added YS, YE, ZM tags
+# 2014_08_28 --> change 139176: Update SAM MD5
+# 2015_03_28 --> change 148101: 148080 update read group id, 148100 update TLEN.
+# 2015_04_09 --> change 148796: update read group id
+# 2015_04_25 --> change 149721, update CIGAR string, replace M with X=
+# 2015_04_26 --> change 149749, add opiton -cigarUseSeqMatch (default: false). If -cigarUseSeqMatch is turned on, CIGAR strings use '=' and 'X' to represent sequence match and mismatch instead of 'M'.
diff --git a/ctest/useccsallBestN1.t b/ctest/useccsallBestN1.t
new file mode 100644
index 0000000..37b1305
--- /dev/null
+++ b/ctest/useccsallBestN1.t
@@ -0,0 +1,11 @@
+Set up
+ $ . $TESTDIR/setup.sh
+
+Test -useccsall with bestn = 1
+ $ $EXEC $DATDIR/ccstest.fofn $DATDIR/ccstest_ref.fasta -bestn 1 -useccsall -sam -out $OUTDIR/useccsall.sam -holeNumbers 76772
+ [INFO]* (glob)
+ [INFO]* (glob)
+ $ sed -n '9,$ p' $OUTDIR/useccsall.sam > $TMP1
+ $ sed -n '9,$ p' $STDDIR/$UPDATEDATE/useccsall.sam > $TMP2
+ $ diff $TMP1 $TMP2
+ $ rm $TMP1 $TMP2
diff --git a/ctest/useccsallLargeGenome.t b/ctest/useccsallLargeGenome.t
new file mode 100644
index 0000000..5ab7ac1
--- /dev/null
+++ b/ctest/useccsallLargeGenome.t
@@ -0,0 +1,13 @@
+Set up
+ $ . $TESTDIR/setup.sh
+
+Test -useccsall with Large genome.
+ $ BASFILE=/mnt/data3/vol53/2450530/0014/Analysis_Results/m130507_052228_42161_c100519212550000001823079909281305_s1_p0.3.bax.h5
+ $ REFDIR=/mnt/secondary/Smrtpipe/repository/hg19_M_sorted/sequence
+ $ REFFA=$REFDIR/hg19_M_sorted.fasta
+ $ REFSA=$REFDIR/hg19_M_sorted.fasta.sa
+ $ OUTFILE=$OUTDIR/intflow.m4
+ $ $EXEC $BASFILE $REFFA -out $OUTFILE -m 4 -sa $REFSA -holeNumbers 109020
+ [INFO]* (glob)
+ [INFO]* (glob)
+ $ diff $STDDIR/intflow_2014_06_10.m4 $OUTFILE
diff --git a/ctest/verbose.t b/ctest/verbose.t
new file mode 100644
index 0000000..19e508a
--- /dev/null
+++ b/ctest/verbose.t
@@ -0,0 +1,9 @@
+Set up
+ $ . $TESTDIR/setup.sh
+
+Test alignment score
+ $ $EXEC $DATDIR/lambda_bax.fofn $DATDIR/lambda_ref.fasta -holeNumbers 1-200 -V 3 > $TMP1
+ [INFO]* (glob)
+ [INFO]* (glob)
+ $ echo $?
+ 0
diff --git a/extrautils/BasH5Simulator.cpp b/extrautils/BasH5Simulator.cpp
new file mode 100644
index 0000000..969f933
--- /dev/null
+++ b/extrautils/BasH5Simulator.cpp
@@ -0,0 +1,524 @@
+#include <string>
+#include <sstream>
+#include <iostream>
+#include "utils.hpp"
+#include "Enumerations.h"
+#include "DNASequence.hpp"
+#include "FASTAReader.hpp"
+#include "CommandLineParser.hpp"
+#include "metagenome/TitleTable.hpp"
+#include "metagenome/FindRandomSequence.hpp"
+#include "statistics/StatUtils.hpp"
+#include "HDFBasWriter.hpp"
+#include "HDFRegionTableWriter.hpp"
+#include "simulator/LengthHistogram.hpp"
+#include "simulator/OutputSampleListSet.hpp"
+#include "simulator/ContextOutputList.hpp"
+
+using namespace std;
+
+void SetHelp(string & str) {
+ stringstream helpStream;
+ helpStream
+ << "usage: alchemy outputModel [ options ]" << endl
+ << " options: " << endl
+ << " -genome genome.fasta" << endl
+ << " Simulate reads from the reference genome 'genome.fasta'." << endl << endl
+ << " -numBasesPerFile numBasesPerFile" << endl
+ << " Limit the number of bases per output file to this." << endl << endl
+ << " -sourceReads filename " << endl
+ << " When set, simulate reads by reading from 'filename', " << endl
+ << " rather than simulating from a genome." << endl
+ << " The format of the fasta titles should be >read_index|chr|start_pos|end_pos" << endl << endl
+ << " -lengthModel" << endl
+ << " Use lengths from the alchemy model, rather than the read length. This " << endl
+ << " is used in conjunction with the sourceReadsFile, to modulate the lenghts" << endl
+ << " of the reads." << endl << endl
+ << " -fixedLength length " << endl
+ << " Set simulated read length to a fixed value of 'length', rather than " << endl
+ << " sampling from a length mode." << endl
+ << " -movieName name (\"simulated_movie\")" << endl
+ << " Use 'name' for movies rather than m000_000..." << endl << endl
+ << " -titleTable name" <<endl
+ << " Read in the titleTable to assign chromosome indices from " << endl
+ << " simulated reads." << endl << endl
+ << " -baseFileName name (\"simulated\")" << endl
+ << " Use an alternative name for the output file, rather than 'simulated'" << endl << endl
+ << " -nFiles N (1)" << endl
+ << " The number of files to simulate. " << endl << endl
+ << " -meanLength L(0)" << endl
+ << " When set, scales the length of the average read to L." << endl << endl
+ << " -posMap filename " << endl
+ << " Use this when running alignment through compareSequences.py " << endl
+ << " and writing to cmp.h5. Specify a map between movie names and " << endl
+ << " chromosome/positions. " << endl << endl
+ << " When set, the simulated positions are not sored in " << endl
+ << " the bas.h5 files and instead printed to 'filename'" << endl << endl
+ << " -printPercentRepeat" << endl
+ << " Add to the title table a field that has the percent " << endl
+ << " repeat content of the read shown by lower case in " << endl
+ << " the reference." << endl << endl;
+ str = helpStream.str();
+}
+
+int main(int argc, char* argv[]) {
+ string refGenomeFileName = "";
+ string lengthModelFileName = "";
+ string outputModelFileName = "";
+ DNALength numBasesPerFile = 0;
+ string sourceReadsFileName = "";
+ string titleTableFileName = "";
+ int numBasH5Files = 1;
+ string basH5BaseFileName = "simulated";
+ string movieName = "m101211_092754_00114_cSIM_s1_p0";
+ bool doRandGenInit = true;
+ bool usePosMap = false;
+ bool printPercentRepeat = false;
+ string posMapFileName = "";
+ vector<string> movieNames;
+ bool useLengthModel = false;
+ bool useFixedLength = false;
+ ofstream posMapFile;
+ int scaledLength = 0;
+ int fixedLength = 0;
+ int nBasFiles = 1;
+ bool useLengthsModel = true;
+ bool printHelp = false;
+
+
+ // Look to see if the refAsReads flag is specified anywhere before
+ // parsing the command line.
+
+ CommandLineParser clp;
+ string commandLine;
+ string helpString;
+ SetHelp(helpString);
+ vector<string> fns;
+
+ clp.RegisterStringOption("genome", &refGenomeFileName, "");
+ clp.RegisterIntOption("numBasesPerFile", (int*)&numBasesPerFile, "",
+ CommandLineParser::PositiveInteger);
+ clp.RegisterStringOption("sourceReads", &sourceReadsFileName, "");
+ clp.RegisterStringOption("lengthModel", &lengthModelFileName, "");
+ clp.RegisterIntOption("fixedLength", &fixedLength, "",
+ CommandLineParser::PositiveInteger);
+ clp.RegisterFlagOption("lengthModel", &useLengthModel, "");
+ clp.RegisterStringOption("movieName", &movieName, "");
+ clp.RegisterStringOption("titleTable", &titleTableFileName, "");
+ clp.RegisterStringOption("baseFileName", &basH5BaseFileName, "");
+ clp.RegisterIntOption("nFiles", &nBasFiles, "",
+ CommandLineParser::PositiveInteger);
+ clp.RegisterIntOption("meanLength", &scaledLength, "",
+ CommandLineParser::PositiveInteger);
+ clp.RegisterStringOption("posMap", &posMapFileName, "");
+ clp.RegisterFlagOption("printPercentRepeat", &printPercentRepeat, "");
+ clp.RegisterFlagOption("h", &printHelp, "");
+
+ clp.SetHelp(helpString);
+ clp.ParseCommandLine(argc, argv, fns);
+ clp.CommandLineToString(argc, argv, commandLine);
+
+ clp.SetProgramName("alchemy");
+
+ outputModelFileName = fns[0];
+ if (argc <= 1 or printHelp or outputModelFileName == "") {
+ cout << helpString << endl;
+ exit(0);
+ }
+
+ if (usePosMap) {
+ CrucialOpen(posMapFileName, posMapFile, std::ios::out);
+ }
+
+ if (sourceReadsFileName == "" and fixedLength == 0) {
+ useLengthModel = true;
+ }
+
+ if (useLengthModel and fixedLength != 0) {
+ cout << "ERROR! You must either use a length model or a fixed length." << endl;
+ exit(1);
+ }
+
+ if (sourceReadsFileName == "" and numBasesPerFile == 0) {
+ cout << "ERROR! You must specify either a set of read to use as " << endl
+ << "original reads for simulation or the total number of bases " << endl
+ << "to simulate in each bas.h5 file." << endl;
+ exit(1);
+ }
+
+ if (sourceReadsFileName == "" and refGenomeFileName == "") {
+ cout << "ERROR! You must specify a genome to sample reads from or a set of read "<<endl
+ << "to use as original reads for simulation." << endl;
+ exit(1);
+ }
+
+ if (fixedLength != 0 and refGenomeFileName == "") {
+ cout << "ERROR! You must specify a genome file if using a fixed length." << endl;
+ exit(1);
+ }
+
+ if ((fixedLength != 0 or scaledLength != 0) and sourceReadsFileName != "") {
+ cout << "ERROR! You cannot specify a fixed length nor mean length with a source " << endl
+ << "reads file. The read lengths are taken from the source reads or the length model." << endl;
+ exit(1);
+ }
+
+ LengthHistogram lengthHistogram;
+ OutputSampleListSet outputModel(0);
+ TitleTable titleTable;
+
+ if (doRandGenInit) {
+ InitializeRandomGeneratorWithTime();
+ }
+
+ //
+ // Read models.
+ //
+ if (titleTableFileName != "") {
+ titleTable.Read(titleTableFileName);
+ }
+
+
+ outputModel.Read(outputModelFileName);
+
+ if (useLengthModel) {
+ lengthHistogram.BuildFromAlignmentLengths(outputModel.lengths);
+ }
+
+
+ vector<int> alignmentLengths;
+ int meanAlignmentLength;
+
+
+ if (scaledLength != 0 and useLengthModel) {
+ //
+ // Scale the histogram so that the average length is 'scaledLength'.
+ //
+
+ // 1. Integrate histogram
+ long totalLength = 0;
+ long totalSamples = 0;
+ int hi;
+ for (hi = 0; hi < lengthHistogram.lengthHistogram.cdf.size()-1; hi++) {
+ int ni;
+ ni = lengthHistogram.lengthHistogram.cdf[hi+1] - lengthHistogram.lengthHistogram.cdf[hi];
+ totalLength += ni * lengthHistogram.lengthHistogram.data[hi];
+ }
+ totalSamples = lengthHistogram.lengthHistogram.cdf[lengthHistogram.lengthHistogram.cdf.size()-1];
+
+ float meanSampleLength = totalLength / (1.0*totalSamples);
+ float fractionIncrease = scaledLength / meanSampleLength;
+
+ for (hi = 0; hi < lengthHistogram.lengthHistogram.cdf.size(); hi++) {
+ lengthHistogram.lengthHistogram.data[hi] *= fractionIncrease;
+ }
+ }
+
+ FASTAReader inReader, seqReader;
+ vector<FASTASequence> reference;
+ DNALength refLength = 0;
+ int i;
+ if (refGenomeFileName != "") {
+ inReader.Init(refGenomeFileName);
+ inReader.ReadAllSequences(reference);
+
+ for (i = 0; i < reference.size(); i++) {
+ refLength += reference[i].length;
+ }
+ }
+
+ if (sourceReadsFileName != "") {
+ seqReader.Init(sourceReadsFileName);
+ }
+
+ ofstream readsFile;
+
+ //
+ // Create and simulate bas.h5 files.
+ //
+ int baseFileIndex;
+ bool readsRemain = true;
+ for (baseFileIndex = 0; ((sourceReadsFileName == "" and baseFileIndex < nBasFiles) // case 1 is reads are generated by file
+ or (sourceReadsFileName != "" and readsRemain)); // case 2 is reads are generated by an input file.
+ baseFileIndex++) {
+ //
+ // Prep the base file for writing.
+ //
+ stringstream fileNameStrm, movieNameStrm;
+ //string movieName = "m000000_000000_00000_cSIMULATED_s";
+ movieNameStrm << movieName << baseFileIndex << "_p0";
+ string fullMovieName = movieNameStrm.str();
+ fileNameStrm << fullMovieName << ".bas.h5";
+
+
+ HDFBasWriter basWriter;
+ HDFRegionTableWriter regionWriter;
+ //
+ // This is mainly used to create the atributes.
+ //
+ RegionTable regionTable;
+ regionTable.CreateDefaultAttributes();
+
+ basWriter.SetPlatform(Springfield);
+ //
+ // Use a fixed set of fields for now.
+ //
+
+ // These are all pulled from the outputModel.
+ basWriter.IncludeField("Basecall");
+ basWriter.IncludeField("QualityValue");
+ basWriter.IncludeField("SubstitutionQV");
+ basWriter.IncludeField("SubstitutionTag");
+ basWriter.IncludeField("InsertionQV");
+ basWriter.IncludeField("DeletionQV");
+ basWriter.IncludeField("DeletionTag");
+ basWriter.IncludeField("WidthInFrames");
+ basWriter.IncludeField("PreBaseFrames");
+ basWriter.IncludeField("PulseIndex");
+
+ vector<unsigned char> qualityValue, substitutionQV, substitutionTag, insertionQV, deletionQV, deletionTag;
+ vector<HalfWord> widthInFrames, preBaseFrames, pulseIndex;
+
+ // Just go from 0 .. hole Number
+ basWriter.IncludeField("HoleNumber");
+ // Fixed to 0.
+ basWriter.IncludeField("HoleXY");
+ if (usePosMap == false) {
+ basWriter.IncludeField("SimulatedSequenceIndex");
+ basWriter.IncludeField("SimulatedCoordinate");
+ }
+ basWriter.SetChangeListID("1.3.0.50.104380");
+
+
+ DNALength numSimulatedBases = 0;
+ FASTASequence sampleSeq;
+ //sampleSeq.length = readLength;
+ int maxRetry = 10000000;
+ int retryNumber = 0;
+ int numReads = 0;
+ int readLength = 0;
+
+ while (numBasesPerFile == 0 or numSimulatedBases < numBasesPerFile) {
+ DNALength seqIndex, seqPos;
+ if (useLengthModel or fixedLength) {
+ if (useLengthModel) {
+ lengthHistogram.GetRandomLength(readLength);
+ }
+ else {
+ readLength = fixedLength;
+ }
+ }
+ if (refGenomeFileName != "") {
+ FindRandomPos(reference, seqIndex, seqPos, readLength + (outputModel.keyLength - 1));
+ sampleSeq.seq = &reference[seqIndex].seq[seqPos];
+ sampleSeq.length = readLength + (outputModel.keyLength - 1);
+ assert(reference[seqIndex].length >= sampleSeq.length);
+ }
+ else if (sourceReadsFileName != "") {
+ if (seqReader.GetNext(sampleSeq) == false) {
+ readsRemain = false;
+ break;
+ }
+ if (sampleSeq.length < outputModel.keyLength) {
+ continue;
+ }
+ //
+ // Now attempt to parse the position from the fasta title.
+ //
+
+ if (useLengthModel) {
+ int tryNumber = 0;
+ readLength = 0;
+ int maxNTries = 1000;
+ int tryBuffer[5] = {-1,-1,-1,-1,-1};
+ while (tryNumber < maxNTries and readLength < outputModel.keyLength) {
+ lengthHistogram.GetRandomLength(readLength);
+ readLength = sampleSeq.length = min(sampleSeq.length, (unsigned int) readLength);
+ tryBuffer[tryNumber%5] = readLength;
+ tryNumber++;
+ }
+ if (tryNumber >= maxNTries) {
+ cout << "ERROR. Could not generate a read length greater than the " << outputModel.keyLength << " requried " <<endl
+ << "minimum number of bases using the length model specified in the alchemy." <<endl
+ << "model. Something is either wrong with the model or the context length is too large." <<endl;
+ cout << "The last few tries were: " << tryBuffer[0] << " " << tryBuffer[1] << " " << tryBuffer[2] << " " << tryBuffer[3] << " " << tryBuffer[4] << endl;
+ exit(1);
+ }
+ }
+
+ readLength = sampleSeq.length;
+ vector<string> tokens;
+ Splice(sampleSeq.title, "|", tokens);
+ if (tokens.size() == 4) {
+ seqPos = atoi(tokens[2].c_str());
+ if (titleTableFileName == "") {
+ seqIndex = 0;
+ }
+ else {
+ int index;
+ titleTable.Lookup(tokens[1], index);
+ seqIndex = index;
+ }
+ }
+ else {
+ seqPos = 0;
+ }
+ }
+
+ //
+ // If this is the first read printed to the base file, initialize it.
+ //
+ if (numSimulatedBases == 0) {
+ basWriter.Initialize(fileNameStrm.str(), movieNameStrm.str(), Springfield);
+ regionWriter.Initialize(basWriter.pulseDataGroup);
+ }
+
+ numSimulatedBases += readLength;
+
+ int p;
+ // create the sample sequence
+ int contextLength = outputModel.keyLength;
+ int contextMiddle = contextLength / 2;
+ string outputString;
+
+ int nDel = 0;
+ int nIns = 0;
+
+ //
+ // Simulate to beyond the sample length.
+ //
+ qualityValue.clear();
+ substitutionQV.clear();
+ substitutionTag.clear();
+ insertionQV.clear();
+ deletionQV.clear();
+ deletionTag.clear();
+ pulseIndex.clear();
+ widthInFrames.clear();
+ preBaseFrames.clear();
+ assert(sampleSeq.length > contextMiddle + 1);
+ for (p = contextMiddle;
+ p < sampleSeq.length - contextMiddle - 1; p++) {
+ string refContext;
+ refContext.assign((const char*) &sampleSeq.seq[p-contextMiddle], contextLength);
+
+ string outputContext;
+ int contextWasFound;
+ OutputSample sample;
+ int i;
+ for (i = 0; i < refContext.size(); i++) { refContext[i] = toupper(refContext[i]);}
+ outputModel.SampleRandomSample(refContext, sample);
+
+ if (sample.type == OutputSample::Deletion ) {
+ //
+ // There was a deletion. Advance in reference, then output
+ // the base after the deletion.
+ //
+ p++;
+ ++nDel;
+ }
+
+ int cp;
+ //
+ // Add the sampled context, possibly multiple characters because of an insertion.
+ //
+ for (i = 0; i < sample.nucleotides.size(); i++) {
+ outputString.push_back(sample.nucleotides[i]);
+ qualityValue.push_back(sample.qualities[i].qv[0]);
+ deletionQV.push_back(sample.qualities[i].qv[1]);
+ insertionQV.push_back(sample.qualities[i].qv[2]);
+ substitutionQV.push_back(sample.qualities[i].qv[3]);
+ deletionTag.push_back(sample.qualities[i].tags[0]);
+ substitutionTag.push_back(sample.qualities[i].tags[1]);
+ pulseIndex.push_back(sample.qualities[i].frameValues[0]);
+ preBaseFrames.push_back(sample.qualities[i].frameValues[1]);
+ widthInFrames.push_back(sample.qualities[i].frameValues[2]);
+ }
+ nIns += sample.qualities.size() - 1;
+ }
+ if (outputString.find('N') != outputString.npos or
+ outputString.find('n') != outputString.npos) {
+ cout << "WARNING! The sampled string " << endl << outputString << endl
+ << "should not contain N's, but it seems to. This is being ignored "<<endl
+ << "for now so that simulation may continue, but this shouldn't happen"<<endl
+ << "and is really a bug." << endl;
+ numSimulatedBases -= readLength;
+ continue;
+ }
+ //
+ // Ok, done creating the read, now time to create some quality values!!!!!
+ //
+ SMRTSequence read;
+ read.length = outputString.size();
+ read.Allocate(read.length);
+ memcpy(read.seq, outputString.c_str(), read.length * sizeof(unsigned char));
+ assert(qualityValue.size() == read.length * sizeof(unsigned char));
+ memcpy(read.qual.data, &qualityValue[0], read.length * sizeof(unsigned char));
+ memcpy(read.deletionQV.data, &deletionQV[0], read.length * sizeof(unsigned char));
+ memcpy(read.insertionQV.data, &insertionQV[0], read.length * sizeof(unsigned char));
+ memcpy(read.substitutionQV.data, &substitutionQV[0], read.length * sizeof(unsigned char));
+ memcpy(read.deletionTag, &deletionTag[0], read.length * sizeof(unsigned char));
+ memcpy(read.substitutionTag, &substitutionTag[0], read.length * sizeof(unsigned char));
+ memcpy(read.pulseIndex, &pulseIndex[0], read.length * sizeof(int));
+ memcpy(read.preBaseFrames, &preBaseFrames[0], read.length * sizeof(HalfWord));
+ memcpy(read.widthInFrames, &widthInFrames[0], read.length * sizeof(HalfWord));
+
+ //
+ // The pulse index for now is just fake data.
+ //
+ int i;
+ for (i = 0; i < read.length; i++) {
+ read.pulseIndex[i] = 1;
+ }
+ read.xy[0] = seqIndex;
+ read.xy[1] = seqPos;
+ read.zmwData.holeNumber = numReads;
+
+ basWriter.Write(read);
+ // Record where this was simulated from.
+ if (usePosMap == false) {
+ basWriter.WriteSimulatedCoordinate(seqPos);
+ basWriter.WriteSimulatedSequenceIndex(seqIndex);
+ }
+ else {
+ posMapFile << fullMovieName << "/" << numReads << "/0_" << read.length << " " << seqIndex << " "<< seqPos;
+ if (printPercentRepeat) {
+ DNALength nRepeat = sampleSeq.GetRepeatContent();
+ posMapFile << " " << nRepeat*1.0/sampleSeq.length;
+ }
+ posMapFile << endl;
+ }
+ RegionAnnotation region;
+ region.row[0] = read.zmwData.holeNumber;
+ region.row[1] = 1;
+ region.row[2] = 0;
+ region.row[3] = read.length;
+ region.row[4] = 1000; // Should be enough.
+ regionWriter.Write(region);
+ region.row[1] = 2; // Rewrite for hq region encompassing everything.
+ regionWriter.Write(region);
+ if (sourceReadsFileName != "") {
+ sampleSeq.Free();
+ }
+ read.Free();
+ ++numReads;
+ }
+ regionWriter.Finalize(regionTable.columnNames,
+ regionTable.regionTypes,
+ regionTable.regionDescriptions,
+ regionTable.regionSources);
+ basWriter.Close();
+ numReads = 0;
+ //
+ // The bas writer should automatically flush on closing.
+ //
+ }
+ if (usePosMap) {
+ posMapFile.close();
+ }
+
+ for (i = 0; i < reference.size(); i++) {
+ reference[i].Free();
+ }
+}
+
diff --git a/extrautils/BuildSequenceDB.cpp b/extrautils/BuildSequenceDB.cpp
new file mode 100644
index 0000000..2532b2c
--- /dev/null
+++ b/extrautils/BuildSequenceDB.cpp
@@ -0,0 +1,52 @@
+#include <string>
+#include "utils.hpp"
+#include "metagenome/SequenceIndexDatabase.hpp"
+#include "CommandLineParser.hpp"
+#include "FASTAReader.hpp"
+#include "utils/FileOfFileNames.hpp"
+
+using namespace std;
+
+int main(int argc, char* argv[]) {
+
+ CommandLineParser clp;
+ string fastaFileName, indexFileName;
+ vector<string> fastaFileNames;
+ vector<string> opts;
+ clp.SetProgramName("bsdb");
+ clp.SetProgramSummary("Build an index database on a file of sequences.\n"
+ " The index is used to map to reads given alignment positions.\n");
+ clp.RegisterStringOption("fasta", &fastaFileName, "A file with sequences to build an index.");
+ clp.RegisterStringOption("index", &indexFileName, "The index file.");
+ clp.RegisterPreviousFlagsAsHidden();
+
+ clp.ParseCommandLine(argc, argv, opts);
+
+ ifstream fastaIn;
+ ofstream indexOut;
+
+ if (FileOfFileNames::IsFOFN(fastaFileName)) {
+ FileOfFileNames::FOFNToList(fastaFileName, fastaFileNames);
+ }
+ else {
+ fastaFileNames.push_back(fastaFileName);
+ }
+
+ CrucialOpen(indexFileName, indexOut, std::ios::out | std::ios::binary);
+ SequenceIndexDatabase<FASTASequence> seqDB;
+
+ int fileNameIndex;
+ for (fileNameIndex = 0; fileNameIndex < fastaFileNames.size(); fileNameIndex++){
+ FASTAReader reader;
+ FASTASequence seq;
+ reader.Init(fastaFileNames[fileNameIndex]);
+ int i = 0;
+ while (reader.GetNext(seq)) {
+ seqDB.AddSequence(seq);
+ i++;
+ }
+ }
+ seqDB.Finalize();
+ seqDB.WriteDatabase(indexOut);
+ return 0;
+}
diff --git a/extrautils/BwtToSuffixArray.cpp b/extrautils/BwtToSuffixArray.cpp
new file mode 100644
index 0000000..12df5c4
--- /dev/null
+++ b/extrautils/BwtToSuffixArray.cpp
@@ -0,0 +1,33 @@
+#include "bwt/BWT.hpp"
+#include "suffixarray/SuffixArray.hpp"
+#include "suffixarray/SuffixArrayTypes.hpp"
+
+
+#include <string>
+#include <cstring>
+#include <iostream>
+
+using namespace std;
+
+int main(int argc, char* argv[]) {
+
+ string bwtFileName, saFileName;
+ if (argc < 3) {
+ cout << "usage: bwt2sa bwtfile safile " << endl;
+ exit(1);
+ }
+ bwtFileName = argv[1];
+ saFileName = argv[2];
+
+ Bwt<PackedDNASequence, FASTASequence> bwt;
+ DNASuffixArray suffixArray;
+
+ bwt.Read(bwtFileName);
+ suffixArray.AllocateSuffixArray(bwt.bwtSequence.length-1);
+ SAIndex index;
+ for (index = 1; index < bwt.bwtSequence.length+1; index++) {
+ suffixArray.index[index-1] = bwt.Locate(index);
+ }
+ suffixArray.Write(saFileName);
+
+}
diff --git a/extrautils/CCSH5ToBam.cpp b/extrautils/CCSH5ToBam.cpp
new file mode 100644
index 0000000..7593cc9
--- /dev/null
+++ b/extrautils/CCSH5ToBam.cpp
@@ -0,0 +1,135 @@
+#include "utils/FileOfFileNames.hpp"
+#include "datastructures/alignmentset/SAMSupplementalQVList.hpp"
+#include "format/SAMHeaderPrinter.hpp"
+#include "format/BAMPrinter.hpp"
+#include "pbbam/BamWriter.h"
+#include "CommandLineParser.hpp"
+
+using namespace PacBio::BAM;
+using namespace std;
+
+string DISCLAIM =
+"THIS TOOL IS CREATED FOR DEVELOPERS USE ONLY AND IT MAY OR MAY NOT "
+"BREAK AT ANY TIME. USE AT YOUR OWN RISK.";
+
+string GetVersion(void) {
+ return "1.0";
+}
+
+void CCSReadToBamRecord(CCSSequence & ccsRead, BamRecord & bamRecord, SupplementalQVList & samQVList) {
+//m140905_042212_sidney_c100564852550000001823085912221377_s1_X0/1650/1920_2155 4 * 0 255 * * 0 0
+ bamRecord.Impl().Name(ccsRead.GetTitle());
+ bamRecord.Impl().Flag(static_cast<uint32_t>(4));
+ string seqString;
+ seqString.assign((char*)ccsRead.seq, ccsRead.length);
+
+ bamRecord.Impl().SetSequenceAndQualities(seqString, ccsRead.qual.ToString());
+ // bamRecord.Impl().CigarData(Cigar::FromStdString("*"));
+ bamRecord.Impl().Bin(0);
+ bamRecord.Impl().InsertSize(0);
+ bamRecord.Impl().MatePosition(static_cast<PacBio::BAM::Position>(-1));
+ bamRecord.Impl().MateReferenceId(static_cast<int32_t>(-1));
+ bamRecord.Impl().Position(static_cast<PacBio::BAM::Position>(-1));
+ bamRecord.Impl().ReferenceId(static_cast<int32_t>(-1));
+ TagCollection tags;
+ tags["RG"] = ccsRead.GetReadGroupId();
+ tags["np"] = ccsRead.numPasses;
+ tags["zm"] = ccsRead.zmwData.holeNumber;
+ tags["qs"] = 0;
+ tags["qe"] = ccsRead.length;
+
+ samQVList.FormatQVOptionalFields(ccsRead);
+ // Add QVs to BamRecordImpl.
+ string insertionQVs, deletionQVs, substitutionQVs, mergeQVs, substitutionTags, deletionTags;
+ if (ccsRead.GetQVs("InsertionQV", insertionQVs)) {
+ tags["iq"] = insertionQVs;
+ }
+ if (ccsRead.GetQVs("DeletionQV", deletionQVs)) {
+ tags["dq"] = deletionQVs;
+ }
+ if (ccsRead.GetQVs("SubstitutionQV", substitutionQVs)) {
+ tags["sq"] = substitutionQVs;
+ }
+ if (ccsRead.GetQVs("MergeQV", mergeQVs)) {
+ tags["mq"] = mergeQVs;
+ }
+ // substitutionTag is not included by default
+ if (ccsRead.GetQVs("DeletionTag", deletionTags)) {
+ tags["dt"] = deletionTags;
+ }
+ bamRecord.Impl().Tags(tags);
+}
+
+int main(int argc, char* argv[]) {
+ string progName = "ccsh5tobam";
+ CommandLineParser clp;
+ clp.SetHelp("Convert ccs.h5 to bam.\n" + DISCLAIM);
+ clp.SetConciseHelp("ccsh5tobam ccs.h5|fofn out.bam\n" + DISCLAIM);
+ clp.SetProgramName(progName);
+ clp.SetVersion(GetVersion());
+ string fofn, bamOutName;
+ clp.RegisterStringOption("in.ccs.h5", &fofn, "Input ccs.h5|fofn file.", true);
+ clp.RegisterStringOption("out.bam", &bamOutName, "Output bam file.", true);
+ clp.RegisterPreviousFlagsAsHidden();
+ clp.ParseCommandLine(argc, argv);
+
+ //cerr << "[INFO] " << GetTimestamp() << " [" << progName << "] started." << endl;
+
+ vector<string> ccsFileNames;
+ FileOfFileNames::StoreFileOrFileList(fofn, ccsFileNames);
+
+ string so = "UNKNOWN"; // sorting order;
+ string version = GetVersion();
+ string commandLineString;
+ clp.CommandLineToString(argc, argv, commandLineString);
+
+ SupplementalQVList samQVList;
+ samQVList.SetDefaultQV();
+ SequenceIndexDatabase<FASTASequence> seqdb;
+ SAMHeaderPrinter shp(so, seqdb,
+ ccsFileNames, ReadType::ReadTypeEnum::CCS,
+ samQVList, "ccsh52bam", version,
+ commandLineString);
+ string headerString = shp.ToString();// SAM/BAM header
+
+ BamHeader header = BamHeader(headerString);
+ // Both file name and SAMHeader are required in order to create a BamWriter.
+ BamWriter * bamWriterPtr = new BamWriter(bamOutName, header);
+
+ for (string ccsFileName: ccsFileNames) {
+ ReaderAgglomerate reader;
+ reader.SetReadFileName(ccsFileName);
+ reader.SetReadType(ReadType::ReadTypeEnum::CCS);
+
+ // Initialize using already set file names.
+ int initReturnValue = reader.Initialize();
+ if (initReturnValue <= 0) {
+ cerr << "WARNING! Could not open file " << ccsFileName << endl;
+ continue;
+ }
+
+ // Check whether use ccs only.
+ assert (reader.GetFileType() == HDFCCSONLY);
+ int randint = 0;
+ CCSSequence ccsRead;
+ while(reader.GetNext(ccsRead, randint) != 0) {
+ if (ccsRead.length > 0) {
+ BamRecord bamRecord;
+ CCSReadToBamRecord(ccsRead, bamRecord, samQVList);
+ bamWriterPtr->Write(bamRecord);
+ }
+ }
+ }
+
+ try {
+ bamWriterPtr->TryFlush();
+ delete bamWriterPtr;
+ bamWriterPtr = NULL;
+ } catch (std::exception e) {
+ cout << "Error, could not flush bam records to bam file." << endl;
+ exit(1);
+ }
+
+ //cerr << "[INFO] " << GetTimestamp() << " [" << progName << "] ended." << endl;
+ return 0;
+}
diff --git a/extrautils/Evolve.cpp b/extrautils/Evolve.cpp
new file mode 100644
index 0000000..31bd06b
--- /dev/null
+++ b/extrautils/Evolve.cpp
@@ -0,0 +1,169 @@
+#include <vector>
+#include <sstream>
+#include "utils.hpp"
+#include "FASTAReader.hpp"
+#include "FASTASequence.hpp"
+#include "CommandLineParser.hpp"
+#include "statistics/StatUtils.hpp"
+
+using namespace std;
+/*
+ref000001 . SNV 9454 9454 0.00 . . reference=C;confidence=0;Name=9454C>A;coverage=0;variantseq=A
+ref000001 . deletion 20223 20223 0.00 . . reference=T;length=1;confidence=0;coverage=0;Name=20222delT
+ref000001 . insertion 35089 35089 0.00 . . confidence=0;Name=35089_35090insC;reference=.;length=1;coverage=0;variantseq=C
+*/
+
+char ToLower(char c, bool useToLower) {
+ if (useToLower) {
+ return tolower(c);
+ }
+ else {
+ return toupper(c);
+ }
+}
+
+
+int main(int argc, char* argv[]) {
+ CommandLineParser clp;
+
+ string refGenomeName;
+ string mutGenomeName;
+ string gffFileName;
+ float insRate = 0;
+ float delRate = 0;
+ float mutRate = 0;
+ bool lower = false;
+ gffFileName = "";
+ clp.RegisterStringOption("refGenome", &refGenomeName, "Reference genome.", true);
+ clp.RegisterStringOption("mutGenome", &mutGenomeName, "Mutated genome.", true);
+ clp.RegisterPreviousFlagsAsHidden();
+ clp.RegisterStringOption("gff", &gffFileName, "GFF file describing the modifications made to the genome.");
+ clp.RegisterFloatOption("i", &insRate, "Insertion rate: (0-1].",
+ CommandLineParser::NonNegativeFloat, false);
+ clp.RegisterFloatOption("d", &delRate, "Deletion rate: (0-1]",
+ CommandLineParser::NonNegativeFloat, false);
+ clp.RegisterFloatOption("m", &mutRate, "Mutation rate, even across all nucleotides: (0-1]",
+ CommandLineParser::NonNegativeFloat, false);
+ clp.RegisterFlagOption("lower", &lower, "Make mutations in lower case", false);
+ vector<string> leftovers;
+ clp.ParseCommandLine(argc, argv, leftovers);
+
+ FASTAReader reader;
+ FASTASequence refGenome;
+
+ reader.Init(refGenomeName);
+ ofstream mutGenomeOut;
+ CrucialOpen(mutGenomeName, mutGenomeOut, std::ios::out);
+ ofstream gffOut;
+ if (gffFileName != "") {
+ CrucialOpen(gffFileName, gffOut, std::ios::out);
+ }
+
+ vector<int> insIndices, delIndices, subIndices;
+ int readIndex = 0;
+ InitializeRandomGeneratorWithTime();
+ while (reader.GetNext(refGenome)) {
+ insIndices.resize(refGenome.length);
+ delIndices.resize(refGenome.length);
+ subIndices.resize(refGenome.length);
+ std::fill(insIndices.begin(), insIndices.end(), false);
+ std::fill(delIndices.begin(), delIndices.end(), false);
+ std::fill(subIndices.begin(), subIndices.end(), 0);
+
+ enum ChangeType { Ins, Del, Mut, None};
+ float changeProb[4];
+ changeProb[Ins] = insRate;
+ changeProb[Del] = changeProb[Ins] + delRate;
+ changeProb[Mut] = changeProb[Del] + mutRate;
+ changeProb[None] = 1;
+
+ if (changeProb[Mut] > 1) {
+ cout << "ERROR! The sum of the error probabilities must be less than 1" << endl;
+ exit(1);
+ }
+ DNALength pos;
+ float randomNumber;
+ int numIns = 0;
+ int numDel = 0;
+ int numMut = 0;
+ for (pos =0 ; pos < refGenome.length; pos++) {
+ randomNumber = Random();
+ if (randomNumber < changeProb[Ins]) {
+ insIndices[pos] = true;
+ numIns++;
+ }
+ else if (randomNumber < changeProb[Del]) {
+ delIndices[pos] = true;
+ numDel++;
+ }
+ else if (randomNumber < changeProb[Mut]){
+ Nucleotide newNuc = TwoBitToAscii[RandomInt(4)];
+ int maxIts = 100000;
+ int it = 0;
+ while (newNuc == refGenome.seq[pos]) {
+ newNuc = TwoBitToAscii[RandomInt(4)];
+ if (it == maxIts) {
+ cout << "ERROR, something is wrong with the random number generation, it took too many tries to generate a new nucleotide" << endl;
+ exit(1);
+ }
+ }
+ subIndices[pos] = refGenome[pos];
+ refGenome.seq[pos] = ToLower(newNuc,lower);
+ ++numMut;
+ }
+ }
+ // cout << readIndex << " m " << numMut << " i " << numIns << " d " << numDel << endl;
+ if (readIndex % 100000 == 0 && readIndex > 0) {
+ cout << readIndex << endl;
+ }
+ //
+ // Now add the insertions and deletions.
+ //
+ FASTASequence newSequence;
+ DNALength newPos;
+ if (numIns - numDel + refGenome.length < 0) {
+ cout << "ERROR, the genome has been deleted to nothing." << endl;
+ exit(1);
+ }
+ ResizeSequence(newSequence, refGenome.length + (numIns - numDel));
+ newPos = 0;
+ pos = 0;
+ for (pos = 0; pos < refGenome.length; pos++) {
+ assert(newPos < newSequence.length or delIndices[pos] == true);
+ if (subIndices[pos] != 0 and gffFileName != "") {
+ gffOut << refGenome.GetName() << " . SNV " << newPos << " " << newPos <<" 0.00 . . reference=" << (char)subIndices[pos] << ";confidence=10;Name=" << newPos << (char)subIndices[pos] << ">" << refGenome.seq[pos] <<";coverage=10;variantseq=" << refGenome.seq[pos] << endl;
+ }
+
+ if (insIndices[pos] == true) {
+ newSequence.seq[newPos] = ToLower(TwoBitToAscii[RandomInt(4)], lower);
+ newPos++;
+ newSequence.seq[newPos] = refGenome.seq[pos];
+
+ assert(newSequence.seq[newPos] != '1');
+ assert(newSequence.seq[newPos] != 1);
+ if (gffFileName != "") {
+ gffOut << refGenome.GetName() << " . deletion " << newPos << " " << newPos << " 0.00 . . reference=" << newSequence.seq[newPos] << ";length=1;confidence=10;coverage=0;Name="<< newPos << "del" << newSequence.seq[newPos] << endl;
+ }
+ newPos++;
+ }
+ else if (delIndices[pos] == true) {
+ // no-op, skip
+ if (gffFileName != "") {
+ gffOut << refGenome.GetName() << " . insertion " << newPos << " " << newPos << " 0.00 . . confidence=10;Name=" << newPos << "_ins" << refGenome.seq[pos] << ";reference=.;length=1;coverage=0;variantseq=" << refGenome.seq[newPos] << endl;
+ //ref000001 . deletion 20223 20223 0.00 . . reference=T;length=1;confidence=0;coverage=0;Name=20222delT
+ }
+ }
+ else {
+ newSequence.seq[newPos] = refGenome.seq[pos];
+ newPos++;
+ }
+ }
+ stringstream titlestrm;
+ titlestrm << " mutated ins " << insRate << " del " << delRate << " mut " << mutRate;
+ newSequence.CopyTitle(refGenome.title);
+ newSequence.AppendToTitle(titlestrm.str());
+ newSequence.PrintSeq(mutGenomeOut);
+ newSequence.Free();
+ readIndex++;
+ }
+}
diff --git a/extrautils/ExciseRepeats.cpp b/extrautils/ExciseRepeats.cpp
new file mode 100644
index 0000000..50436dc
--- /dev/null
+++ b/extrautils/ExciseRepeats.cpp
@@ -0,0 +1,69 @@
+#include <sstream>
+#include "FASTAReader.hpp"
+#include "FASTASequence.hpp"
+#include "utils.hpp"
+
+using namespace std;
+
+int main(int argc, char* argv[]) {
+ string seqInName, seqOutName, dotOutName;
+ if (argc < 4) {
+ cout << "usage: exciseRepeats inName repMaskOutFile outName" << endl;
+ exit(1);
+ }
+
+ seqInName = argv[1];
+ dotOutName = argv[2];
+ seqOutName = argv[3];
+ FASTAReader reader;
+ reader.Initialize(seqInName);
+ FASTASequence origSeq;
+ reader.GetNext(origSeq);
+
+ ifstream dotOutFile;
+ CrucialOpen(dotOutName, dotOutFile);
+ ofstream seqOutFile;
+ ofstream seqOut;
+ CrucialOpen(seqOutName, seqOut, std::ios::out);
+ string dotOutLine;
+ getline(dotOutFile, dotOutLine);
+ getline(dotOutFile, dotOutLine);
+ getline(dotOutFile, dotOutLine);
+ while(getline(dotOutFile, dotOutLine)) {
+ stringstream lineStrm(dotOutLine);
+ int swScore;
+ float pctDiv, pctDel, pctIns;
+ string query;
+ int qPosBegin, qPosEnd;
+ string left;
+ char strand;
+ string matchingRepeat;
+ string repClass;
+ string repPos, repEnd, repLeft;
+ int id;
+ lineStrm >> swScore >> pctDiv >> pctDel >> pctIns >> query >> qPosBegin >> qPosEnd >> left >> strand >> matchingRepeat >> repClass >> repPos >> repEnd >> repLeft >> id;
+ DNALength seqPos;
+ for (seqPos = qPosBegin; seqPos < qPosEnd; seqPos++) {
+ origSeq.seq[seqPos] = 'X';
+ }
+ }
+
+ DNALength seqPos, unexPos;
+ unexPos = 0;
+ for (seqPos = 0; seqPos < origSeq.length; seqPos++) {
+ if (origSeq.seq[seqPos] != 'X') {
+ origSeq.seq[unexPos] = origSeq.seq[seqPos];
+ unexPos++;
+ }
+ }
+ origSeq.length = unexPos;
+
+ origSeq.PrintSeq(seqOut);
+ return 0;
+}
+
+
+
+
+
+
diff --git a/extrautils/GNUmakefile b/extrautils/GNUmakefile
new file mode 100644
index 0000000..5d7da34
--- /dev/null
+++ b/extrautils/GNUmakefile
@@ -0,0 +1,45 @@
+.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
new file mode 100644
index 0000000..0e05bd5
--- /dev/null
+++ b/extrautils/Makefile
@@ -0,0 +1,78 @@
+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/PrintTupleCountTable.cpp b/extrautils/PrintTupleCountTable.cpp
new file mode 100644
index 0000000..04d999c
--- /dev/null
+++ b/extrautils/PrintTupleCountTable.cpp
@@ -0,0 +1,65 @@
+#include <string>
+#include <vector>
+#include <iostream>
+#include <fstream>
+
+#include "utils.hpp"
+#include "FASTASequence.hpp"
+#include "FASTAReader.hpp"
+#include "CommandLineParser.hpp"
+#include "tuples/DNATuple.hpp"
+#include "tuples/CompressedDNATuple.hpp"
+#include "tuples/TupleMetrics.hpp"
+#include "tuples/TupleCountTable.hpp"
+
+
+#ifdef COMPRESSED
+typedef TupleCountTable<FASTASequence, CompressedDNATuple<FASTASequence> > CountTable;
+#else
+typedef TupleCountTable<FASTASequence, DNATuple> CountTable;
+#endif
+
+int main(int argc, char* argv[]) {
+ CommandLineParser clp;
+ string tableFileName;
+ vector<string> sequenceFiles;
+ TupleMetrics tm;
+ int tupleSize = 8;
+ clp.SetProgramName("printTupleCountTable");
+ clp.SetProgramSummary("Count the number of occurrences of every k-mer in a file.");
+ clp.RegisterStringOption("table", &tableFileName, "Output table name.", true);
+ clp.RegisterIntOption("wordsize", &tupleSize, "Size of words to count",
+ CommandLineParser::NonNegativeInteger, false);
+ clp.RegisterStringListOption("reads", &sequenceFiles, "All sequences.", false);
+ clp.RegisterPreviousFlagsAsHidden();
+ vector<string> opts;
+
+ if (argc == 2) {
+ string fastaFileName = argv[1];
+ sequenceFiles.push_back(fastaFileName);
+ tableFileName = fastaFileName + ".ctab";
+ }
+ else {
+ clp.ParseCommandLine(argc, argv, opts);
+ }
+
+ tm.tupleSize = tupleSize;
+ tm.InitializeMask();
+ ofstream tableOut;
+ CrucialOpen(tableFileName, tableOut, std::ios::out| std::ios::binary);
+ CountTable table;
+ table.InitCountTable(tm);
+ int i;
+ FASTASequence seq;
+ for (i = 0; i < sequenceFiles.size(); i++ ){
+ FASTAReader reader;
+ reader.Init(sequenceFiles[i]);
+ while (reader.GetNext(seq)) {
+ seq.ToUpper();
+ table.AddSequenceTupleCountsLR(seq);
+ }
+ }
+ table.Write(tableOut);
+
+ return 0;
+}
diff --git a/extrautils/SALS.cpp b/extrautils/SALS.cpp
new file mode 100644
index 0000000..608fea0
--- /dev/null
+++ b/extrautils/SALS.cpp
@@ -0,0 +1,40 @@
+#include <string>
+#include <iostream>
+#include "utils.hpp"
+#include "suffixarray/SuffixArray.hpp"
+#include "suffixarray/SuffixArrayTypes.hpp"
+
+using namespace std;
+
+int main(int argc, char* argv[]) {
+
+ if (argc <= 1) {
+ cout << "sals checks if a suffix array has lookup table or not." <<endl;
+ cout << "usage sals genome.sa" <<endl;
+ exit(1);
+ }
+
+ string saFileName = argv[1];
+
+ DNASuffixArray sa;
+ if (!sa.LightRead(saFileName)) {
+ cout << "The file is not in a sa format." << endl;
+ exit(1);
+ }
+
+ if (sa.componentList[DNASuffixArray::CompArray]) {
+ cout << " * has a suffix array." << endl;
+ }
+ else {
+ cout << " * does not contain a suffix array." << endl;
+ }
+
+ if (sa.componentList[DNASuffixArray::CompLookupTable]) {
+ cout << " * has a lookup table for word size. " << sa.lookupPrefixLength
+ << endl;
+ }
+ else {
+ cout << " * does not have a lookup table." << endl;
+ }
+}
+
diff --git a/extrautils/SAModify.cpp b/extrautils/SAModify.cpp
new file mode 100644
index 0000000..a29966b
--- /dev/null
+++ b/extrautils/SAModify.cpp
@@ -0,0 +1,77 @@
+#include <vector>
+#include <string>
+#include "NucConversion.hpp"
+#include "FASTASequence.hpp"
+#include "FASTAReader.hpp"
+#include "suffixarray/SuffixArray.hpp"
+#include "suffixarray/SuffixArrayTypes.hpp"
+#include "suffixarray/ssort.hpp"
+#include "algorithms/sorting/qsufsort.hpp"
+
+
+void PrintUsage() {
+ cout << "samodify changes word size of input suffix array." << endl;
+ cout << "Usage: samodify in.sa genome.fasta out.sa [-blt p]" << endl;
+ cout << " -blt p Build a lookup table on prefixes of length 'p' " << endl;
+}
+
+int main(int argc, char* argv[]) {
+
+ if (argc < 4) {
+ PrintUsage();
+ exit(1);
+ }
+ int argi = 1;
+ string saInFile = argv[argi++];
+ string genomeFileName = argv[argi++];
+ string saOutFile = argv[argi++];
+ vector<string> inFiles;
+
+ int doBLT = 0;
+ int doBLCP = 0;
+ int bltPrefixLength = 0;
+ int lcpLength = 0;
+ int parsingOptions = 0;
+
+ while (argi < argc) {
+ if (strcmp(argv[argi], "-blt") == 0) {
+ doBLT = 1;
+ bltPrefixLength = atoi(argv[++argi]);
+ }
+ else if (strcmp(argv[argi], "-blcp") == 0) {
+ doBLCP = 1;
+ lcpLength = atoi(argv[++argi]);
+ }
+ else {
+ PrintUsage();
+ cout << "Bad option: " << argv[argi] << endl;
+ exit(1);
+ }
+ ++argi;
+ }
+
+ //
+ // Read the suffix array to modify.
+ //
+
+ DNASuffixArray sa;
+ sa.Read(saInFile);
+
+ FASTAReader reader;
+ reader.Initialize(genomeFileName);
+ FASTASequence seq;
+ reader.ReadAllSequencesIntoOne(seq);
+
+
+ if (doBLT) {
+ sa.BuildLookupTable(seq.seq, seq.length, bltPrefixLength);
+ }
+
+ if (doBLCP) {
+ cout << "LCP Table not yet implemented." << endl;
+ }
+
+ sa.Write(saOutFile);
+
+}
+
diff --git a/extrautils/SWMatcher.cpp b/extrautils/SWMatcher.cpp
new file mode 100644
index 0000000..0649adf
--- /dev/null
+++ b/extrautils/SWMatcher.cpp
@@ -0,0 +1,180 @@
+#include <assert.h>
+#include <string>
+#include <iostream>
+#include <vector>
+
+#include "FASTAReader.hpp"
+#include "FASTASequence.hpp"
+#include "algorithms/alignment/AlignmentUtils.hpp"
+#include "algorithms/alignment/DistanceMatrixScoreFunction.hpp"
+#include "algorithms/alignment/IDSScoreFunction.hpp"
+#include "algorithms/alignment/SWAlign.hpp"
+#include "format/StickAlignmentPrinter.hpp"
+
+using namespace std;
+
+int main(int argc, char* argv[]) {
+ if (argc < 3) {
+ cout << "usage: swMatcher query target [-indel i] [-local] [-showalign] " << endl
+ << " [-type queryfit|overlap|global] [-match m ] [-mismatch m]" << endl
+ << " or [-local] [-queryfit] [-overlap] [-fixedtarget] [-fixedquery]" << endl
+ << " [-printmatrix]"<< endl
+ << " Unless -showalign is specified, output is tabular and in the formt:"<<endl
+ << " query_length target_length align_score query_start query_end target_start target_end"<<endl;
+ exit(1);
+ }
+
+ string queryName, targetName;
+ queryName = argv[1];
+ targetName = argv[2];
+ int argi = 3;
+ int indelCost = 3;
+ int showAlign = 0;
+ AlignmentType alignType = Global;
+ int match = 0;
+ int mismatch = 0;
+ int fixedTarget = 0;
+ int fixedQuery = 0;
+ bool printMatrix = false;
+ int insertion = 4;
+ int deletion = 5;
+ while (argi < argc) {
+ if (strcmp(argv[argi], "-insertion") == 0) {
+ insertion = atoi(argv[++argi]);
+ }
+ else if (strcmp(argv[argi], "-deletion") == 0) {
+ deletion = atoi(argv[++argi]);
+ }
+ else if (strcmp(argv[argi], "-local") == 0) {
+ alignType = Local;
+ }
+ else if (strcmp(argv[argi], "-showalign") == 0) {
+ showAlign = 1;
+ }
+ else if (strcmp(argv[argi], "-fixedtarget") == 0) {
+ fixedTarget = 1;
+ }
+ else if (strcmp(argv[argi], "-fixedquery") == 0) {
+ fixedQuery = 1;
+ }
+ else if (strcmp(argv[argi], "-type") == 0) {
+ ++argi;
+ if (strcmp(argv[argi], "queryfit") == 0) {
+ alignType = QueryFit;
+ }
+ else if (strcmp(argv[argi], "targetfit") == 0) {
+ alignType = TargetFit;
+ }
+ else if (strcmp(argv[argi], "overlap") == 0) {
+ alignType = Overlap;
+ }
+ else if (strcmp(argv[argi], "global") == 0) {
+ alignType = Global;
+ }
+ else if (strcmp(argv[argi], "tpqs") == 0) {
+ alignType = TPrefixQSuffix;
+ }
+ else if (strcmp(argv[argi], "tsqp") == 0 ){
+ alignType = TSuffixQPrefix;
+ }
+ else {
+ cout <<" ERROR, aligntype must be one of queryfit, overlap, or global" << endl;
+ exit(1);
+ }
+ }
+ else if(strcmp(argv[argi], "-printmatrix") == 0) {
+ printMatrix = true;
+ }
+ else if (strcmp(argv[argi], "-local") == 0) {
+ alignType = Local;
+ }
+ else if (strcmp(argv[argi], "-queryfit") == 0) {
+ alignType = QueryFit;
+ }
+ else if (strcmp(argv[argi], "-overlap") == 0) {
+ alignType = Overlap;
+ }
+ else if (strcmp(argv[argi], "-match") == 0) {
+ match = atoi(argv[++argi]);
+ }
+ else if (strcmp(argv[argi], "-mismatch") == 0) {
+ mismatch = atoi(argv[++argi]);
+ }
+ ++argi;
+ }
+ DistanceMatrixScoreFunction<FASTASequence, FASTASequence> scoreFn(
+ SMRTDistanceMatrix, insertion, deletion);
+
+ FASTASequence query, target;
+ FASTAReader queryReader, targetReader;
+ queryReader.Init(queryName);
+
+ targetReader.Init(targetName);
+
+ if (fixedTarget) {
+ targetReader.GetNext(target);
+ }
+ if (fixedQuery) {
+ queryReader.GetNext(query);
+ }
+ //
+ // Prepare the target database;
+ //
+
+ //
+ // Prepare the query match set.
+ //
+
+ int seqIndex = 0;
+
+ vector<int> scoreMat;
+ vector<Arrow> pathMat;
+ int alignScore;
+ MatchedAlignment alignment;
+
+ if (match != 0) {
+ int i;
+ for (i = 0; i < 4; i++ ) {
+ LocalAlignLowMutationMatrix[i][i] = match;
+ }
+ }
+
+ int i,j;
+ for (i = 0; i < 5; i++) {
+ for (j = 0; j < 5 ; j++) {
+ if (i == j) continue;
+ SMRTDistanceMatrix[i][j] += 3;
+ }
+ }
+
+ cout << "qlen tlen score" << endl;
+ while ((fixedQuery or queryReader.GetNext(query)) and
+ (fixedTarget or targetReader.GetNext(target))) {
+ alignment.qName.assign(query.title, query.titleLength);
+ alignment.tName.assign(target.title, target.titleLength);
+ alignment.blocks.clear();
+ alignment.qPos = 0;
+ alignment.tPos = 0;
+ alignment.qStart = 0;
+ alignment.tStart = 0;
+ if (query.length == 0 or target.length == 0)
+ continue;
+
+ alignScore = SWAlign(query, target, scoreMat, pathMat,
+ alignment, scoreFn, alignType, false, printMatrix);
+
+ cout << query.length << " " << target.length << " " << alignScore << endl;
+ cout << alignment.qPos << " " << alignment.QEnd()
+ << " " << alignment.tPos << " " << alignment.TEnd() << endl;
+
+ if (showAlign) {
+ ComputeAlignmentStats(alignment, query.seq, target.seq, scoreFn);
+ //SMRTDistanceMatrix, indelCost, indelCost);
+ PrintAlignmentStats(alignment, cout);
+ StickPrintAlignment(alignment, query, target, cout);
+ }
+ ++seqIndex;
+ }
+
+ return 0;
+}
diff --git a/extrautils/SimpleShredder.cpp b/extrautils/SimpleShredder.cpp
new file mode 100644
index 0000000..321e053
--- /dev/null
+++ b/extrautils/SimpleShredder.cpp
@@ -0,0 +1,159 @@
+#include <string>
+#include <sstream>
+#include "utils.hpp"
+#include "FASTAReader.hpp"
+#include "FASTQSequence.hpp"
+#include "FASTASequence.hpp"
+#include "CommandLineParser.hpp"
+#include "metagenome/FindRandomSequence.hpp"
+#include "statistics/StatUtils.hpp"
+
+using namespace std;
+
+int main(int argc, char* argv[]) {
+ string inFileName, readsFileName;
+ DNALength readLength;
+ float coverage = 0;
+ bool noRandInit = false;
+ int numReads = -1;
+ CommandLineParser clp;
+ int qualityValue = 20;
+ bool printFastq = false;
+ int stratify = 0;
+ string titleType = "pacbio";
+ string fastqType = "illumina"; // or "sanger"
+ clp.RegisterStringOption("inFile", &inFileName, "Reference sequence", 0);
+ clp.RegisterPreviousFlagsAsHidden();
+ clp.RegisterIntOption("readLength", (int*) &readLength, "The length of reads to simulate. The length is fixed.",
+ CommandLineParser::PositiveInteger, "Length of every read.", 0);
+ clp.RegisterFloatOption("coverage", &coverage, "Total coverage (from which the number of reads is calculated",
+ CommandLineParser::PositiveFloat, 0);
+ clp.RegisterFlagOption("nonRandInit", &noRandInit, "Skip initializing the random number generator with time.");
+ clp.RegisterIntOption("nReads", &numReads, "Total number of reads (from which coverage is calculated)", CommandLineParser::PositiveInteger, 0);
+ clp.RegisterStringOption("readsFile", &readsFileName, "Reads output file", 0);
+ clp.RegisterFlagOption("fastq", &printFastq, "Fake fastq output with constant quality value (20)");
+ clp.RegisterIntOption("quality", &qualityValue, "Value to use for fastq quality", CommandLineParser::PositiveInteger);
+ clp.RegisterIntOption("stratify", &stratify, "Sample a read every 'stratify' bases, rather than randomly.", CommandLineParser::PositiveInteger);
+ clp.RegisterStringOption("titleType", &titleType, "Set the name of the title: 'pacbio'|'illumina'");
+ clp.RegisterStringOption("fastqType", &fastqType, "Set the type of fastq: 'illumina'|'sanger'");
+ vector<string> leftovers;
+ clp.ParseCommandLine(argc, argv, leftovers);
+
+ if (!noRandInit) {
+ InitializeRandomGeneratorWithTime();
+ }
+
+ FASTAReader inReader;
+ inReader.Init(inFileName);
+ vector<FASTASequence> reference;
+
+ inReader.ReadAllSequences(reference);
+ ofstream readsFile;
+ if (readsFileName == "") {
+ cout << "ERROR. You must specify a reads file." << endl;
+ exit(1);
+ }
+ CrucialOpen(readsFileName, readsFile, std::ios::out);
+
+ ofstream sangerFastqFile;
+ if (fastqType == "sanger") {
+ string sangerFastqFileName = readsFileName + ".fastq";
+ CrucialOpen(sangerFastqFileName, sangerFastqFile, std::ios::out);
+ }
+
+ DNALength refLength = 0;
+ int i;
+ for (i = 0; i < reference.size(); i++) {
+ refLength += reference[i].length;
+ }
+ if (numReads == -1 and coverage == 0 and stratify == 0) {
+ cout << "ERROR, you must specify either coverage, nReads, or stratify." << endl;
+ exit(1);
+ }
+ else if (numReads == -1) {
+ numReads = (refLength / readLength) * coverage;
+ }
+
+ if (stratify) {
+ if (!readLength) {
+ cout << "ERROR. If you are using stratification, a read length must be specified." << endl;
+ exit(1);
+ }
+ }
+
+ DNASequence sampleSeq;
+ sampleSeq.length = readLength;
+ int maxRetry = 10000000;
+ int retryNumber = 0;
+ DNALength seqIndex, seqPos;
+ if (stratify) {
+ seqIndex = 0;
+ seqPos = 0;
+ }
+ DNALength origReadLength = readLength;
+ for (i = 0; stratify or i < numReads; i++) {
+ if (stratify == 0) {
+ FindRandomPos(reference, seqIndex, seqPos, readLength );
+ }
+ else {
+ //
+ // find the next start pos, or bail if done
+ //
+ if (seqPos >= reference[seqIndex].length) {
+ if (seqIndex == reference.size() - 1) {
+ break;
+ }
+ else {
+ seqIndex = seqIndex + 1;
+ seqPos = 0;
+ continue;
+ }
+ }
+ readLength = min(reference[seqIndex].length - seqPos, origReadLength);
+ }
+ sampleSeq.seq = &reference[seqIndex].seq[seqPos];
+ int j;
+ int gappedRead = 0;
+ string title;
+ stringstream titleStrm;
+ if (titleType == "pacbio") {
+ titleStrm << i << "|"<< reference[seqIndex].GetName() << "|" << seqPos << "|" << seqPos + readLength;
+ }
+ else if (titleType == "illumina") {
+ titleStrm << "SE_" << i << "_0@" << seqPos << "-"<<seqPos+readLength <<"/1";
+ }
+ else {
+ cout << "ERROR. Bad title type " << titleType << endl;
+ exit(1);
+ }
+ title = titleStrm.str();
+ sampleSeq.length = readLength;
+ if (!printFastq) {
+ readsFile << ">" << title << endl;
+ sampleSeq.PrintSeq(readsFile);
+ }
+ else {
+ FASTQSequence fastqSampleSeq;
+ fastqSampleSeq.CopyTitle(title);
+ fastqSampleSeq.seq = sampleSeq.seq;
+ fastqSampleSeq.length = sampleSeq.length;
+ fastqSampleSeq.qual.data = new unsigned char[sampleSeq.length];
+ fill(fastqSampleSeq.qual.data, fastqSampleSeq.qual.data + sampleSeq.length, qualityValue);
+ if (fastqType == "illumina") {
+ fastqSampleSeq.PrintFastq(readsFile, fastqSampleSeq.length+1);
+ }
+ else {
+ fastqSampleSeq.PrintSeq(readsFile);
+ fastqSampleSeq.PrintQual(sangerFastqFile);
+ }
+ delete[] fastqSampleSeq.qual.data;
+ delete[] fastqSampleSeq.title;
+ }
+
+ if (stratify) {
+ seqPos += readLength;
+ }
+
+ }
+ return 0;
+}
diff --git a/extrautils/StoreQualityByContextFromCmpH5.cpp b/extrautils/StoreQualityByContextFromCmpH5.cpp
new file mode 100644
index 0000000..04d5d79
--- /dev/null
+++ b/extrautils/StoreQualityByContextFromCmpH5.cpp
@@ -0,0 +1,283 @@
+#include "files/ReaderAgglomerate.hpp"
+#include "SMRTSequence.hpp"
+#include "utils/FileOfFileNames.hpp"
+#include "simulator/ContextSet.hpp"
+#include "simulator/OutputSampleListSet.hpp"
+#include "datastructures/alignment/CmpFile.hpp"
+#include "HDFCmpFile.hpp"
+#include "format/StickAlignmentPrinter.hpp"
+
+class ScoredLength {
+public:
+ int score, length;
+ int operator<(const ScoredLength &rhs) const {
+ return score < rhs.score;
+ }
+ ScoredLength(int s, int l) : score(s), length(l) {}
+ ScoredLength() {}
+};
+
+void PrintUsage() {
+ cout << "cmpH5StoreQualityByContext - grab quality values from cmp.h5 files until minimum requirements for the number of times a context has been sampled are met." << endl;
+ cout << "usage: cmpH5StoreQualityByContext aligned_reads.cmp.h5 output.qbc [options] " << endl;
+ cout << "options: " << endl
+ << " -contextLength L The length of the context to sample (default: 5) " << endl
+ << " -minSamples S(500) Report pass if all contexts are sampled" << endl
+ << " at least S times." << endl
+ << " -maxSamples S(1000) Stop sampling a context once it has reached" << endl
+ << " S samples." << endl
+ << " -onlyMaxLength" <<endl
+ << " Whether or not to store only the length of the" << endl
+ << " longest subread as part of the length model." << endl << endl;
+}
+
+int main(int argc, char* argv[]) {
+ string outFileName;
+ int contextLength = 5;
+ int minSamples = 500;
+ int maxSamples = 1000;
+ if (argc < 3) {
+ PrintUsage();
+ exit(1);
+ }
+
+ int argi = 1;
+ string cmpH5FileName;
+ cmpH5FileName = argv[argi++];
+ outFileName = argv[argi++];
+ int minAverageQual = 0;
+ bool onlyMaxLength = false;
+
+ while (argi < argc) {
+ if (strcmp(argv[argi], "-contextLength") == 0) {
+ contextLength = atoi(argv[++argi]);
+ }
+ else if (strcmp(argv[argi], "-minSamples") == 0) {
+ minSamples = atoi(argv[++argi]);
+ }
+ else if (strcmp(argv[argi], "-maxSamples") == 0) {
+ maxSamples = atoi(argv[++argi]);
+ }
+ else if (strcmp(argv[argi], "-onlyMaxLength") == 0) {
+ onlyMaxLength = true;
+ }
+ else {
+ PrintUsage();
+ cout << "ERROR, bad option: " << argv[argi] << endl;
+ exit(1);
+ }
+ ++argi;
+ }
+ map<string, ScoredLength> maxLengthMap;
+ OutputSampleListSet samples(contextLength);
+ SMRTSequence read;
+
+ ofstream sampleOut;
+ CrucialOpen(outFileName, sampleOut, std::ios::out|std::ios::binary);
+ int fileNameIndex;
+
+ int numContextsReached = 0;
+ int numContexts = 1 << (contextLength*2);
+ ReaderAgglomerate reader;
+ samples.keyLength = contextLength;
+ HDFCmpFile<CmpAlignment> cmpReader;
+ cmpReader.IncludeField("QualityValue");
+ cmpReader.IncludeField("DeletionQV");
+ cmpReader.IncludeField("InsertionQV");
+ cmpReader.IncludeField("SubstitutionQV");
+ cmpReader.IncludeField("SubstitutionTag");
+ cmpReader.IncludeField("DeletionTag");
+ cmpReader.IncludeField("PulseIndex");
+ cmpReader.IncludeField("WidthInFrames");
+ cmpReader.IncludeField("PreBaseFrames");
+
+ if (cmpReader.Initialize(cmpH5FileName, H5F_ACC_RDWR) == 0) {
+ cout << "ERROR, could not open the cmp file." << endl;
+ exit(1);
+ }
+ cout << "Reading cmp file." << endl;
+
+ CmpFile cmpFile;
+
+ cmpReader.ReadAlignmentDescriptions(cmpFile);
+ cmpReader.ReadStructure(cmpFile);
+ cout << "done reading structure."<<endl;
+ int alignmentIndex;
+ int nAlignments = cmpReader.alnInfoGroup.GetNAlignments();
+ vector<int> alignmentToBaseMap;
+
+ for (alignmentIndex = 0;
+ alignmentIndex < nAlignments and
+ !samples.Sufficient();
+ alignmentIndex++) {
+ //
+ // For ease of use, store the length of the alignment to make another model.
+ //
+
+ ByteAlignment alignmentArray;
+ cmpReader.ReadAlignmentArray(alignmentIndex, alignmentArray);
+ Alignment alignment;
+ ByteAlignmentToAlignment(alignmentArray, alignment);
+ string readSequence, refSequence;
+ readSequence.resize(alignmentArray.size());
+ refSequence.resize(alignmentArray.size());
+ DNASequence readDNA, refDNA;
+
+ ByteAlignmentToQueryString(&alignmentArray[0], alignmentArray.size(), &readSequence[0]);
+ ByteAlignmentToRefString(&alignmentArray[0], alignmentArray.size(), &refSequence[0]);
+ RemoveGaps(readSequence, readSequence);
+ RemoveGaps(refSequence, refSequence);
+
+ readDNA.seq = (Nucleotide*) readSequence.c_str();
+ readDNA.length = readSequence.size();
+ refDNA.seq = (Nucleotide*) refSequence.c_str();
+ refDNA.length = refSequence.size();
+ CmpAlignment cmpAlignment;
+
+ cmpReader.ImportReadFromCmpH5(alignmentIndex, cmpAlignment, read);
+
+ CreateAlignmentToSequenceMap(alignmentArray, alignmentToBaseMap);
+
+ if (read.length < contextLength) {
+ continue;
+ }
+ int subreadLength = (cmpFile.alnInfo.alignments[alignmentIndex].GetQueryEnd() -
+ cmpFile.alnInfo.alignments[alignmentIndex].GetQueryStart());
+ if (onlyMaxLength == false) {
+ samples.lengths.push_back(subreadLength);
+ }
+ else {
+ int score = (cmpAlignment.GetNMatch() -
+ cmpAlignment.GetNMismatch() -
+ cmpAlignment.GetNInsertions() -
+ cmpAlignment.GetNDeletions());
+ stringstream nameStrm;
+ nameStrm << cmpAlignment.GetMovieId() << "_" << cmpAlignment.GetHoleNumber();
+ string nameStr = nameStrm.str();
+ if (maxLengthMap.find(nameStr) == maxLengthMap.end()) {
+ maxLengthMap[nameStr] = ScoredLength(score, subreadLength);
+ }
+ }
+
+ int sampleEnd = alignmentArray.size() - contextLength/2;
+ int a;
+ for (a = contextLength/2; a < sampleEnd; a++) {
+
+ // Make sure the context begins on a real nucleotide.
+ while (a < sampleEnd and
+ ((RefChar[alignmentArray[a]] == ' '))) {a++;}
+
+ //
+ // Move ab back to an index where there are contextLength/2 non-gap
+ // characters, counted by nb
+ //
+ int ab; //num bases
+ int ae; //alignment end
+ ab = a-1;
+ int nb = 0, ne = 0;
+ while (true) {
+ if (RefChar[alignmentArray[ab]] != ' ') {
+ nb++;
+ }
+ if (ab == 0 or nb == contextLength/2) break;
+ ab--;
+ }
+
+ //
+ // Advance ae to an index where there are contextLength/2 non-gap
+ // characters, counted by ne.
+ //
+ ae = a + 1;
+ while (ae < alignmentArray.size() and ne < contextLength/ 2) {
+ if (RefChar[alignmentArray[ae]] != ' ') {
+ ne++;
+ }
+ ae++;
+ }
+
+ //
+ // Make sure there are no edge effects that prevent a context of the correct length from being assigned.
+ //
+ if (nb + ne + 1 != contextLength) {
+ continue;
+ }
+ int ai;
+ string context;
+ for (ai = ab; ai < ae; ai++) {
+ if (RefChar[alignmentArray[ai]] != ' ') {
+ context.push_back(RefChar[alignmentArray[ai]]);
+ }
+ }
+ assert(context.size() == contextLength);
+ //
+ // Now create the context.
+ //
+ OutputSample sample;
+
+ //
+ // This context is a deletion, create that.
+ //
+ sample.type = OutputSample::Deletion;
+
+ //
+ // This context is either an insertion or substitution
+ //
+ // Look to see if the previous aligned position was an
+ // insertion, and move back as far as the insertion extends.
+ int aq = a-1;
+ int sampleLength;
+
+ if (QueryChar[alignmentArray[a]] == ' ') {
+ sample.type = OutputSample::Deletion;
+ sampleLength = 0;
+ }
+ else if (RefChar[alignmentArray[aq]] == ' ') {
+
+ while (aq > 0
+ and RefChar[alignmentArray[aq]] == ' '
+ and QueryChar[alignmentArray[aq]] != ' ') {
+ aq--;
+ }
+ sample.type = OutputSample::Insertion;
+ sampleLength = a - aq;
+ }
+ else if (QueryChar[alignmentArray[a]] == RefChar[alignmentArray[aq]]) {
+ sample.type = OutputSample::Match;
+ sampleLength = 1;
+ }
+ else {
+ sample.type = OutputSample::Substitution;
+ sampleLength = 1;
+ }
+
+ sample.Resize(sampleLength);
+ if (sampleLength > 0) {
+ int seqPos = alignmentToBaseMap[aq];
+ if (seqPos < read.length) {
+ sample.CopyFromSeq(read, seqPos, sampleLength);
+ string nucs;
+ int n;
+ for (n = 0; n < sample.nucleotides.size(); n++) {
+ char c = sample.nucleotides[n];
+ assert(c == 'A' or c == 'T' or c == 'G' or c == 'C');
+ nucs.push_back(sample.nucleotides[n]);
+ }
+ }
+ }
+ samples.AppendOutputSample(context, sample);
+ }
+ read.Free();
+ }
+
+ if (onlyMaxLength) {
+ map<string, ScoredLength>::iterator maxScoreIt;
+ for (maxScoreIt = maxLengthMap.begin(); maxScoreIt != maxLengthMap.end(); ++maxScoreIt) {
+ cout << maxScoreIt->second.length << endl;
+ samples.lengths.push_back(maxScoreIt->second.length);
+ }
+ }
+
+ samples.Write(sampleOut);
+
+ return 0;
+}
diff --git a/extrautils/SuffixArrayToBWT.cpp b/extrautils/SuffixArrayToBWT.cpp
new file mode 100644
index 0000000..6fddecc
--- /dev/null
+++ b/extrautils/SuffixArrayToBWT.cpp
@@ -0,0 +1,48 @@
+#include "FASTASequence.hpp"
+#include "FASTAReader.hpp"
+
+#include "suffixarray/SuffixArrayTypes.hpp"
+#include "suffixarray/SuffixArray.hpp"
+#include "bwt/BWT.hpp"
+
+#include <iostream>
+#include <fstream>
+
+
+using namespace std;
+int main(int argc, char* argv[]) {
+ if (argc < 4) {
+ cout << "usage: sa2bwt genomeFileName suffixArray bwt [-debug]" << endl;
+ exit(1);
+ }
+ string genomeFileName = argv[1];
+ string suffixArrayFileName = argv[2];
+ string bwtFileName = argv[3];
+ int storeDebugInformation = 0;
+ int argi = 4;
+ while(argi < argc) {
+ if (strcmp(argv[argi], "-debug") == 0) {
+ storeDebugInformation = 1;
+ }
+ ++argi;
+ }
+
+ ofstream bwtOutFile;
+ CrucialOpen(bwtFileName, bwtOutFile, std::ios::out|std::ios::binary);
+
+ FASTAReader reader;
+ reader.Init(genomeFileName);
+ FASTASequence seq;
+ reader.ReadAllSequencesIntoOne(seq);
+
+
+ DNASuffixArray suffixArray;
+ suffixArray.Read(suffixArrayFileName);
+
+ Bwt<PackedDNASequence, FASTASequence> bwt;
+ bwt.InitializeFromSuffixArray(seq, suffixArray.index, storeDebugInformation );
+ bwt.Write(bwtOutFile);
+
+ return 0;
+}
+
diff --git a/extrautils/ctest/alchemy.t b/extrautils/ctest/alchemy.t
new file mode 100644
index 0000000..d792e7e
--- /dev/null
+++ b/extrautils/ctest/alchemy.t
@@ -0,0 +1,20 @@
+Set up
+ $ . $TESTDIR/setup.sh
+
+Set up the executable: alchemy.
+ $ EXEC=$TESTDIR/../alchemy
+
+test_alchemy.cmp.h5 was generated by
+pbalign.py $DATDIR/test_alchemy_read.fa $DATDIR/test_alchemy_ref.fa test_alchemy.cmp.h5
+
+$ ./cmpH5StoreQualityByContext $DATDIR/test_alchemy.cmp.h5 $OUTDIR/test_alchemy.qbc -contextLength 3
+
+ $ $EXEC $DATDIR/ecoli_out.qbc -genome $DATDIR/ecoli_reference.fasta -numBasesPerFile 100000 -baseFileName 'this_bas_file' -movieName $OUTDIR/alchemy_
+ $ echo $?
+ 0
+
+pls2fasta can be successfully applied to the simulated bas.h5 file.
+$ pls2fasta *.bas.h5 $OUTDIR/test_alchemy_pls2fasta.fa
+[INFO] * [pls2fasta] started. (glob)
+[INFO] * [pls2fasta] ended. (glob)
+
diff --git a/extrautils/ctest/bwt2sa.t b/extrautils/ctest/bwt2sa.t
new file mode 100644
index 0000000..47ddb91
--- /dev/null
+++ b/extrautils/ctest/bwt2sa.t
@@ -0,0 +1,21 @@
+Set up
+ $ . $TESTDIR/setup.sh
+
+Noticed that pipeline fa->sa->bwt works OK, however fa->sa->bwt->sa
+does not generate identical suffix array.
+Set up the executable: bwt2sa.
+ $ EXEC=$TESTDIR/../bwt2sa
+
+Define tmporary files
+ $ TMP1=$OUTDIR/$$.tmp.out
+ $ TMP2=$OUTDIR/$$.tmp.stdout
+
+Make OUTDIR
+ $ mkdir -p $OUTDIR
+
+ $ SA=$OUTDIR/ecoli_reference.bwt2sa.sa
+ $ BWT=$DATDIR/ecoli_reference.bwt
+ $ $EXEC $BWT $SA
+ $ echo $?
+ 0
+
diff --git a/extrautils/ctest/ccsh5tobam.t b/extrautils/ctest/ccsh5tobam.t
new file mode 100644
index 0000000..5770cca
--- /dev/null
+++ b/extrautils/ctest/ccsh5tobam.t
@@ -0,0 +1,10 @@
+Set up
+ $ . $TESTDIR/setup.sh
+
+Set up the executable: ccsh5tobam
+ $ EXEC=$TESTDIR/../ccsh5tobam
+ $ SMRTWRAP=/mnt/secondary/Smrtpipe/builds/Internal_Mainline_Nightly_LastSuccessfulBuild/smrtcmds/bin/smrtwrap
+
+ $ $SMRTWRAP python $SCRIPTDIR/test_ccsh5tobam.py $EXEC $DATDIR/test_ccsh5tobam/input.fofn $OUTDIR/test_ccsh5tobam.bam
+ $ echo $?
+ 0
diff --git a/extrautils/ctest/cmpH5StoreQualityByContext.t b/extrautils/ctest/cmpH5StoreQualityByContext.t
new file mode 100644
index 0000000..63e0cb3
--- /dev/null
+++ b/extrautils/ctest/cmpH5StoreQualityByContext.t
@@ -0,0 +1,16 @@
+Set up
+ $ . $TESTDIR/setup.sh
+
+Set up the executable: cmpH5StoreQualityByContext.
+ $ EXEC=$TESTDIR/../cmpH5StoreQualityByContext
+
+Define tmporary files
+ $ TMP1=$OUTDIR/$$.tmp.out
+ $ TMP2=$OUTDIR/$$.tmp.stdout
+
+Make OUTDIR
+ $ mkdir -p $OUTDIR
+
+ $ $EXEC $DATDIR/ecoli_out.cmp.h5 $OUTDIR/ecoli_out.qbc -contextLength 8 -onlyMaxLength -minSamples 600 -maxSamples 1500 > $TMP1
+ $ echo $?
+ 0
diff --git a/extrautils/ctest/printTupleCountTable.t b/extrautils/ctest/printTupleCountTable.t
new file mode 100644
index 0000000..2229e1b
--- /dev/null
+++ b/extrautils/ctest/printTupleCountTable.t
@@ -0,0 +1,20 @@
+Set up
+ $ . $TESTDIR/setup.sh
+
+Set up the executable: printTupleCountTable.
+ $ EXEC=$TESTDIR/../printTupleCountTable
+
+Define tmporary files
+ $ TMP1=$OUTDIR/$$.tmp.out
+ $ TMP2=$OUTDIR/$$.tmp.stdout
+
+Make OUTDIR
+ $ mkdir -p $OUTDIR
+
+ $ $EXEC $OUTDIR/ecoli_tuple.table $DATDIR/ecoli_reference.fasta
+ $ echo $?
+ 0
+
+ $ md5sum $OUTDIR/ecoli_tuple.table |cut -f 1 -d ' '
+ 3f1ae70fd009827d6d6e56050341b5df
+
diff --git a/extrautils/ctest/sa2bwt.t b/extrautils/ctest/sa2bwt.t
new file mode 100644
index 0000000..3fbb3a4
--- /dev/null
+++ b/extrautils/ctest/sa2bwt.t
@@ -0,0 +1,19 @@
+Set up
+ $ . $TESTDIR/setup.sh
+
+Set up the executable: sa2bwt.
+ $ EXEC=$TESTDIR/../sa2bwt
+
+Define tmporary files
+ $ TMP1=$OUTDIR/$$.tmp.out
+ $ TMP2=$OUTDIR/$$.tmp.stdout
+
+Make OUTDIR
+ $ mkdir -p $OUTDIR
+
+ $ FA=$DATDIR/ecoli_reference.fasta
+ $ SA=$DATDIR/ecoli_reference.sa
+ $ BWT=$OUTDIR/ecoli_reference.bwt
+ $ $EXEC $FA $SA $BWT
+ $ echo $?
+ 0
diff --git a/extrautils/ctest/sals.t b/extrautils/ctest/sals.t
new file mode 100644
index 0000000..aef617a
--- /dev/null
+++ b/extrautils/ctest/sals.t
@@ -0,0 +1,18 @@
+Set up
+ $ . $TESTDIR/setup.sh
+
+Set up the executable: sals.
+ $ EXEC=$TESTDIR/../sals
+
+Define tmporary files
+ $ TMP1=$OUTDIR/$$.tmp.out
+ $ TMP2=$OUTDIR/$$.tmp.stdout
+
+Make OUTDIR
+ $ mkdir -p $OUTDIR
+
+ $ $EXEC $DATDIR/ecoli_reference.sa
+ * has a suffix array.
+ * has a lookup table for word size. 8
+ $ echo $?
+ 0
diff --git a/extrautils/ctest/samodify.t b/extrautils/ctest/samodify.t
new file mode 100644
index 0000000..5b4050a
--- /dev/null
+++ b/extrautils/ctest/samodify.t
@@ -0,0 +1,19 @@
+Set up
+ $ . $TESTDIR/setup.sh
+
+Set up the executable: samodify.
+ $ EXEC=$TESTDIR/../samodify
+
+Define tmporary files
+ $ TMP1=$OUTDIR/$$.tmp.out
+ $ TMP2=$OUTDIR/$$.tmp.stdout
+
+Make OUTDIR
+ $ mkdir -p $OUTDIR
+
+ $ $EXEC $DATDIR/ecoli_reference.sa $DATDIR/ecoli_reference.fasta $OUTDIR/ecoli_reference_blt13.sa -blt 13
+ $ echo $?
+ 0
+
+ $ md5sum $OUTDIR/ecoli_reference_blt13.sa | cut -f 1 -d ' '
+ ac70eef5a6e03ae8177f27b3aeacc4c5
diff --git a/extrautils/ctest/setup.sh b/extrautils/ctest/setup.sh
new file mode 100755
index 0000000..ab2f01a
--- /dev/null
+++ b/extrautils/ctest/setup.sh
@@ -0,0 +1,15 @@
+# Set up directories
+CURDIR=$TESTDIR
+REMOTEDIR=/mnt/secondary-siv/testdata/BlasrTestData/ctest
+DATDIR=$REMOTEDIR/data
+OUTDIR=$CURDIR/out
+STDDIR=$REMOTEDIR/stdout
+SCRIPTDIR=$REMOTEDIR/scripts/
+
+# Define tmporary files
+TMP1=$OUTDIR/$$.tmp.out
+TMP2=$OUTDIR/$$.tmp.stdout
+
+# Make OUTDIR
+mkdir -p $OUTDIR
+
diff --git a/extrautils/ctest/swmatcher.t b/extrautils/ctest/swmatcher.t
new file mode 100644
index 0000000..162d3ca
--- /dev/null
+++ b/extrautils/ctest/swmatcher.t
@@ -0,0 +1,20 @@
+Set up
+ $ . $TESTDIR/setup.sh
+
+Set up the executable: swMather.
+ $ EXEC=$TESTDIR/../swMatcher
+
+Define tmporary files
+ $ TMP1=$OUTDIR/$$.tmp.out
+ $ TMP2=$OUTDIR/$$.tmp.stdout
+
+Make OUTDIR
+ $ mkdir -p $OUTDIR
+
+ $ FA=$DATDIR/ecoli_subset.fasta
+ $ $EXEC $FA $FA 10 -local > $OUTDIR/swmatcher.out
+ $ echo $?
+ 0
+ $ diff $OUTDIR/swmatcher.out $STDDIR/swmatcher.stdout
+
+
diff --git a/extrautils/p4.mk b/extrautils/p4.mk
new file mode 100644
index 0000000..7e41029
--- /dev/null
+++ b/extrautils/p4.mk
@@ -0,0 +1,79 @@
+# 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 $(DEPS)
diff --git a/libcpp.makefile b/libcpp.makefile
new file mode 100644
index 0000000..d4f9c40
--- /dev/null
+++ b/libcpp.makefile
@@ -0,0 +1,9 @@
+include defines.mk
+
+# Note that, for now, HDF5_LIB is a directory here, and a file in libcpp.
+# I do not know why buildctl has set that up, but we follow the mobs
+# adaptors for now.
+
+pblib: libcpp/configure.py libcpp/makefile
+ cd libcpp && NOPBBAM=true HDF5_LIB=${HDF5_LIB}/libhdf5.so ./configure.py
+ ${MAKE} -C libcpp
diff --git a/libcpp/.gitignore b/libcpp/.gitignore
new file mode 100644
index 0000000..d67c0ce
--- /dev/null
+++ b/libcpp/.gitignore
@@ -0,0 +1,7 @@
+*.o
+*.d
+*.a
+*.so
+defines.mk
+/pbdata/libconfig.h
+/hdf/hdf5-1.8.12-headers/
diff --git a/libcpp/.travis.yml b/libcpp/.travis.yml
new file mode 100644
index 0000000..5efbc08
--- /dev/null
+++ b/libcpp/.travis.yml
@@ -0,0 +1,22 @@
+language: cpp
+script:
+ - NOPBBAM=1 ./configure.py
+ - make -j all
+# - make -j gtest
+compiler:
+ - gcc
+# - clang
+install:
+- if [ "$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
new file mode 100644
index 0000000..91745bc
--- /dev/null
+++ b/libcpp/README.md
@@ -0,0 +1,47 @@
+[](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
new file mode 100644
index 0000000..1a5650e
--- /dev/null
+++ b/libcpp/alignment/MappingMetrics.cpp
@@ -0,0 +1,299 @@
+#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
new file mode 100644
index 0000000..83bc07c
--- /dev/null
+++ b/libcpp/alignment/MappingMetrics.hpp
@@ -0,0 +1,133 @@
+#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
new file mode 100644
index 0000000..4080489
--- /dev/null
+++ b/libcpp/alignment/algorithms/alignment/AffineGuidedAlign.hpp
@@ -0,0 +1,589 @@
+#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
new file mode 100644
index 0000000..82ba5f7
--- /dev/null
+++ b/libcpp/alignment/algorithms/alignment/AffineKBandAlign.hpp
@@ -0,0 +1,406 @@
+#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
new file mode 100644
index 0000000..b645b94
--- /dev/null
+++ b/libcpp/alignment/algorithms/alignment/AlignmentFormats.hpp
@@ -0,0 +1,6 @@
+#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
new file mode 100644
index 0000000..7912783
--- /dev/null
+++ b/libcpp/alignment/algorithms/alignment/AlignmentUtils.cpp
@@ -0,0 +1,43 @@
+#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
new file mode 100644
index 0000000..0daa80f
--- /dev/null
+++ b/libcpp/alignment/algorithms/alignment/AlignmentUtils.hpp
@@ -0,0 +1,139 @@
+#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
new file mode 100644
index 0000000..30f434b
--- /dev/null
+++ b/libcpp/alignment/algorithms/alignment/AlignmentUtilsImpl.hpp
@@ -0,0 +1,548 @@
+#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
new file mode 100644
index 0000000..339b454
--- /dev/null
+++ b/libcpp/alignment/algorithms/alignment/BaseScoreFunction.cpp
@@ -0,0 +1,11 @@
+#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
new file mode 100644
index 0000000..1d5c35c
--- /dev/null
+++ b/libcpp/alignment/algorithms/alignment/BaseScoreFunction.hpp
@@ -0,0 +1,17 @@
+#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
new file mode 100644
index 0000000..ed932ab
--- /dev/null
+++ b/libcpp/alignment/algorithms/alignment/DistanceMatrixScoreFunction.hpp
@@ -0,0 +1,40 @@
+#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
new file mode 100644
index 0000000..97bacad
--- /dev/null
+++ b/libcpp/alignment/algorithms/alignment/DistanceMatrixScoreFunctionImpl.hpp
@@ -0,0 +1,96 @@
+#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
new file mode 100644
index 0000000..1a17664
--- /dev/null
+++ b/libcpp/alignment/algorithms/alignment/ExtendAlign.cpp
@@ -0,0 +1,79 @@
+#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
new file mode 100644
index 0000000..a5430bc
--- /dev/null
+++ b/libcpp/alignment/algorithms/alignment/ExtendAlign.hpp
@@ -0,0 +1,416 @@
+#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
new file mode 100644
index 0000000..a49395c
--- /dev/null
+++ b/libcpp/alignment/algorithms/alignment/FullQVAlign.hpp
@@ -0,0 +1,132 @@
+#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
new file mode 100644
index 0000000..ddd1a4e
--- /dev/null
+++ b/libcpp/alignment/algorithms/alignment/GraphPaper.hpp
@@ -0,0 +1,31 @@
+#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
new file mode 100644
index 0000000..c57d5a8
--- /dev/null
+++ b/libcpp/alignment/algorithms/alignment/GraphPaperImpl.hpp
@@ -0,0 +1,175 @@
+#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
new file mode 100644
index 0000000..2904720
--- /dev/null
+++ b/libcpp/alignment/algorithms/alignment/GuidedAlign.cpp
@@ -0,0 +1,226 @@
+#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
new file mode 100644
index 0000000..3296a21
--- /dev/null
+++ b/libcpp/alignment/algorithms/alignment/GuidedAlign.hpp
@@ -0,0 +1,600 @@
+#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
new file mode 100644
index 0000000..cc40a5f
--- /dev/null
+++ b/libcpp/alignment/algorithms/alignment/IDSScoreFunction.cpp
@@ -0,0 +1,158 @@
+#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
new file mode 100644
index 0000000..3b6b5e5
--- /dev/null
+++ b/libcpp/alignment/algorithms/alignment/IDSScoreFunction.hpp
@@ -0,0 +1,109 @@
+#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
new file mode 100644
index 0000000..c25bb92
--- /dev/null
+++ b/libcpp/alignment/algorithms/alignment/KBandAlign.cpp
@@ -0,0 +1,30 @@
+#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
new file mode 100644
index 0000000..456c985
--- /dev/null
+++ b/libcpp/alignment/algorithms/alignment/KBandAlign.hpp
@@ -0,0 +1,381 @@
+#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
new file mode 100644
index 0000000..33405e6
--- /dev/null
+++ b/libcpp/alignment/algorithms/alignment/OneGapAlignment.hpp
@@ -0,0 +1,374 @@
+#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
new file mode 100644
index 0000000..c73b49e
--- /dev/null
+++ b/libcpp/alignment/algorithms/alignment/QualityValueScoreFunction.cpp
@@ -0,0 +1,90 @@
+#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
new file mode 100644
index 0000000..670b42f
--- /dev/null
+++ b/libcpp/alignment/algorithms/alignment/QualityValueScoreFunction.hpp
@@ -0,0 +1,56 @@
+#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
new file mode 100644
index 0000000..14c3b23
--- /dev/null
+++ b/libcpp/alignment/algorithms/alignment/SDPAlign.hpp
@@ -0,0 +1,64 @@
+#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
new file mode 100644
index 0000000..140b667
--- /dev/null
+++ b/libcpp/alignment/algorithms/alignment/SDPAlignImpl.hpp
@@ -0,0 +1,614 @@
+#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
new file mode 100644
index 0000000..a92b60b
--- /dev/null
+++ b/libcpp/alignment/algorithms/alignment/SWAlign.hpp
@@ -0,0 +1,17 @@
+#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
new file mode 100644
index 0000000..b30ec10
--- /dev/null
+++ b/libcpp/alignment/algorithms/alignment/SWAlignImpl.hpp
@@ -0,0 +1,389 @@
+#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
new file mode 100644
index 0000000..5aa06cc
--- /dev/null
+++ b/libcpp/alignment/algorithms/alignment/ScoreMatrices.cpp
@@ -0,0 +1,58 @@
+#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
new file mode 100644
index 0000000..e948cf6
--- /dev/null
+++ b/libcpp/alignment/algorithms/alignment/ScoreMatrices.hpp
@@ -0,0 +1,18 @@
+#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
new file mode 100644
index 0000000..ea48abe
--- /dev/null
+++ b/libcpp/alignment/algorithms/alignment/StringToScoreMatrix.cpp
@@ -0,0 +1,26 @@
+#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
new file mode 100644
index 0000000..b1f415c
--- /dev/null
+++ b/libcpp/alignment/algorithms/alignment/StringToScoreMatrix.hpp
@@ -0,0 +1,9 @@
+#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
new file mode 100644
index 0000000..f665833
--- /dev/null
+++ b/libcpp/alignment/algorithms/alignment/sdp/FragmentSort.hpp
@@ -0,0 +1,19 @@
+#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
new file mode 100644
index 0000000..b9a3aa8
--- /dev/null
+++ b/libcpp/alignment/algorithms/alignment/sdp/FragmentSortImpl.hpp
@@ -0,0 +1,16 @@
+#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
new file mode 100644
index 0000000..148c16d
--- /dev/null
+++ b/libcpp/alignment/algorithms/alignment/sdp/NonoverlappingSparseDynamicProgramming.h
@@ -0,0 +1,193 @@
+#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
new file mode 100644
index 0000000..6ae674e
--- /dev/null
+++ b/libcpp/alignment/algorithms/alignment/sdp/SDPColumn.hpp
@@ -0,0 +1,23 @@
+#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
new file mode 100644
index 0000000..861144e
--- /dev/null
+++ b/libcpp/alignment/algorithms/alignment/sdp/SDPFragment.cpp
@@ -0,0 +1,27 @@
+#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
new file mode 100644
index 0000000..23b0e1c
--- /dev/null
+++ b/libcpp/alignment/algorithms/alignment/sdp/SDPFragment.hpp
@@ -0,0 +1,132 @@
+#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
new file mode 100644
index 0000000..866dbfb
--- /dev/null
+++ b/libcpp/alignment/algorithms/alignment/sdp/SDPSet.hpp
@@ -0,0 +1,52 @@
+#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
new file mode 100644
index 0000000..6dbe709
--- /dev/null
+++ b/libcpp/alignment/algorithms/alignment/sdp/SDPSetImpl.hpp
@@ -0,0 +1,113 @@
+#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
new file mode 100644
index 0000000..9325491
--- /dev/null
+++ b/libcpp/alignment/algorithms/alignment/sdp/SparseDynamicProgramming.cpp
@@ -0,0 +1,18 @@
+#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
new file mode 100644
index 0000000..8f42113
--- /dev/null
+++ b/libcpp/alignment/algorithms/alignment/sdp/SparseDynamicProgramming.hpp
@@ -0,0 +1,37 @@
+#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
new file mode 100644
index 0000000..a227c70
--- /dev/null
+++ b/libcpp/alignment/algorithms/alignment/sdp/SparseDynamicProgrammingImpl.hpp
@@ -0,0 +1,266 @@
+#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
new file mode 100644
index 0000000..618b25e
--- /dev/null
+++ b/libcpp/alignment/algorithms/alignment/sdp/VariableLengthSDPFragment.h
@@ -0,0 +1,51 @@
+#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
new file mode 100644
index 0000000..16ea57c
--- /dev/null
+++ b/libcpp/alignment/algorithms/anchoring/BWTSearch.cpp
@@ -0,0 +1,85 @@
+#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
new file mode 100644
index 0000000..e3e0366
--- /dev/null
+++ b/libcpp/alignment/algorithms/anchoring/BWTSearch.hpp
@@ -0,0 +1,35 @@
+#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
new file mode 100644
index 0000000..ec71552
--- /dev/null
+++ b/libcpp/alignment/algorithms/anchoring/BWTSearchImpl.hpp
@@ -0,0 +1,14 @@
+#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
new file mode 100644
index 0000000..28ffaae
--- /dev/null
+++ b/libcpp/alignment/algorithms/anchoring/BasicEndpoint.hpp
@@ -0,0 +1,50 @@
+#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
new file mode 100644
index 0000000..dd61377
--- /dev/null
+++ b/libcpp/alignment/algorithms/anchoring/BasicEndpointImpl.hpp
@@ -0,0 +1,78 @@
+#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
new file mode 100644
index 0000000..0dc61dc
--- /dev/null
+++ b/libcpp/alignment/algorithms/anchoring/ClusterProbability.cpp
@@ -0,0 +1,45 @@
+#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
new file mode 100644
index 0000000..23d4e4e
--- /dev/null
+++ b/libcpp/alignment/algorithms/anchoring/ClusterProbability.hpp
@@ -0,0 +1,13 @@
+#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
new file mode 100644
index 0000000..9e6f624
--- /dev/null
+++ b/libcpp/alignment/algorithms/anchoring/Coordinate.cpp
@@ -0,0 +1,12 @@
+#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
new file mode 100644
index 0000000..1e86e29
--- /dev/null
+++ b/libcpp/alignment/algorithms/anchoring/Coordinate.hpp
@@ -0,0 +1,45 @@
+#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
new file mode 100644
index 0000000..cc9ca5b
--- /dev/null
+++ b/libcpp/alignment/algorithms/anchoring/FindMaxInterval.cpp
@@ -0,0 +1,23 @@
+#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
new file mode 100644
index 0000000..3f64505
--- /dev/null
+++ b/libcpp/alignment/algorithms/anchoring/FindMaxInterval.hpp
@@ -0,0 +1,175 @@
+#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
new file mode 100644
index 0000000..65b2922
--- /dev/null
+++ b/libcpp/alignment/algorithms/anchoring/FindMaxIntervalImpl.hpp
@@ -0,0 +1,945 @@
+#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
new file mode 100644
index 0000000..b3565ec
--- /dev/null
+++ b/libcpp/alignment/algorithms/anchoring/GlobalChain.hpp
@@ -0,0 +1,37 @@
+#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
new file mode 100644
index 0000000..49c7788
--- /dev/null
+++ b/libcpp/alignment/algorithms/anchoring/GlobalChainImpl.hpp
@@ -0,0 +1,225 @@
+#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
new file mode 100644
index 0000000..1a0e9ab
--- /dev/null
+++ b/libcpp/alignment/algorithms/anchoring/LISPValue.hpp
@@ -0,0 +1,24 @@
+#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
new file mode 100644
index 0000000..613381c
--- /dev/null
+++ b/libcpp/alignment/algorithms/anchoring/LISPValueImpl.hpp
@@ -0,0 +1,165 @@
+#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
new file mode 100644
index 0000000..85213ff
--- /dev/null
+++ b/libcpp/alignment/algorithms/anchoring/LISPValueWeightor.hpp
@@ -0,0 +1,52 @@
+#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
new file mode 100644
index 0000000..2e06940
--- /dev/null
+++ b/libcpp/alignment/algorithms/anchoring/LISPValueWeightorImpl.hpp
@@ -0,0 +1,112 @@
+#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
new file mode 100644
index 0000000..fd537ca
--- /dev/null
+++ b/libcpp/alignment/algorithms/anchoring/LISQValueWeightor.hpp
@@ -0,0 +1,35 @@
+#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
new file mode 100644
index 0000000..fa71bd0
--- /dev/null
+++ b/libcpp/alignment/algorithms/anchoring/LISSizeWeightor.hpp
@@ -0,0 +1,14 @@
+#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
new file mode 100644
index 0000000..ff778f5
--- /dev/null
+++ b/libcpp/alignment/algorithms/anchoring/LISSizeWeightorImpl.hpp
@@ -0,0 +1,13 @@
+#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
new file mode 100644
index 0000000..ef8c920
--- /dev/null
+++ b/libcpp/alignment/algorithms/anchoring/LongestIncreasingSubsequence.hpp
@@ -0,0 +1,31 @@
+#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
new file mode 100644
index 0000000..acda550
--- /dev/null
+++ b/libcpp/alignment/algorithms/anchoring/LongestIncreasingSubsequenceImpl.hpp
@@ -0,0 +1,135 @@
+#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
new file mode 100644
index 0000000..ce8ac39
--- /dev/null
+++ b/libcpp/alignment/algorithms/anchoring/MapBySuffixArray.hpp
@@ -0,0 +1,44 @@
+#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
new file mode 100644
index 0000000..6cbac02
--- /dev/null
+++ b/libcpp/alignment/algorithms/anchoring/MapBySuffixArrayImpl.hpp
@@ -0,0 +1,315 @@
+#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
new file mode 100644
index 0000000..e9f4c69
--- /dev/null
+++ b/libcpp/alignment/algorithms/anchoring/PrioritySearchTree.hpp
@@ -0,0 +1,69 @@
+#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
new file mode 100644
index 0000000..baa5b5b
--- /dev/null
+++ b/libcpp/alignment/algorithms/anchoring/PrioritySearchTreeImpl.hpp
@@ -0,0 +1,296 @@
+#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
new file mode 100644
index 0000000..5d11504
--- /dev/null
+++ b/libcpp/alignment/algorithms/anchoring/ScoreAnchors.hpp
@@ -0,0 +1,46 @@
+#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
new file mode 100644
index 0000000..2debcbf
--- /dev/null
+++ b/libcpp/alignment/algorithms/anchoring/ScoreAnchorsImpl.hpp
@@ -0,0 +1,179 @@
+#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
new file mode 100644
index 0000000..18170c7
--- /dev/null
+++ b/libcpp/alignment/algorithms/compare/CompareStrings.hpp
@@ -0,0 +1,81 @@
+#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
new file mode 100644
index 0000000..09a4be7
--- /dev/null
+++ b/libcpp/alignment/algorithms/sorting/DifferenceCovers.cpp
@@ -0,0 +1,15 @@
+#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
new file mode 100644
index 0000000..3ed502a
--- /dev/null
+++ b/libcpp/alignment/algorithms/sorting/DifferenceCovers.hpp
@@ -0,0 +1,16 @@
+#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
new file mode 100644
index 0000000..a02f70a
--- /dev/null
+++ b/libcpp/alignment/algorithms/sorting/Karkkainen.hpp
@@ -0,0 +1,134 @@
+#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
new file mode 100644
index 0000000..eb0e607
--- /dev/null
+++ b/libcpp/alignment/algorithms/sorting/LightweightSuffixArray.cpp
@@ -0,0 +1,405 @@
+#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
new file mode 100644
index 0000000..e312671
--- /dev/null
+++ b/libcpp/alignment/algorithms/sorting/LightweightSuffixArray.hpp
@@ -0,0 +1,103 @@
+#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
new file mode 100644
index 0000000..40936ee
--- /dev/null
+++ b/libcpp/alignment/algorithms/sorting/MultikeyQuicksort.cpp
@@ -0,0 +1,197 @@
+#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
new file mode 100644
index 0000000..c09a10b
--- /dev/null
+++ b/libcpp/alignment/algorithms/sorting/MultikeyQuicksort.hpp
@@ -0,0 +1,48 @@
+#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
new file mode 100644
index 0000000..aa23e85
--- /dev/null
+++ b/libcpp/alignment/algorithms/sorting/qsufsort.cpp
@@ -0,0 +1,302 @@
+/* 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
new file mode 100644
index 0000000..5525fe4
--- /dev/null
+++ b/libcpp/alignment/algorithms/sorting/qsufsort.hpp
@@ -0,0 +1,376 @@
+#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
new file mode 100644
index 0000000..ec7ac62
--- /dev/null
+++ b/libcpp/alignment/anchoring/AnchorParameters.hpp
@@ -0,0 +1,35 @@
+#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
new file mode 120000
index 0000000..2247f36
--- /dev/null
+++ b/libcpp/alignment/build.mk
@@ -0,0 +1 @@
+makefile
\ No newline at end of file
diff --git a/libcpp/alignment/bwt/BWT.hpp b/libcpp/alignment/bwt/BWT.hpp
new file mode 100644
index 0000000..ef91a3a
--- /dev/null
+++ b/libcpp/alignment/bwt/BWT.hpp
@@ -0,0 +1,316 @@
+#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
new file mode 100644
index 0000000..0e2640b
--- /dev/null
+++ b/libcpp/alignment/bwt/Occ.hpp
@@ -0,0 +1,217 @@
+#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
new file mode 100644
index 0000000..f1fa540
--- /dev/null
+++ b/libcpp/alignment/bwt/PackedHash.hpp
@@ -0,0 +1,350 @@
+#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
new file mode 100644
index 0000000..06f6882
--- /dev/null
+++ b/libcpp/alignment/bwt/Pos.hpp
@@ -0,0 +1,47 @@
+#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
new file mode 100644
index 0000000..588e832
--- /dev/null
+++ b/libcpp/alignment/datastructures/alignment/AlignedPair.h
@@ -0,0 +1,19 @@
+#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
new file mode 100644
index 0000000..d40aa39
--- /dev/null
+++ b/libcpp/alignment/datastructures/alignment/Alignment.cpp
@@ -0,0 +1,512 @@
+#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
new file mode 100644
index 0000000..a10bbb6
--- /dev/null
+++ b/libcpp/alignment/datastructures/alignment/Alignment.hpp
@@ -0,0 +1,184 @@
+#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
new file mode 100644
index 0000000..111cfc9
--- /dev/null
+++ b/libcpp/alignment/datastructures/alignment/AlignmentCandidate.cpp
@@ -0,0 +1,26 @@
+#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
new file mode 100644
index 0000000..2e27142
--- /dev/null
+++ b/libcpp/alignment/datastructures/alignment/AlignmentCandidate.hpp
@@ -0,0 +1,370 @@
+#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
new file mode 100644
index 0000000..913a689
--- /dev/null
+++ b/libcpp/alignment/datastructures/alignment/AlignmentContext.cpp
@@ -0,0 +1,35 @@
+#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
new file mode 100644
index 0000000..69c57ce
--- /dev/null
+++ b/libcpp/alignment/datastructures/alignment/AlignmentContext.hpp
@@ -0,0 +1,32 @@
+#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
new file mode 100644
index 0000000..47fb01c
--- /dev/null
+++ b/libcpp/alignment/datastructures/alignment/AlignmentGapList.h
@@ -0,0 +1,26 @@
+#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
new file mode 100644
index 0000000..7e39d0b
--- /dev/null
+++ b/libcpp/alignment/datastructures/alignment/AlignmentMap.cpp
@@ -0,0 +1,22 @@
+#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
new file mode 100644
index 0000000..57752fc
--- /dev/null
+++ b/libcpp/alignment/datastructures/alignment/AlignmentMap.hpp
@@ -0,0 +1,20 @@
+#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
new file mode 100644
index 0000000..3da5fe5
--- /dev/null
+++ b/libcpp/alignment/datastructures/alignment/AlignmentStats.cpp
@@ -0,0 +1,29 @@
+#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
new file mode 100644
index 0000000..7f52e14
--- /dev/null
+++ b/libcpp/alignment/datastructures/alignment/AlignmentStats.hpp
@@ -0,0 +1,25 @@
+#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
new file mode 100644
index 0000000..c5c34c9
--- /dev/null
+++ b/libcpp/alignment/datastructures/alignment/ByteAlignment.h
@@ -0,0 +1,347 @@
+#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
new file mode 100644
index 0000000..9270fc9
--- /dev/null
+++ b/libcpp/alignment/datastructures/alignment/CmpFile.cpp
@@ -0,0 +1,6 @@
+#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
new file mode 100644
index 0000000..76682e4
--- /dev/null
+++ b/libcpp/alignment/datastructures/alignment/CmpFile.hpp
@@ -0,0 +1,33 @@
+#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
new file mode 100644
index 0000000..2530a40
--- /dev/null
+++ b/libcpp/alignment/datastructures/alignment/CmpIndexedStringTable.h
@@ -0,0 +1,67 @@
+#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
new file mode 100644
index 0000000..92a070c
--- /dev/null
+++ b/libcpp/alignment/datastructures/alignment/CmpReadGroupTable.h
@@ -0,0 +1,22 @@
+#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
new file mode 100644
index 0000000..91caf1b
--- /dev/null
+++ b/libcpp/alignment/datastructures/alignment/CmpRefSeqTable.h
@@ -0,0 +1,22 @@
+#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
new file mode 100644
index 0000000..16f4bff
--- /dev/null
+++ b/libcpp/alignment/datastructures/alignment/FilterCriteria.cpp
@@ -0,0 +1,371 @@
+/*
+ * =====================================================================================
+ *
+ * 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
new file mode 100644
index 0000000..778e659
--- /dev/null
+++ b/libcpp/alignment/datastructures/alignment/FilterCriteria.hpp
@@ -0,0 +1,165 @@
+#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
new file mode 100644
index 0000000..a71b605
--- /dev/null
+++ b/libcpp/alignment/datastructures/alignment/Path.h
@@ -0,0 +1,23 @@
+#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
new file mode 100644
index 0000000..32de362
--- /dev/null
+++ b/libcpp/alignment/datastructures/alignment/SAMToAlignmentCandidateAdapter.cpp
@@ -0,0 +1,461 @@
+#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
new file mode 100644
index 0000000..344aa60
--- /dev/null
+++ b/libcpp/alignment/datastructures/alignment/SAMToAlignmentCandidateAdapter.hpp
@@ -0,0 +1,79 @@
+#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
new file mode 100644
index 0000000..9884edc
--- /dev/null
+++ b/libcpp/alignment/datastructures/alignmentset/AlignmentSetToCmpH5Adapter.hpp
@@ -0,0 +1,84 @@
+#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
new file mode 100644
index 0000000..6604930
--- /dev/null
+++ b/libcpp/alignment/datastructures/alignmentset/AlignmentSetToCmpH5AdapterImpl.hpp
@@ -0,0 +1,256 @@
+#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
new file mode 100644
index 0000000..05e867d
--- /dev/null
+++ b/libcpp/alignment/datastructures/alignmentset/SAMQVConversion.cpp
@@ -0,0 +1,27 @@
+#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
new file mode 100644
index 0000000..1a8312f
--- /dev/null
+++ b/libcpp/alignment/datastructures/alignmentset/SAMQVConversion.hpp
@@ -0,0 +1,15 @@
+#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
new file mode 100644
index 0000000..2f0558e
--- /dev/null
+++ b/libcpp/alignment/datastructures/alignmentset/SAMSupplementalQVList.cpp
@@ -0,0 +1,71 @@
+#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
new file mode 100644
index 0000000..1ea8baa
--- /dev/null
+++ b/libcpp/alignment/datastructures/alignmentset/SAMSupplementalQVList.hpp
@@ -0,0 +1,27 @@
+#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
new file mode 100644
index 0000000..8b435b9
--- /dev/null
+++ b/libcpp/alignment/datastructures/anchoring/AnchorParameters.cpp
@@ -0,0 +1,44 @@
+#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
new file mode 100644
index 0000000..8ca5474
--- /dev/null
+++ b/libcpp/alignment/datastructures/anchoring/AnchorParameters.hpp
@@ -0,0 +1,35 @@
+#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
new file mode 100644
index 0000000..f562ed6
--- /dev/null
+++ b/libcpp/alignment/datastructures/anchoring/ClusterList.cpp
@@ -0,0 +1,75 @@
+#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
new file mode 100644
index 0000000..055446f
--- /dev/null
+++ b/libcpp/alignment/datastructures/anchoring/ClusterList.hpp
@@ -0,0 +1,25 @@
+#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
new file mode 100644
index 0000000..e6d7ec3
--- /dev/null
+++ b/libcpp/alignment/datastructures/anchoring/MatchPos.cpp
@@ -0,0 +1,59 @@
+#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
new file mode 100644
index 0000000..513b3d2
--- /dev/null
+++ b/libcpp/alignment/datastructures/anchoring/MatchPos.hpp
@@ -0,0 +1,192 @@
+#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
new file mode 100644
index 0000000..173eb89
--- /dev/null
+++ b/libcpp/alignment/datastructures/anchoring/WeightedInterval.cpp
@@ -0,0 +1,181 @@
+#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
new file mode 100644
index 0000000..052da90
--- /dev/null
+++ b/libcpp/alignment/datastructures/anchoring/WeightedInterval.hpp
@@ -0,0 +1,85 @@
+#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
new file mode 100644
index 0000000..ec39903
--- /dev/null
+++ b/libcpp/alignment/files/BaseSequenceIO.cpp
@@ -0,0 +1,77 @@
+#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
new file mode 100644
index 0000000..1b187d2
--- /dev/null
+++ b/libcpp/alignment/files/BaseSequenceIO.hpp
@@ -0,0 +1,26 @@
+#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
new file mode 100644
index 0000000..7edf650
--- /dev/null
+++ b/libcpp/alignment/files/CCSIterator.cpp
@@ -0,0 +1,28 @@
+#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
new file mode 100644
index 0000000..6f97641
--- /dev/null
+++ b/libcpp/alignment/files/CCSIterator.hpp
@@ -0,0 +1,21 @@
+#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
new file mode 100644
index 0000000..d02876c
--- /dev/null
+++ b/libcpp/alignment/files/FragmentCCSIterator.cpp
@@ -0,0 +1,109 @@
+#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
new file mode 100644
index 0000000..620491f
--- /dev/null
+++ b/libcpp/alignment/files/FragmentCCSIterator.hpp
@@ -0,0 +1,23 @@
+#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
new file mode 100644
index 0000000..ff04a08
--- /dev/null
+++ b/libcpp/alignment/files/ReaderAgglomerate.cpp
@@ -0,0 +1,505 @@
+#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
new file mode 100644
index 0000000..0955498
--- /dev/null
+++ b/libcpp/alignment/files/ReaderAgglomerate.hpp
@@ -0,0 +1,136 @@
+#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
new file mode 100644
index 0000000..c50fafa
--- /dev/null
+++ b/libcpp/alignment/files/ReaderAgglomerateImpl.hpp
@@ -0,0 +1,44 @@
+#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
new file mode 100644
index 0000000..db70308
--- /dev/null
+++ b/libcpp/alignment/format/BAMPrinter.hpp
@@ -0,0 +1,29 @@
+#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
new file mode 100644
index 0000000..9dd66c6
--- /dev/null
+++ b/libcpp/alignment/format/BAMPrinterImpl.hpp
@@ -0,0 +1,168 @@
+#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
new file mode 100644
index 0000000..581664a
--- /dev/null
+++ b/libcpp/alignment/format/CompareSequencesPrinter.cpp
@@ -0,0 +1,10 @@
+#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
new file mode 100644
index 0000000..bd5fe34
--- /dev/null
+++ b/libcpp/alignment/format/CompareSequencesPrinter.hpp
@@ -0,0 +1,21 @@
+#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
new file mode 100644
index 0000000..e285780
--- /dev/null
+++ b/libcpp/alignment/format/CompareSequencesPrinterImpl.hpp
@@ -0,0 +1,77 @@
+#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
new file mode 100644
index 0000000..e9cd328
--- /dev/null
+++ b/libcpp/alignment/format/IntervalPrinter.cpp
@@ -0,0 +1,70 @@
+#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
new file mode 100644
index 0000000..a1efdfc
--- /dev/null
+++ b/libcpp/alignment/format/IntervalPrinter.hpp
@@ -0,0 +1,21 @@
+#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
new file mode 100644
index 0000000..c5c8eca
--- /dev/null
+++ b/libcpp/alignment/format/SAMHeaderPrinter.cpp
@@ -0,0 +1,432 @@
+#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
new file mode 100644
index 0000000..0b95da1
--- /dev/null
+++ b/libcpp/alignment/format/SAMHeaderPrinter.hpp
@@ -0,0 +1,311 @@
+#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
new file mode 100644
index 0000000..c44c40a
--- /dev/null
+++ b/libcpp/alignment/format/SAMPrinter.cpp
@@ -0,0 +1,188 @@
+#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
new file mode 100644
index 0000000..c47f8ec
--- /dev/null
+++ b/libcpp/alignment/format/SAMPrinter.hpp
@@ -0,0 +1,93 @@
+#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
new file mode 100644
index 0000000..f83d1a9
--- /dev/null
+++ b/libcpp/alignment/format/SAMPrinterImpl.hpp
@@ -0,0 +1,304 @@
+#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
new file mode 100644
index 0000000..11f6b39
--- /dev/null
+++ b/libcpp/alignment/format/StickAlignmentPrinter.hpp
@@ -0,0 +1,123 @@
+#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
new file mode 100644
index 0000000..6704bce
--- /dev/null
+++ b/libcpp/alignment/format/SummaryPrinter.cpp
@@ -0,0 +1,26 @@
+#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
new file mode 100644
index 0000000..5cc9c29
--- /dev/null
+++ b/libcpp/alignment/format/SummaryPrinter.hpp
@@ -0,0 +1,14 @@
+#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
new file mode 100644
index 0000000..a4505cf
--- /dev/null
+++ b/libcpp/alignment/format/VulgarPrinter.hpp
@@ -0,0 +1,53 @@
+#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
new file mode 100644
index 0000000..076518e
--- /dev/null
+++ b/libcpp/alignment/format/XMLPrinter.hpp
@@ -0,0 +1,84 @@
+#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
new file mode 100644
index 0000000..5599b63
--- /dev/null
+++ b/libcpp/alignment/ipc/SharedMemoryAllocator.hpp
@@ -0,0 +1,33 @@
+#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
new file mode 100644
index 0000000..0cfd1d6
--- /dev/null
+++ b/libcpp/alignment/makefile
@@ -0,0 +1,52 @@
+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 $(dependencies)
diff --git a/libcpp/alignment/old.Makefile b/libcpp/alignment/old.Makefile
new file mode 100644
index 0000000..099a7d0
--- /dev/null
+++ b/libcpp/alignment/old.Makefile
@@ -0,0 +1,113 @@
+
+include ../common.mk
+
+# To enable building a shared library, invoke as "make SHARED_LIB=true ..."
+ifneq ($(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
new file mode 100644
index 0000000..f1c3c2f
--- /dev/null
+++ b/libcpp/alignment/qvs/QualityValueProfile.cpp
@@ -0,0 +1,41 @@
+#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
new file mode 100644
index 0000000..a410fe9
--- /dev/null
+++ b/libcpp/alignment/qvs/QualityValueProfile.hpp
@@ -0,0 +1,23 @@
+#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
new file mode 100644
index 0000000..9a66a51
--- /dev/null
+++ b/libcpp/alignment/simulator/CDFMap.hpp
@@ -0,0 +1,44 @@
+#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
new file mode 100644
index 0000000..5023463
--- /dev/null
+++ b/libcpp/alignment/simulator/ContextOutputList.hpp
@@ -0,0 +1,100 @@
+#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
new file mode 100644
index 0000000..798df30
--- /dev/null
+++ b/libcpp/alignment/simulator/ContextSample.cpp
@@ -0,0 +1,53 @@
+#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
new file mode 100644
index 0000000..c7aa5c2
--- /dev/null
+++ b/libcpp/alignment/simulator/ContextSample.hpp
@@ -0,0 +1,30 @@
+#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
new file mode 100644
index 0000000..1d84d72
--- /dev/null
+++ b/libcpp/alignment/simulator/ContextSet.cpp
@@ -0,0 +1,35 @@
+#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
new file mode 100644
index 0000000..7441f08
--- /dev/null
+++ b/libcpp/alignment/simulator/ContextSet.hpp
@@ -0,0 +1,19 @@
+#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
new file mode 100644
index 0000000..e135db2
--- /dev/null
+++ b/libcpp/alignment/simulator/LengthHistogram.cpp
@@ -0,0 +1,58 @@
+#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
new file mode 100644
index 0000000..28c5e51
--- /dev/null
+++ b/libcpp/alignment/simulator/LengthHistogram.hpp
@@ -0,0 +1,24 @@
+#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
new file mode 100644
index 0000000..352c047
--- /dev/null
+++ b/libcpp/alignment/simulator/OutputList.hpp
@@ -0,0 +1,57 @@
+#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
new file mode 100644
index 0000000..528ecd3
--- /dev/null
+++ b/libcpp/alignment/simulator/OutputSample.hpp
@@ -0,0 +1,59 @@
+#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
new file mode 100644
index 0000000..f2da93f
--- /dev/null
+++ b/libcpp/alignment/simulator/OutputSampleList.hpp
@@ -0,0 +1,33 @@
+#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
new file mode 100644
index 0000000..dbfe8d0
--- /dev/null
+++ b/libcpp/alignment/simulator/OutputSampleListSet.hpp
@@ -0,0 +1,123 @@
+#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
new file mode 100644
index 0000000..1f15b95
--- /dev/null
+++ b/libcpp/alignment/simulator/QualitySample.cpp
@@ -0,0 +1,77 @@
+#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
new file mode 100644
index 0000000..3f0a181
--- /dev/null
+++ b/libcpp/alignment/simulator/QualitySample.hpp
@@ -0,0 +1,28 @@
+#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
new file mode 100644
index 0000000..c789b4d
--- /dev/null
+++ b/libcpp/alignment/statistics/AnchorDistributionTable.hpp
@@ -0,0 +1,43518 @@
+#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,
+17.49,17.83,17.75,17.79,18.08,17.96,18.09,18.25,18.27,18.09,
+18.35,18.56,18.59,18.75,18.67,18.93,18.97,19.12,19.01,19.23,
+19.32,19.48,19.41,19.47,19.72,19.68,19.83,19.94,19.88,20.18,
+20.19,20.11,20.14,20.50,20.35,20.65,20.74,20.77,20.91,20.83,
+20.78,20.91,21.19,21.12,21.21,21.39,21.52,21.27,21.62,21.96,
+21.96,21.59,22.06,21.96,22.24,22.45,22.18,22.63,22.50,22.83,
+22.57,22.77,22.71,22.70,23.02,23.00,23.06,23.24,23.33,23.42,
+23.57,23.61,23.95,23.48,23.88,23.82,24.00,24.08,23.96,24.24,
+24.36,24.41,24.75,24.72,24.59,24.57,24.82,24.71,25.22,24.88,
+0.59,0.65,0.70,0.76,0.82,0.87,0.95,0.98,1.17,1.11,
+1.18,1.22,1.27,1.32,1.48,1.53,1.59,1.60,1.65,1.67,
+1.78,1.80,1.92,1.97,2.07,2.07,2.09,2.18,2.31,2.29,
+2.42,2.49,2.46,2.51,2.56,2.67,2.75,2.79,2.84,2.85,
+2.94,3.01,3.04,3.18,3.22,3.34,3.27,3.39,3.40,3.53,
+3.49,3.61,3.60,3.71,3.77,3.71,3.85,3.98,4.05,4.04,
+4.13,4.24,4.33,4.35,4.37,4.41,4.49,4.55,4.59,4.59,
+4.74,4.89,4.79,4.81,4.82,5.00,5.10,5.11,5.07,5.23,
+5.31,5.39,5.55,5.40,5.47,5.63,5.63,5.73,5.73,5.91,
+5.89,5.94,6.02,5.94,6.13,6.26,6.31,6.29,6.58,6.45,
+6.46,6.41,6.56,6.77,6.79,6.70,6.82,6.84,7.14,7.03,
+6.94,7.00,7.27,7.23,7.35,7.29,7.37,7.28,7.48,7.52,
+7.53,7.74,7.92,7.76,7.85,8.00,7.86,8.04,8.02,8.08,
+8.35,8.32,8.41,8.39,8.34,8.56,8.61,8.67,8.66,8.81,
+8.70,8.87,8.81,8.75,9.33,9.09,9.10,9.00,9.35,9.28,
+9.27,9.44,9.54,9.60,9.60,9.65,9.72,9.77,9.91,9.90,
+10.11,9.90,10.13,10.13,10.21,10.39,10.34,10.22,10.46,10.64,
+10.40,10.84,10.89,10.70,10.98,10.79,10.75,10.96,11.09,11.12,
+11.26,11.40,11.34,11.28,11.32,11.45,11.55,11.80,11.61,11.67,
+11.74,11.69,11.95,11.92,11.92,11.88,11.98,12.26,12.25,12.13,
+12.19,12.16,12.24,12.51,12.52,12.48,12.63,12.90,12.85,12.79,
+12.77,13.16,13.05,13.13,13.12,13.13,13.41,13.37,13.46,13.35,
+13.44,13.65,13.61,13.58,13.74,13.67,13.98,13.97,13.95,13.92,
+14.07,13.87,14.15,14.41,14.36,14.44,14.38,14.54,14.69,14.78,
+14.72,14.90,14.77,14.85,14.84,14.96,15.08,15.04,15.21,15.08,
+15.23,15.29,15.42,15.36,15.29,15.58,15.71,15.78,15.55,15.98,
+16.01,15.88,15.89,16.07,16.11,16.44,16.32,16.29,16.37,16.50,
+16.58,16.38,16.55,16.54,16.54,16.55,16.80,16.77,16.81,16.95,
+16.89,17.43,17.14,17.19,17.04,17.35,17.34,17.40,17.27,17.73,
+0.41,0.47,0.52,0.54,0.56,0.61,0.66,0.72,0.77,0.79,
+0.81,0.90,0.88,0.92,1.01,1.12,1.03,1.09,1.16,1.20,
+1.25,1.25,1.40,1.31,1.37,1.43,1.43,1.51,1.48,1.62,
+1.68,1.73,1.66,1.74,1.82,1.84,1.86,1.94,2.04,2.02,
+2.06,2.14,2.18,2.18,2.17,2.25,2.30,2.25,2.36,2.37,
+2.42,2.50,2.59,2.54,2.63,2.64,2.70,2.88,2.74,2.76,
+2.88,2.91,3.07,2.96,3.09,3.12,3.17,3.14,3.24,3.35,
+3.22,3.27,3.43,3.39,3.38,3.52,3.45,3.56,3.66,3.75,
+3.71,3.69,3.77,3.92,3.90,3.87,3.86,3.99,4.06,4.11,
+4.05,4.18,4.16,4.29,4.31,4.42,4.40,4.47,4.61,4.52,
+4.42,4.54,4.59,4.65,4.71,4.74,4.71,4.88,4.81,4.88,
+4.95,5.00,5.11,5.14,5.18,5.11,5.15,5.32,5.30,5.27,
+5.39,5.45,5.54,5.53,5.52,5.50,5.55,5.67,5.64,5.70,
+5.64,5.84,5.83,5.73,5.93,5.95,6.03,6.21,6.12,6.04,
+6.16,6.14,6.30,6.26,6.24,6.48,6.51,6.33,6.42,6.46,
+6.60,6.59,6.61,6.72,6.83,6.78,6.83,6.91,6.89,6.94,
+6.90,6.99,7.01,7.15,7.19,7.18,7.26,7.11,7.25,7.33,
+7.40,7.34,7.64,7.62,7.51,7.66,7.84,7.69,7.79,7.73,
+7.92,7.83,7.90,7.95,8.08,8.01,8.15,8.24,8.10,8.25,
+8.13,8.15,8.40,8.47,8.45,8.43,8.31,8.52,8.58,8.68,
+8.69,8.53,8.69,8.71,8.69,8.97,8.92,8.80,8.86,8.99,
+9.04,9.08,9.15,9.19,9.32,9.12,9.15,9.47,9.31,9.42,
+9.39,9.54,9.56,9.60,9.70,9.81,9.78,9.68,9.68,9.91,
+9.90,9.69,9.89,9.91,10.12,10.16,10.22,10.25,10.26,10.21,
+10.32,10.34,10.35,10.33,10.37,10.44,10.52,10.53,10.60,10.76,
+10.61,10.79,10.80,10.87,10.84,10.80,10.94,10.90,10.85,11.04,
+11.09,11.20,11.03,11.08,11.16,11.42,11.14,11.30,11.54,11.36,
+11.52,11.43,11.53,11.68,11.62,11.67,11.80,11.83,11.94,12.01,
+11.90,11.94,11.77,12.01,12.08,12.09,12.13,12.33,12.26,12.06,
+0.28,0.33,0.37,0.39,0.41,0.48,0.50,0.49,0.52,0.51,
+0.58,0.63,0.65,0.66,0.68,0.71,0.68,0.79,0.83,0.84,
+0.89,0.90,0.91,0.95,1.02,1.04,1.08,1.04,1.08,1.19,
+1.08,1.22,1.20,1.21,1.30,1.27,1.36,1.35,1.37,1.45,
+1.41,1.44,1.54,1.49,1.54,1.55,1.56,1.65,1.68,1.71,
+1.71,1.78,1.80,1.81,1.85,1.86,1.87,1.87,1.97,1.96,
+2.12,2.07,2.09,2.17,2.14,2.19,2.21,2.27,2.27,2.25,
+2.24,2.36,2.29,2.33,2.44,2.35,2.48,2.45,2.63,2.58,
+2.60,2.64,2.67,2.67,2.69,2.74,2.77,2.84,2.78,2.87,
+3.02,2.88,3.05,2.94,3.05,3.04,3.16,3.15,3.12,3.12,
+3.22,3.28,3.17,3.27,3.22,3.40,3.32,3.34,3.47,3.45,
+3.44,3.49,3.60,3.69,3.63,3.52,3.53,3.69,3.70,3.68,
+3.74,3.78,3.83,3.87,3.96,3.72,3.86,3.95,4.00,3.92,
+4.07,4.03,4.04,4.03,4.12,4.14,4.22,4.17,4.20,4.22,
+4.36,4.31,4.41,4.43,4.46,4.45,4.48,4.53,4.54,4.53,
+4.59,4.71,4.64,4.72,4.78,4.75,4.70,4.85,4.83,4.90,
+4.86,4.98,4.90,5.05,5.04,4.90,5.08,5.16,5.04,5.21,
+5.23,5.09,5.26,5.24,5.29,5.29,5.34,5.46,5.45,5.39,
+5.39,5.53,5.49,5.54,5.42,5.57,5.51,5.64,5.75,5.64,
+5.76,5.76,5.84,5.95,5.89,6.02,5.84,5.99,5.90,6.16,
+6.14,5.97,5.99,6.27,6.06,6.10,6.27,6.31,6.18,6.18,
+6.24,6.32,6.35,6.39,6.54,6.52,6.49,6.51,6.57,6.68,
+6.70,6.57,6.63,6.74,6.72,6.69,6.72,6.96,6.85,6.81,
+6.92,6.79,6.95,7.11,6.98,7.02,6.97,7.06,7.02,7.15,
+7.17,7.20,7.20,7.34,7.35,7.18,7.24,7.46,7.38,7.35,
+7.50,7.52,7.60,7.71,7.47,7.43,7.68,7.65,7.71,7.80,
+7.76,7.78,7.81,7.68,7.98,7.98,8.05,7.86,8.13,8.02,
+8.16,8.19,8.09,8.19,8.09,8.07,8.07,8.19,8.20,8.38,
+8.36,8.51,8.50,8.38,8.37,8.51,8.57,8.34,8.52,8.65,
+0.19,0.22,0.23,0.26,0.28,0.32,0.36,0.34,0.37,0.41,
+0.42,0.42,0.45,0.46,0.51,0.50,0.55,0.53,0.62,0.57,
+0.60,0.59,0.67,0.69,0.75,0.69,0.78,0.77,0.80,0.79,
+0.76,0.89,0.89,0.86,0.94,0.92,0.97,0.93,1.00,1.00,
+1.04,1.07,1.04,1.01,1.11,1.12,1.10,1.18,1.15,1.22,
+1.25,1.26,1.22,1.24,1.33,1.36,1.30,1.39,1.47,1.44,
+1.38,1.42,1.38,1.47,1.49,1.55,1.53,1.58,1.54,1.55,
+1.62,1.64,1.67,1.68,1.70,1.73,1.77,1.84,1.74,1.81,
+1.77,1.81,1.92,1.87,1.95,1.88,1.91,2.00,1.96,1.98,
+2.02,2.10,2.05,2.05,2.08,2.14,2.17,2.14,2.21,2.13,
+2.17,2.19,2.17,2.21,2.23,2.19,2.34,2.29,2.39,2.41,
+2.44,2.42,2.53,2.53,2.45,2.53,2.60,2.59,2.67,2.60,
+2.54,2.62,2.55,2.73,2.74,2.75,2.68,2.74,2.75,2.77,
+2.82,2.81,2.88,2.83,2.97,3.01,2.90,2.98,2.94,3.01,
+3.04,3.06,3.00,3.13,3.06,3.22,3.25,3.23,3.24,3.22,
+3.28,3.31,3.33,3.29,3.28,3.30,3.29,3.41,3.32,3.30,
+3.45,3.38,3.38,3.48,3.45,3.50,3.50,3.61,3.50,3.75,
+3.68,3.57,3.58,3.64,3.66,3.79,3.71,3.71,3.69,3.79,
+3.77,3.85,3.81,3.80,3.85,3.96,4.03,3.91,4.07,4.08,
+3.96,3.93,4.02,4.13,4.09,4.12,4.17,4.13,4.21,4.16,
+4.30,4.17,4.38,4.23,4.29,4.22,4.40,4.39,4.46,4.35,
+4.40,4.43,4.43,4.56,4.49,4.58,4.60,4.49,4.61,4.57,
+4.71,4.59,4.71,4.84,4.72,4.67,4.76,4.79,4.69,4.85,
+4.85,4.82,4.80,4.93,4.94,4.89,4.95,5.06,5.02,5.00,
+5.10,5.06,5.08,5.09,5.14,5.17,5.19,5.23,5.22,5.21,
+5.21,5.23,5.13,5.41,5.37,5.32,5.27,5.33,5.45,5.40,
+5.37,5.53,5.46,5.51,5.56,5.64,5.60,5.49,5.55,5.57,
+5.60,5.72,5.47,5.70,5.68,5.71,5.75,5.76,5.79,5.93,
+5.80,5.80,5.94,5.98,5.89,5.98,5.89,6.07,5.93,6.03,
+0.14,0.14,0.16,0.18,0.18,0.22,0.23,0.25,0.23,0.30,
+0.30,0.31,0.28,0.34,0.36,0.38,0.35,0.41,0.39,0.42,
+0.45,0.45,0.44,0.47,0.48,0.49,0.50,0.50,0.54,0.55,
+0.53,0.57,0.57,0.64,0.64,0.66,0.64,0.69,0.68,0.69,
+0.68,0.70,0.76,0.71,0.76,0.81,0.78,0.78,0.82,0.77,
+0.83,0.87,0.87,0.92,0.90,0.90,0.95,0.96,1.02,0.97,
+0.95,1.02,1.02,1.10,1.03,1.03,1.16,1.12,1.07,1.13,
+1.14,1.14,1.13,1.16,1.20,1.21,1.16,1.21,1.26,1.23,
+1.31,1.24,1.32,1.29,1.31,1.31,1.32,1.44,1.39,1.41,
+1.41,1.40,1.49,1.41,1.46,1.46,1.56,1.52,1.49,1.62,
+1.52,1.54,1.59,1.57,1.61,1.62,1.62,1.74,1.68,1.72,
+1.73,1.74,1.72,1.68,1.74,1.75,1.75,1.85,1.81,1.81,
+1.80,1.85,1.92,1.91,1.95,1.91,1.85,1.98,1.97,2.00,
+2.00,2.00,2.03,2.04,2.11,2.07,2.08,2.07,2.15,2.10,
+2.10,2.08,2.11,2.20,2.17,2.19,2.23,2.14,2.26,2.26,
+2.25,2.22,2.27,2.33,2.30,2.35,2.33,2.36,2.35,2.36,
+2.37,2.42,2.38,2.51,2.45,2.44,2.53,2.55,2.54,2.51,
+2.54,2.51,2.53,2.55,2.65,2.62,2.65,2.61,2.73,2.70,
+2.60,2.68,2.73,2.72,2.67,2.74,2.74,2.82,2.79,2.83,
+2.85,2.82,2.90,2.83,2.89,2.93,2.92,2.94,2.90,2.92,
+3.03,2.93,2.95,2.98,3.03,3.02,3.17,3.09,3.12,3.09,
+3.12,3.14,3.18,3.20,3.18,3.07,3.21,3.21,3.19,3.23,
+3.28,3.30,3.27,3.21,3.35,3.35,3.44,3.34,3.29,3.35,
+3.42,3.37,3.48,3.43,3.36,3.45,3.43,3.52,3.49,3.51,
+3.54,3.62,3.47,3.66,3.56,3.55,3.55,3.70,3.56,3.61,
+3.65,3.66,3.64,3.69,3.65,3.77,3.75,3.68,3.79,3.73,
+3.68,3.77,3.81,3.84,3.81,3.85,3.85,3.90,3.91,3.92,
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+};
+
+static float sdNumAnchors[] = {
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+};
+
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+1664.35,1663.02,1669.93,1675.42,1687.93,1689.50,1689.51,1694.24,1707.42,1709.69
+};
+
+static float sdNumAnchorBases[] = {
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+101.67,102.87,101.72,98.49,101.43,101.41,100.22,103.89,100.99,105.75,
+101.07,98.99,104.25,102.52,104.86,103.80,104.92,103.79,101.65,103.20,
+102.89,104.67,106.89,105.80,105.61,104.55,107.32,103.27,107.57,110.36,
+109.51,109.84,107.80,109.31,110.47,109.96,109.94,107.07,108.45,109.20,
+108.50,113.23,108.78,106.94,113.69,113.44,112.49,111.78,110.61,116.81,
+112.93,116.00,113.52,111.28,115.21,113.07,113.20,119.81,115.68,114.04,
+116.31,118.31,114.34,115.67,117.17,118.59,115.31,118.66,113.93,118.53,
+117.43,119.18,117.39,118.27,118.75,124.14,121.16,122.18,122.06,119.87,
+122.61,120.04,117.15,120.14,118.33,118.92,122.24,122.57,121.25,123.10,
+125.56,125.13,118.02,123.79,125.28,126.20,121.65,130.40,123.33,122.77,
+121.70,124.70,127.60,128.75,127.56,128.62,126.73,128.47,124.05,131.51,
+129.88,128.05,128.05,127.04,130.92,128.43,132.38,129.23,130.55,130.54,
+129.32,126.45,131.19,130.83,131.27,130.50,128.80,132.68,132.52,128.92,
+132.20,129.82,126.80,135.35,130.81,132.95,137.47,132.99,139.06,133.83,
+31.15,32.18,32.96,33.25,35.89,37.73,36.70,36.97,38.94,38.77,
+39.05,40.46,41.50,42.74,42.60,44.42,45.83,46.11,46.05,48.09,
+49.91,46.24,47.46,50.36,50.83,51.57,51.36,51.30,52.46,54.36,
+53.05,54.40,54.88,52.29,55.46,56.15,59.74,59.26,58.87,58.01,
+60.00,59.94,58.71,62.05,62.57,61.68,62.01,64.98,64.13,64.76,
+63.80,65.43,63.94,65.09,66.64,66.31,68.95,67.71,69.00,68.81,
+67.83,69.49,69.50,68.41,68.23,70.00,71.61,72.73,72.34,71.13,
+74.33,73.18,73.60,76.67,75.45,77.67,76.93,80.32,81.15,76.90,
+77.58,77.64,79.05,78.06,78.58,80.70,81.93,76.72,81.60,82.41,
+75.70,81.11,82.93,82.21,81.57,80.88,83.84,83.64,84.85,86.48,
+85.82,85.00,91.27,86.79,89.92,90.21,90.73,88.19,87.84,89.28,
+89.44,89.02,91.07,91.29,91.81,92.17,92.00,92.69,87.45,92.50,
+97.21,91.01,88.76,92.59,95.41,94.74,95.42,94.34,94.21,97.13,
+95.78,97.01,97.27,100.79,97.02,95.24,97.86,99.36,100.30,99.46,
+96.97,99.21,99.66,102.67,99.27,102.79,103.69,99.81,105.94,103.94,
+99.41,102.09,104.51,104.37,99.28,102.10,102.67,98.87,104.03,110.31,
+106.01,106.46,103.60,105.32,111.15,100.73,111.34,107.33,107.77,105.41,
+106.86,112.07,105.77,113.30,108.58,110.84,113.72,113.70,108.91,108.18,
+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
new file mode 100644
index 0000000..ebab522
--- /dev/null
+++ b/libcpp/alignment/statistics/LookupAnchorDistribution.cpp
@@ -0,0 +1,58 @@
+#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
new file mode 100644
index 0000000..cfc9e35
--- /dev/null
+++ b/libcpp/alignment/statistics/LookupAnchorDistribution.hpp
@@ -0,0 +1,10 @@
+#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
new file mode 100644
index 0000000..cc6bf79
--- /dev/null
+++ b/libcpp/alignment/statistics/StatUtils.cpp
@@ -0,0 +1,45 @@
+#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
new file mode 100644
index 0000000..40ba2a5
--- /dev/null
+++ b/libcpp/alignment/statistics/StatUtils.hpp
@@ -0,0 +1,165 @@
+#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
new file mode 100644
index 0000000..3d1cc76
--- /dev/null
+++ b/libcpp/alignment/statistics/StatUtilsImpl.hpp
@@ -0,0 +1,57 @@
+#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
new file mode 100644
index 0000000..068bc62
--- /dev/null
+++ b/libcpp/alignment/statistics/VarianceAccumulator.hpp
@@ -0,0 +1,28 @@
+#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
new file mode 100644
index 0000000..98bda35
--- /dev/null
+++ b/libcpp/alignment/statistics/VarianceAccumulatorImpl.hpp
@@ -0,0 +1,60 @@
+#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
new file mode 100644
index 0000000..ab37322
--- /dev/null
+++ b/libcpp/alignment/statistics/cdfs.cpp
@@ -0,0 +1,53 @@
+#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
new file mode 100644
index 0000000..b7ac3d2
--- /dev/null
+++ b/libcpp/alignment/statistics/cdfs.hpp
@@ -0,0 +1,418 @@
+#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,
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+ 0.967843225204386, 0.968557237019247, 0.969258091070534, 0.9699459610388, 0.97062101995959,
+ 0.971283440183998, 0.971933393340228, 0.972571050296163, 0.973196581122945, 0.973810155059547,
+ 0.974411940478361, 0.97500210485178, 0.975580814719778, 0.976148235658492, 0.976704532249788,
+ 0.977249868051821, 0.977784405570569, 0.978308306232353, 0.978821730357328, 0.97932483713393,
+ 0.979817784594296, 0.980300729590623, 0.980773827772483, 0.981237233565062, 0.98169110014834,
+ 0.982135579437183, 0.982570822062343, 0.982996977352367, 0.983414193316395, 0.983822616627834,
+ 0.98422239260891, 0.984613665216075, 0.984996577026268, 0.98537126922401, 0.985737881589331,
+ 0.986096552486501, 0.98644741885358, 0.986790616192744, 0.987126278561398, 0.987454538564053,
+ 0.987775527344955, 0.988089374581453, 0.988396208478096, 0.988696155761447, 0.988989341675589,
+ 0.989275889978324, 0.98955592293805, 0.98982956133128, 0.990096924440836, 0.990358130054642,
+ 0.990613294465161, 0.990862532469427, 0.991105957369663, 0.991343680974483, 0.991575813600654,
+ 0.991802464075404, 0.992023739739266, 0.992239746449446, 0.99245058858369, 0.992656369044652,
+ 0.992857189264729, 0.993053149211376, 0.99324434739286, 0.993430880864453, 0.993612845235057,
+ 0.993790334674224, 0.993963441919587, 0.994132258284667, 0.99429687366705, 0.994457376556917,
+ 0.994613854045933, 0.994766391836444, 0.99491507425101, 0.99505998424223, 0.995201203402874,
+ 0.995338811976281, 0.995472888867033, 0.995603511651879, 0.99573075659091, 0.995854698638964,
+ 0.995975411457242, 0.996092967425147, 0.996207437652315, 0.996318891990825, 0.9964273990476,
+ 0.99653302619696, 0.996635839593331, 0.996735904184109, 0.996833283722642, 0.99692804078135,
+ 0.997020236764945, 0.997109931923774, 0.997197185367235, 0.997282055077299, 0.997364597922095,
+ 0.997444869669572, 0.997522925001214, 0.99759881752581, 0.997672599793268, 0.997744323308458,
+ 0.997814038545087, 0.997881794959595, 0.99794764100506, 0.998011624145106, 0.998073790867812,
+ 0.998134186699616, 0.998192856219194, 0.998249843071324, 0.998305189980723, 0.998358938765843,
+ 0.998411130352635, 0.998461804788262, 0.998511001254763, 0.99855875808266, 0.998605112764508,
+ 0.99865010196837, 0.99869376155123, 0.998736126572328, 0.998777231306408, 0.998817109256896,
+ 0.998855793168977, 0.99889331504259, 0.998929706145321, 0.998964997025197, 0.998999217523386,
+ 0.999032396786782, 0.999064563280486, 0.999095744800178, 0.999125968484368, 0.999155260826541,
+ 0.999183647687171, 0.999211154305624, 0.999237805311933, 0.999263624738446, 0.999288636031355,
+ 0.999312862062084, 0.99933632513856, 0.99935904701634, 0.999381048909613, 0.999402351502066,
+ 0.99942297495761, 0.999442938930975, 0.99946226257817, 0.999480964566793, 0.999499063086214,
+ 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
new file mode 100644
index 0000000..1e066d1
--- /dev/null
+++ b/libcpp/alignment/statistics/pdfs.cpp
@@ -0,0 +1,36 @@
+#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
new file mode 100644
index 0000000..5f760c6
--- /dev/null
+++ b/libcpp/alignment/statistics/pdfs.hpp
@@ -0,0 +1,18 @@
+#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
new file mode 100644
index 0000000..85037f2
--- /dev/null
+++ b/libcpp/alignment/suffixarray/LCPTable.hpp
@@ -0,0 +1,182 @@
+#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
new file mode 100644
index 0000000..dd31437
--- /dev/null
+++ b/libcpp/alignment/suffixarray/SharedSuffixArray.hpp
@@ -0,0 +1,83 @@
+#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
new file mode 100644
index 0000000..907bf1b
--- /dev/null
+++ b/libcpp/alignment/suffixarray/SuffixArray.hpp
@@ -0,0 +1,1197 @@
+#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
new file mode 100644
index 0000000..a9047dc
--- /dev/null
+++ b/libcpp/alignment/suffixarray/SuffixArrayTypes.hpp
@@ -0,0 +1,17 @@
+#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
new file mode 100644
index 0000000..0a6f9b8
--- /dev/null
+++ b/libcpp/alignment/suffixarray/ssort.hpp
@@ -0,0 +1,449 @@
+/****************************************************************
+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
new file mode 100644
index 0000000..fefbab7
--- /dev/null
+++ b/libcpp/alignment/tuples/BaseTuple.cpp
@@ -0,0 +1,53 @@
+#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
new file mode 100644
index 0000000..0a6a9ea
--- /dev/null
+++ b/libcpp/alignment/tuples/BaseTuple.hpp
@@ -0,0 +1,27 @@
+#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
new file mode 100644
index 0000000..c60a838
--- /dev/null
+++ b/libcpp/alignment/tuples/CompressedDNATuple.hpp
@@ -0,0 +1,63 @@
+#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
new file mode 100644
index 0000000..acb997e
--- /dev/null
+++ b/libcpp/alignment/tuples/CountedTuple.h
@@ -0,0 +1,16 @@
+#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
new file mode 100644
index 0000000..cf779dd
--- /dev/null
+++ b/libcpp/alignment/tuples/DNATuple.cpp
@@ -0,0 +1,94 @@
+#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
new file mode 100644
index 0000000..57a12ff
--- /dev/null
+++ b/libcpp/alignment/tuples/DNATuple.hpp
@@ -0,0 +1,103 @@
+#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
new file mode 100644
index 0000000..4ba748e
--- /dev/null
+++ b/libcpp/alignment/tuples/DNATupleImpl.hpp
@@ -0,0 +1,200 @@
+#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
new file mode 100644
index 0000000..a5b0dae
--- /dev/null
+++ b/libcpp/alignment/tuples/DNATupleList.h
@@ -0,0 +1,53 @@
+#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
new file mode 100644
index 0000000..8695844
--- /dev/null
+++ b/libcpp/alignment/tuples/HashedTupleList.hpp
@@ -0,0 +1,61 @@
+#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
new file mode 100644
index 0000000..41d9832
--- /dev/null
+++ b/libcpp/alignment/tuples/HashedTupleListImpl.hpp
@@ -0,0 +1,144 @@
+#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
new file mode 100644
index 0000000..603ccd9
--- /dev/null
+++ b/libcpp/alignment/tuples/TupleCountTable.hpp
@@ -0,0 +1,33 @@
+#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
new file mode 100644
index 0000000..805dc66
--- /dev/null
+++ b/libcpp/alignment/tuples/TupleCountTableImpl.hpp
@@ -0,0 +1,101 @@
+#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
new file mode 100644
index 0000000..2f9eef0
--- /dev/null
+++ b/libcpp/alignment/tuples/TupleList.hpp
@@ -0,0 +1,64 @@
+#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
new file mode 100644
index 0000000..fdbf91f
--- /dev/null
+++ b/libcpp/alignment/tuples/TupleListImpl.hpp
@@ -0,0 +1,134 @@
+
+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
new file mode 100644
index 0000000..f731db1
--- /dev/null
+++ b/libcpp/alignment/tuples/TupleMask.h
@@ -0,0 +1,13 @@
+#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
new file mode 100644
index 0000000..dd8c01e
--- /dev/null
+++ b/libcpp/alignment/tuples/TupleMatching.hpp
@@ -0,0 +1,25 @@
+#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
new file mode 100644
index 0000000..c89a247
--- /dev/null
+++ b/libcpp/alignment/tuples/TupleMatchingImpl.hpp
@@ -0,0 +1,106 @@
+#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
new file mode 100644
index 0000000..5b00a7b
--- /dev/null
+++ b/libcpp/alignment/tuples/TupleMetrics.cpp
@@ -0,0 +1,16 @@
+#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
new file mode 100644
index 0000000..841aaf2
--- /dev/null
+++ b/libcpp/alignment/tuples/TupleMetrics.hpp
@@ -0,0 +1,19 @@
+#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
new file mode 100644
index 0000000..2c7d13e
--- /dev/null
+++ b/libcpp/alignment/tuples/TupleOperations.h
@@ -0,0 +1,7 @@
+#ifndef TUPLE_OPERATIONS_H_
+#define TUPLE_OPERATIONS_H_
+
+
+#endif
+
+
diff --git a/libcpp/alignment/tuples/TupleTranslations.h b/libcpp/alignment/tuples/TupleTranslations.h
new file mode 100644
index 0000000..a96cf15
--- /dev/null
+++ b/libcpp/alignment/tuples/TupleTranslations.h
@@ -0,0 +1,4 @@
+#ifndef TUPLE_OPERATIONS_H_
+#define TUPLE_OPERATIONS_H_
+
+
diff --git a/libcpp/alignment/tuples/tuple.h b/libcpp/alignment/tuples/tuple.h
new file mode 100644
index 0000000..5063f08
--- /dev/null
+++ b/libcpp/alignment/tuples/tuple.h
@@ -0,0 +1,82 @@
+#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
new file mode 100644
index 0000000..da738bd
--- /dev/null
+++ b/libcpp/alignment/utils/FileOfFileNames.cpp
@@ -0,0 +1,102 @@
+#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
new file mode 100644
index 0000000..2aef7c6
--- /dev/null
+++ b/libcpp/alignment/utils/FileOfFileNames.hpp
@@ -0,0 +1,27 @@
+#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
new file mode 100644
index 0000000..84813e8
--- /dev/null
+++ b/libcpp/alignment/utils/FileUtils.cpp
@@ -0,0 +1,61 @@
+#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
new file mode 100644
index 0000000..7457b33
--- /dev/null
+++ b/libcpp/alignment/utils/FileUtils.hpp
@@ -0,0 +1,27 @@
+#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
new file mode 100644
index 0000000..018d7bc
--- /dev/null
+++ b/libcpp/alignment/utils/LogUtils.cpp
@@ -0,0 +1,55 @@
+#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
new file mode 100644
index 0000000..16f2ecd
--- /dev/null
+++ b/libcpp/alignment/utils/LogUtils.hpp
@@ -0,0 +1,15 @@
+#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
new file mode 100644
index 0000000..b2653d0
--- /dev/null
+++ b/libcpp/alignment/utils/PhredUtils.cpp
@@ -0,0 +1,13 @@
+#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
new file mode 100644
index 0000000..c90dbdd
--- /dev/null
+++ b/libcpp/alignment/utils/PhredUtils.hpp
@@ -0,0 +1,8 @@
+#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
new file mode 100644
index 0000000..90a1458
--- /dev/null
+++ b/libcpp/alignment/utils/RangeUtils.cpp
@@ -0,0 +1,107 @@
+
+#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
new file mode 100644
index 0000000..b0a41ba
--- /dev/null
+++ b/libcpp/alignment/utils/RangeUtils.hpp
@@ -0,0 +1,56 @@
+/*
+ * ============================================================================
+ *
+ * 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
new file mode 100644
index 0000000..0448f2e
--- /dev/null
+++ b/libcpp/alignment/utils/RegionUtils.cpp
@@ -0,0 +1,302 @@
+#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
new file mode 100644
index 0000000..f5fb870
--- /dev/null
+++ b/libcpp/alignment/utils/RegionUtils.hpp
@@ -0,0 +1,132 @@
+#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
new file mode 100644
index 0000000..fc4b859
--- /dev/null
+++ b/libcpp/alignment/utils/RegionUtilsImpl.hpp
@@ -0,0 +1,215 @@
+#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
new file mode 100644
index 0000000..020a4bb
--- /dev/null
+++ b/libcpp/alignment/utils/SimpleXMLUtils.hpp
@@ -0,0 +1,99 @@
+#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
new file mode 100644
index 0000000..94f7851
--- /dev/null
+++ b/libcpp/alignment/utils/TimeUtils.cpp
@@ -0,0 +1,20 @@
+#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
new file mode 100644
index 0000000..543d929
--- /dev/null
+++ b/libcpp/alignment/utils/TimeUtils.hpp
@@ -0,0 +1,7 @@
+#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
new file mode 100755
index 0000000..b147c09
--- /dev/null
+++ b/libcpp/configure.py
@@ -0,0 +1,268 @@
+#!/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
new file mode 100644
index 0000000..204d4d7
--- /dev/null
+++ b/libcpp/hdf/BufferedHDF2DArray.cpp
@@ -0,0 +1,79 @@
+#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
new file mode 100644
index 0000000..36a4a33
--- /dev/null
+++ b/libcpp/hdf/BufferedHDF2DArray.hpp
@@ -0,0 +1,158 @@
+#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
new file mode 100644
index 0000000..49336ef
--- /dev/null
+++ b/libcpp/hdf/BufferedHDF2DArrayImpl.hpp
@@ -0,0 +1,379 @@
+#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
new file mode 100644
index 0000000..a23f6f8
--- /dev/null
+++ b/libcpp/hdf/BufferedHDFArray.cpp
@@ -0,0 +1,92 @@
+#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
new file mode 100644
index 0000000..cb1037e
--- /dev/null
+++ b/libcpp/hdf/BufferedHDFArray.hpp
@@ -0,0 +1,207 @@
+#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
new file mode 100644
index 0000000..9f890ca
--- /dev/null
+++ b/libcpp/hdf/BufferedHDFArrayImpl.hpp
@@ -0,0 +1,435 @@
+#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
new file mode 100644
index 0000000..3184e49
--- /dev/null
+++ b/libcpp/hdf/DatasetCollection.cpp
@@ -0,0 +1,61 @@
+#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
new file mode 100644
index 0000000..b3305f7
--- /dev/null
+++ b/libcpp/hdf/DatasetCollection.hpp
@@ -0,0 +1,41 @@
+#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
new file mode 100644
index 0000000..7344e9f
--- /dev/null
+++ b/libcpp/hdf/DatasetCollectionImpl.hpp
@@ -0,0 +1,29 @@
+#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
new file mode 100644
index 0000000..1e76e6e
--- /dev/null
+++ b/libcpp/hdf/HDF2DArray.hpp
@@ -0,0 +1,25 @@
+#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
new file mode 100644
index 0000000..ebdc05e
--- /dev/null
+++ b/libcpp/hdf/HDFAlnGroup.hpp
@@ -0,0 +1,50 @@
+#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
new file mode 100644
index 0000000..959098e
--- /dev/null
+++ b/libcpp/hdf/HDFAlnGroupGroup.cpp
@@ -0,0 +1,52 @@
+#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
new file mode 100644
index 0000000..8045e48
--- /dev/null
+++ b/libcpp/hdf/HDFAlnGroupGroup.hpp
@@ -0,0 +1,27 @@
+#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
new file mode 100644
index 0000000..4beba5f
--- /dev/null
+++ b/libcpp/hdf/HDFAlnInfoGroup.cpp
@@ -0,0 +1,102 @@
+#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
new file mode 100644
index 0000000..4941b1b
--- /dev/null
+++ b/libcpp/hdf/HDFAlnInfoGroup.hpp
@@ -0,0 +1,46 @@
+#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
new file mode 100644
index 0000000..af4c66a
--- /dev/null
+++ b/libcpp/hdf/HDFArray.hpp
@@ -0,0 +1,85 @@
+#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
new file mode 100644
index 0000000..ef23749
--- /dev/null
+++ b/libcpp/hdf/HDFAtom.cpp
@@ -0,0 +1,159 @@
+#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
new file mode 100644
index 0000000..f8934df
--- /dev/null
+++ b/libcpp/hdf/HDFAtom.hpp
@@ -0,0 +1,176 @@
+#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
new file mode 100644
index 0000000..da57d08
--- /dev/null
+++ b/libcpp/hdf/HDFAttributable.cpp
@@ -0,0 +1,41 @@
+#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
new file mode 100644
index 0000000..4b223c7
--- /dev/null
+++ b/libcpp/hdf/HDFAttributable.hpp
@@ -0,0 +1,23 @@
+#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
new file mode 100644
index 0000000..48e375d
--- /dev/null
+++ b/libcpp/hdf/HDFBasReader.cpp
@@ -0,0 +1,46 @@
+#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
new file mode 100644
index 0000000..23fe235
--- /dev/null
+++ b/libcpp/hdf/HDFBasReader.hpp
@@ -0,0 +1,1178 @@
+#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
new file mode 100644
index 0000000..dc4bac9
--- /dev/null
+++ b/libcpp/hdf/HDFBasWriter.hpp
@@ -0,0 +1,390 @@
+#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
new file mode 100644
index 0000000..c93be14
--- /dev/null
+++ b/libcpp/hdf/HDFCCSReader.hpp
@@ -0,0 +1,257 @@
+#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
new file mode 100644
index 0000000..dd9e54e
--- /dev/null
+++ b/libcpp/hdf/HDFCmpData.hpp
@@ -0,0 +1,36 @@
+#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
new file mode 100644
index 0000000..6f6459c
--- /dev/null
+++ b/libcpp/hdf/HDFCmpExperimentGroup.cpp
@@ -0,0 +1,193 @@
+#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
new file mode 100644
index 0000000..05d5cfb
--- /dev/null
+++ b/libcpp/hdf/HDFCmpExperimentGroup.hpp
@@ -0,0 +1,70 @@
+#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
new file mode 100644
index 0000000..d4d6984
--- /dev/null
+++ b/libcpp/hdf/HDFCmpFile.hpp
@@ -0,0 +1,844 @@
+#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
new file mode 100644
index 0000000..f12d2e6
--- /dev/null
+++ b/libcpp/hdf/HDFCmpReader.hpp
@@ -0,0 +1,663 @@
+#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
new file mode 100644
index 0000000..69650ec
--- /dev/null
+++ b/libcpp/hdf/HDFCmpRefAlignmentGroup.hpp
@@ -0,0 +1,102 @@
+#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
new file mode 100644
index 0000000..d84084f
--- /dev/null
+++ b/libcpp/hdf/HDFCmpRootGroup.hpp
@@ -0,0 +1,66 @@
+#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
new file mode 100644
index 0000000..b240d39
--- /dev/null
+++ b/libcpp/hdf/HDFCmpSupportedFields.cpp
@@ -0,0 +1,25 @@
+#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
new file mode 100644
index 0000000..8ac0e87
--- /dev/null
+++ b/libcpp/hdf/HDFCmpSupportedFields.hpp
@@ -0,0 +1,13 @@
+#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
new file mode 100644
index 0000000..2b859eb
--- /dev/null
+++ b/libcpp/hdf/HDFCommonFG.hpp
@@ -0,0 +1,13 @@
+#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
new file mode 100644
index 0000000..6dbd24a
--- /dev/null
+++ b/libcpp/hdf/HDFConfig.hpp
@@ -0,0 +1,7 @@
+#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
new file mode 100644
index 0000000..0283992
--- /dev/null
+++ b/libcpp/hdf/HDFData.cpp
@@ -0,0 +1,74 @@
+#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
new file mode 100644
index 0000000..5ca1455
--- /dev/null
+++ b/libcpp/hdf/HDFData.hpp
@@ -0,0 +1,52 @@
+#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
new file mode 100644
index 0000000..285b8f6
--- /dev/null
+++ b/libcpp/hdf/HDFFile.cpp
@@ -0,0 +1,53 @@
+#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
new file mode 100644
index 0000000..ae67c3e
--- /dev/null
+++ b/libcpp/hdf/HDFFile.hpp
@@ -0,0 +1,32 @@
+#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
new file mode 100644
index 0000000..caaca07
--- /dev/null
+++ b/libcpp/hdf/HDFFileLogGroup.hpp
@@ -0,0 +1,55 @@
+#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
new file mode 100644
index 0000000..396943b
--- /dev/null
+++ b/libcpp/hdf/HDFGroup.cpp
@@ -0,0 +1,58 @@
+#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
new file mode 100644
index 0000000..e9f806c
--- /dev/null
+++ b/libcpp/hdf/HDFGroup.hpp
@@ -0,0 +1,36 @@
+#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
new file mode 100644
index 0000000..988bc95
--- /dev/null
+++ b/libcpp/hdf/HDFMovieInfoGroup.hpp
@@ -0,0 +1,79 @@
+#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
new file mode 100644
index 0000000..14ddc3a
--- /dev/null
+++ b/libcpp/hdf/HDFNewBasReader.cpp
@@ -0,0 +1,72 @@
+#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
new file mode 100644
index 0000000..4992cff
--- /dev/null
+++ b/libcpp/hdf/HDFNewBasReader.hpp
@@ -0,0 +1,39 @@
+#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
new file mode 100644
index 0000000..750be08
--- /dev/null
+++ b/libcpp/hdf/HDFPlsReader.hpp
@@ -0,0 +1,542 @@
+#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
new file mode 100644
index 0000000..9efc92b
--- /dev/null
+++ b/libcpp/hdf/HDFPlsWriter.hpp
@@ -0,0 +1,195 @@
+#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
new file mode 100644
index 0000000..cd88874
--- /dev/null
+++ b/libcpp/hdf/HDFPulseDataFile.cpp
@@ -0,0 +1,151 @@
+#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
new file mode 100644
index 0000000..0cec337
--- /dev/null
+++ b/libcpp/hdf/HDFPulseDataFile.hpp
@@ -0,0 +1,67 @@
+#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
new file mode 100644
index 0000000..727b311
--- /dev/null
+++ b/libcpp/hdf/HDFRefGroupGroup.hpp
@@ -0,0 +1,65 @@
+#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
new file mode 100644
index 0000000..72a85fe
--- /dev/null
+++ b/libcpp/hdf/HDFRefInfoGroup.hpp
@@ -0,0 +1,84 @@
+#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
new file mode 100644
index 0000000..80bc2db
--- /dev/null
+++ b/libcpp/hdf/HDFRegionTableReader.cpp
@@ -0,0 +1,149 @@
+#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
new file mode 100644
index 0000000..470cddf
--- /dev/null
+++ b/libcpp/hdf/HDFRegionTableReader.hpp
@@ -0,0 +1,47 @@
+#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
new file mode 100644
index 0000000..f1c38b9
--- /dev/null
+++ b/libcpp/hdf/HDFRegionTableWriter.hpp
@@ -0,0 +1,140 @@
+#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
new file mode 100644
index 0000000..737f19e
--- /dev/null
+++ b/libcpp/hdf/HDFSMRTSequenceReader.hpp
@@ -0,0 +1,71 @@
+#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
new file mode 100644
index 0000000..daed4b2
--- /dev/null
+++ b/libcpp/hdf/HDFScanDataReader.cpp
@@ -0,0 +1,262 @@
+#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
new file mode 100644
index 0000000..7da6649
--- /dev/null
+++ b/libcpp/hdf/HDFScanDataReader.hpp
@@ -0,0 +1,101 @@
+#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
new file mode 100644
index 0000000..874aba0
--- /dev/null
+++ b/libcpp/hdf/HDFScanDataWriter.cpp
@@ -0,0 +1,164 @@
+#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
new file mode 100644
index 0000000..f92d8e6
--- /dev/null
+++ b/libcpp/hdf/HDFScanDataWriter.hpp
@@ -0,0 +1,71 @@
+#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
new file mode 100644
index 0000000..71f7de8
--- /dev/null
+++ b/libcpp/hdf/HDFSentinalFile.hpp
@@ -0,0 +1,21 @@
+#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
new file mode 100644
index 0000000..ad0739b
--- /dev/null
+++ b/libcpp/hdf/HDFUtils.cpp
@@ -0,0 +1,82 @@
+#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
new file mode 100644
index 0000000..ee9409e
--- /dev/null
+++ b/libcpp/hdf/HDFUtils.hpp
@@ -0,0 +1,44 @@
+#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
new file mode 100644
index 0000000..3600c5a
--- /dev/null
+++ b/libcpp/hdf/HDFWriteBuffer.hpp
@@ -0,0 +1,52 @@
+#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
new file mode 100644
index 0000000..a79107e
--- /dev/null
+++ b/libcpp/hdf/HDFZMWReader.cpp
@@ -0,0 +1,136 @@
+#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
new file mode 100644
index 0000000..8cd7d2d
--- /dev/null
+++ b/libcpp/hdf/HDFZMWReader.hpp
@@ -0,0 +1,45 @@
+#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
new file mode 120000
index 0000000..2247f36
--- /dev/null
+++ b/libcpp/hdf/build.mk
@@ -0,0 +1 @@
+makefile
\ No newline at end of file
diff --git a/libcpp/hdf/makefile b/libcpp/hdf/makefile
new file mode 100644
index 0000000..c92a229
--- /dev/null
+++ b/libcpp/hdf/makefile
@@ -0,0 +1,28 @@
+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 $(dependencies)
diff --git a/libcpp/hdf/old.Makefile b/libcpp/hdf/old.Makefile
new file mode 100644
index 0000000..1998195
--- /dev/null
+++ b/libcpp/hdf/old.Makefile
@@ -0,0 +1,94 @@
+
+include ../common.mk
+
+# To enable building a shared library, invoke as "make SHARED_LIB=true ..."
+ifneq ($(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
new file mode 100644
index 0000000..64a113b
--- /dev/null
+++ b/libcpp/makefile
@@ -0,0 +1,32 @@
+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
new file mode 100644
index 0000000..1e52e1d
--- /dev/null
+++ b/libcpp/old.Makefile
@@ -0,0 +1,28 @@
+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
new file mode 100644
index 0000000..4c3cf0b
--- /dev/null
+++ b/libcpp/pbdata/.gitignore
@@ -0,0 +1,2 @@
+/libconfig.h
+/defines.mk
diff --git a/libcpp/pbdata/CCSSequence.cpp b/libcpp/pbdata/CCSSequence.cpp
new file mode 100644
index 0000000..1f8e5b9
--- /dev/null
+++ b/libcpp/pbdata/CCSSequence.cpp
@@ -0,0 +1,35 @@
+#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
new file mode 100644
index 0000000..15e89d6
--- /dev/null
+++ b/libcpp/pbdata/CCSSequence.hpp
@@ -0,0 +1,43 @@
+#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
new file mode 100644
index 0000000..2b99c42
--- /dev/null
+++ b/libcpp/pbdata/ChangeListID.cpp
@@ -0,0 +1,64 @@
+#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
new file mode 100644
index 0000000..eda525e
--- /dev/null
+++ b/libcpp/pbdata/ChangeListID.hpp
@@ -0,0 +1,38 @@
+#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
new file mode 100644
index 0000000..2f1c92e
--- /dev/null
+++ b/libcpp/pbdata/CommandLineParser.cpp
@@ -0,0 +1,846 @@
+#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
new file mode 100644
index 0000000..8cc7a8e
--- /dev/null
+++ b/libcpp/pbdata/CommandLineParser.hpp
@@ -0,0 +1,175 @@
+#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
new file mode 100644
index 0000000..f94f37f
--- /dev/null
+++ b/libcpp/pbdata/Compare4BitCompressed.hpp
@@ -0,0 +1,98 @@
+/*
+ * ============================================================================
+ *
+ * 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
new file mode 100644
index 0000000..a3fa6d1
--- /dev/null
+++ b/libcpp/pbdata/CompressedDNASequence.hpp
@@ -0,0 +1,89 @@
+#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
new file mode 100644
index 0000000..45b3aaa
--- /dev/null
+++ b/libcpp/pbdata/CompressedSequence.hpp
@@ -0,0 +1,100 @@
+#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
new file mode 100644
index 0000000..7759541
--- /dev/null
+++ b/libcpp/pbdata/CompressedSequenceImpl.hpp
@@ -0,0 +1,343 @@
+#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
new file mode 100644
index 0000000..cec3fab
--- /dev/null
+++ b/libcpp/pbdata/DNASequence.cpp
@@ -0,0 +1,402 @@
+#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
new file mode 100644
index 0000000..286e7d8
--- /dev/null
+++ b/libcpp/pbdata/DNASequence.hpp
@@ -0,0 +1,183 @@
+#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
new file mode 100644
index 0000000..b51575b
--- /dev/null
+++ b/libcpp/pbdata/Enumerations.h
@@ -0,0 +1,39 @@
+#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
new file mode 100644
index 0000000..6477fc0
--- /dev/null
+++ b/libcpp/pbdata/FASTAReader.cpp
@@ -0,0 +1,420 @@
+#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
new file mode 100644
index 0000000..6cc5ca9
--- /dev/null
+++ b/libcpp/pbdata/FASTAReader.hpp
@@ -0,0 +1,80 @@
+#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
new file mode 100644
index 0000000..4b579cc
--- /dev/null
+++ b/libcpp/pbdata/FASTASequence.cpp
@@ -0,0 +1,246 @@
+#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
new file mode 100644
index 0000000..bfadb58
--- /dev/null
+++ b/libcpp/pbdata/FASTASequence.hpp
@@ -0,0 +1,91 @@
+#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
new file mode 100644
index 0000000..324d57a
--- /dev/null
+++ b/libcpp/pbdata/FASTQReader.cpp
@@ -0,0 +1,89 @@
+#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
new file mode 100644
index 0000000..4caeab3
--- /dev/null
+++ b/libcpp/pbdata/FASTQReader.hpp
@@ -0,0 +1,24 @@
+#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
new file mode 100644
index 0000000..26789ac
--- /dev/null
+++ b/libcpp/pbdata/FASTQSequence.cpp
@@ -0,0 +1,651 @@
+#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
new file mode 100644
index 0000000..f94b2b0
--- /dev/null
+++ b/libcpp/pbdata/FASTQSequence.hpp
@@ -0,0 +1,146 @@
+#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
new file mode 100644
index 0000000..d9f36e1
--- /dev/null
+++ b/libcpp/pbdata/GFFFile.cpp
@@ -0,0 +1,39 @@
+#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
new file mode 100644
index 0000000..2e410ec
--- /dev/null
+++ b/libcpp/pbdata/GFFFile.hpp
@@ -0,0 +1,33 @@
+#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
new file mode 100644
index 0000000..dd1f45a
--- /dev/null
+++ b/libcpp/pbdata/MD5Utils.cpp
@@ -0,0 +1,464 @@
+
+// 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
new file mode 100644
index 0000000..8957933
--- /dev/null
+++ b/libcpp/pbdata/MD5Utils.hpp
@@ -0,0 +1,113 @@
+#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
new file mode 100644
index 0000000..3e8f78e
--- /dev/null
+++ b/libcpp/pbdata/MD5UtilsImpl.hpp
@@ -0,0 +1,57 @@
+#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
new file mode 100644
index 0000000..ba46f6b
--- /dev/null
+++ b/libcpp/pbdata/NucConversion.cpp
@@ -0,0 +1,409 @@
+#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
new file mode 100644
index 0000000..892dd07
--- /dev/null
+++ b/libcpp/pbdata/NucConversion.hpp
@@ -0,0 +1,50 @@
+#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
new file mode 100644
index 0000000..957839b
--- /dev/null
+++ b/libcpp/pbdata/PackedDNASequence.cpp
@@ -0,0 +1,233 @@
+#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
new file mode 100644
index 0000000..d780c0e
--- /dev/null
+++ b/libcpp/pbdata/PackedDNASequence.hpp
@@ -0,0 +1,60 @@
+#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
new file mode 100644
index 0000000..5179735
--- /dev/null
+++ b/libcpp/pbdata/ReverseCompressIndex.cpp
@@ -0,0 +1,40 @@
+#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
new file mode 100644
index 0000000..bfa2601
--- /dev/null
+++ b/libcpp/pbdata/ReverseCompressIndex.hpp
@@ -0,0 +1,25 @@
+#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
new file mode 100644
index 0000000..baabf57
--- /dev/null
+++ b/libcpp/pbdata/SMRTSequence.cpp
@@ -0,0 +1,283 @@
+#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
new file mode 100644
index 0000000..f7cff1c
--- /dev/null
+++ b/libcpp/pbdata/SMRTSequence.hpp
@@ -0,0 +1,115 @@
+#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
new file mode 100644
index 0000000..8e0b087
--- /dev/null
+++ b/libcpp/pbdata/SeqUtils.hpp
@@ -0,0 +1,17 @@
+#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
new file mode 100644
index 0000000..35754d9
--- /dev/null
+++ b/libcpp/pbdata/SeqUtilsImpl.hpp
@@ -0,0 +1,47 @@
+#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
new file mode 100644
index 0000000..2b008d4
--- /dev/null
+++ b/libcpp/pbdata/StringUtils.cpp
@@ -0,0 +1,133 @@
+#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
new file mode 100644
index 0000000..ea895a2
--- /dev/null
+++ b/libcpp/pbdata/StringUtils.hpp
@@ -0,0 +1,71 @@
+#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
new file mode 100644
index 0000000..54fb856
--- /dev/null
+++ b/libcpp/pbdata/Types.h
@@ -0,0 +1,21 @@
+#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
new file mode 100644
index 0000000..c654c9d
--- /dev/null
+++ b/libcpp/pbdata/VectorUtils.hpp
@@ -0,0 +1,17 @@
+#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
new file mode 100644
index 0000000..d3569d4
--- /dev/null
+++ b/libcpp/pbdata/alignment/CmpAlignment.cpp
@@ -0,0 +1,219 @@
+#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
new file mode 100644
index 0000000..484bfa1
--- /dev/null
+++ b/libcpp/pbdata/alignment/CmpAlignment.hpp
@@ -0,0 +1,126 @@
+#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
new file mode 100644
index 0000000..e8b9a5f
--- /dev/null
+++ b/libcpp/pbdata/alignment/CmpAlignmentImpl.hpp
@@ -0,0 +1,6 @@
+
+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
new file mode 100644
index 0000000..2817bce
--- /dev/null
+++ b/libcpp/pbdata/amos/AfgBasWriter.cpp
@@ -0,0 +1,102 @@
+#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
new file mode 100644
index 0000000..c945f88
--- /dev/null
+++ b/libcpp/pbdata/amos/AfgBasWriter.hpp
@@ -0,0 +1,59 @@
+#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
new file mode 120000
index 0000000..2247f36
--- /dev/null
+++ b/libcpp/pbdata/build.mk
@@ -0,0 +1 @@
+makefile
\ No newline at end of file
diff --git a/libcpp/pbdata/defs.h b/libcpp/pbdata/defs.h
new file mode 100644
index 0000000..c01d625
--- /dev/null
+++ b/libcpp/pbdata/defs.h
@@ -0,0 +1,19 @@
+#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
new file mode 100644
index 0000000..1e95a46
--- /dev/null
+++ b/libcpp/pbdata/loadpulses/MetricField.cpp
@@ -0,0 +1,87 @@
+#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
new file mode 100644
index 0000000..a930017
--- /dev/null
+++ b/libcpp/pbdata/loadpulses/MetricField.hpp
@@ -0,0 +1,115 @@
+#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
new file mode 100644
index 0000000..51140d3
--- /dev/null
+++ b/libcpp/pbdata/loadpulses/MovieAlnIndexLookupTable.cpp
@@ -0,0 +1,54 @@
+#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
new file mode 100644
index 0000000..f69811c
--- /dev/null
+++ b/libcpp/pbdata/loadpulses/MovieAlnIndexLookupTable.hpp
@@ -0,0 +1,117 @@
+/*
+ * =====================================================================================
+ *
+ * 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
new file mode 100644
index 0000000..fd4a65c
--- /dev/null
+++ b/libcpp/pbdata/makefile
@@ -0,0 +1,40 @@
+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
new file mode 100644
index 0000000..1664f9e
--- /dev/null
+++ b/libcpp/pbdata/matrix/FlatMatrix.hpp
@@ -0,0 +1,98 @@
+#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
new file mode 100644
index 0000000..5536cb7
--- /dev/null
+++ b/libcpp/pbdata/matrix/FlatMatrixImpl.hpp
@@ -0,0 +1,192 @@
+#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
new file mode 100644
index 0000000..3ef6bca
--- /dev/null
+++ b/libcpp/pbdata/matrix/Matrix.hpp
@@ -0,0 +1,50 @@
+#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
new file mode 100644
index 0000000..c66aaf4
--- /dev/null
+++ b/libcpp/pbdata/matrix/MatrixImpl.hpp
@@ -0,0 +1,117 @@
+#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
new file mode 100644
index 0000000..cb5ab3c
--- /dev/null
+++ b/libcpp/pbdata/metagenome/FindRandomSequence.hpp
@@ -0,0 +1,70 @@
+#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
new file mode 100644
index 0000000..7a43cba
--- /dev/null
+++ b/libcpp/pbdata/metagenome/SequenceIndexDatabase.hpp
@@ -0,0 +1,96 @@
+#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
new file mode 100644
index 0000000..e26f61e
--- /dev/null
+++ b/libcpp/pbdata/metagenome/SequenceIndexDatabaseImpl.hpp
@@ -0,0 +1,347 @@
+#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
new file mode 100644
index 0000000..078da23
--- /dev/null
+++ b/libcpp/pbdata/metagenome/TitleTable.cpp
@@ -0,0 +1,109 @@
+#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
new file mode 100644
index 0000000..14b23a7
--- /dev/null
+++ b/libcpp/pbdata/metagenome/TitleTable.hpp
@@ -0,0 +1,39 @@
+#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
new file mode 100755
index 0000000..e438893
--- /dev/null
+++ b/libcpp/pbdata/mklibconfig.sh
@@ -0,0 +1,32 @@
+#!/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" > $fn
+fi
diff --git a/libcpp/pbdata/old.Makefile b/libcpp/pbdata/old.Makefile
new file mode 100644
index 0000000..a01c77e
--- /dev/null
+++ b/libcpp/pbdata/old.Makefile
@@ -0,0 +1,87 @@
+# Let common.mk know that that the third party checks should be ignored
+COMMON_NO_THIRD_PARTY_REQD := true
+
+include ../common.mk
+
+CXXOPTS := -std=c++11 -pedantic -MMD -MP
+INCLUDES := -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment
+
+# To enable building a shared library, invoke as "make SHARED_LIB=true ..."
+ifneq ($(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
new file mode 100644
index 0000000..45ec117
--- /dev/null
+++ b/libcpp/pbdata/qvs/QualityTransform.cpp
@@ -0,0 +1,23 @@
+#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
new file mode 100644
index 0000000..73c8f27
--- /dev/null
+++ b/libcpp/pbdata/qvs/QualityTransform.hpp
@@ -0,0 +1,26 @@
+#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
new file mode 100644
index 0000000..e9f1775
--- /dev/null
+++ b/libcpp/pbdata/qvs/QualityValue.cpp
@@ -0,0 +1,65 @@
+#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
new file mode 100644
index 0000000..9def8e5
--- /dev/null
+++ b/libcpp/pbdata/qvs/QualityValue.hpp
@@ -0,0 +1,31 @@
+#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
new file mode 100644
index 0000000..8e3ae5d
--- /dev/null
+++ b/libcpp/pbdata/qvs/QualityValueVector.hpp
@@ -0,0 +1,47 @@
+#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
new file mode 100644
index 0000000..7d33266
--- /dev/null
+++ b/libcpp/pbdata/qvs/QualityValueVectorImpl.hpp
@@ -0,0 +1,99 @@
+#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
new file mode 100644
index 0000000..bf4c56a
--- /dev/null
+++ b/libcpp/pbdata/reads/BaseFile.cpp
@@ -0,0 +1,82 @@
+#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
new file mode 100644
index 0000000..d3b6afb
--- /dev/null
+++ b/libcpp/pbdata/reads/BaseFile.hpp
@@ -0,0 +1,49 @@
+#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
new file mode 100644
index 0000000..b09c927
--- /dev/null
+++ b/libcpp/pbdata/reads/BaseFileImpl.hpp
@@ -0,0 +1,11 @@
+#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
new file mode 100644
index 0000000..ff9d1f7
--- /dev/null
+++ b/libcpp/pbdata/reads/HoleXY.cpp
@@ -0,0 +1,14 @@
+#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
new file mode 100644
index 0000000..5386c72
--- /dev/null
+++ b/libcpp/pbdata/reads/HoleXY.hpp
@@ -0,0 +1,14 @@
+#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
new file mode 100644
index 0000000..437a0fb
--- /dev/null
+++ b/libcpp/pbdata/reads/PulseBaseCommon.cpp
@@ -0,0 +1,37 @@
+#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
new file mode 100644
index 0000000..e8b86fc
--- /dev/null
+++ b/libcpp/pbdata/reads/PulseBaseCommon.hpp
@@ -0,0 +1,26 @@
+#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
new file mode 100644
index 0000000..7d2db0b
--- /dev/null
+++ b/libcpp/pbdata/reads/PulseFile.cpp
@@ -0,0 +1,76 @@
+#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
new file mode 100644
index 0000000..d5c4d89
--- /dev/null
+++ b/libcpp/pbdata/reads/PulseFile.hpp
@@ -0,0 +1,53 @@
+#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
new file mode 100644
index 0000000..7fc1f8d
--- /dev/null
+++ b/libcpp/pbdata/reads/PulseFileImpl.hpp
@@ -0,0 +1,21 @@
+#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
new file mode 100644
index 0000000..c21838f
--- /dev/null
+++ b/libcpp/pbdata/reads/ReadInterval.hpp
@@ -0,0 +1,18 @@
+#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
new file mode 100644
index 0000000..7e15ce0
--- /dev/null
+++ b/libcpp/pbdata/reads/ReadType.cpp
@@ -0,0 +1,43 @@
+#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
new file mode 100644
index 0000000..02279da
--- /dev/null
+++ b/libcpp/pbdata/reads/ReadType.hpp
@@ -0,0 +1,18 @@
+#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
new file mode 100644
index 0000000..54582a7
--- /dev/null
+++ b/libcpp/pbdata/reads/RegionTable.cpp
@@ -0,0 +1,159 @@
+#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
new file mode 100644
index 0000000..497e625
--- /dev/null
+++ b/libcpp/pbdata/reads/RegionTable.hpp
@@ -0,0 +1,95 @@
+#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
new file mode 100644
index 0000000..3114376
--- /dev/null
+++ b/libcpp/pbdata/reads/ScanData.cpp
@@ -0,0 +1,12 @@
+#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
new file mode 100644
index 0000000..8cf07ea
--- /dev/null
+++ b/libcpp/pbdata/reads/ScanData.hpp
@@ -0,0 +1,20 @@
+#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
new file mode 100644
index 0000000..64381ed
--- /dev/null
+++ b/libcpp/pbdata/reads/ZMWGroupEntry.cpp
@@ -0,0 +1,8 @@
+#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
new file mode 100644
index 0000000..05234df
--- /dev/null
+++ b/libcpp/pbdata/reads/ZMWGroupEntry.hpp
@@ -0,0 +1,17 @@
+#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
new file mode 100644
index 0000000..9f680cb
--- /dev/null
+++ b/libcpp/pbdata/saf/AlnGroup.cpp
@@ -0,0 +1,12 @@
+#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
new file mode 100644
index 0000000..e941b19
--- /dev/null
+++ b/libcpp/pbdata/saf/AlnGroup.hpp
@@ -0,0 +1,14 @@
+#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
new file mode 100644
index 0000000..6d59ad2
--- /dev/null
+++ b/libcpp/pbdata/saf/AlnInfo.hpp
@@ -0,0 +1,17 @@
+#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
new file mode 100644
index 0000000..f76a386
--- /dev/null
+++ b/libcpp/pbdata/saf/MovieInfo.cpp
@@ -0,0 +1,13 @@
+#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
new file mode 100644
index 0000000..c92f819
--- /dev/null
+++ b/libcpp/pbdata/saf/MovieInfo.hpp
@@ -0,0 +1,19 @@
+#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
new file mode 100644
index 0000000..fcd9bbf
--- /dev/null
+++ b/libcpp/pbdata/saf/RefGroup.cpp
@@ -0,0 +1,25 @@
+#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
new file mode 100644
index 0000000..7c3b012
--- /dev/null
+++ b/libcpp/pbdata/saf/RefGroup.hpp
@@ -0,0 +1,21 @@
+#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
new file mode 100644
index 0000000..48259a7
--- /dev/null
+++ b/libcpp/pbdata/saf/RefInfo.cpp
@@ -0,0 +1,20 @@
+#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
new file mode 100644
index 0000000..39cda75
--- /dev/null
+++ b/libcpp/pbdata/saf/RefInfo.hpp
@@ -0,0 +1,26 @@
+#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
new file mode 100644
index 0000000..6e8bc49
--- /dev/null
+++ b/libcpp/pbdata/sam/AlignmentSet.hpp
@@ -0,0 +1,31 @@
+#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
new file mode 100644
index 0000000..ddd0e5d
--- /dev/null
+++ b/libcpp/pbdata/sam/AlignmentSetImpl.hpp
@@ -0,0 +1,31 @@
+#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
new file mode 100644
index 0000000..979e125
--- /dev/null
+++ b/libcpp/pbdata/sam/CigarString.h
@@ -0,0 +1,23 @@
+#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
new file mode 100644
index 0000000..161e2c3
--- /dev/null
+++ b/libcpp/pbdata/sam/ReadGroup.cpp
@@ -0,0 +1,51 @@
+#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
new file mode 100644
index 0000000..24d6941
--- /dev/null
+++ b/libcpp/pbdata/sam/ReadGroup.hpp
@@ -0,0 +1,40 @@
+#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
new file mode 100644
index 0000000..6da44b9
--- /dev/null
+++ b/libcpp/pbdata/sam/ReferenceSequence.cpp
@@ -0,0 +1,47 @@
+#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
new file mode 100644
index 0000000..b5bb380
--- /dev/null
+++ b/libcpp/pbdata/sam/ReferenceSequence.hpp
@@ -0,0 +1,72 @@
+#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
new file mode 100644
index 0000000..e362d65
--- /dev/null
+++ b/libcpp/pbdata/sam/SAMAlignment.cpp
@@ -0,0 +1,199 @@
+#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
new file mode 100644
index 0000000..a4183fd
--- /dev/null
+++ b/libcpp/pbdata/sam/SAMAlignment.hpp
@@ -0,0 +1,97 @@
+#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
new file mode 100644
index 0000000..10b311d
--- /dev/null
+++ b/libcpp/pbdata/sam/SAMFlag.h
@@ -0,0 +1,48 @@
+#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
new file mode 100644
index 0000000..00c3d33
--- /dev/null
+++ b/libcpp/pbdata/sam/SAMHeader.cpp
@@ -0,0 +1,31 @@
+#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
new file mode 100644
index 0000000..0a862a3
--- /dev/null
+++ b/libcpp/pbdata/sam/SAMHeader.hpp
@@ -0,0 +1,18 @@
+#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
new file mode 100644
index 0000000..c034228
--- /dev/null
+++ b/libcpp/pbdata/sam/SAMKeywordValuePair.cpp
@@ -0,0 +1,51 @@
+#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
new file mode 100644
index 0000000..b4610f8
--- /dev/null
+++ b/libcpp/pbdata/sam/SAMKeywordValuePair.hpp
@@ -0,0 +1,50 @@
+#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
new file mode 100644
index 0000000..624acc5
--- /dev/null
+++ b/libcpp/pbdata/sam/SAMKeywordValuePairImpl.hpp
@@ -0,0 +1,32 @@
+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
new file mode 100644
index 0000000..16688d8
--- /dev/null
+++ b/libcpp/pbdata/sam/SAMReader.hpp
@@ -0,0 +1,61 @@
+#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
new file mode 100644
index 0000000..b92ffc1
--- /dev/null
+++ b/libcpp/pbdata/sam/SAMReaderImpl.hpp
@@ -0,0 +1,197 @@
+#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
new file mode 100644
index 0000000..9686cb5
--- /dev/null
+++ b/libcpp/pbdata/utils.hpp
@@ -0,0 +1,20 @@
+#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
new file mode 100644
index 0000000..0bc4bf3
--- /dev/null
+++ b/libcpp/pbdata/utils/BitUtils.cpp
@@ -0,0 +1,99 @@
+#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
new file mode 100644
index 0000000..3914b7c
--- /dev/null
+++ b/libcpp/pbdata/utils/BitUtils.hpp
@@ -0,0 +1,14 @@
+#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
new file mode 100644
index 0000000..b2430b0
--- /dev/null
+++ b/libcpp/pbdata/utils/SMRTReadUtils.cpp
@@ -0,0 +1,45 @@
+
+#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
new file mode 100644
index 0000000..bbf0d9c
--- /dev/null
+++ b/libcpp/pbdata/utils/SMRTReadUtils.hpp
@@ -0,0 +1,18 @@
+#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
new file mode 100644
index 0000000..d1c3262
--- /dev/null
+++ b/libcpp/pbdata/utils/SMRTTitle.cpp
@@ -0,0 +1,52 @@
+#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
new file mode 100644
index 0000000..33b108b
--- /dev/null
+++ b/libcpp/pbdata/utils/SMRTTitle.hpp
@@ -0,0 +1,24 @@
+#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
new file mode 100644
index 0000000..ee899cd
--- /dev/null
+++ b/libcpp/pbdata/utilsImpl.hpp
@@ -0,0 +1,32 @@
+#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
new file mode 100644
index 0000000..c836d78
--- /dev/null
+++ b/libcpp/rules.mk
@@ -0,0 +1,17 @@
+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
new file mode 100644
index 0000000..e725a6e
--- /dev/null
+++ b/libcpp/simple.mk
@@ -0,0 +1,16 @@
+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
new file mode 100644
index 0000000..26ca380
--- /dev/null
+++ b/libcpp/unittest/.gitignore
@@ -0,0 +1 @@
+/test-runner
diff --git a/libcpp/unittest/Makefile b/libcpp/unittest/Makefile
new file mode 100644
index 0000000..fe48ef7
--- /dev/null
+++ b/libcpp/unittest/Makefile
@@ -0,0 +1,151 @@
+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
new file mode 100644
index 0000000..154ab5e
--- /dev/null
+++ b/libcpp/unittest/alignment/Makefile
@@ -0,0 +1,35 @@
+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
new file mode 100644
index 0000000..52bdb2b
--- /dev/null
+++ b/libcpp/unittest/alignment/datastructures/alignment/AlignmentMap_gtest.cpp
@@ -0,0 +1,63 @@
+/*
+ * =====================================================================================
+ *
+ * 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
new file mode 100644
index 0000000..7080876
--- /dev/null
+++ b/libcpp/unittest/alignment/datastructures/alignment/CmpIndexedStringTable_gtest.cpp
@@ -0,0 +1,143 @@
+/*
+ * =====================================================================================
+ *
+ * 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
new file mode 100644
index 0000000..eba2a24
--- /dev/null
+++ b/libcpp/unittest/alignment/files/CCSIterator_gtest.cpp
@@ -0,0 +1,66 @@
+/*
+ * =====================================================================================
+ *
+ * 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
new file mode 100644
index 0000000..e1b2d0c
--- /dev/null
+++ b/libcpp/unittest/alignment/files/FragmentCCSIterator_gtest.cpp
@@ -0,0 +1,104 @@
+/*
+ * =====================================================================================
+ *
+ * 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
new file mode 100644
index 0000000..f27eb16
--- /dev/null
+++ b/libcpp/unittest/alignment/files/ReaderAgglomerate_gtest.cpp
@@ -0,0 +1,129 @@
+/*
+ * =====================================================================================
+ *
+ * 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
new file mode 100644
index 0000000..7547254
--- /dev/null
+++ b/libcpp/unittest/alignment/format/SAMHeaderPrinter_gtest.cpp
@@ -0,0 +1,138 @@
+/*
+ * =====================================================================================
+ *
+ * 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
new file mode 100644
index 0000000..63331b7
--- /dev/null
+++ b/libcpp/unittest/alignment/format/SAMPrinter_gtest.cpp
@@ -0,0 +1,45 @@
+/*
+ * =====================================================================================
+ *
+ * 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
new file mode 100644
index 0000000..1b2ea3b
--- /dev/null
+++ b/libcpp/unittest/alignment/utils/FileUtils_gtest.cpp
@@ -0,0 +1,54 @@
+/*
+ * =====================================================================================
+ *
+ * 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
new file mode 100644
index 0000000..482e586
--- /dev/null
+++ b/libcpp/unittest/alignment/utils/RangeUtils_gtest.cpp
@@ -0,0 +1,63 @@
+/*
+ * =====================================================================================
+ *
+ * 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
new file mode 100644
index 0000000..2daaa86
--- /dev/null
+++ b/libcpp/unittest/alignment/utils/RegionUtils_gtest.cpp
@@ -0,0 +1,236 @@
+/*
+ * =====================================================================================
+ *
+ * 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
new file mode 100644
index 0000000..a8dde8f
--- /dev/null
+++ b/libcpp/unittest/build.mk
@@ -0,0 +1,27 @@
+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
new file mode 100644
index 0000000..5337ea9
--- /dev/null
+++ b/libcpp/unittest/common.mk
@@ -0,0 +1,64 @@
+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
new file mode 100644
index 0000000..96b27b6
--- /dev/null
+++ b/libcpp/unittest/hdf/HDF2DArray_gtest.cpp
@@ -0,0 +1,96 @@
+/*
+ * ==========================================================================
+ *
+ * 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
new file mode 100644
index 0000000..a196395
--- /dev/null
+++ b/libcpp/unittest/hdf/HDFBasReader_gtest.cpp
@@ -0,0 +1,56 @@
+/*
+ * ============================================================================
+ *
+ * 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
new file mode 100644
index 0000000..1ff04c1
--- /dev/null
+++ b/libcpp/unittest/hdf/HDFCCSReader_gtest.cpp
@@ -0,0 +1,68 @@
+/*
+ * ============================================================================
+ *
+ * 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
new file mode 100644
index 0000000..a4f63a2
--- /dev/null
+++ b/libcpp/unittest/hdf/HDFPlsReader_gtest.cpp
@@ -0,0 +1,49 @@
+/*
+ * ============================================================================
+ *
+ * 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
new file mode 100644
index 0000000..9beb6b1
--- /dev/null
+++ b/libcpp/unittest/hdf/HDFScanDataReader_gtest.cpp
@@ -0,0 +1,52 @@
+#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
new file mode 100644
index 0000000..15831ca
--- /dev/null
+++ b/libcpp/unittest/hdf/HDFScanDataWriter_gtest.cpp
@@ -0,0 +1,36 @@
+/*
+ * ============================================================================
+ *
+ * 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
new file mode 100644
index 0000000..7fab6d7
--- /dev/null
+++ b/libcpp/unittest/hdf/HDFUtils_gtest.cpp
@@ -0,0 +1,38 @@
+/*
+ * ============================================================================
+ *
+ * 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
new file mode 100644
index 0000000..63b8f6d
--- /dev/null
+++ b/libcpp/unittest/hdf/HDFZMWReader_gtest.cpp
@@ -0,0 +1,125 @@
+/*
+ * ==========================================================================
+ *
+ * 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
new file mode 100644
index 0000000..d942d8f
--- /dev/null
+++ b/libcpp/unittest/hdf/Makefile
@@ -0,0 +1,26 @@
+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
new file mode 100644
index 0000000..798365f
--- /dev/null
+++ b/libcpp/unittest/normal.Makefile
@@ -0,0 +1,9 @@
+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
new file mode 100644
index 0000000..a8264c4
--- /dev/null
+++ b/libcpp/unittest/normal.defines.mk
@@ -0,0 +1,54 @@
+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
new file mode 100644
index 0000000..02e72cd
--- /dev/null
+++ b/libcpp/unittest/pbdata/CCSSequence_gtest.cpp
@@ -0,0 +1,117 @@
+/*
+ * =====================================================================================
+ *
+ * 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
new file mode 100644
index 0000000..18cc8b6
--- /dev/null
+++ b/libcpp/unittest/pbdata/ChangeListID_gtest.cpp
@@ -0,0 +1,34 @@
+/*
+ * =====================================================================================
+ *
+ * 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
new file mode 100644
index 0000000..6d16f01
--- /dev/null
+++ b/libcpp/unittest/pbdata/DNASequence_gtest.cpp
@@ -0,0 +1,279 @@
+/*
+ * =====================================================================================
+ *
+ * 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
new file mode 100644
index 0000000..f8aa7de
--- /dev/null
+++ b/libcpp/unittest/pbdata/FASTAReader_gtest.cpp
@@ -0,0 +1,65 @@
+/*
+ * =====================================================================================
+ *
+ * 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
new file mode 100644
index 0000000..4161e76
--- /dev/null
+++ b/libcpp/unittest/pbdata/FASTASequence_gtest.cpp
@@ -0,0 +1,143 @@
+/*
+ * =====================================================================================
+ *
+ * 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
new file mode 100644
index 0000000..2fbbaca
--- /dev/null
+++ b/libcpp/unittest/pbdata/FASTQReader_gtest.cpp
@@ -0,0 +1,90 @@
+/*
+ * =====================================================================================
+ *
+ * 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
new file mode 100644
index 0000000..a6474af
--- /dev/null
+++ b/libcpp/unittest/pbdata/Makefile
@@ -0,0 +1,31 @@
+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
new file mode 100644
index 0000000..b1df999
--- /dev/null
+++ b/libcpp/unittest/pbdata/NucConversion_gtest.cpp
@@ -0,0 +1,105 @@
+/*
+ * =====================================================================================
+ *
+ * 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
new file mode 100644
index 0000000..43f40d9
--- /dev/null
+++ b/libcpp/unittest/pbdata/SMRTSequence_gtest.cpp
@@ -0,0 +1,62 @@
+/*
+ * =====================================================================================
+ *
+ * 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
new file mode 100644
index 0000000..1a3bdbb
--- /dev/null
+++ b/libcpp/unittest/pbdata/ScanData_gtest.cpp
@@ -0,0 +1,31 @@
+/*
+ * =====================================================================================
+ *
+ * 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
new file mode 100644
index 0000000..e83c955
--- /dev/null
+++ b/libcpp/unittest/pbdata/SeqUtils_gtest.cpp
@@ -0,0 +1,50 @@
+/*
+ * =====================================================================================
+ *
+ * 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
new file mode 100644
index 0000000..abd6622
--- /dev/null
+++ b/libcpp/unittest/pbdata/StringUtils_gtest.cpp
@@ -0,0 +1,80 @@
+/*
+ * ==================================================================
+ *
+ * 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
new file mode 100644
index 0000000..70d9463
--- /dev/null
+++ b/libcpp/unittest/pbdata/VectorUtils_gtest.cpp
@@ -0,0 +1,38 @@
+/*
+ * =====================================================================================
+ *
+ * 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
new file mode 100644
index 0000000..f81686b
--- /dev/null
+++ b/libcpp/unittest/pbdata/defs_gtest.cpp
@@ -0,0 +1,44 @@
+/*
+ * =====================================================================================
+ *
+ * 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
new file mode 100644
index 0000000..e4132a7
--- /dev/null
+++ b/libcpp/unittest/pbdata/metagenome/TitleTable_gtest.cpp
@@ -0,0 +1,32 @@
+/*
+ * =====================================================================================
+ *
+ * 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
new file mode 100644
index 0000000..4119c93
--- /dev/null
+++ b/libcpp/unittest/pbdata/qvs/QualityValueVector_gtest.cpp
@@ -0,0 +1,50 @@
+/*
+ * =====================================================================================
+ *
+ * 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
new file mode 100644
index 0000000..50f6a54
--- /dev/null
+++ b/libcpp/unittest/pbdata/reads/ReadType_gtest.cpp
@@ -0,0 +1,57 @@
+/*
+ * ==================================================================
+ *
+ * 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
new file mode 100644
index 0000000..d0daed4
--- /dev/null
+++ b/libcpp/unittest/pbdata/saf/AlnGroup_gtest.cpp
@@ -0,0 +1,44 @@
+/*
+ * =====================================================================================
+ *
+ * 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
new file mode 100644
index 0000000..02a2642
--- /dev/null
+++ b/libcpp/unittest/pbdata/saf/MovieInfo_gtest.cpp
@@ -0,0 +1,43 @@
+/*
+ * =====================================================================================
+ *
+ * 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
new file mode 100644
index 0000000..0e25e99
--- /dev/null
+++ b/libcpp/unittest/pbdata/saf/RefInfo_gtest.cpp
@@ -0,0 +1,45 @@
+/*
+ * =====================================================================================
+ *
+ * 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
new file mode 100644
index 0000000..ec208f4
--- /dev/null
+++ b/libcpp/unittest/pbdata/testdata.h
@@ -0,0 +1,71 @@
+/* * ============================================================================
+ *
+ * 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
new file mode 100644
index 0000000..5618258
--- /dev/null
+++ b/libcpp/unittest/pbdata/utils/SMRTTitle_gtest.cpp
@@ -0,0 +1,28 @@
+#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
new file mode 100644
index 0000000..a2f6b77
--- /dev/null
+++ b/libcpp/unittest/pbdata/utils_gtest.cpp
@@ -0,0 +1,37 @@
+/*
+ * =====================================================================================
+ *
+ * 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/p4.common.mk b/p4.common.mk
new file mode 100644
index 0000000..c913f27
--- /dev/null
+++ b/p4.common.mk
@@ -0,0 +1,147 @@
+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
new file mode 100644
index 0000000..c171051
--- /dev/null
+++ b/p4.fetch.tmpmk
@@ -0,0 +1,10 @@
+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
new file mode 100644
index 0000000..60941d6
--- /dev/null
+++ b/p4.mk
@@ -0,0 +1,76 @@
+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
new file mode 100644
index 0000000..39c8309
--- /dev/null
+++ b/rules.mk
@@ -0,0 +1,31 @@
+INCDIRS := \
+ ${LIBBLASR_INCLUDE} \
+ ${LIBPBDATA_INCLUDE} \
+ ${LIBPBIHDF_INCLUDE} \
+ ${PBBAM_INCLUDE} \
+ ${HDF5_INCLUDE} \
+ ${HTSLIB_INCLUDE} \
+ ${BOOST_INCLUDE}
+LIBDIRS := \
+ ${LIBBLASR_LIB} \
+ ${LIBPBDATA_LIB} \
+ ${LIBPBIHDF_LIB} \
+ ${PBBAM_LIB} \
+ ${HDF5_LIB} \
+ ${HTSLIB_LIB} \
+ ${ZLIB_LIB}
+LDLIBS+= \
+ ${LIBPBIHDF_LIBFLAGS} \
+ ${LIBBLASR_LIBFLAGS} \
+ ${LIBPBDATA_LIBFLAGS} \
+ ${LIBPBIHDF_LIBFLAGS} \
+ ${PBBAM_LIBFLAGS} \
+ ${HDF5_LIBFLAGS} \
+ ${HTSLIB_LIBFLAGS} \
+ ${ZLIB_LIBFLAGS} \
+ ${PTHREAD_LIBFLAGS} \
+ ${DL_LIBFLAGS}
+# We repeat LIBPBIHDF_LIBFLAGS because of a circular dependency. See #77.
+
+CPPFLAGS+=$(patsubst %,-I%,${INCDIRS})
+LDFLAGS+=$(patsubst %,-L%,${LIBDIRS})
diff --git a/travis.sh b/travis.sh
new file mode 100755
index 0000000..4e27de9
--- /dev/null
+++ b/travis.sh
@@ -0,0 +1,9 @@
+#!/usr/bin/env bash
+# This will not work within Travis until have have pre-compiled HDF5
+# (or least headers?). But it shows the steps.
+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}
+make -j4 init-submodule
+make --debug=b -j4 all
diff --git a/utils/GNUmakefile b/utils/GNUmakefile
new file mode 100644
index 0000000..3413244
--- /dev/null
+++ b/utils/GNUmakefile
@@ -0,0 +1,43 @@
+.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 = loadPulses pls2fasta samtoh5 samtom4 samFilter toAfg sawriter sdpMatcher
+
+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}
+
+loadPulses: LoadPulses.cpp
+pls2fasta: PulseToFasta.cpp
+samtoh5: SamToCmpH5.cpp
+samtom4: SamToM4.cpp
+samFilter: SamFilter.cpp
+toAfg: ToAfg.cpp
+sawriter: SAWriter.cpp
+sdpMatcher: SDPMatcher.cpp
+
+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
diff --git a/utils/LoadPulses.cpp b/utils/LoadPulses.cpp
new file mode 100644
index 0000000..34fc0ab
--- /dev/null
+++ b/utils/LoadPulses.cpp
@@ -0,0 +1,2643 @@
+#define __FAST_MATH__
+
+#include "HDFCmpFile.hpp"
+#include "HDFBasReader.hpp"
+#include "HDFPlsReader.hpp"
+#include "HDFCCSReader.hpp"
+#include "datastructures/alignment/CmpFile.hpp"
+#include "alignment/CmpAlignment.hpp"
+#include "datastructures/alignment/ByteAlignment.h"
+#include "datastructures/alignment/AlignmentMap.hpp"
+#include "reads/BaseFile.hpp"
+#include "reads/PulseFile.hpp"
+#include "reads/ReadType.hpp"
+#include "loadpulses/MetricField.hpp"
+#include "loadpulses/MovieAlnIndexLookupTable.hpp"
+#include "utils/FileOfFileNames.hpp"
+#include "utils/TimeUtils.hpp"
+#include "files/BaseSequenceIO.hpp"
+#include "CommandLineParser.hpp"
+#include <map>
+#include <set>
+#include <string>
+#include <algorithm>
+#include <assert.h>
+#include <numeric>
+#include <stdio.h>
+
+using namespace std;
+
+typedef map<string, int> MovieNameToArrayIndex;
+typedef map<string, bool> MetricOptionsMap;
+typedef map<string, vector<string> > RequirementMap;
+
+
+char VERSION[] = "v1.1.0";
+char PERFORCE_VERSION_STRING[] = "$Change: 126407 $";
+
+// define default values for metrics
+const float NaN = 0.0/0.0;
+const UChar missingQualityValue = 255;
+const unsigned char maxQualityValue = 100;
+const HalfWord missingFrameRateValue = USHRT_MAX;
+const unsigned int missingPulseIndex = UINT_MAX;
+
+
+void CapQualityValue(QualityValueVector<QualityValue> &vect, DNALength length, unsigned char maxQualityValue=100) {
+ unsigned int i;
+ if (vect.data == NULL) {
+ return;
+ }
+ for (i = 0; i < length; i++) {
+ vect.data[i] = min(vect.data[i], maxQualityValue);
+ }
+}
+
+
+void CapQualityValues(SMRTSequence &seq, unsigned char maxQualityValue = 100) {
+ CapQualityValue(seq.qual, seq.length, maxQualityValue);
+ CapQualityValue(seq.deletionQV, seq.length, maxQualityValue);
+ CapQualityValue(seq.preBaseDeletionQV, seq.length, maxQualityValue);
+ CapQualityValue(seq.insertionQV, seq.length, maxQualityValue);
+ CapQualityValue(seq.substitutionQV, seq.length, maxQualityValue);
+ CapQualityValue(seq.mergeQV, seq.length, maxQualityValue);
+}
+
+
+int CheckCmpFileFormat(CmpFile &cmpFile) {
+ if (cmpFile.readType != ReadType::Standard) {
+ cout << "ERROR! Reading pulse information into a cmp.h5 file generated from circular " << endl
+ << "consensus called sequences is not supported." << endl;
+ exit(1);
+ }
+ return 1;
+}
+
+void BuildRequirementMap(RequirementMap &fieldRequirements) {
+ fieldRequirements["StartTimeOffset"].push_back("StartFrame");
+ fieldRequirements["StartTimeOffset"].push_back("NumEvent");
+ fieldRequirements["StartFrame"].push_back("PreBaseFrames");
+ fieldRequirements["StartFrame"].push_back("WidthInFrames");
+ fieldRequirements["PulseWidth"].push_back("WidthInFrames");
+ fieldRequirements["pkmid"].push_back("MidSignal");
+ fieldRequirements["pkmid"].push_back("NumEvent");
+ fieldRequirements["IPD"].push_back("StartFrame");
+ fieldRequirements["IPD"].push_back("NumEvent");
+ fieldRequirements["IPD"].push_back("PreBaseFrames");
+ fieldRequirements["IPD"].push_back("WidthInFrames");
+ fieldRequirements["Light"].push_back("MeanSignal");
+ fieldRequirements["Light"].push_back("NumEvent");
+ fieldRequirements["Light"].push_back("WidthInFrames");
+
+ // Build requirementMap for sneaky metrics
+ fieldRequirements["StartFrameBase"].push_back("PreBaseFrames");
+ fieldRequirements["StartFrameBase"].push_back("WidthInFrames");
+ fieldRequirements["StartFramePulse"].push_back("PreBaseFrames");
+ fieldRequirements["StartFramePulse"].push_back("WidthInFrames");
+}
+
+void ExclusivelyAdd(const char *value, vector<string> &vect) {
+ if (find(vect.begin(), vect.end(), value) == vect.end()) {
+ vect.push_back(value);
+ }
+}
+
+bool AnyFieldRequiresFrameRate(vector<string> &fields) {
+ int i;
+ for (i = 0; i < fields.size(); i++ ) {
+ if (fields[i] == "PulseWidth" or
+ fields[i] == "IPD" or
+ fields[i] == "Light" or
+ fields[i] == "StartTimeOffset" or
+ fields[i] == "StartFrame" or
+ fields[i] == "PulseWidth" or
+ fields[i] == "PreBaseFrames" or
+ fields[i] == "WidthInFrames") {
+ return true;
+ }
+ }
+ return false;
+}
+
+template<typename T>
+void Free(T* &buf) {
+ if (buf != NULL){
+ delete[] buf;
+ }
+ buf = NULL;
+}
+
+// Return all eighteen metrics that can be loaded.
+// StartTimeOffset QualityValue InsertionQV MergeQV
+// DeletionQV DeletionTag PulseIndex SubstitutionTag
+// SubstitutionQV ClassifierQV StartFrame PulseWidth
+// PreBaseFrames WidthInFrames pkmid IPD
+// Light WhenStarted
+vector<string> GetAllSupportedMetrics(bool isSneakyMetricsIncluded = true) {
+ // The order of metrics matters. With -bymetric option, all fields
+ // which are required for computing a metric are cached before WriteMetric()
+ // and cleared afterwards. If two neighboring metrics share a subset of
+ // required fields, then the cached fields can be re-used. Arrange metrics
+ // in an order that maximizes reuse of cached fields.
+ vector<string> supportedMetrics;
+ supportedMetrics.push_back("WhenStarted");
+
+ supportedMetrics.push_back("QualityValue");
+ supportedMetrics.push_back("InsertionQV");
+ supportedMetrics.push_back("MergeQV");
+ supportedMetrics.push_back("DeletionQV");
+ supportedMetrics.push_back("DeletionTag");
+ supportedMetrics.push_back("SubstitutionTag");
+ supportedMetrics.push_back("SubstitutionQV");
+ supportedMetrics.push_back("PreBaseFrames");
+ // Sneaky metrics for internal use Only
+ if (isSneakyMetricsIncluded) {
+ supportedMetrics.push_back("StartFrameBase");
+ }
+ supportedMetrics.push_back("IPD");
+ supportedMetrics.push_back("StartFrame");
+ if (isSneakyMetricsIncluded) {
+ supportedMetrics.push_back("StartFramePulse");
+ }
+ // Disable metric StartTimeOffset for now.
+ // StartTimeOffset is placed at the same level as AlnArray, However, the
+ // size of StartTimeOffset is far less than AlnArray, while cmp.h5 spec
+ // requires all datasets at that level to have the same size.
+
+ // supportedMetrics.push_back("StartTimeOffset");
+
+ supportedMetrics.push_back("PulseWidth");
+ supportedMetrics.push_back("WidthInFrames");
+ supportedMetrics.push_back("Light");
+ supportedMetrics.push_back("pkmid");
+ supportedMetrics.push_back("ClassifierQV");
+ supportedMetrics.push_back("PulseIndex");
+
+ return supportedMetrics;
+}
+
+// Return metrics to load by default.
+vector<string> GetDefaultMetrics() {
+ vector<string> defaultMetrics;
+ defaultMetrics.push_back("QualityValue");
+ defaultMetrics.push_back("ClassifierQV");
+ defaultMetrics.push_back("StartFrame");
+ defaultMetrics.push_back("PulseWidth");
+ defaultMetrics.push_back("WidthInFrames");
+ defaultMetrics.push_back("pkmid");
+ defaultMetrics.push_back("IPD");
+ return defaultMetrics;
+}
+
+// Return metrics that can be computed from PulseCalls.
+vector<string> GetPulseMetrics() {
+ vector<string> pulseMetrics;
+ pulseMetrics.push_back("StartFrame");
+ pulseMetrics.push_back("StartTimeOffset");
+ pulseMetrics.push_back("ClassifierQV");
+ pulseMetrics.push_back("PulseWidth");
+ pulseMetrics.push_back("WidthInFrames");
+ pulseMetrics.push_back("IPD");
+ pulseMetrics.push_back("pkmid");
+ pulseMetrics.push_back("Light");
+ pulseMetrics.push_back("StartFramePulse");
+ return pulseMetrics;
+}
+
+// Return true if this metric can be computed from PulseCalls.
+bool IsPulseMetric(const string & metric) {
+ vector<string> pulseMetrics = GetPulseMetrics();
+ for (int i = 0; i < pulseMetrics.size(); i++) {
+ if (pulseMetrics[i] == metric)
+ return true;
+ }
+ return false;
+}
+
+// Return all metrics that are
+// (1) supported,
+// (2) requested to load, and
+// (3) computable with all required fields available
+// in either bas.h5 or pls.h5.
+vector<string> GetMetricsToLoad(map<string, bool> & metricOptions) {
+ vector<string> metricsToLoad;
+ // Get all supported metrics.
+ vector<string> supportedMetrics = GetAllSupportedMetrics();
+ map<string, bool>::iterator metricIt;
+ for (int i = 0; i < supportedMetrics.size(); i++) {
+ string metric = supportedMetrics[i];
+ metricIt = metricOptions.find(metric);
+ if (metricIt!=metricOptions.end() and metricIt->second) {
+ // Get metrics that are required and computable
+ metricsToLoad.push_back(metricIt->first);
+ }
+ }
+ return metricsToLoad;
+}
+
+void StoreDatasetFieldsFromPulseFields(MetricOptionsMap &fieldSet,
+ RequirementMap &fieldRequirements,
+ vector<string> &datasetFields) {
+ int f;
+ int d;
+ MetricOptionsMap::iterator optionsIt;
+ for (optionsIt = fieldSet.begin(); optionsIt != fieldSet.end(); ++optionsIt) {
+ if (optionsIt->second == true) {
+ if (fieldRequirements.find(optionsIt->first) == fieldRequirements.end()) {
+ ExclusivelyAdd(optionsIt->first.c_str(), datasetFields);
+ }
+ else {
+ for (d = 0; d < fieldRequirements[optionsIt->first].size(); d++) {
+ ExclusivelyAdd(fieldRequirements[optionsIt->first][d].c_str(), datasetFields );
+ }
+ }
+ }
+ }
+}
+
+void ParseMetricsList(string metricListString, MetricOptionsMap &metricOptions) {
+ vector<string> metrics;
+ Splice(metricListString, ",", metrics);
+ int m;
+ for (m = 0; m < metrics.size(); m++) {
+ if (metricOptions.find(metrics[m]) != metricOptions.end()) {
+ metricOptions[metrics[m]] = true;
+ }
+ else {
+ cout << "ERROR! Metric " << metrics[m] << " is not supported." << endl;
+ exit(1);
+ }
+ }
+}
+
+// Set default metric options to true
+void SetDefaultMetricOptions(map<string, bool> & metricOptions) {
+ vector<string> defaultMetrics = GetDefaultMetrics();
+ for (int i = 0; i < defaultMetrics.size(); i++) {
+ metricOptions[defaultMetrics[i]] = true;
+ }
+}
+
+
+// Initialize all supported metric options and set all to false
+void CreateMetricOptions(map<string, bool> &metricOptions) {
+ vector<string> supportedMetrics = GetAllSupportedMetrics();
+ for (int i = 0; i < supportedMetrics.size(); i++) {
+ metricOptions[supportedMetrics[i]] = false;
+ }
+}
+
+// Check whether all fields are available or not.
+bool AreAllFieldsAvailable(
+ vector <Field> & requiredFields,
+ HDFBasReader & hdfBasReader,
+ HDFPlsReader & hdfPlsReader,
+ const bool & useBaseFile,
+ const bool & usePulseFile) {
+ bool allAvailable = true;
+
+ for (int i = 0; i < requiredFields.size(); i++) {
+ Field field = requiredFields[i];
+ if (field.type == BasField) {
+ if (!useBaseFile or !hdfBasReader.FieldIsIncluded(field.name)
+ or !hdfBasReader.includedFields[field.name]) {
+ allAvailable = false;
+ break;
+ }
+ } else if (field.type == PlsField) {
+ if (!usePulseFile or !hdfPlsReader.FieldIsIncluded(field.name)
+ or !hdfPlsReader.includedFields[field.name]) {
+ allAvailable = false;
+ break;
+ }
+ }
+ }
+ return allAvailable;
+}
+
+//
+// Check whether a metric is computable or not.
+// fieldsToBeUsed = all fields that will be used for computing a metric.
+// If a metric can be computed from both bas and pls files (e.g.
+// StartFrame, IPD, PulseWidth, WidthInFrame), only compute it from pls.
+//
+bool CanThisMetricBeComputed (
+ const string & metricName,
+ HDFBasReader & hdfBasReader,
+ HDFPlsReader & hdfPlsReader,
+ const bool & useBaseFile,
+ const bool & usePulseFile,
+ vector<Field> & fieldsToBeUsed) {
+ fieldsToBeUsed.clear();
+
+ FieldsRequirement fieldsRequirement = FieldsRequirement(metricName);
+
+ bool metricMayBeComputedFromPls = true;
+ if (fieldsRequirement.fieldsUsePlsFile.size() != 0 && usePulseFile) {
+ metricMayBeComputedFromPls = AreAllFieldsAvailable(
+ fieldsRequirement.fieldsUsePlsFile,
+ hdfBasReader, hdfPlsReader,
+ useBaseFile, usePulseFile);
+ } else {
+ metricMayBeComputedFromPls = false;
+ }
+
+ bool metricMayBeComputedFromBas = true;
+ if (fieldsRequirement.fieldsUseBasFile.size() != 0 && useBaseFile) {
+ metricMayBeComputedFromBas = AreAllFieldsAvailable(
+ fieldsRequirement.fieldsUseBasFile,
+ hdfBasReader, hdfPlsReader,
+ useBaseFile, usePulseFile);
+ } else {
+ metricMayBeComputedFromBas = false;
+ }
+
+ bool metricMayBeComputed = true;
+ if (!metricMayBeComputedFromBas and !metricMayBeComputedFromPls) {
+ metricMayBeComputed = false;
+ }
+
+ // Compute from pls if possible
+ if (metricMayBeComputedFromPls) {
+ fieldsToBeUsed = fieldsRequirement.fieldsUsePlsFile;
+ } else if (metricMayBeComputedFromBas) {
+ fieldsToBeUsed = fieldsRequirement.fieldsUseBasFile;
+ }
+
+ if (metricName == "StartTimeOffset") {
+ metricMayBeComputed = false;
+ // Disable StartTimeOffset for now.
+ }
+ if (metricName == "WhenStarted") {
+ // WhenStarted requires no fields from neither bas nor pls.
+ metricMayBeComputed = true;
+ }
+
+ return metricMayBeComputed;
+}
+
+//
+// Check whether metrics are computable or not. If a metric is not
+// computable, disable it with a warning or exit with an error.
+//
+void CanMetricsBeComputed(
+ MetricOptionsMap & metricOptions,
+ HDFBasReader & hdfBasReader,
+ HDFPlsReader & hdfPlsReader,
+ const bool & useBaseFile,
+ const bool & usePulseFile,
+ const bool & failOnMissingData,
+ const string & movieName) {
+
+ map<string,bool>::iterator metricIt;
+ for (metricIt = metricOptions.begin(); metricIt != metricOptions.end(); ++metricIt) {
+ string metricName = metricIt->first;
+ if (metricName == "") {
+ metricIt->second == false;
+ }
+
+ if (metricIt->second == false) {
+ continue;
+ }
+ vector<Field> fieldsToBeUsed;
+ bool metricMayBeComputed = CanThisMetricBeComputed(metricName,
+ hdfBasReader, hdfPlsReader, useBaseFile, usePulseFile,
+ fieldsToBeUsed);
+
+ if (metricMayBeComputed == false) {
+ if (failOnMissingData) {
+ cout << "ERROR";
+ }
+ else {
+ cout << "WARNING";
+ }
+ cout << ": There is insufficient data to compute metric: "
+ << metricName << " in the file " << movieName << " ";
+ cout << " It will be ignored." << endl;
+ if (failOnMissingData) {
+ exit(1);
+ }
+ metricOptions[metricName] = false;
+ }
+ }
+}
+
+// Return size of a single field in KB.
+UInt ComputeRequiredMemoryForThisField(
+ Field & thisField,
+ HDFBasReader & hdfBasReader,
+ HDFPlsReader & hdfPlsReader,
+ const bool & useBaseFile,
+ const bool & usePulseFile) {
+ UInt memory = 0;
+ if (thisField.type == BasField) {
+ assert(useBaseFile);
+ return hdfBasReader.GetFieldSize(thisField.name);
+ }
+ if (thisField.type == PlsField) {
+ assert(usePulseFile);
+ return hdfPlsReader.GetFieldSize(thisField.name);
+ }
+ assert(false);
+}
+
+//
+// Return estimated memory peak (in KB) for buffering all data using -bymetric.
+//
+UInt ComputeRequiredMemory(
+ vector<string> & metricsToLoad,
+ HDFBasReader & hdfBasReader,
+ HDFPlsReader & hdfPlsReader,
+ const bool & useBaseFile,
+ const bool & usePulseFile,
+ HDFCmpFile<CmpAlignment> & cmpReader,
+ UInt & totalAlnLength) {
+ UInt maxMemory = 0;
+ for (int i = 0; i < metricsToLoad.size(); i++) {
+ UInt memoryForThisMetric = 0;
+ vector<Field> fieldsToBeUsed;
+ bool canBeComputed = CanThisMetricBeComputed(
+ metricsToLoad[i], hdfBasReader, hdfPlsReader,
+ useBaseFile, usePulseFile, fieldsToBeUsed);
+
+ for (int j = 0; j < fieldsToBeUsed.size(); j++) {
+ UInt memoryForThisField = ComputeRequiredMemoryForThisField(
+ fieldsToBeUsed[j], hdfBasReader, hdfPlsReader,
+ useBaseFile, usePulseFile);
+ memoryForThisMetric += memoryForThisField;
+ }
+ maxMemory = max(maxMemory, memoryForThisMetric);
+ }
+ //
+ // AlnIndex will be buffered. Some other datastructures also need
+ // to be buffered for quick look up. Approximately double the size.
+ //
+ UInt totalAlnIndexMem = 2 * cmpReader.alnInfoGroup.GetAlnIndexSize();
+
+ //
+ // AlnArray and metrics to load needs to be buffered in KB.
+ //
+ UInt totalAlnArrayMem = totalAlnLength / 1024 *
+ (sizeof(unsigned int) + sizeof(unsigned char));
+
+ //
+ // It's diffcult to estimate how much memory will be used by hdf5.
+ // Assume memory consumed by hdf5 scales with AlnIndex and AlnArray datasets.
+ //
+ UInt hdf5Mem = totalAlnIndexMem / 2 + totalAlnLength / 1024 * sizeof(unsigned int);
+
+ maxMemory += totalAlnIndexMem + totalAlnArrayMem + hdf5Mem;
+
+ //cout << "The estimated peak memory for buffering fields is "
+ // << maxMemory << " KB." << endl;
+ //cout << "The estimated memory for buffering AlnIndex related data is "
+ // << totalAlnIndexMem << " KB."<< endl;
+ //cout << "The estimated memory for buffering AlnArray related data is "
+ // << totalAlnArrayMem << " KB." << endl;
+ //cout << "The estimated memory for hdf5 is "
+ // << hdf5Mem << " KB." << endl;
+ //cout << "The estimated total memory is "
+ // << maxMemory << " KB." << endl;
+ return maxMemory;
+}
+
+//
+// Get aligned sequence for this alignment from cmpFile
+//
+string GetAlignedSequenceFromCmpFile(
+ const HDFCmpFile<CmpAlignment> & cmpReader,
+ MovieAlnIndexLookupTable & lookupTable) {
+ string alignedSequence;
+ vector <unsigned char> byteAlignment;
+ int alignedSequenceLength = lookupTable.offsetEnd - lookupTable.offsetBegin;
+ if (alignedSequenceLength >= 0 ) {
+ alignedSequence.resize(alignedSequenceLength);
+ byteAlignment.resize(alignedSequenceLength);
+ }
+ //
+ // Read the alignment string. All alignments
+ //
+ cmpReader.refAlignGroups[lookupTable.refGroupIndex]->readGroups[lookupTable.readGroupIndex]->alignmentArray.Read(
+ lookupTable.offsetBegin,
+ lookupTable.offsetEnd,
+ &byteAlignment[0]);
+
+ //
+ // Convert to something we can compare easily.
+ //
+ ByteAlignmentToQueryString(&byteAlignment[0], byteAlignment.size(), &alignedSequence[0]);
+ return alignedSequence;
+}
+
+//
+// Store info necessary for loading pulses to lookupTable.
+//
+void BuildLookupTable(
+ const int & movieAlignmentIndex,
+ CmpFile & cmpFile,
+ BaseFile & baseFile,
+ const bool & usePulseFile,
+ PulseFile & pulseFile,
+ HDFCmpFile<CmpAlignment> & cmpReader,
+ const vector<int> & movieAlnIndex,
+ const vector< pair<int,int> > & toFrom,
+ const set<uint32_t> & moviePartHoleNumbers,
+ MovieAlnIndexLookupTable & lookupTable) {
+ //
+ // Query the cmp file for a way to look up a read based on
+ // coordinate information. For Astro reads, the coords are
+ // based on x and y. For Springfield, it is read index. The
+ // base files should be able to look up reads by x,y or by
+ // index.
+ //
+ if (cmpFile.platformId == Astro) {
+ cout << "ASTRO pulse loading is deprecated." << endl;
+ exit(1);
+ }
+
+ int alignmentIndex = movieAlnIndex[toFrom[movieAlignmentIndex].second];
+
+ //
+ // Alignments are grouped by ref group id then movie id.
+ //
+ int refGroupId = cmpFile.alnInfo.alignments[alignmentIndex].GetRefGroupId();
+ int movieId = cmpFile.alnInfo.alignments[alignmentIndex].GetMovieId();
+ UInt holeNumber = cmpFile.alnInfo.alignments[alignmentIndex].GetHoleNumber();
+ int alnGroupId = cmpFile.alnInfo.alignments[alignmentIndex].GetAlnGroupId();
+
+ if (cmpReader.refGroupIdToArrayIndex.find(refGroupId) ==
+ cmpReader.refGroupIdToArrayIndex.end()) {
+ cout << "ERROR! An alignment " << alignmentIndex
+ << " is specified with reference group " << endl
+ << refGroupId << " that is not found as an alignment group." << endl;
+ exit(1);
+ }
+ int refGroupIndex = cmpReader.refGroupIdToArrayIndex[refGroupId];
+
+ //
+ // Now find the group containing the alignment.
+ //
+ if (cmpReader.alnGroupIdToReadGroupName.find(alnGroupId) ==
+ cmpReader.alnGroupIdToReadGroupName.end()) {
+ cout << "ERROR! An alignment " << alignmentIndex
+ << " is specified with alignment group " << endl
+ << alnGroupId << " that is not found." << endl;
+ exit(1);
+ }
+
+ string readGroupName = cmpReader.alnGroupIdToReadGroupName[alnGroupId];
+ if (cmpReader.refAlignGroups[refGroupIndex]->experimentNameToIndex.find(readGroupName) ==
+ cmpReader.refAlignGroups[refGroupIndex]->experimentNameToIndex.end()) {
+ cout << "ERROR! An alignment " << alignmentIndex
+ << " is specified with read group name " << endl
+ << readGroupName << " that is not found." << endl;
+ exit(1);
+ }
+
+ int readGroupIndex = cmpReader.refAlignGroups[refGroupIndex]->experimentNameToIndex[readGroupName];
+
+ UInt offsetBegin = cmpFile.alnInfo.alignments[alignmentIndex].GetOffsetBegin();
+ UInt offsetEnd = cmpFile.alnInfo.alignments[alignmentIndex].GetOffsetEnd();
+
+ //
+ // First pull out the bases corresponding to this read.
+ //
+ int queryStart = cmpFile.alnInfo.alignments[alignmentIndex].GetQueryStart();
+ int queryEnd = cmpFile.alnInfo.alignments[alignmentIndex].GetQueryEnd();
+
+ bool skip = false;
+ int readIndex, readStart, readLength, plsReadIndex;
+ readIndex = readStart = readLength = plsReadIndex = -1;
+ //
+ // Since the movie may be split into multiple parts, look to see
+ // if this hole number is one of the ones covered by this
+ // set. If it is not, just continue. It will be loaded on
+ // another pass through a different movie part.
+ //
+ if (moviePartHoleNumbers.find(holeNumber) == moviePartHoleNumbers.end()) {
+ skip = true;
+ } else {
+ if (!baseFile.LookupReadIndexByHoleNumber(holeNumber, readIndex)) {
+ cout << "ERROR! Alignment has hole number " << holeNumber
+ << " that is not in the movie. " << endl;
+ exit(1);
+ }
+ readStart = baseFile.readStartPositions[readIndex];
+ readLength = baseFile.readStartPositions[readIndex+1] -
+ baseFile.readStartPositions[readIndex];
+ if (usePulseFile) {
+ if (!pulseFile.LookupReadIndexByHoleNumber(holeNumber, plsReadIndex)) {
+ cout << "ERROR! Alignment has hole number " << holeNumber
+ << " that is not in the movie. " << endl;
+ exit(1);
+ }
+ assert(pulseFile.holeNumbers[plsReadIndex] ==
+ baseFile.holeNumbers[readIndex]);
+ }
+ }
+ // Save info to lookupTable
+ lookupTable.SetValue(skip, // Skip processing this or not
+ movieAlignmentIndex,
+ alignmentIndex,
+ refGroupIndex,
+ readGroupIndex,
+ holeNumber, // cmp.h5 /AlnInfo/AlnIndex column 7
+ offsetBegin, // cmp.h5 /AlnInfo/AlnIndex column 18
+ offsetEnd, // cmp.h5 /AlnInfo/AlnIndex column 19
+ queryStart, // cmp.h5 /AlnInfo/AlnIndex column 11
+ queryEnd, // cmp.h5 /AlnInfo/AlnIndex column 12
+ readIndex, // hole Index in BaseCalls/ZMW/HoleNumber
+ readStart, // readStart in BaseCalls/* (e.g. *=Basecall)
+ readLength, // readLength in BaseCalls/*
+ plsReadIndex); // readIndex in PulseCalls/ZMW/HoleNumber
+}
+
+//
+// Map bases of a read to pulse indices.
+//
+void MapBaseToPulseIndex(
+ BaseFile & baseFile,
+ PulseFile & pulseFile,
+ MovieAlnIndexLookupTable & table,
+ vector<int> & baseToPulseIndexMap) {
+ baseToPulseIndexMap.resize(table.readLength);
+
+ int pulseStart = pulseFile.pulseStartPositions[table.plsReadIndex];
+ //
+ // Copy the subset of pulses that correspond to the ones called as bases.
+ //
+ int i;
+ for (i = 0; i < table.readLength; i++) {
+ baseToPulseIndexMap[i] = pulseStart + baseFile.pulseIndex[table.readStart + i];
+ }
+}
+
+//
+// Get source read from the bas/pls file.
+//
+void GetSourceRead(CmpFile & cmpFile,
+ BaseFile & baseFile,
+ PulseFile & pulseFile,
+ HDFBasReader & hdfBasReader,
+ HDFPlsReader & hdfPlsReader,
+ HDFCCSReader<SMRTSequence> & hdfCcsReader,
+ const bool & useBaseFile,
+ const bool & usePulseFile,
+ const bool & useCcsOnly,
+ //const bool & byRead,
+ MovieAlnIndexLookupTable & table,
+ const string & alignedSequence,
+ SMRTSequence & sourceRead,
+ unsigned int & numPasses) {
+
+ assert(!table.skip);
+ //
+ // These are not allocated in the regular allocate function
+ // since they are only used in loadPulses. (maybe I should
+ // subclass SMRTSequence here).
+ //
+ //if (byRead) {
+ // Read in the data from the bas file if it exsts.
+ if (useBaseFile) {
+ hdfBasReader.GetReadAt(table.readIndex, sourceRead);
+ if (cmpFile.readType == ReadType::CCS or useCcsOnly) {
+ numPasses = hdfCcsReader.GetNumPasses(table.readIndex);
+ }
+ }
+ // Read in the data from the pls file if it exists.
+ if (usePulseFile) {
+ hdfPlsReader.GetReadAt(table.plsReadIndex, sourceRead.pulseIndex, sourceRead);
+ }
+ // }
+ // else {
+ // This is deprecated
+ // //
+ // // The entire base/pulse file was read in, so copy data from that into a read
+ // // For the data used in the read, it is possible to simply
+ // // reference the data, but for the pls file it is necessary
+ // // to copy since there is a packing of data.
+ // //
+ // if (useBaseFile) {
+ // baseFile.CopyReadAt(table.readIndex, sourceRead);
+ // if (cmpFile.readType == ReadType::CCS or useCcsOnly) {
+ // numPasses = hdfCcsReader.GetNumPasses(table.readIndex);
+ // }
+ // }
+ // if (usePulseFile) {
+ // vector<int> baseToPulseIndexMap;
+ // MapBaseToPulseIndex(baseFile, pulseFile, table, baseToPulseIndexMap);
+ // pulseFile.CopyReadAt(table.readIndex, &baseToPulseIndexMap[0], sourceRead);
+ // }
+ //}
+ CapQualityValues(sourceRead);
+}
+
+//
+// Build lookup tables for all alignments whose indices in
+// AlnArray are saved in movieAlnIndex.
+// Also check whether the bas file and the cmp file match.
+//
+void BuildLookupTablesAndMakeSane(
+ CmpFile & cmpFile,
+ BaseFile & baseFile,
+ PulseFile & pulseFile,
+ HDFCmpFile<CmpAlignment> & cmpReader,
+ HDFBasReader & hdfBasReader,
+ HDFPlsReader & hdfPlsReader,
+ HDFCCSReader<SMRTSequence> & hdfCcsReader,
+ const bool & useBaseFile,
+ const bool & usePulseFile,
+ const bool & useCcsOnly,
+ const vector<int> & movieAlnIndex,
+ const vector< pair<int,int> > & toFrom,
+ const set<uint32_t> & moviePartHoleNumbers,
+ vector<MovieAlnIndexLookupTable> & lookupTables) {
+
+ lookupTables.resize(movieAlnIndex.size());
+ int movieAlignmentIndex = 0;
+ for (movieAlignmentIndex = 0; movieAlignmentIndex < movieAlnIndex.size(); movieAlignmentIndex++) {
+ BuildLookupTable(movieAlignmentIndex,
+ cmpFile,
+ baseFile,
+ usePulseFile,
+ pulseFile,
+ cmpReader,
+ movieAlnIndex,
+ toFrom,
+ moviePartHoleNumbers,
+ lookupTables[movieAlignmentIndex]);
+ }
+
+ //
+ // Load entire Basecall from pls/bas to memory, and
+ // check whether aligned sequences in cmp.h5 matches
+ // sequences in pls/bas or not
+ //
+ hdfBasReader.ReadField(baseFile, "Basecall");
+
+ //
+ // For each alignment, do sanity check and
+ // cache aligned sequence in MovieAlnIndexLookupTable
+ //
+ for (movieAlignmentIndex = 0; movieAlignmentIndex < movieAlnIndex.size(); movieAlignmentIndex++) {
+ MovieAlnIndexLookupTable & table = lookupTables[movieAlignmentIndex];
+ if (table.skip) continue;
+ //
+ // Get aligned sequence for this alignment from cmpFile
+ //
+ string alignedSequence = GetAlignedSequenceFromCmpFile(cmpReader, table);
+
+ // Save the aligned sequence in the table
+ table.alignedSequence = alignedSequence;
+
+ RemoveGaps(alignedSequence, alignedSequence);
+
+ //
+ // Get sequence for this alignment from baseFile
+ //
+ Nucleotide * seq = new Nucleotide[table.readLength];
+ baseFile.CopyArray(baseFile.baseCalls, table.readStart, table.readLength, seq);
+
+ string readSequence;
+ readSequence.resize(table.queryEnd - table.queryStart);
+ copy((char*) (seq + table.queryStart),
+ (char*) (seq + table.queryEnd),
+ readSequence.begin());
+ delete seq;
+
+ //
+ // Do a sanity check to make sure the pulses and the alignment
+ // make sense. The main check is to see if the query sequence
+ // in the alignment is the same as the query sequence in the
+ // read.
+ //
+ if (alignedSequence.size() != readSequence.size() or alignedSequence != readSequence) {
+ cout << "ERROR, the query sequence does not match the aligned query sequence." << endl
+ << "HoleNumber: " << cmpFile.alnInfo.alignments[table.alignmentIndex].GetHoleNumber()
+ << ", MovieName: " << baseFile.GetMovieName()
+ << ", ReadIndex: " << table.readIndex
+ << ", qStart: " << table.queryStart
+ << ", qEnd: " << table.queryEnd << endl
+ << "Aligned sequence: " << endl
+ << alignedSequence << endl
+ << "Original sequence: "<< endl
+ << readSequence << endl;
+ exit(1);
+ }
+ }
+
+ hdfBasReader.ClearField(baseFile, "Basecall");
+}
+
+// Given a vector of lookupTables in which items with the same
+// refGroupIndex and readGroupIndex are grouped, find index boundaries
+// of each group and save these boundaries to groupedLookupTablesIndexPairs
+// The index boundary of each group consists of:
+// 1, index (0 based, inclusive) of the very first item of a group
+// 2, index (0 based, exclusive) of the very last item of a group
+//
+// Assume that lookupTables satisfy the following criteria.
+// 1, items are already grouped by refGroupIndex and readGroupIndex
+// 2, items which have the same alnGroupIndex, should have
+// the same refGroupIndex and readGroupIndex
+// Note that:
+// 1, alnGroupIndex represents index of AlnGroupID, (i.e. dataset
+// /AlnInfo/AlnIndex column 1);
+// refGroupIndex represents index of RefGroupID, (i.e. dataset
+// /AlnInfo/AlnIndex column 3);
+// readGroupIndex represents index of an experiment group within
+// a refGroup (e.g. if a refGroup /ref0001 contains two experiment
+// groups /ref0001/movie1 and /ref0001/movie2, then readGroupIndex
+// for these two groups are 0 and 1.).
+// 2, within each grouped item, offsetBegin may not begin from 0,
+// and offsets may not be continugous.
+//
+void GroupLookupTables(
+ vector<MovieAlnIndexLookupTable> & lookupTables,
+ vector<pair<UInt, UInt> > & groupedLookupTablesIndexPairs) {
+
+ vector<pair<UInt, UInt> > refGroupIndexReadGroupIndexPairs;
+ UInt movieAlignmentIndex = 0;
+ UInt preRefGroupIndex = 0;
+ UInt preReadGroupIndex = 0;
+ UInt pairFirst = 0;
+ bool isVeryFirstGroup = true;
+
+ for (movieAlignmentIndex = 0; movieAlignmentIndex < lookupTables.size(); movieAlignmentIndex++) {
+ MovieAlnIndexLookupTable & lookupTable = lookupTables[movieAlignmentIndex];
+
+ if (isVeryFirstGroup or
+ (lookupTable.refGroupIndex != preRefGroupIndex or
+ lookupTable.readGroupIndex != preReadGroupIndex)) {
+ // Find a new group
+ if (isVeryFirstGroup) {
+ // This is the very first group
+ isVeryFirstGroup = false;
+ } else
+ if (lookupTable.refGroupIndex == preRefGroupIndex &&
+ lookupTable.readGroupIndex != preReadGroupIndex) {
+ // Assumption (1) has been violated
+ cout << "ERROR! lookupTables should have been sorted by reference"
+ << "group index and read group index." << endl;
+ exit(1);
+ } else {
+ // Find the first lookupTable of a new group, save indices of [first and last)
+ // lookupTables of the last group.
+ groupedLookupTablesIndexPairs.push_back(pair<UInt,UInt> (pairFirst, movieAlignmentIndex));
+ // Save refGroupIndex and readGroupIndex of the last group
+ pair<UInt,UInt> refGroupIndexReadGroupIndexPair(preRefGroupIndex, preReadGroupIndex);
+ refGroupIndexReadGroupIndexPairs.push_back(refGroupIndexReadGroupIndexPair);
+ }
+
+ // Store index of the first lookupTable of the new group in lookupTables
+ pairFirst = movieAlignmentIndex;
+ // Store refGroupIndex and readGroupIndex of the new group
+ preRefGroupIndex = lookupTable.refGroupIndex;
+ preReadGroupIndex = lookupTable.readGroupIndex;
+ }
+ }
+ if (not isVeryFirstGroup) {
+ // Save indices of [first and last) lookupTables of the very last group
+ groupedLookupTablesIndexPairs.push_back(pair<UInt,UInt> (pairFirst, movieAlignmentIndex));
+ // Save refGroupIndex and readGroupIndex of the very last group
+ pair<UInt,UInt> refGroupIndexReadGroupIndexPair(preRefGroupIndex, preReadGroupIndex);
+ refGroupIndexReadGroupIndexPairs.push_back(refGroupIndexReadGroupIndexPair);
+ } // Do nothing, if no lookupTable exists
+
+
+ // Double check all assumptions are met
+ for (int i = 0; i < refGroupIndexReadGroupIndexPairs.size(); i++) {
+ for (int j = i+1; j < refGroupIndexReadGroupIndexPairs.size(); j++) {
+ // Assure that assumption (1) is met. If this assertion fails,
+ // then alignments in the input cmp.h5 are not grouped by
+ // reference. Check /AlnInfo/AlnIndex dataset column 3.
+ assert(refGroupIndexReadGroupIndexPairs[i] != refGroupIndexReadGroupIndexPairs[j]);
+ }
+ }
+ assert(groupedLookupTablesIndexPairs.size() == refGroupIndexReadGroupIndexPairs.size());
+ int i ;
+ for (i = 0; i < groupedLookupTablesIndexPairs.size(); i++) {
+ UInt firstIndex = groupedLookupTablesIndexPairs[i].first;
+ UInt lastIndex = groupedLookupTablesIndexPairs[i].second;
+ UInt refGroupIndex = refGroupIndexReadGroupIndexPairs[i].first;
+ UInt readGroupIndex = refGroupIndexReadGroupIndexPairs[i].second;
+ for(UInt index = firstIndex; index < lastIndex; index++) {
+ assert(lookupTables[index].refGroupIndex == refGroupIndex);
+ assert(lookupTables[index].readGroupIndex == readGroupIndex);
+ }
+ }
+}
+
+
+//
+// Read all required fields for computing the specified metric into memory,
+// unless the fields have been cached.
+//
+void CacheRequiredFieldsForMetric(
+ BaseFile & baseFile,
+ PulseFile & pulseFile,
+ HDFBasReader & hdfBasReader,
+ HDFPlsReader & hdfPlsReader,
+ HDFCCSReader<SMRTSequence> & hdfCcsReader,
+ const bool & useBaseFile,
+ const bool & usePulseFile,
+ const bool & useCcsOnly,
+ vector<Field> & cachedFields,
+ const string & curMetric) {
+
+ vector<Field> fieldsToBeUsed;
+ bool canBeComputed = CanThisMetricBeComputed(
+ curMetric, hdfBasReader, hdfPlsReader,
+ useBaseFile, usePulseFile, fieldsToBeUsed);
+ assert(canBeComputed);
+
+ // Cache all required fields
+ for (int i = 0; i < fieldsToBeUsed.size(); i++) {
+ bool isFieldCached = false;
+ for (int j = 0; j < cachedFields.size(); j++) {
+ if (fieldsToBeUsed[i] == cachedFields[j]) {
+ isFieldCached = true;
+ break;
+ }
+ }
+ if (isFieldCached) {
+ continue;
+ }
+ string & curField = fieldsToBeUsed[i].name;
+ FieldType & fieldType= fieldsToBeUsed[i].type;
+
+ if (fieldType == BasField and useBaseFile
+ and hdfBasReader.FieldIsIncluded(curField)
+ and hdfBasReader.includedFields[curField]) {
+ hdfBasReader.ReadField(baseFile, curField);
+ cachedFields.push_back(fieldsToBeUsed[i]);
+ } else
+ if (fieldType == PlsField and usePulseFile
+ and hdfPlsReader.FieldIsIncluded(curField)
+ and hdfPlsReader.includedFields[curField]) {
+ hdfPlsReader.ReadField(pulseFile, curField);
+ cachedFields.push_back(fieldsToBeUsed[i]);
+ }
+ }
+}
+
+//
+// Clear cached fields unless they are also required for computing
+// the next metric.
+//
+void ClearCachedFields(
+ BaseFile & baseFile,
+ PulseFile & pulseFile,
+ HDFBasReader & hdfBasReader,
+ HDFPlsReader & hdfPlsReader,
+ HDFCCSReader<SMRTSequence> & hdfCcsReader,
+ const bool & useBaseFile,
+ const bool & usePulseFile,
+ const bool & useCcsOnly,
+ vector<Field> & cachedFields,
+ const string & curMetric,
+ const string & nextMetric) {
+
+
+ vector<Field> nextRequiredFields;
+ if (nextMetric != "") {
+ bool canBeComputed = CanThisMetricBeComputed(
+ nextMetric, hdfBasReader, hdfPlsReader,
+ useBaseFile, usePulseFile, nextRequiredFields);
+ assert(canBeComputed);
+ }
+ for (int i = 0; i < cachedFields.size(); i++) {
+ bool isRequiredForNextMetric = false;
+ for (int j = 0; j < nextRequiredFields.size(); j++) {
+ if (cachedFields[i] == nextRequiredFields[j]) {
+ isRequiredForNextMetric = true;
+ break;
+ }
+ }
+ if (isRequiredForNextMetric) {
+ continue;
+ }
+ string & curField = cachedFields[i].name;
+ FieldType & fieldType= cachedFields[i].type;
+
+ if (fieldType == BasField and useBaseFile and
+ hdfBasReader.FieldIsIncluded(curField) and
+ hdfBasReader.includedFields[curField]) {
+ hdfBasReader.ClearField(baseFile, curField);
+ // Remove it from cachedFields
+ cachedFields.erase(cachedFields.begin()+i);
+ i--;
+ } else
+ if (fieldType == PlsField and usePulseFile and
+ hdfPlsReader.FieldIsIncluded(curField) and
+ hdfPlsReader.includedFields[curField]) {
+ if (curField == "NumEvent") {
+ // Always keep NumEvent
+ continue;
+ }
+ hdfPlsReader.ClearField(pulseFile, curField);
+ // Remove it from cachedFields
+ cachedFields.erase(cachedFields.begin()+i);
+ i--;
+ }
+ }
+}
+
+// Compute StartFrame from BaseCalls only.
+// Return true if succeed, false otherwise.
+bool ComputeStartFrameFromBase(
+ BaseFile & baseFile,
+ HDFBasReader & hdfBasReader,
+ const bool & useBaseFile,
+ MovieAlnIndexLookupTable & lookupTable,
+ vector<UInt> & newStartFrame) {
+ newStartFrame.resize(lookupTable.readLength);
+ if (useBaseFile and hdfBasReader.FieldIsIncluded("PreBaseFrames")
+ and hdfBasReader.includedFields["PreBaseFrames"]
+ and baseFile.preBaseFrames.size() > 0) {
+ // baseFile.preBaseFrame data type = uint16
+ // startFrame data type = uint32
+ for (int i = 0; i < lookupTable.readLength; i++) {
+ newStartFrame[i] = baseFile.preBaseFrames[lookupTable.readStart+i];
+ }
+ for (int i = 0; i < lookupTable.readLength-1; i++) {
+ newStartFrame[i+1] += baseFile.basWidthInFrames[lookupTable.readStart+i];
+ }
+ partial_sum(&newStartFrame[0], &newStartFrame[lookupTable.readLength], &newStartFrame[0]);
+ return true;
+ }
+ return false;
+}
+
+// Compute StartFrame from PulseCalls only.
+// Return true if succeed, false otherwise.
+bool ComputeStartFrameFromPulse(
+ PulseFile & pulseFile,
+ HDFPlsReader & hdfPlsReader,
+ const bool & usePulseFile,
+ MovieAlnIndexLookupTable & lookupTable,
+ vector<int> & baseToPulseIndexMap,
+ vector<UInt> & newStartFrame) {
+ newStartFrame.resize(lookupTable.readLength);
+ if (usePulseFile) {
+ assert(pulseFile.startFrame.size() > 0);
+ hdfPlsReader.CopyFieldAt(pulseFile, "StartFrame", lookupTable.plsReadIndex,
+ &baseToPulseIndexMap[0], &newStartFrame[0],
+ lookupTable.readLength);
+ return true;
+ }
+ return false;
+}
+
+
+// Compute StartFrame from either (1) BaseCalls or (2) PulseCalls.
+// (1) Uses baseFile.preBaseFrames and baseFile.basWidthInFrames
+// (2) Uses pulseFile.startFrame
+// In theory, the generated results using both methods should
+// be exactly the same. However, they can be different in practice
+// because PreBaseFrames is of data type uint_16, while its
+// value can exceed maximum uint_16 (65535).
+// When possible, always use PulseCalls.
+void ComputeStartFrame(
+ BaseFile & baseFile,
+ PulseFile & pulseFile,
+ HDFBasReader & hdfBasReader,
+ HDFPlsReader & hdfPlsReader,
+ bool useBaseFile,
+ bool usePulseFile,
+ MovieAlnIndexLookupTable & lookupTable,
+ vector<int> & baseToPulseIndexMap,
+ vector<UInt> & newStartFrame) {
+
+ if (!ComputeStartFrameFromPulse(pulseFile, hdfPlsReader, usePulseFile,
+ lookupTable, baseToPulseIndexMap, newStartFrame)) {
+ if (!ComputeStartFrameFromBase(baseFile, hdfBasReader, useBaseFile,
+ lookupTable, newStartFrame)) {
+ cout << "ERROR! There is insufficient data to compute metric: StartFrame." << endl;
+ exit(1);
+ }
+ }
+}
+
+//
+// Compute and write an entire metric to cmp.h5.
+// Assume that all required fields have been loaded.
+//
+void WriteMetric(
+ CmpFile & cmpFile,
+ BaseFile & baseFile,
+ PulseFile & pulseFile,
+ HDFCmpFile<CmpAlignment> & cmpReader,
+ HDFBasReader & hdfBasReader,
+ HDFPlsReader & hdfPlsReader,
+ HDFCCSReader<SMRTSequence> & hdfCcsReader,
+ const bool & useBaseFile,
+ const bool & usePulseFile,
+ const bool & useCcsOnly,
+ vector<MovieAlnIndexLookupTable> & lookupTables,
+ vector<pair<UInt, UInt> > & groupedLookupTablesIndexPairs,
+ const string & curMetric ) {
+
+ int movieAlignmentIndex = 0;
+ for (int index = 0; index < groupedLookupTablesIndexPairs.size(); index++) {
+ // Group[index] contains all items in lookupTables[firstIndex...lastIndex)
+ UInt firstIndex = groupedLookupTablesIndexPairs[index].first;
+ UInt lastIndex = groupedLookupTablesIndexPairs[index].second;
+
+ assert(lookupTables.size() > firstIndex);
+ UInt refGroupIndex = lookupTables[firstIndex].refGroupIndex;
+ UInt readGroupIndex = lookupTables[firstIndex].readGroupIndex;
+ // Obtain alignment array length from *.cmp.h5/refGroup/readGroup/AlnArray.
+ HDFCmpExperimentGroup* expGroup = cmpReader.refAlignGroups[refGroupIndex]->readGroups[readGroupIndex];
+ UInt alnArrayLength = expGroup->alignmentArray.size();
+
+ //
+ // Compute any necessary data fields. These usually involve
+ // using differences of pulse indices, pulse widths, etc..
+ // Missing fields are stored as 0's.
+ //
+ vector<UInt> startTimeOffsetMetric;
+ // pulseIndex's data type is uint16 in ICD,
+ // but I have seen it defined as uint32 in a bas file.
+ vector<UInt> pulseMetric;
+ vector<UChar> qvMetric;
+ vector<HalfWord> frameRateMetric;
+ vector<UInt> timeMetric;
+ vector<char> tagMetric;
+ vector<float> floatMetric;
+
+ /*
+ if (curMetric == "StartTimeOffset") {
+ startTimeOffsetMetric.resize(alnNum);
+ HDFArray<UInt> * data = (HDFArray<UInt>*) expGroup->fields[curMetric];
+ if (data->IsInitialized()) {
+ assert(data->size() == alnNum);
+ data->UpdateH5Dataspace();
+ data->Read(0, alnNum-1, &StartTimeOffsetMetric[0]);
+ } else {
+ data->Initialize(expGroup->experimentGroup, curMetric);
+ fill(startTimeOffsetMetric.begin(), startTimeOffsetMetric.end(), );
+ }
+
+ } else */
+ if (curMetric == "QualityValue" || curMetric == "InsertionQV" ||
+ curMetric == "DeletionQV" || curMetric == "MergeQV" ||
+ curMetric == "SubstitutionQV") {
+ qvMetric.resize(alnArrayLength);
+ HDFArray<UChar> * data = (HDFArray<UChar>*) expGroup->fields[curMetric];
+ if (data->IsInitialized()) {
+ assert(data->size() == alnArrayLength);
+ data->UpdateH5Dataspace();
+ data->Read(0, alnArrayLength-1, &qvMetric[0]);
+ } else {
+ data->Initialize(expGroup->experimentGroup, curMetric);
+ //fill(qvMetric.begin(), qvMetric.end(), missingQualityValue);
+ }
+
+ } else if (curMetric == "ClassifierQV" || curMetric == "pkmid" ) {
+ // Note that data type of pkmid=midSignal, which is uint_8 in bas/pls files,
+ // has been changed to float in cmp.h5. Why?
+ floatMetric.resize(alnArrayLength);
+ HDFArray<float> * data = (HDFArray<float>*) expGroup->fields[curMetric];
+ if (data->IsInitialized()) {
+ assert(data->size() == alnArrayLength);
+ data->UpdateH5Dataspace();
+ data->Read(0, alnArrayLength-1, &floatMetric[0]);
+ } else {
+ data->Initialize(expGroup->experimentGroup, curMetric);
+ //fill(floatMetric.begin(), floatMetric.end(), NaN);
+ }
+
+ } else if (curMetric == "PulseIndex" ) {
+ pulseMetric.resize(alnArrayLength);
+ HDFArray<UInt> * data = (HDFArray<UInt>*) expGroup->fields[curMetric];
+ if (data->IsInitialized()) {
+ assert(data->size() == alnArrayLength);
+ data->UpdateH5Dataspace();
+ data->Read(0, alnArrayLength-1, &pulseMetric[0]);
+ } else {
+ data->Initialize(expGroup->experimentGroup, curMetric);
+ //fill(pulseMetric.begin(), pulseMetric.end(), 0);
+ }
+
+ } else if (curMetric == "DeletionTag" || curMetric == "SubstitutionTag") {
+ tagMetric.resize(alnArrayLength);
+ HDFArray<char> * data = (HDFArray<char>*) expGroup->fields[curMetric];
+ if (data->IsInitialized()) {
+ assert(data->size() == alnArrayLength);
+ data->UpdateH5Dataspace();
+ data->Read(0, alnArrayLength-1, &tagMetric[0]);
+ } else {
+ data->Initialize(expGroup->experimentGroup, curMetric);
+ //fill(tagMetric.begin(), tagMetric.end(), '-');
+ }
+
+ } else if (curMetric == "StartFrame" || curMetric == "StartFrameBase" ||
+ curMetric == "StartFramePulse") {
+ timeMetric.resize(alnArrayLength);
+ HDFArray<UInt> * data = (HDFArray<UInt>*) expGroup->fields[curMetric];
+ if (data->IsInitialized()) {
+ assert(data->size() == alnArrayLength);
+ data->UpdateH5Dataspace();
+ data->Read(0, alnArrayLength-1, &timeMetric[0]);
+ } else {
+ data->Initialize(expGroup->experimentGroup, curMetric);
+ //fill(timeMetric.begin(), timeMetric.end(), missingPulseIndex);
+ }
+
+ } else if (curMetric == "PulseWidth" || curMetric == "PreBaseFrames" ||
+ curMetric == "WidthInFrames"|| curMetric == "IPD" ||
+ curMetric == "Light") {
+ frameRateMetric.resize(alnArrayLength);
+ HDFArray<HalfWord> * data = (HDFArray<HalfWord>*) expGroup->fields[curMetric];
+ if (data->IsInitialized()) {
+ assert(data->size() == alnArrayLength);
+ data->UpdateH5Dataspace();
+ data->Read(0, alnArrayLength-1, &frameRateMetric[0]);
+ } else {
+ data->Initialize(expGroup->experimentGroup, curMetric);
+ //fill(frameRateMetric.begin(), frameRateMetric.end(), missingFrameRateValue);
+ }
+ } else {
+ cout << "ERROR, metric " << curMetric << " is not supported." << endl;
+ exit(1);
+ }
+
+ for (movieAlignmentIndex = firstIndex; movieAlignmentIndex < lastIndex; movieAlignmentIndex++) {
+ MovieAlnIndexLookupTable & lookupTable = lookupTables[movieAlignmentIndex];
+ if (lookupTable.skip) continue;
+
+ const UInt alignedSequenceLength = lookupTable.offsetEnd - lookupTable.offsetBegin;
+ const UInt ungappedAlignedSequenceLength = lookupTable.queryEnd - lookupTable.queryStart;
+ const UInt & readIndex = lookupTable.readIndex;
+ const UInt & plsReadIndex = lookupTable.plsReadIndex;
+ const UInt & readStart = lookupTable.readStart;
+ const UInt & readLength = lookupTable.readLength;
+ const UInt & queryStart = lookupTable.queryStart;
+ const UInt & offsetBegin = lookupTable.offsetBegin;
+ const UInt & offsetEnd = lookupTable.offsetEnd;
+ assert (offsetEnd <= alnArrayLength);
+ assert (offsetBegin+alignedSequenceLength <= alnArrayLength);
+
+ // Condense gaps and get ungapped aligned sequence.
+ string ungappedAlignedSequence = lookupTable.alignedSequence;
+ RemoveGaps(ungappedAlignedSequence, ungappedAlignedSequence);
+
+ vector<int> baseToAlignmentMap;
+ // Map bases in the aligned sequence to their positions in the alignment.
+ CreateSequenceToAlignmentMap(lookupTable.alignedSequence, baseToAlignmentMap);
+
+ vector<int> baseToPulseIndexMap;
+ if (usePulseFile && IsPulseMetric(curMetric)) {
+ // Map bases in the read to pulse indices.
+ MapBaseToPulseIndex(baseFile, pulseFile, lookupTable, baseToPulseIndexMap);
+ }
+
+ UInt i;
+ if (curMetric == "QualityValue") {
+ assert(baseFile.qualityValues.size() > 0 &&
+ baseFile.qualityValues.size() >= readStart + readLength);
+ fill(&qvMetric[offsetBegin], &qvMetric[offsetEnd], missingPulseIndex);
+ for (i = 0; i < ungappedAlignedSequenceLength; i++ ) {
+ // cap quality value
+ qvMetric[offsetBegin+baseToAlignmentMap[i]] = min(maxQualityValue, baseFile.qualityValues[readStart+queryStart+i]);
+ }
+ qvMetric[offsetBegin+alignedSequenceLength] = 0;
+
+ } else if (curMetric == "InsertionQV") {
+ assert(baseFile.insertionQV.size() > 0 &&
+ baseFile.insertionQV.size() >= readStart + readLength);
+ fill(&qvMetric[offsetBegin], &qvMetric[offsetEnd], missingPulseIndex);
+ for (i = 0; i < ungappedAlignedSequenceLength; i++) {
+ // cap quality value
+ qvMetric[offsetBegin+baseToAlignmentMap[i]] = min(maxQualityValue, baseFile.insertionQV[readStart+queryStart+i]);
+ }
+ qvMetric[offsetBegin+alignedSequenceLength] = 0;
+
+ } else if (curMetric == "MergeQV") {
+ assert(baseFile.mergeQV.size() > 0 &&
+ baseFile.mergeQV.size() >= readStart + readLength);
+ fill(&qvMetric[offsetBegin], &qvMetric[offsetEnd], missingPulseIndex);
+ for (i = 0; i < ungappedAlignedSequenceLength; i++ ) {
+ // cap quality value
+ qvMetric[offsetBegin+baseToAlignmentMap[i]] = min(maxQualityValue, baseFile.mergeQV[readStart+queryStart+i]);
+ }
+ qvMetric[offsetBegin+alignedSequenceLength] = 0;
+
+ } else if (curMetric == "DeletionQV") {
+ assert(baseFile.deletionQV.size() > 0 &&
+ baseFile.deletionQV.size() >= readStart + readLength);
+ fill(&qvMetric[offsetBegin], &qvMetric[offsetEnd], missingPulseIndex);
+ for (i = 0; i < ungappedAlignedSequenceLength; i++) {
+ // cap quality value
+ qvMetric[offsetBegin+baseToAlignmentMap[i]] = min(maxQualityValue, baseFile.deletionQV[readStart+queryStart+i]);
+ }
+ qvMetric[offsetBegin+alignedSequenceLength] = 0;
+
+ } else if (curMetric == "DeletionTag") {
+ assert(baseFile.deletionTag.size() > 0 &&
+ baseFile.deletionTag.size() >= readStart + readLength);
+ fill(&tagMetric[offsetBegin], &tagMetric[offsetEnd], '-');
+ for (i = 0; i < ungappedAlignedSequenceLength; i++ ) {
+ assert(offsetBegin+baseToAlignmentMap[i] < tagMetric.size());
+ tagMetric[offsetBegin+baseToAlignmentMap[i]] = baseFile.deletionTag[readStart+queryStart+i];
+ }
+ tagMetric[offsetBegin+alignedSequenceLength] = 0;
+
+ } else if (curMetric == "PulseIndex") {
+ assert(baseFile.pulseIndex.size() > 0 &&
+ baseFile.pulseIndex.size() >= readStart + readLength);
+ fill(&pulseMetric[offsetBegin], &pulseMetric[offsetEnd], 0);
+ for (i = 0; i < ungappedAlignedSequenceLength; i++ ) {
+ pulseMetric[offsetBegin+baseToAlignmentMap[i]] = baseFile.pulseIndex[readStart+queryStart+i];
+ }
+ pulseMetric[offsetBegin+alignedSequenceLength] = 0;
+
+ } else if (curMetric == "SubstitutionTag") {
+ assert(baseFile.substitutionTag.size() > 0 &&
+ baseFile.substitutionTag.size() >= readStart + readLength);
+ fill(&tagMetric[offsetBegin], &tagMetric[offsetEnd], '-');
+ for (i = 0; i < ungappedAlignedSequenceLength; i++ ) {
+ tagMetric[offsetBegin+baseToAlignmentMap[i]] = baseFile.substitutionTag[readStart+queryStart+i];
+ }
+ tagMetric[offsetBegin+alignedSequenceLength] = 0;
+
+ } else if (curMetric == "SubstitutionQV") {
+ assert(baseFile.substitutionQV.size() > 0 &&
+ baseFile.substitutionQV.size() >= readStart + readLength);
+ fill(&qvMetric[offsetBegin], &qvMetric[offsetEnd], missingPulseIndex);
+ for (i = 0; i < ungappedAlignedSequenceLength; i++ ) {
+ qvMetric[offsetBegin+baseToAlignmentMap[i]] = min(maxQualityValue, baseFile.substitutionQV[readStart+queryStart+i]);
+ }
+ qvMetric[offsetBegin+alignedSequenceLength] = 0;
+
+ } else if (curMetric == "ClassifierQV") {
+ assert(pulseFile.classifierQV.size() > 0 &&
+ pulseFile.classifierQV.size() >= readStart + readLength);
+ vector<float> newClassifierQV;
+ newClassifierQV.resize(ungappedAlignedSequenceLength);
+ // For the data used for this table, it is possible to simply
+ // reference the data for the bas file, but for the pls file,
+ // it is necessary to copy since there is a packing of data.
+ hdfPlsReader.CopyFieldAt(pulseFile, "ClassifierQV", plsReadIndex,
+ &baseToPulseIndexMap[queryStart], &newClassifierQV[0],
+ ungappedAlignedSequenceLength);
+
+ fill(&floatMetric[offsetBegin], &floatMetric[offsetEnd], NaN);
+ for (i = 0; i < ungappedAlignedSequenceLength; i++ ) {
+ floatMetric[offsetBegin+baseToAlignmentMap[i]] = newClassifierQV[i];
+ }
+ floatMetric[offsetBegin+alignedSequenceLength] = 0;
+
+/* } else if (curMetric == "StartTimeOffset") {
+ // StartTimeOffset is a subset of StartFrame.
+ vector<UInt> newStartFrame;
+ ComputeStartFrame(baseFile, pulseFile, hdfBasReader, hdfPlsReader,
+ useBaseFile, usePulseFile, lookupTable,
+ baseToPulseIndexMap, newStartFrame);
+
+ startTimeOffsetMetric[offsetBegin] = newStartFrame[queryStart];
+*/
+ } else if (curMetric == "StartFrame") {
+ vector<UInt> newStartFrame;
+ ComputeStartFrame(baseFile, pulseFile, hdfBasReader, hdfPlsReader,
+ useBaseFile, usePulseFile, lookupTable,
+ baseToPulseIndexMap, newStartFrame);
+ fill(&timeMetric[offsetBegin], &timeMetric[offsetEnd], missingPulseIndex);
+ for (i = 0; i < ungappedAlignedSequenceLength; i++ ) {
+ timeMetric[offsetBegin+baseToAlignmentMap[i]] = newStartFrame[queryStart+i];
+ }
+ timeMetric[offsetBegin+alignedSequenceLength] = 0;
+
+ } else if (curMetric == "StartFrameBase") {
+ // Sneaky metric, compute StartFrame from BaseCalls only.
+ vector<UInt> newStartFrame;
+ ComputeStartFrameFromBase(baseFile, hdfBasReader, useBaseFile,
+ lookupTable, newStartFrame);
+ fill(&timeMetric[offsetBegin], &timeMetric[offsetEnd], missingPulseIndex);
+ for (i = 0; i < ungappedAlignedSequenceLength; i++ ) {
+ timeMetric[offsetBegin+baseToAlignmentMap[i]] = newStartFrame[queryStart+i];
+ }
+ timeMetric[offsetBegin+alignedSequenceLength] = 0;
+
+ } else if (curMetric == "StartFramePulse") {
+ // Sneaky metric, compute StartFrame from PulseCalls only.
+ vector<UInt> newStartFrame;
+ ComputeStartFrameFromPulse(pulseFile, hdfPlsReader, usePulseFile,
+ lookupTable, baseToPulseIndexMap, newStartFrame);
+ fill(&timeMetric[offsetBegin], &timeMetric[offsetEnd], missingPulseIndex);
+ for (i = 0; i < ungappedAlignedSequenceLength; i++ ) {
+ timeMetric[offsetBegin+baseToAlignmentMap[i]] = newStartFrame[queryStart+i];
+ }
+ timeMetric[offsetBegin+alignedSequenceLength] = 0;
+
+ } else if (curMetric == "PreBaseFrames") {
+ // Directly load baseFile.PreBaseFrames.
+ // DON'T compute it from PulseCalls even if you can.
+ assert(baseFile.preBaseFrames.size() > 0 &&
+ baseFile.preBaseFrames.size() >= readStart + readLength);
+ fill(&frameRateMetric[offsetBegin], &frameRateMetric[offsetEnd], missingFrameRateValue);
+ for (i = 0; i < ungappedAlignedSequenceLength; i++ ) {
+ frameRateMetric[offsetBegin+baseToAlignmentMap[i]] = baseFile.preBaseFrames[readStart+queryStart+i];
+ }
+ frameRateMetric[offsetBegin+alignedSequenceLength] = 0;
+
+ } else if (curMetric == "WidthInFrames" || curMetric == "PulseWidth") {
+ // For legacy reasons, it's possible the width in frames is
+ // stored in the bas file. If this is the case, use the width
+ // in frames there. Otherwise, use the width in frames stored
+ // in the pls file.
+ vector<uint16_t> newWidthInFrames;
+ newWidthInFrames.resize(ungappedAlignedSequenceLength);
+ if (usePulseFile) {
+ hdfPlsReader.CopyFieldAt(pulseFile, "WidthInFrames", plsReadIndex,
+ &baseToPulseIndexMap[queryStart], &newWidthInFrames[0],
+ ungappedAlignedSequenceLength);
+ } else
+ if (useBaseFile) {
+ // basWidthInFrames data type uint16
+ copy(&baseFile.basWidthInFrames[readStart+queryStart],
+ &baseFile.basWidthInFrames[readStart+queryStart+ungappedAlignedSequenceLength],
+ &newWidthInFrames[0]);
+ }
+
+ fill(&frameRateMetric[offsetBegin], &frameRateMetric[offsetEnd], missingFrameRateValue);
+ for (i = 0; i < ungappedAlignedSequenceLength; i++ ) {
+ frameRateMetric[offsetBegin+baseToAlignmentMap[i]] = newWidthInFrames[i];
+ }
+ frameRateMetric[offsetBegin+alignedSequenceLength] = 0;
+
+ } else if (curMetric == "pkmid") {
+ // pkmid in cmp.h5 is MidSignal in pls.h5, but
+ // data type of MidSignal is uint16 in pls files,
+ // data type of pkmid is float in cmp files.
+ assert(usePulseFile);
+ vector<HalfWord> newMidSignal;
+ newMidSignal.resize(ungappedAlignedSequenceLength);
+ hdfPlsReader.CopyFieldAt(pulseFile, "MidSignal", plsReadIndex,
+ &baseToPulseIndexMap[queryStart], &newMidSignal[0],
+ ungappedAlignedSequenceLength, ungappedAlignedSequence);
+
+ fill(&floatMetric[offsetBegin], &floatMetric[offsetEnd], NaN);
+ for (i = 0; i < ungappedAlignedSequenceLength; i++ ) {
+ floatMetric[offsetBegin+baseToAlignmentMap[i]] = newMidSignal[i];
+ }
+ floatMetric[offsetBegin+alignedSequenceLength] = 0;
+
+ } else if (curMetric == "IPD") {
+ fill(&frameRateMetric[offsetBegin], &frameRateMetric[offsetEnd], missingFrameRateValue);
+
+ // IPD can be either (1) copied from baseFile.preBaseFrames
+ // or (2) computed from pulseFile.StartFrame and pulseFile.WidthInFrames
+ // Always use method (2) when possible as it is more accurate.
+ if (usePulseFile) {
+ // Need to read StartFrame & WidthInFrames for the entire read,
+ // not only for a subset of bases in the alignment
+ assert(pulseFile.startFrame.size() > 0);
+ assert(pulseFile.plsWidthInFrames.size() > 0);
+ vector<UInt> newStartFrame;
+ newStartFrame.resize(readLength);
+ hdfPlsReader.CopyFieldAt(pulseFile, "StartFrame", plsReadIndex,
+ &baseToPulseIndexMap[0], &newStartFrame[0], readLength);
+
+ vector<uint16_t> newWidthInFrames;
+ newWidthInFrames.resize(readLength);
+ hdfPlsReader.CopyFieldAt(pulseFile, "WidthInFrames", plsReadIndex,
+ &baseToPulseIndexMap[0], &newWidthInFrames[0], readLength);
+
+ for (i = 0; i < ungappedAlignedSequenceLength; i++) {
+ // The IPD is undefined for the first base in a read.
+ if (queryStart == 0 and i == 0) {
+ frameRateMetric[offsetBegin+baseToAlignmentMap[i]] = 0;
+ } else {
+ frameRateMetric[offsetBegin+baseToAlignmentMap[i]] = newStartFrame[queryStart+i]
+ - newStartFrame[i+queryStart-1] - newWidthInFrames[i+queryStart-1];
+ }
+ }
+ } else
+ if (useBaseFile) {
+ assert(baseFile.preBaseFrames.size() > 0);
+ assert(baseFile.preBaseFrames.size() >= readStart + readLength);
+
+ for (i = 0; i < ungappedAlignedSequenceLength; i++) {
+ frameRateMetric[offsetBegin+baseToAlignmentMap[i]] =
+ baseFile.preBaseFrames[readStart+queryStart+i];
+ }
+ }
+ frameRateMetric[offsetBegin+alignedSequenceLength] = 0;
+
+ } else if (curMetric == "Light") {
+ // Light can be computed from pulseFile.meanSignal and
+ // pulseFile.plsWidthInFrames. Might have been deprecated.
+ assert(usePulseFile);
+ fill(&frameRateMetric[offsetBegin], &frameRateMetric[offsetEnd], missingFrameRateValue);
+
+ vector<uint16_t> newMeanSignal;
+ newMeanSignal.resize(ungappedAlignedSequenceLength);
+ hdfPlsReader.CopyFieldAt(pulseFile, "MeanSignal", plsReadIndex,
+ &baseToPulseIndexMap[queryStart], &newMeanSignal[0],
+ ungappedAlignedSequenceLength, ungappedAlignedSequence);
+
+ vector<uint16_t> newWidthInFrames;
+ newWidthInFrames.resize(ungappedAlignedSequenceLength);
+ hdfPlsReader.CopyFieldAt(pulseFile, "WidthInFrames", plsReadIndex,
+ &baseToPulseIndexMap[queryStart], &newWidthInFrames[0],
+ ungappedAlignedSequenceLength);
+
+ for (i = 0; i < ungappedAlignedSequenceLength; i++ ) {
+ frameRateMetric[offsetBegin+baseToAlignmentMap[i]] = newMeanSignal[i] * newWidthInFrames[i];
+ }
+ frameRateMetric[offsetBegin+alignedSequenceLength] = 0;
+
+ } else {
+ cout << "ERROR, unknown metric " << curMetric << endl;
+ exit(1);
+ }
+ }
+
+ // Write the computed metric to cmp.h5.
+ /*if (curMetric == "StartTimeOffset") {
+ expGroup->startTimeOffset.WriteToPos(&startTimeOffsetMetric[0], startTimeOffsetMetric.size(), 0);
+ } else */
+ if (curMetric == "QualityValue" || curMetric == "InsertionQV" ||
+ curMetric == "DeletionQV" || curMetric == "MergeQV" ||
+ curMetric == "SubstitutionQV") {
+ HDFArray<UChar> * data = (HDFArray<UChar> *) expGroup->fields[curMetric];
+ data->WriteToPos(&qvMetric[0], qvMetric.size(), 0);
+
+ } else if (curMetric == "ClassifierQV" || curMetric == "pkmid" ) {
+ HDFArray<float> * data = (HDFArray<float> *) expGroup->fields[curMetric];
+ data->WriteToPos(&floatMetric[0], floatMetric.size(), 0);
+
+ } else if (curMetric == "PulseIndex") {
+ HDFArray<UInt> * data = (HDFArray<UInt> *) expGroup->fields[curMetric];
+ data->WriteToPos(&pulseMetric[0], pulseMetric.size(), 0);
+
+ } else if (curMetric == "DeletionTag" || curMetric == "SubstitutionTag") {
+ HDFArray<char> * data = (HDFArray<char> *) expGroup->fields[curMetric];
+ data->WriteToPos(&tagMetric[0], tagMetric.size(), 0);
+
+ } else if (curMetric == "StartFrame" || curMetric == "StartFrameBase"||
+ curMetric == "StartFramePulse") {
+ HDFArray<UInt> * data = (HDFArray<UInt>*) expGroup->fields[curMetric];
+ data->WriteToPos(&timeMetric[0], timeMetric.size(), 0);
+
+ } else if (curMetric == "PulseWidth" || curMetric == "PreBaseFrames" ||
+ curMetric == "WidthInFrames"|| curMetric == "IPD" ||
+ curMetric == "Light") {
+ HDFArray<HalfWord> * data = (HDFArray<HalfWord>*) expGroup->fields[curMetric];
+ data->WriteToPos(&frameRateMetric[0], frameRateMetric.size(), 0);
+
+ } else {
+ cout << "ERROR, unknown metric " << curMetric << endl;
+ exit(1);
+ }
+ }
+}
+
+//
+// Write "WhenStarted" from pls.h5 and write to cmp.h5
+//
+void WriteMetricWhenStarted(
+ HDFCmpFile<CmpAlignment> & cmpReader,
+ HDFPlsReader & hdfPlsReader,
+ const string & movieName) {
+ string metric = "WhenStarted";
+ string whenStarted;
+ if (hdfPlsReader.scanDataReader.useWhenStarted == false) {
+ cout << "ERROR! Attempting to read WhenStarted from "
+ << movieName
+ << " but the attriubte does not exist." << endl;
+ exit(1);
+ }
+ hdfPlsReader.scanDataReader.ReadWhenStarted(whenStarted);
+
+ if (!cmpReader.movieInfoGroup.whenStartedArray.IsInitialized()) {
+ cmpReader.movieInfoGroup.whenStartedArray.Initialize(cmpReader.movieInfoGroup.movieInfoGroup, metric);
+ }
+ cmpReader.movieInfoGroup.whenStartedArray.Write(&whenStarted, 1);
+}
+
+//
+// Print metrics.
+//
+string MetricsToString(const vector<string> & metrics) {
+ string ret = "";
+ int j = 0;
+ for (int i = 0; i < metrics.size(); i++) {
+ ret += metrics[i];
+ if (i != metrics.size()-1) ret += ",";
+ if (i % 4 == 3) ret += "\n";
+ }
+ return ret;
+}
+
+//
+// Print usage.
+//
+void PrintUsage() {
+ cout << " loadPulses - Load pulse information and quality values into a Compare file" << endl;
+ cout << "usage: loadPulses movieFile cmpFile [-metrics m1,m2,...] [-byread]" << endl;
+ cout << " movieFile may be a movie file or a fofn of movie file names." << endl;
+ cout << " metrics m1,m2,... is a comma-separated list (without spaces) of metrics " << endl
+ << " to print to the pulse file." << endl;
+ cout << " Valid metrics are: " << endl;
+ cout << MetricsToString(GetAllSupportedMetrics(false)) << endl;
+ // << " QualityValue, ClassifierQV, MergeQV," << endl
+ // << " StartFrame, PulseWidth, pkmid, IPD, Light" << endl
+ // << " WhenStarted, StartTimeOffset, PreBaseFrames," << endl
+ // << " InsertionQV, DeletionQV, DeletionTag, SubstitutionQV" << endl
+ // << " SubstitutionTag, PulseIndex, WidthInFrames" << endl;
+ cout << " By default, " << MetricsToString(GetDefaultMetrics()) << " are added" << endl;
+ // Deprecate -useccs, an option for old data.
+ // cout << " -useccs This option is for older cmp.h5 files that do not have the read type " << endl
+ // << " stored. Newer cmp.h5 files have a read type that indicates the cmp.h5 file " << endl
+ // << " has alignments generated from de novo ccs sequences. Using this flag assuems"<<endl
+ // << " ALL alignments in the cmp.h5 file are from ccs sequences, and loads the "<< endl
+ // << " quality values from ccs instead of the raw sequence. "<<endl
+ // << " The only metrics that are allowed for de novo ccs sequences are QualityValue, " << endl
+ // << " InsertionQV, DeletionQV, and SubstitutionQV" << endl;
+ cout << " -byread Reads pulse/base fields by read, rather than reading an entire " << endl
+ << " movie first. This uses considerably less memory than the defualt mode" << endl
+ << " but is slow." << endl;
+ cout << " -byMetric Loads every pls/base field for each movie entirely before loading " << endl
+ << " another field. This uses more memory than -byread, but can be faster." << endl
+ << " This opiton is experimental. " << endl;
+ cout << " Using hdf version " << H5_VERS_MAJOR << "." << H5_VERS_MINOR << "." << H5_VERS_RELEASE << endl;
+}
+
+
+//
+// The main function.
+//
+int main(int argc, char* argv[]) {
+ string program = "loadPulses";
+ string versionStr(VERSION);
+ AppendPerforceChangelist(PERFORCE_VERSION_STRING, versionStr);
+
+ string cmpFileName, movieFileName;
+ int argi = 3;
+ int numMetrics = 8;
+ map<string,bool> metricOptions;
+ int maxElements = 0;
+ //Maximum Memory allowed for bymetric is 6 GB
+ int maxMemory = 4;
+ //
+ // Default is all options are false
+ //
+ CreateMetricOptions(metricOptions);
+ string metricList = "";
+ bool useCcsOnly = false;
+ bool byRead = false;
+ bool byMetric = false;
+ bool failOnMissingData = false;
+
+ CommandLineParser clp;
+ clp.SetProgramName(program);
+ clp.SetVersion(versionStr);
+
+ clp.RegisterStringOption("basFileName", &movieFileName,
+ "The input {bas,pls}.h5 or input.fofn.", true);
+ clp.RegisterStringOption("cmpFileName", &cmpFileName,
+ "The cmp.h5 file to load pulse information into.", true);
+ clp.RegisterPreviousFlagsAsHidden();
+
+ string metricsDescription = "A comma separated list of metrics (with no spaces).\nValid options are:\n";
+ metricsDescription += MetricsToString(GetAllSupportedMetrics(false));
+ metricsDescription += "\nDefault options are:\n";
+ metricsDescription += MetricsToString(GetDefaultMetrics());
+
+ clp.RegisterStringOption("metrics", &metricList, metricsDescription);
+ clp.RegisterFlagOption("failOnMissingData", &failOnMissingData,
+ "Exit if any data fields are missing from the bas.h5 or pls.h5 "
+ "input that are required to load a metric. Defualt is a warning.");
+ clp.RegisterFlagOption("byread", &byRead,
+ "Load pulse information by read rather than buffering metrics.");
+ clp.RegisterFlagOption("bymetric", & byMetric,
+ "Load pulse information by metric rather than by read. "
+ "This uses more memory than -byread, but can be faster.");
+ clp.RegisterIntOption("maxElements", &maxElements,
+ "Set a limit on the size of pls/bas file to buffer in with -bymetric "
+ "(default value: maximum int). Use -byread if the limit is exceeded.",
+ CommandLineParser::PositiveInteger);
+ clp.RegisterIntOption("maxMemory", & maxMemory,
+ "Set a limit (in GB) on the memory to buffer data with -bymetric "
+ "(default value: 4 GB). Use -byread if the limit is exceeded.",
+ CommandLineParser::PositiveInteger);
+ int metaNElements, rawChunkSize, rawNElements;
+ metaNElements = rawChunkSize = metaNElements = 0;
+ clp.RegisterIntOption("metaNElements", & metaNElements,
+ "Set number of elements in meta data cache for reading bas/bax/pls.h5 file.",
+ CommandLineParser::PositiveInteger);
+ clp.RegisterIntOption("rawNElements", & rawNElements,
+ "Set number of elements in raw data cache for reading bas/bax/pls.h5 file.",
+ CommandLineParser::PositiveInteger);
+ clp.RegisterIntOption("rawChunkSize", & rawChunkSize,
+ "Set chunk size of raw data cache for reading bas/bax/pls.h5 file.",
+ CommandLineParser::PositiveInteger);
+
+ string progSummary = ("Loads pulse information such as inter pulse "
+ "distance, or quality information into the cmp.h5 file. This allows "
+ "one to analyze kinetic and quality information by alignment column.");
+ clp.SetProgramSummary(progSummary);
+ clp.ParseCommandLine(argc, argv);
+
+ cerr << "[INFO] " << GetTimestamp() << " [" << program << "] started." << endl;
+ //use byMetric by default unless byRead is specified.
+ byMetric = true;
+ if (byRead) {
+ byMetric = false;
+ }
+
+ if (metricList == "") {
+ SetDefaultMetricOptions(metricOptions);
+ }
+ else {
+ ParseMetricsList(metricList, metricOptions);
+ }
+
+ //
+ // Always read in basecalls since they are used to check the sanity
+ // of the alignment indices.
+ //
+ metricOptions["Basecall"] = true;
+
+ //
+ // Translate from the metrics to be loaded to the ones that are
+ // required to compute them.
+ // Need to be refactored.
+ //
+ vector<string> datasetFields;
+ RequirementMap fieldRequirements;
+ BuildRequirementMap(fieldRequirements);
+ StoreDatasetFieldsFromPulseFields(metricOptions, fieldRequirements, datasetFields);
+
+
+ //e.g. /PATH_TO_FILE/m120321_032600_42142_c100310572550000001523013208061210_s1_p0.bas.h5
+ // /PATH_TO_FILE/m120321_032600_42142_c100310572550000001523013208061210_s2_p0.bas.h5
+ vector<string> movieFileNames;
+
+ //e.g. m120321_032600_42142_c100310572550000001523013208061210_s1_p0
+ // m120321_032600_42142_c100310572550000001523013208061210_s2_p0
+ vector<string> fofnMovieNames;
+
+ FileOfFileNames::StoreFileOrFileList(movieFileName, movieFileNames);
+
+ HDFBasReader hdfBasReader;
+ HDFPlsReader hdfPlsReader;
+ HDFCCSReader<SMRTSequence> hdfCcsReader;
+
+ vector<string> baseFileFields, pulseFileFields;
+ int fieldIndex;
+ bool useBaseFile = false, usePulseFile = false;
+ for (fieldIndex = 0; fieldIndex < datasetFields.size(); fieldIndex++) {
+ if (hdfBasReader.ContainsField(datasetFields[fieldIndex])) {
+ useBaseFile = true;
+ baseFileFields.push_back(datasetFields[fieldIndex]);
+ }
+ }
+
+ if (maxElements != 0) {
+ hdfBasReader.maxAllocNElements = maxElements;
+ hdfPlsReader.maxAllocNElements = maxElements;
+ }
+
+ //
+ // For now, all runs will attempt to use information from a .bas
+ // file, since it's assumed that if one has alignments, one has a
+ // .bas file.
+ //
+ useBaseFile = true;
+ //
+ // Add some default fields.
+ //
+ hdfBasReader.IncludeField("Basecall");
+ hdfBasReader.IncludeField("PulseIndex");
+ hdfBasReader.InitializeFields(baseFileFields);
+
+ for (fieldIndex = 0; fieldIndex < datasetFields.size(); fieldIndex++) {
+ if (hdfPlsReader.ContainsField(datasetFields[fieldIndex])) {
+ usePulseFile = true;
+ pulseFileFields.push_back(datasetFields[fieldIndex]);
+ }
+ }
+ if (usePulseFile) {
+ // set hdfPlsReader.includedFields[fieldX] to true if fieldX is
+ // in pulseFileFields
+ hdfPlsReader.InitializeFields(pulseFileFields);
+ }
+ hdfPlsReader.IncludeField("NumEvent");
+
+ int nMovies = movieFileNames.size();
+ int movieIndex;
+ MovieNameToArrayIndex movieNameMap;
+ //
+ // Initialize movies. This accomplishes two tasks. First, all movie
+ // files are opened and initialized, so that if there are data
+ // fields missing the program will exit now rather than in the
+ // middle of loading pulses.
+ // Next, a list of movie names is created in fofnMovieNames. The
+ // cmp file does not necessarily index movies in the order of the
+ // fofn, and so when loading pulses from a movie indexed by a cmp
+ // file, one needs to look up the file name of the movie. This is
+ // done by scanning the fofnMovieNames list in order until the movie
+ // is found.
+
+ //
+ // h5 file access property list can be customized here.
+ //
+ H5::FileAccPropList fileAccPropList = H5::FileAccPropList::DEFAULT;
+ // h5: number of items in meta data cache
+ int mdc_nelmts = (metaNElements==0)?(4096):(metaNElements);
+ // h5: number of items in raw data chunk cache
+ size_t rdcc_nelmts = (rawNElements==0)?(4096):(rawNElements);
+ // h5: raw data chunk cache size (in bytes) per dataset
+ size_t rdcc_nbytes = (rawChunkSize==0)?(9192):(rawChunkSize);
+ double rdcc_w0 = 0.75; // h5: preemption policy
+ // fileAccPropList.getCache(mdc_nelmts, rdcc_nelmts, rdcc_nbytes, rdcc_w0);
+ fileAccPropList.setCache(mdc_nelmts, rdcc_nelmts, rdcc_nbytes, rdcc_w0);
+ // fileAccPropList.setCache(4096, 4096, 8388608, rdcc_w0);
+
+
+ // If one of the h5 in the fofn is a ccs.h5 file, then only load pulse
+ // information from group /PulseData/ConsensusBaseCalls.
+ for (movieIndex = 0; movieIndex < nMovies; movieIndex++) {
+ FileType fileType;
+ BaseSequenceIO::DetermineFileTypeByExtension(movieFileNames[movieIndex], fileType, true);
+ if (fileType == HDFCCSONLY) {
+ useCcsOnly = true;
+ }
+ }
+
+ for (movieIndex = 0; movieIndex < nMovies; movieIndex++) {
+ if (useCcsOnly) {
+ hdfCcsReader.SetReadBasesFromCCS();
+ hdfBasReader.SetReadBasesFromCCS();
+ }
+ if (!hdfBasReader.Initialize(movieFileNames[movieIndex], fileAccPropList)) {
+ cout << "ERROR, could not initialize HDF file "
+ << movieFileNames[movieIndex] << " for reading bases." << endl;
+ exit(1);
+ }
+ else {
+ fofnMovieNames.push_back(hdfBasReader.GetMovieName());
+ movieNameMap[hdfBasReader.GetMovieName()] = movieIndex;
+ hdfBasReader.Close();
+ }
+
+ //
+ // The pulse file is optional.
+ //
+ if (usePulseFile) {
+ if (hdfPlsReader.Initialize(movieFileNames[movieIndex], fileAccPropList) == 0) {
+ usePulseFile = false;
+ }
+ }
+ }
+
+ CmpFile cmpFile;
+
+ //
+ // These readers pull information from the same pls file.
+ //
+ HDFCmpFile<CmpAlignment> cmpReader;
+
+ if (cmpReader.Initialize(cmpFileName, H5F_ACC_RDWR) == 0) {
+ cout << "ERROR, could not open the cmp file." << endl;
+ exit(1);
+ }
+
+ if (cmpReader.HasNoAlignments()) {
+ cout << "WARNING, there is no alignment in the cmp file." << endl;
+ if (useBaseFile) {
+ hdfBasReader.Close();
+ }
+ if (usePulseFile) {
+ hdfPlsReader.Close();
+ }
+ cmpReader.Close();
+ cerr << "[INFO] " << GetTimestamp() << " [" << program << "] ended." << endl;
+ exit(0);
+ }
+
+ cmpReader.Read(cmpFile, false);
+
+ // Sanity check: if there is a ccs.h5 file in the fofn and
+ // cmp.h5 file's readType is not CCS, something is wrong.
+ if (cmpFile.readType != ReadType::CCS and useCcsOnly) {
+ cout << "ERROR, there is a ccs.h5 file in the fofn, while read type of"
+ << " the cmp.h5 file is not CCS." << endl;
+ exit(1);
+ }
+
+ string commandLine;
+ clp.CommandLineToString(argc, argv, commandLine);
+ cmpReader.fileLogGroup.AddEntry(commandLine, "Loading pulse metrics", program, GetTimestamp(), versionStr);
+
+ //
+ // Group alignment indices by movie so that they may be processed one movie at a time
+ // later on. The movie indices set keeps track of all indices
+ // listed in alignment files. This keeps a reference to all
+ // alignments in memory at once. At the time of writing this, most
+ // projects will have at most a few million alignments, and so the
+ // size of this structure is modest.
+ // Each movieIndexSets[$movieId] contains indices of all the alignments, which
+ // are associated with a movie whose id in dataset /MovieInfo/ID equals $movieId
+ //
+ UInt alignmentIndex;
+ map<int, vector<int> > movieIndexSets;
+
+ for (alignmentIndex = 0; alignmentIndex < cmpFile.alnInfo.alignments.size(); alignmentIndex++) {
+ movieIndexSets[cmpFile.alnInfo.alignments[alignmentIndex].GetMovieId()].push_back(alignmentIndex);
+ }
+
+ //
+ // Load pulses from movies in order they appear in the input fofn.
+ //
+ int m;
+ int fofnMovieIndex;
+ for (fofnMovieIndex = 0; fofnMovieIndex < fofnMovieNames.size(); fofnMovieIndex++) {
+ bool byMetricForThisMovie = byMetric;
+
+ if (cmpFile.readType == ReadType::CCS or useCcsOnly) {
+ hdfBasReader.SetReadBasesFromCCS();
+ hdfCcsReader.Initialize(movieFileNames[fofnMovieIndex], fileAccPropList);
+ }
+ hdfBasReader.Initialize(movieFileNames[fofnMovieIndex], fileAccPropList);
+
+ BaseFile baseFile;
+ PulseFile pulseFile;
+
+ //
+ // Deprecate reading the entire bas.h5 file. Reads are scanned
+ // one by one or by metric, instead of caching all.
+ // It is still necessary to read in some of the datasets entirely,
+ // in particular the start positions and hole numbers.
+ //
+ hdfBasReader.ReadBaseFileInit(baseFile);
+
+ set<uint32_t> moviePartHoleNumbers;
+ copy(baseFile.holeNumbers.begin(), baseFile.holeNumbers.end(), inserter(moviePartHoleNumbers, moviePartHoleNumbers.begin()));
+
+ if (usePulseFile) {
+ hdfPlsReader.Initialize(movieFileNames[fofnMovieIndex], fileAccPropList);
+ hdfPlsReader.IncludeField("NumEvent");
+ hdfPlsReader.IncludeField("StartFrame");
+ //
+ // Deprecate reading the entire pls.h5 file.
+ // Reads are scanned by read or by metric instead of caching all.
+ // It is still necessary to read in some of the datasets entirely,
+ // in particular the start positions and hole numbers.
+ //
+ hdfPlsReader.ReadPulseFileInit(pulseFile);
+ }
+
+ string cmpFileMovieName;
+
+ for (m = 0; m < cmpFile.movieInfo.name.size(); m++) {
+ //
+ // First find the file name for the movie 'm'
+ //
+ cmpFileMovieName = cmpFile.movieInfo.name[m];
+
+ if (baseFile.GetMovieName() == cmpFileMovieName) {
+ break;
+ }
+ }
+
+ //
+ // If the movie specified in the input.fofn is not found in the
+ // cmp file, that indicates something bad is happeing. Either the
+ // input.fofn was not used to generate the cmp.h5 file, or no
+ // alignments were found between the input bas.h5 and the
+ // reference. That shouldn't happen.
+ //
+ if (m == cmpFile.movieInfo.name.size()) {
+ cout << "WARNING: Could not find any alignments for file " << movieFileNames[fofnMovieIndex] << endl;
+ continue;
+ }
+
+ //
+ // Open the movie and load its pulses into memory.
+ //
+ movieIndex = cmpFile.movieInfo.id[m];
+ UInt movieAlignmentIndex;
+
+ //
+ // Since usePulseFile is set when the input file is a pulseFile,
+ // and ReadType::CCS becomes the read type when the alignments are
+ // ccs, when pulse files are specified for de novo ccs alignments,
+ // they will be opened as pulse files. Since the de novo ccs
+ // sequences do not have pulse file information, the auto-reading
+ // of pulse files needs to be disabled. Do that here.
+ //
+ if (cmpFile.readType == ReadType::CCS or useCcsOnly) {
+ usePulseFile = false;
+ }
+
+ // Check whether all metrics are computable or not.
+ CanMetricsBeComputed(metricOptions, hdfBasReader, hdfPlsReader, useBaseFile,
+ usePulseFile, failOnMissingData, movieFileNames[fofnMovieIndex]);
+
+ // Get all metrics that are (1) supported, (2) required and (3) can be loaded.
+ vector<string> metricsToLoad = GetMetricsToLoad(metricOptions);
+
+ //
+ // An index set is a set of indices into the alignment array that
+ // are of reads generated by this movie. Load pulses for all
+ // alignments generated for this movie.
+ //
+ // Movie index sets should be sorted by alignment index. Build a lookup table for this.
+ //
+
+ std::vector<std::pair<int,int> > toFrom;
+ UInt totalAlnLength = 0;
+ for (movieAlignmentIndex = 0; movieAlignmentIndex < movieIndexSets[movieIndex].size(); movieAlignmentIndex++) {
+ alignmentIndex = movieIndexSets[movieIndex][movieAlignmentIndex];
+ totalAlnLength += cmpFile.alnInfo.alignments[alignmentIndex].GetOffsetEnd() - \
+ cmpFile.alnInfo.alignments[alignmentIndex].GetOffsetBegin();
+ toFrom.push_back(std::pair<int,int>(cmpFile.alnInfo.alignments[alignmentIndex].GetAlignmentId(), movieAlignmentIndex));
+ }
+
+ // orders by first by default.
+ std::sort(toFrom.begin(), toFrom.end());
+
+ //
+ // Check metric dataset size in this movie and the required memory
+ // consumption, if either limit is exceeded, switch to byread.
+ //
+ if (byMetricForThisMovie)
+ {
+ UInt requiredMem = ComputeRequiredMemory(metricsToLoad, hdfBasReader,
+ hdfPlsReader, useBaseFile, usePulseFile, cmpReader, totalAlnLength);
+ if (hdfBasReader.baseArray.arrayLength > hdfBasReader.maxAllocNElements or
+ (usePulseFile and
+ hdfPlsReader.GetStartFrameSize() > hdfPlsReader.maxAllocNElements) or
+ ((float)requiredMem / 1024 / 1024) > maxMemory) {
+ cout << "Either the number of elements exceeds maxElement ("
+ << hdfPlsReader.maxAllocNElements << "). Or the estimated memory " << endl
+ << "consumption exceeds maxMemory (" << maxMemory << " GB)." << endl
+ << "Loading pulses from " << movieFileNames[fofnMovieIndex]
+ << " by read." << endl;
+ byMetricForThisMovie = false;
+ }
+ }
+
+ if (((metricOptions.find("StartFrameBase") != metricOptions.end() and
+ metricOptions["StartFrameBase"]) or
+ (metricOptions.find("StartFramePulse")!= metricOptions.end() and
+ metricOptions["StartFramePulse"])) and !byMetricForThisMovie) {
+ // Sneaky metrics StartFrameBase and StartFramePulse can used
+ // with -bymetric only
+ cout << "ERROR: Internal metrics StartFrameBase and StartFramePulse "
+ << "can only be loaded with -bymetric." << endl;
+ exit(1);
+ }
+
+ // Load "WhenStarted" before processing the others.
+ if (metricOptions["WhenStarted"]) {
+ WriteMetricWhenStarted(cmpReader, hdfPlsReader, movieFileNames[fofnMovieIndex]);
+ }
+
+ // Now load frame rate.
+ // if (AnyFieldRequiresFrameRate(datasetFields)) {
+ // Load frame rate anyway to ensure that cmp.h5 files are consistent.
+ if (useBaseFile) {
+ cmpReader.movieInfoGroup.StoreFrameRate(m, baseFile.GetFrameRate());
+ } else
+ if (usePulseFile) {
+ cmpReader.movieInfoGroup.StoreFrameRate(m, pulseFile.GetFrameRate());
+ }
+
+ //
+ // Load metrics for alignments from movie 'movieIndex'.
+ //
+ cout << "loading " << movieIndexSets[movieIndex].size() << " alignments for movie " << movieIndex << endl;
+
+ UInt i;
+ if (byMetricForThisMovie) {
+ //
+ // Build lookup tables for all alignments which
+ // are generated by the movie and check whether
+ // pls/bas.h5 and cmp.h5 match.
+ //
+ vector<MovieAlnIndexLookupTable> lookupTables;
+
+ BuildLookupTablesAndMakeSane(cmpFile,
+ baseFile,
+ pulseFile,
+ cmpReader,
+ hdfBasReader,
+ hdfPlsReader,
+ hdfCcsReader,
+ useBaseFile,
+ usePulseFile,
+ useCcsOnly,
+ movieIndexSets[movieIndex],
+ toFrom,
+ moviePartHoleNumbers,
+ lookupTables);
+
+ //
+ // Group lookup tables by refGroupIndex and readGroupIndex.
+ //
+ vector<pair<UInt, UInt> > groupedLookupTablesIndexPairs;
+ GroupLookupTables(lookupTables, groupedLookupTablesIndexPairs);
+
+ if (cmpFile.readType == ReadType::CCS or useCcsOnly) {
+ vector<unsigned int> numPassesMetric;
+ numPassesMetric.resize(lookupTables.size());
+ UInt index = 0;
+ for (index = 0; index < lookupTables.size(); index++) {
+ if (lookupTables[index].skip) {
+ continue;
+ }
+ numPassesMetric[index] = hdfCcsReader.GetNumPasses(lookupTables[index].readIndex);
+ }
+ if (!cmpReader.alnInfoGroup.numPasses.IsInitialized()) {
+ cmpReader.alnInfoGroup.InitializeNumPasses();
+ // Clear /AlnInfo/NumPasses dataset.
+ cmpReader.alnInfoGroup.numPasses.Resize(0);
+ }
+ // Append numPasses of this movie to the end of /AlnInfo/NumPasses.
+ UInt numPassesSize = cmpReader.alnInfoGroup.numPasses.size();
+ cmpReader.alnInfoGroup.numPasses.WriteToPos(
+ &numPassesMetric[0],
+ numPassesMetric.size(),
+ numPassesSize);
+ }
+
+ // Keep a list of currently cached fields.
+ vector<Field> cachedFields;
+ if (usePulseFile) {
+ // PulseCalls/ZMW/NumEvent is always cached in plsFile.
+ cachedFields.push_back(Field("NumEvent", PlsField));
+ }
+
+ for (int metricsToLoadIndex = 0; metricsToLoadIndex < metricsToLoad.size(); metricsToLoadIndex++) {
+ string curMetric = metricsToLoad[metricsToLoadIndex];
+ // Metric "WhenStarted" should have been loaded before getting here.
+ if (curMetric == "WhenStarted") {
+ continue;
+ }
+ // Get the next metric to load.
+ string nextMetric = "";
+ if (metricsToLoadIndex+1 < metricsToLoad.size()) {
+ nextMetric = metricsToLoad[metricsToLoadIndex+1];
+ }
+
+ // Cache all required data for computing this metric.
+ CacheRequiredFieldsForMetric(baseFile,
+ pulseFile,
+ hdfBasReader,
+ hdfPlsReader,
+ hdfCcsReader,
+ useBaseFile,
+ usePulseFile,
+ useCcsOnly,
+ cachedFields,
+ curMetric);
+
+ // Compute the metric and write it to cmp.h5.
+ WriteMetric(cmpFile,
+ baseFile,
+ pulseFile,
+ cmpReader,
+ hdfBasReader,
+ hdfPlsReader,
+ hdfCcsReader,
+ useBaseFile,
+ usePulseFile,
+ useCcsOnly,
+ lookupTables,
+ groupedLookupTablesIndexPairs,
+ curMetric);
+
+ // Clear cached fields unless they are required by the next metric.
+ ClearCachedFields(baseFile,
+ pulseFile,
+ hdfBasReader,
+ hdfPlsReader,
+ hdfCcsReader,
+ useBaseFile,
+ usePulseFile,
+ useCcsOnly,
+ cachedFields,
+ curMetric,
+ nextMetric);
+ }
+
+ // Clear the default field "NumEvent"
+ if (usePulseFile) {
+ hdfPlsReader.ClearField(pulseFile, "NumEvent");
+ }
+
+ } else { // byRead for this movie
+ for (movieAlignmentIndex = 0; movieAlignmentIndex < movieIndexSets[movieIndex].size(); movieAlignmentIndex++) {
+ MovieAlnIndexLookupTable lookupTable;
+ BuildLookupTable(movieAlignmentIndex,
+ cmpFile,
+ baseFile,
+ usePulseFile,
+ pulseFile,
+ cmpReader,
+ movieIndexSets[movieIndex],
+ toFrom,
+ moviePartHoleNumbers,
+ lookupTable);
+
+ // Skip this alignment if it is not generated by this movie
+ if (lookupTable.skip) {
+ continue;
+ }
+
+ UInt & alignmentIndex = lookupTable.alignmentIndex;
+ int & refGroupIndex = lookupTable.refGroupIndex;
+ int & readGroupIndex = lookupTable.readGroupIndex;
+ UInt & holeNumber = lookupTable.holeNumber;
+ int & readIndex = lookupTable.readIndex;
+ int & queryStart = lookupTable.queryStart;
+ int & queryEnd = lookupTable.queryEnd;
+ int & readStart = lookupTable.readStart;
+ int & readLength = lookupTable.readLength;
+ UInt & offsetBegin = lookupTable.offsetBegin;
+ UInt & offsetEnd = lookupTable.offsetEnd;
+
+ string alignedSequence = GetAlignedSequenceFromCmpFile(cmpReader, lookupTable);
+
+ // Create a map of where.
+ vector<int> baseToAlignmentMap;
+ CreateSequenceToAlignmentMap(alignedSequence, baseToAlignmentMap);
+
+ // Condense gaps in the alignment for easy comparison.
+ RemoveGaps(alignedSequence, alignedSequence);
+
+ // Get source read.
+ unsigned int numPasses;
+ SMRTSequence sourceRead;
+ GetSourceRead(cmpFile,
+ baseFile ,
+ pulseFile ,
+ hdfBasReader,
+ hdfPlsReader,
+ hdfCcsReader,
+ useBaseFile ,
+ usePulseFile,
+ useCcsOnly ,
+ //byRead ,
+ lookupTable ,
+ alignedSequence,
+ sourceRead ,
+ numPasses);
+
+ string readSequence;
+ readSequence.resize(queryEnd - queryStart);
+ copy((char*) (sourceRead.seq + queryStart),
+ (char*) (sourceRead.seq + queryEnd),
+ readSequence.begin());
+
+ if (alignedSequence.size() != readSequence.size() or alignedSequence != readSequence) {
+ cout << "ERROR, the query sequence does not match the aligned query sequence." << endl;
+ cout << "HoleNumber: "<< holeNumber << ", MovieName: " << cmpFileMovieName;
+ cout << ", ReadIndex: " << (int) readIndex;
+ cout << ", qStart: "<< queryStart << ", qEnd: " << queryEnd << endl;
+ cout << "Aligned sequence: "<< endl;
+ cout << alignedSequence << endl;
+ cout << "Original sequence: " << endl;
+ cout << readSequence << endl;
+ assert(0);
+ }
+
+ //
+ // Compute any necessary data fields. These usually involve
+ // using differences of pulse indices, pulse widths, etc..
+ // Missing fields are stored as 0's.
+ //
+
+ vector<float> readPulseMetric;
+ vector<float> floatMetric;
+ vector<UChar> qvMetric;
+ vector<HalfWord> frameRateMetric;
+ vector<uint32_t> timeMetric;
+ int ungappedAlignedSequenceLength = alignedSequence.size();
+ assert(ungappedAlignedSequenceLength == queryEnd - queryStart);
+
+ int alignedSequenceLength = offsetEnd - offsetBegin;
+ readPulseMetric.resize(alignedSequenceLength+1);
+ qvMetric.resize(alignedSequenceLength+1);
+ frameRateMetric.resize(alignedSequenceLength+1);
+ timeMetric.resize(alignedSequenceLength+1);
+
+ UInt i;
+ UInt pi;
+
+ HDFCmpExperimentGroup* expGroup = cmpReader.refAlignGroups[refGroupIndex]->readGroups[readGroupIndex];
+ UInt alnArrayLength = expGroup->alignmentArray.size();
+
+ if (cmpFile.readType == ReadType::CCS or useCcsOnly) {
+ if (!cmpReader.alnInfoGroup.numPasses.IsInitialized()) {
+ cmpReader.alnInfoGroup.InitializeNumPasses();
+ }
+ cmpReader.alnInfoGroup.numPasses.WriteToPos(&numPasses, 1, alignmentIndex);
+ }
+
+ if (metricOptions["StartTimeOffset"] == true) {
+ if (!expGroup->startTimeOffset.IsInitialized()) {
+ expGroup->startTimeOffset.Initialize(expGroup->experimentGroup, "StartTimeOffset");
+ }
+ unsigned int readStartTimeOffset = sourceRead.startFrame[queryStart];
+ expGroup->startTimeOffset.WriteToPos(&readStartTimeOffset, 1, alignmentIndex);
+ }
+
+ if (metricOptions["QualityValue"] == true) {
+ if (!expGroup->qualityValue.IsInitialized()) {
+ expGroup->qualityValue.Initialize(expGroup->experimentGroup, "QualityValue", true, alnArrayLength);
+ }
+ // Store QualityValue.
+ fill(qvMetric.begin(), qvMetric.end(), missingQualityValue);
+ for (i = 0; i < ungappedAlignedSequenceLength; i++ ) {
+ qvMetric[baseToAlignmentMap[i]] = sourceRead.qual[queryStart + i];
+ }
+ qvMetric[qvMetric.size()-1] = 0;
+ expGroup->qualityValue.WriteToPos(&qvMetric[0], qvMetric.size(), offsetBegin);
+ }
+
+ if (metricOptions["InsertionQV"] == true) {
+ if (!expGroup->insertionQV.IsInitialized()) {
+ expGroup->insertionQV.Initialize(expGroup->experimentGroup, "InsertionQV", true, alnArrayLength);
+ }
+ // Store InsertionQV.
+ fill(qvMetric.begin(), qvMetric.end(), missingQualityValue);
+ for (i = 0; i < ungappedAlignedSequenceLength; i++ ) {
+ qvMetric[baseToAlignmentMap[i]] = sourceRead.insertionQV[queryStart+ i];
+ }
+ qvMetric[qvMetric.size()-1] = 0;
+ expGroup->insertionQV.WriteToPos(&qvMetric[0], qvMetric.size(), offsetBegin);
+ }
+
+ if (metricOptions["MergeQV"] == true) {
+ if (!expGroup->mergeQV.IsInitialized()) {
+ expGroup->mergeQV.Initialize(expGroup->experimentGroup, "MergeQV", true, alnArrayLength);
+ }
+ // Store MergeQV.
+ fill(qvMetric.begin(), qvMetric.end(), missingQualityValue);
+ for (i = 0; i < ungappedAlignedSequenceLength; i++ ) {
+ qvMetric[baseToAlignmentMap[i]] = sourceRead.mergeQV[queryStart+ i];
+ }
+ qvMetric[qvMetric.size()-1] = 0;
+ expGroup->mergeQV.WriteToPos(&qvMetric[0], qvMetric.size(), offsetBegin);
+ }
+
+ if (metricOptions["DeletionQV"] == true) {
+ if (!expGroup->deletionQV.IsInitialized()) {
+ expGroup->deletionQV.Initialize(expGroup->experimentGroup, "DeletionQV", true, alnArrayLength);
+ }
+ // Store DeletionQV.
+ fill(qvMetric.begin(), qvMetric.end(), missingQualityValue);
+ for (i = 0; i < ungappedAlignedSequenceLength; i++ ) {
+ qvMetric[baseToAlignmentMap[i]] = sourceRead.deletionQV[queryStart+i];
+ }
+ qvMetric[qvMetric.size()-1] = 0;
+ expGroup->deletionQV.WriteToPos(&qvMetric[0], qvMetric.size(), offsetBegin);
+ }
+
+ if (metricOptions["DeletionTag"] == true) {
+ if (!expGroup->deletionTag.IsInitialized()) {
+ expGroup->deletionTag.Initialize(expGroup->experimentGroup, "DeletionTag", true, alnArrayLength);
+ }
+ vector<char> readDeletionTagMetric;
+ readDeletionTagMetric.resize(readPulseMetric.size());
+ // Store DeletionTag.
+ for (i = 0; i < readDeletionTagMetric.size()-1; i++ ) {
+ readDeletionTagMetric[i] = '-';
+ }
+ readDeletionTagMetric[i] = '\0';
+ for (i = 0; i < ungappedAlignedSequenceLength; i++ ) {
+ assert(baseToAlignmentMap[i] < readDeletionTagMetric.size());
+ readDeletionTagMetric[baseToAlignmentMap[i]] = sourceRead.deletionTag[queryStart+i];
+ }
+ readDeletionTagMetric[readDeletionTagMetric.size()-1] = 0;
+ expGroup->deletionTag.WriteToPos(&readDeletionTagMetric[0], readDeletionTagMetric.size(), offsetBegin);
+ }
+
+ if (metricOptions["PulseIndex"] == true) {
+ if (!expGroup->pulseIndex.IsInitialized()) {
+ expGroup->pulseIndex.Initialize(expGroup->experimentGroup, "PulseIndex", true, alnArrayLength);
+ }
+ vector<uint32_t> readPulseIndexMetric;
+ fill(readPulseIndexMetric.begin(), readPulseIndexMetric.end(), missingPulseIndex);
+ readPulseIndexMetric.resize(readPulseMetric.size());
+ // Store Pulse Index.
+ assert(readPulseIndexMetric.size() > 0);
+ for (i = 0; i < readPulseIndexMetric.size(); i++ ) {
+ readPulseIndexMetric[i] = 0;
+ }
+ for (i = 0; i < ungappedAlignedSequenceLength; i++ ) {
+ readPulseIndexMetric[baseToAlignmentMap[i]] = sourceRead.pulseIndex[queryStart+i];
+ }
+ readPulseIndexMetric[readPulseIndexMetric.size()-1] = 0;
+ expGroup->pulseIndex.WriteToPos(&readPulseIndexMetric[0], readPulseIndexMetric.size(), offsetBegin);
+ }
+
+ if (metricOptions["SubstitutionTag"] == true) {
+ if (!expGroup->substitutionTag.IsInitialized()) {
+ expGroup->substitutionTag.Initialize(expGroup->experimentGroup, "SubstitutionTag", true, alnArrayLength);
+ }
+ vector<char> readSubstitutionTagMetric;
+ readSubstitutionTagMetric.resize(readPulseMetric.size());
+ // Store substitutionTag
+ for (i = 0; i < readSubstitutionTagMetric.size()-1; i++ ) {
+ readSubstitutionTagMetric[i] = '-';
+ }
+ readSubstitutionTagMetric[i] = '\0';
+ for (i = 0; i < ungappedAlignedSequenceLength; i++ ) {
+ readSubstitutionTagMetric[baseToAlignmentMap[i]] = sourceRead.substitutionTag[queryStart+i];
+ }
+ readSubstitutionTagMetric[readSubstitutionTagMetric.size()-1] = 0;
+ expGroup->substitutionTag.WriteToPos(&readSubstitutionTagMetric[0], readSubstitutionTagMetric.size(), offsetBegin);
+ }
+
+ if (metricOptions["SubstitutionQV"] == true) {
+ if (!expGroup->substitutionQV.IsInitialized()) {
+ expGroup->substitutionQV.Initialize(expGroup->experimentGroup, "SubstitutionQV", true, alnArrayLength);
+ }
+
+ // Store start time normalized to frame rate.
+ fill(qvMetric.begin(), qvMetric.end(), missingQualityValue);
+
+ for (i = 0; i < ungappedAlignedSequenceLength; i++ ) {
+ qvMetric[baseToAlignmentMap[i]] = sourceRead.substitutionQV[queryStart+i];
+ }
+ qvMetric[qvMetric.size()-1] = 0;
+ expGroup->substitutionQV.WriteToPos(&qvMetric[0], qvMetric.size(), offsetBegin);
+ }
+
+ if (metricOptions["ClassifierQV"] == true) {
+ if (!expGroup->classifierQV.IsInitialized()) {
+ expGroup->classifierQV.Initialize(expGroup->experimentGroup, "ClassifierQV", true, alnArrayLength);
+ }
+ fill(floatMetric.begin(), floatMetric.end(), NaN);
+
+ for (i = 0; i < ungappedAlignedSequenceLength; i++ ) {
+ floatMetric[baseToAlignmentMap[i]] = sourceRead.classifierQV[i+queryStart];
+ }
+ qvMetric[qvMetric.size()-1] = 0;
+ expGroup->classifierQV.WriteToPos(&floatMetric[0], floatMetric.size(), offsetBegin);
+ }
+
+ if (metricOptions["StartFrame"] == true) {
+ if (!expGroup->startTime.IsInitialized()) {
+ expGroup->startTime.Initialize(expGroup->experimentGroup, "StartFrame", true, alnArrayLength);
+ }
+
+ // StartFrame used to be computed from baseFile.preBaseFrame and
+ // baseFile.basWidthInFrames, whenever possible. But a more accurate
+ // way is to obtain StartFrame directly from pulseFile.StartFrame
+ // when a pulseFile is provided.
+ if (usePulseFile) {
+ assert(sourceRead.startFrame);
+ } else if (useBaseFile) {
+ if (sourceRead.startFrame) {
+ Free(sourceRead.startFrame);
+ }
+ sourceRead.startFrame = new unsigned int[sourceRead.length];
+ copy(sourceRead.preBaseFrames, &sourceRead.preBaseFrames[sourceRead.length], sourceRead.startFrame);
+ for (i = 0; i < sourceRead.length-1; i++) {
+ sourceRead.startFrame[i+1] += sourceRead.widthInFrames[i];
+ }
+ partial_sum(sourceRead.startFrame, &sourceRead.startFrame[sourceRead.length], sourceRead.startFrame);
+ }
+
+ fill(timeMetric.begin(), timeMetric.end(), missingPulseIndex);
+ for (i = 0; i < ungappedAlignedSequenceLength; i++ ) {
+ timeMetric[baseToAlignmentMap[i]] = sourceRead.startFrame[i+queryStart];
+ }
+ timeMetric[timeMetric.size()-1] = 0;
+ expGroup->startTime.WriteToPos(&timeMetric[0], timeMetric.size(), offsetBegin);
+ }
+
+ if (metricOptions["PulseWidth"] == true) {
+ if (!expGroup->pulseWidth.IsInitialized()) {
+ expGroup->pulseWidth.Initialize(expGroup->experimentGroup, "PulseWidth", true, alnArrayLength);
+ }
+ fill(frameRateMetric.begin(), frameRateMetric.end(), missingFrameRateValue);
+
+ // For legacy reasons, it's possible the width in frames is
+ // stored in the bas file. If this is the case, use the width
+ // in frames there. Otherwise, use the width in frames stored
+ // in the pls file.
+ for (i = 0; i < ungappedAlignedSequenceLength; i++ ) {
+ frameRateMetric[baseToAlignmentMap[i]] = sourceRead.widthInFrames[queryStart + i];
+ }
+ frameRateMetric[frameRateMetric.size()-1] = 0;
+ expGroup->pulseWidth.WriteToPos(&frameRateMetric[0], frameRateMetric.size(), offsetBegin);
+ }
+
+ if (metricOptions["PreBaseFrames"] == true) {
+ if (!expGroup->preBaseFrames.IsInitialized()) {
+ expGroup->preBaseFrames.Initialize(expGroup->experimentGroup, "PreBaseFrames", true, alnArrayLength);
+ }
+ fill(frameRateMetric.begin(), frameRateMetric.end(), missingFrameRateValue);
+ for (i = 0; i < ungappedAlignedSequenceLength; i++ ) {
+ frameRateMetric[baseToAlignmentMap[i]] = sourceRead.preBaseFrames[i+queryStart];
+ }
+ frameRateMetric[frameRateMetric.size()-1] = 0;
+ expGroup->preBaseFrames.WriteToPos(&frameRateMetric[0], frameRateMetric.size(), offsetBegin);
+ }
+
+ if (metricOptions["WidthInFrames"] == true) {
+ if (!expGroup->widthInFrames.IsInitialized()) {
+ expGroup->widthInFrames.Initialize(expGroup->experimentGroup, "WidthInFrames", true, alnArrayLength);
+ }
+ // Compute width in frames.
+ fill(frameRateMetric.begin(), frameRateMetric.end(), missingFrameRateValue);
+
+ for (i = 0; i < ungappedAlignedSequenceLength; i++ ) {
+ frameRateMetric[baseToAlignmentMap[i]] = sourceRead.widthInFrames[i+queryStart];
+ }
+ frameRateMetric[frameRateMetric.size()-1] = 0;
+ expGroup->widthInFrames.WriteToPos(&frameRateMetric[0], frameRateMetric.size(), offsetBegin);
+ }
+
+ if (metricOptions["pkmid"] == true) {
+ if (!expGroup->pkmid.IsInitialized()) {
+ expGroup->pkmid.Initialize(expGroup->experimentGroup, "pkmid", true, alnArrayLength);
+ }
+
+ for (i = 0; i < readPulseMetric.size(); i++ ) {
+ readPulseMetric[i] = NaN;
+ }
+
+ for (i = 0; i < ungappedAlignedSequenceLength; i++ ) {
+ readPulseMetric[baseToAlignmentMap[i]] = sourceRead.midSignal[i+queryStart];
+ }
+ readPulseMetric[readPulseMetric.size()-1] = 0;
+ expGroup->pkmid.WriteToPos(&readPulseMetric[0], readPulseMetric.size(), offsetBegin);
+ }
+
+ if (metricOptions["IPD"] == true) {
+ if (!expGroup->ipd.IsInitialized()) {
+ expGroup->ipd.Initialize(expGroup->experimentGroup, "IPD", true, alnArrayLength);
+ }
+ fill(frameRateMetric.begin(), frameRateMetric.end(), missingFrameRateValue);
+
+ for (i = 0; i < ungappedAlignedSequenceLength; i++ ) {
+ //
+ // The IPD is undefined for the first base in a read.
+ //
+ if (usePulseFile ) {
+ if (queryStart == 0 and i == 0) {
+ frameRateMetric[baseToAlignmentMap[i]] = 0;
+ }
+ else {
+ frameRateMetric[baseToAlignmentMap[i]] = (sourceRead.startFrame[i+queryStart]
+ - sourceRead.startFrame[i+queryStart-1]
+ - sourceRead.widthInFrames[i+queryStart-1]);
+ }
+ }
+ else if (useBaseFile) {
+ frameRateMetric[baseToAlignmentMap[i]] = sourceRead.preBaseFrames[i + queryStart];
+ }
+ }
+ frameRateMetric[frameRateMetric.size()-1] = 0;
+ expGroup->ipd.WriteToPos(&frameRateMetric[0], frameRateMetric.size(), offsetBegin);
+ }
+
+ if (metricOptions["Light"] == true) {
+ if (!expGroup->light.IsInitialized()) {
+ expGroup->light.Initialize(expGroup->experimentGroup, "Light", true, alnArrayLength);
+ }
+ fill(frameRateMetric.begin(), frameRateMetric.end(), missingFrameRateValue);
+ for (i = 0; i < ungappedAlignedSequenceLength; i++ ) {
+ frameRateMetric[baseToAlignmentMap[i]] = sourceRead.meanSignal[i+queryStart];
+ frameRateMetric[baseToAlignmentMap[i]] = (frameRateMetric[baseToAlignmentMap[i]] *
+ sourceRead.widthInFrames[i+queryStart]);
+ }
+ frameRateMetric[frameRateMetric.size()-1] = 0;
+ expGroup->light.WriteToPos(&frameRateMetric[0], frameRateMetric.size(), offsetBegin);
+ }
+
+ sourceRead.Free();
+ Free(sourceRead.meanSignal);
+ Free(sourceRead.maxSignal);
+ Free(sourceRead.midSignal);
+ Free(sourceRead.startFrame);
+ Free(sourceRead.classifierQV);
+ Free(sourceRead.widthInFrames);
+ }
+ }
+
+ if (useBaseFile) {
+ hdfBasReader.Close();
+ }
+ if (cmpFile.readType == ReadType::CCS or useCcsOnly) {
+ hdfCcsReader.Close();
+ }
+ if (usePulseFile) {
+ hdfPlsReader.Close();
+ }
+ } // Done loading movies.
+
+ cmpReader.Close();
+ cerr << "[INFO] " << GetTimestamp() << " [" << program << "] ended." << endl;
+}
diff --git a/utils/Makefile b/utils/Makefile
new file mode 100644
index 0000000..53f40fa
--- /dev/null
+++ b/utils/Makefile
@@ -0,0 +1,64 @@
+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/PulseToFasta.cpp b/utils/PulseToFasta.cpp
new file mode 100644
index 0000000..336bfc5
--- /dev/null
+++ b/utils/PulseToFasta.cpp
@@ -0,0 +1,334 @@
+#include <string>
+#include <iostream>
+#include <vector>
+
+#include "HDFPlsReader.hpp"
+#include "HDFUtils.hpp"
+#include "HDFRegionTableReader.hpp"
+#include "reads/RegionTable.hpp"
+#include "reads/ReadInterval.hpp"
+#include "files/ReaderAgglomerate.hpp"
+#include "utils/FileOfFileNames.hpp"
+#include "utils/RegionUtils.hpp"
+#include "utils/TimeUtils.hpp"
+#include "SMRTSequence.hpp"
+#include "utils.hpp"
+#include "CommandLineParser.hpp"
+
+
+using namespace std;
+char VERSION[] = "v1.0.0";
+char PERFORCE_VERSION_STRING[] = "$Change: 126414 $";
+
+int main(int argc, char* argv[]) {
+ string program = "pls2fasta";
+ string versionString = VERSION;
+ AppendPerforceChangelist(PERFORCE_VERSION_STRING, versionString);
+
+ string plsFileName, fastaOutName;
+ vector<string> plsFileNames;
+ bool trimByRegion, maskByRegion;
+ trimByRegion = false;
+ maskByRegion = false;
+ int argi = 3;
+ RegionTable regionTable;
+ string regionsFOFNName = "";
+ vector<string> regionFileNames;
+ bool splitSubreads = true;
+ int minSubreadLength = 0;
+ bool addSimulatedData = false;
+ bool printSimulatedCoordinate = false;
+ bool printSimulatedSequenceIndex = false;
+ bool printFastq = false;
+ bool printCcs = false;
+ int lineLength = 50;
+ int minReadScore = 0;
+ vector<int> holeNumbers;
+ CommandLineParser clp;
+ bool printOnlyBest = false;
+
+ clp.SetProgramName(program);
+ clp.SetVersion(versionString);
+ clp.RegisterStringOption("in.bax.h5", &plsFileName, "Input plx.h5/bax.h5/fofn file.", true);
+ clp.RegisterStringOption("out.fasta", &fastaOutName, "Output fasta/fastq file.", true);
+ clp.RegisterPreviousFlagsAsHidden();
+ clp.RegisterFlagOption("trimByRegion", &trimByRegion, "Trim away low quality regions.");
+ clp.RegisterFlagOption("maskByRegion", &maskByRegion, "Mask low quality regions with 'N'.");
+ clp.RegisterStringOption("regionTable", ®ionsFOFNName, "Optional HDF file with a /PulseData/Regions dataset.");
+ clp.RegisterIntOption("minSubreadLength", &minSubreadLength, "Do not write subreads less than the specified length.", CommandLineParser::PositiveInteger);
+ clp.RegisterFlagOption("noSplitSubreads", &splitSubreads, "Do not split reads on adapter sequences.");
+ clp.RegisterIntListOption("holeNumber", &holeNumbers, "Only print this hole number (or list of numbers).");
+ clp.RegisterFlagOption("fastq", &printFastq, "Print in FASTQ format with quality.");
+ clp.RegisterFlagOption("ccs", &printCcs, "Print de novo CCS sequences");
+ clp.RegisterIntOption("lineLength", &lineLength, "Specify fasta/fastq line length", CommandLineParser::PositiveInteger);
+ clp.RegisterIntOption("minReadScore", &minReadScore, "Minimum read score to print a read. The score is "
+ "a number between 0 and 1000 and represents the expected accuracy percentage * 10. "
+ "A typical value would be between 750 and 800. This does not apply to ccs reads.", CommandLineParser::NonNegativeInteger);
+ clp.RegisterFlagOption("best", &printOnlyBest, "If a CCS sequence exists, print this. Otherwise, print the longest"
+ "subread. This does not support fastq.");
+ string description = ("Converts plx.h5/bax.h5/fofn files to fasta or fastq files. Although fasta files are provided"
+ " with every run, they are not trimmed nor split into subreads. This program takes "
+ "additional annotation information, such as the subread coordinates and high quality regions "
+ "and uses them to create fasta sequences that are substrings of all bases called. Most of the time "
+ "you will want to trim low quality reads, so you should specify -trimByRegion.");
+ clp.SetProgramSummary(description);
+
+ clp.ParseCommandLine(argc, argv);
+
+ cerr << "[INFO] " << GetTimestamp() << " [" << program << "] started." << endl;
+ if (trimByRegion and maskByRegion) {
+ cout << "ERROR! You cannot both trim and mask regions. Use one or the other." << endl;
+ exit(1);
+ }
+
+ if (printFastq) {
+ // Setting lineLength to 0 flags to print on one line.
+ lineLength = 0;
+ }
+
+
+ FileOfFileNames::StoreFileOrFileList(plsFileName, plsFileNames);
+ if (regionsFOFNName == "") {
+ regionFileNames = plsFileNames;
+ }
+ else {
+ FileOfFileNames::StoreFileOrFileList(regionsFOFNName, regionFileNames);
+ }
+
+ ofstream fastaOut;
+ CrucialOpen(fastaOutName, fastaOut);
+ int plsFileIndex;
+ HDFRegionTableReader hdfRegionReader;
+ sort(holeNumbers.begin(), holeNumbers.end());
+
+ vector<int> pls2rgn = MapPls2Rgn(plsFileNames, regionFileNames);
+
+ for (plsFileIndex = 0; plsFileIndex < plsFileNames.size(); plsFileIndex++) {
+ if (trimByRegion or maskByRegion or splitSubreads) {
+ hdfRegionReader.Initialize(regionFileNames[pls2rgn[plsFileIndex]]);
+ hdfRegionReader.ReadTable(regionTable);
+ regionTable.SortTableByHoleNumber();
+ }
+
+ ReaderAgglomerate reader;
+ HDFBasReader ccsReader;
+
+ if (printOnlyBest) {
+ ccsReader.SetReadBasesFromCCS();
+ ccsReader.Initialize(plsFileNames[plsFileIndex]);
+ }
+ if (printCcs == false) {
+ reader.IgnoreCCS();
+ }
+ else {
+ reader.hdfBasReader.SetReadBasesFromCCS();
+ }
+ if (addSimulatedData) {
+ reader.hdfBasReader.IncludeField("SimulatedCoordinate");
+ reader.hdfBasReader.IncludeField("SimulatedSequenceIndex");
+ }
+
+ if (reader.SetReadFileName(plsFileNames[plsFileIndex]) == 0) {
+ cout << "ERROR, could not determine file type."
+ << plsFileNames[plsFileIndex] << endl;
+ exit(1);
+ }
+ if (reader.Initialize() == 0) {
+ cout << "ERROR, could not initialize file "
+ << plsFileNames[plsFileIndex] << endl;
+ exit(1);
+ }
+
+ DNALength simulatedCoordinate;
+ DNALength simulatedSequenceIndex;
+ reader.SkipReadQuality();
+ SMRTSequence seq;
+ vector<ReadInterval> subreadIntervals;;
+ SMRTSequence ccsSeq;
+ while (reader.GetNextBases(seq, printFastq)) {
+ if (printOnlyBest) {
+ ccsReader.GetNext(ccsSeq);
+ }
+
+ if (holeNumbers.size() != 0 and
+ binary_search(holeNumbers.begin(), holeNumbers.end(), seq.zmwData.holeNumber) == false) {
+ continue;
+ }
+
+ if (seq.length == 0) {
+ continue;
+ }
+
+ if (addSimulatedData) {
+ reader.hdfBasReader.simulatedCoordinateArray.Read(reader.hdfBasReader.curRead-1, reader.hdfBasReader.curRead, &simulatedCoordinate);
+ reader.hdfBasReader.simulatedSequenceIndexArray.Read(reader.hdfBasReader.curRead-1, reader.hdfBasReader.curRead, &simulatedSequenceIndex);
+ }
+
+ if (printCcs == true) {
+ if (printFastq == false) {
+ seq.PrintSeq(fastaOut);
+ }
+ else {
+ seq.PrintFastq(fastaOut, lineLength);
+ }
+ continue;
+ }
+
+ //
+ // Determine the high quality boundaries of the read. This is
+ // the full read is no hq regions exist, or it is stated to
+ // ignore regions.
+ //
+ DNALength hqReadStart, hqReadEnd;
+ int hqRegionScore;
+ if (GetReadTrimCoordinates(seq, seq.zmwData, regionTable, hqReadStart, hqReadEnd, hqRegionScore) == false or
+ (trimByRegion == false and maskByRegion == false)) {
+ hqReadStart = 0;
+ hqReadEnd = seq.length;
+ }
+
+ //
+ // Mask off the low quality portions of the reads.
+ //
+ if (maskByRegion) {
+ if (hqReadStart > 0) {
+ fill(&seq.seq[0], &seq.seq[hqReadStart], 'N');
+ }
+ if (hqReadEnd != seq.length) {
+ fill(&seq.seq[hqReadEnd], &seq.seq[seq.length], 'N');
+ }
+ }
+
+
+
+ //
+ // Now possibly print the full read with masking. This could be handled by making a
+ //
+ if (splitSubreads == false) {
+ ReadInterval wholeRead(0, seq.length);
+ // The set of subread intervals is just the entire read.
+ subreadIntervals.clear();
+ subreadIntervals.push_back(wholeRead);
+ }
+ else {
+ //
+ // Print subread coordinates no matter whether or not reads have subreads.
+ //
+ subreadIntervals.clear(); // clear old, new intervals are appended.
+ CollectSubreadIntervals(seq, ®ionTable, subreadIntervals);
+ }
+ //
+ // Output all subreads as separate sequences.
+ //
+ int intvIndex;
+ SMRTSequence bestSubreadSequence;
+ int bestSubreadScore = -1;
+ int bestSubreadIndex = 0;
+ int bestSubreadStart = 0, bestSubreadEnd = 0;
+ SMRTSequence bestSubread;
+ for (intvIndex = 0; intvIndex < subreadIntervals.size(); intvIndex++) {
+ SMRTSequence subreadSequence, subreadSequenceRC;
+
+ subreadSequence.subreadStart = subreadIntervals[intvIndex].start;
+ subreadSequence.subreadEnd = subreadIntervals[intvIndex].end;
+
+ //
+ // When trimming by region, only output the parts of the
+ // subread that overlap the hq region.
+ //
+ if (trimByRegion == true) {
+ subreadSequence.subreadStart = max((DNALength) subreadIntervals[intvIndex].start, hqReadStart);
+ subreadSequence.subreadEnd = min((DNALength) subreadIntervals[intvIndex].end, hqReadEnd);
+ }
+
+ if (subreadSequence.subreadStart >= subreadSequence.subreadEnd or
+ subreadSequence.subreadEnd - subreadSequence.subreadStart <= minSubreadLength) {
+ //
+ // There is no high qualty portion of this subread. Skip it.
+ //
+ continue;
+ }
+
+ if (hqRegionScore < minReadScore) {
+ continue;
+ }
+
+ //
+ // Print the subread, adding the coordinates as part of the title.
+ //
+ subreadSequence.ReferenceSubstring(seq, subreadSequence.subreadStart,
+ subreadSequence.subreadEnd - subreadSequence.subreadStart);
+ stringstream titleStream;
+ titleStream << seq.title;
+ if (splitSubreads) {
+ //
+ // Add the subread coordinates if splitting on subread.
+ //
+ titleStream << "/"
+ << subreadSequence.subreadStart
+ << "_" << subreadSequence.subreadEnd;
+ }
+
+ //
+ // If running on simulated data, add where the values were simulated from.
+ //
+ if (addSimulatedData) {
+ titleStream << ((FASTASequence*)&seq)->title << "/chrIndex_"
+ << simulatedSequenceIndex << "/position_"<< simulatedCoordinate;
+ ((FASTASequence*)&seq)->CopyTitle(titleStream.str());
+ }
+
+ subreadSequence.CopyTitle(titleStream.str());
+
+ //
+ // Eventually replace with WriterAgglomerate.
+ //
+ if (printOnlyBest == false) {
+ if (subreadSequence.length > 0) {
+ if (printFastq == false) {
+ ((FASTASequence*)&subreadSequence)->PrintSeq(fastaOut);
+ }
+ else {
+ subreadSequence.PrintFastq(fastaOut, lineLength);
+ }
+ }
+ }
+ else {
+ int subreadWeightedScore = subreadSequence.length * hqRegionScore;
+ if (subreadWeightedScore > bestSubreadScore) {
+ bestSubreadIndex = intvIndex;
+ bestSubread = subreadSequence;
+ bestSubreadScore = subreadWeightedScore;
+ }
+ }
+ }
+
+ if (printOnlyBest) {
+ if (ccsSeq.length > 0) {
+ if (printFastq == false) {
+ ccsSeq.PrintSeq(fastaOut);
+ }
+ else {
+ ccsSeq.PrintFastq(fastaOut, ccsSeq.length);
+ }
+ }
+ else {
+ if (bestSubreadScore >= 0) {
+ if (printFastq == false) {
+ bestSubread.PrintSeq(fastaOut);
+ }
+ else {
+ bestSubread.PrintFastq(fastaOut, bestSubread.length);
+ }
+ bestSubread.Free();
+ }
+ }
+ ccsSeq.Free();
+ }
+ seq.Free();
+ }
+ reader.Close();
+ hdfRegionReader.Close();
+ }
+ cerr << "[INFO] " << GetTimestamp() << " [" << program << "] ended." << endl;
+}
diff --git a/utils/SAWriter.cpp b/utils/SAWriter.cpp
new file mode 100644
index 0000000..883723c
--- /dev/null
+++ b/utils/SAWriter.cpp
@@ -0,0 +1,231 @@
+#include <vector>
+#include <string>
+#include "suffixarray/SuffixArray.hpp"
+#include "FASTASequence.hpp"
+#include "FASTAReader.hpp"
+#include "NucConversion.hpp"
+#include "Types.h"
+#include "suffixarray/ssort.hpp"
+#include "algorithms/sorting/qsufsort.hpp"
+#include "algorithms/sorting/Karkkainen.hpp"
+#include "CompressedSequence.hpp"
+
+
+void PrintUsage() {
+ cout << "usage: sawriter saOut fastaIn [fastaIn2 fastaIn3 ...] [-blt p] [-larsson] [-4bit] [-manmy] [-kar]" << endl;
+ cout << " or sawriter fastaIn (writes to fastIn.sa)." << endl;
+ cout << " -blt p Build a lookup table on prefixes of length 'p'. This speeds " << endl
+ << " up lookups considerably (more than the LCP table), but misses matches " << endl
+ << " less than p when searching." << endl;
+ cout << " -4bit Read in (one) fasta file as a compressed sequence file." << endl;
+ cout << " -larsson (default) Uses the method of Larsson and Sadakane to build the array." << endl;
+ cout << " -mamy Uses the method of MAnber and MYers to build the array (slower than larsson, " << endl
+ << " and produces the same result. This is mainly for double checking"<<endl
+ << " the correctness of larsson)." << endl
+ << " -kark Use Karkkainen DS3 method for building the suffix array. This will probably be more "<<endl
+ << " slow than larsson, but takes only an extra N/(sqrt 3) extra space." << endl
+ << " -mafe (disabled for now!) Use the lightweight construction algorithm from Manzini and Ferragina" << endl
+ << " -welter Use lightweight (sort of light) suffix array construction. This is a bit more slow than" << endl
+ << " normal larsson." << endl
+ << " -welterweight N use a difference cover of size N for building the suffix array. Valid values are 7,32,64,111, and 2281." << endl;
+
+
+}
+
+int main(int argc, char* argv[]) {
+
+ if (argc < 2) {
+ PrintUsage();
+ exit(1);
+ }
+ int argi = 1;
+ string saFile = argv[argi++];
+ vector<string> inFiles;
+
+ int doBLT = 1;
+ int bltPrefixLength = 8;
+ int parsingOptions = 0;
+ SAType saBuildType = larsson;
+ int read4BitCompressed = 0;
+ int diffCoverSize = 0;
+ while (argi < argc) {
+ if (strlen(argv[argi]) > 0 and
+ argv[argi][0] == '-'){
+ parsingOptions = 1;
+ }
+ if (!parsingOptions) {
+ inFiles.push_back(argv[argi]);
+ }
+ else {
+ if (strcmp(argv[argi], "-blt") == 0) {
+ doBLT = 1;
+ if (argi < argc - 1) {
+ bltPrefixLength = atoi(argv[++argi]);
+ if (bltPrefixLength == 0) {
+ cout << argv[argi] << " is not a valid lookup table length." << endl;
+ exit(1);
+ }
+ }
+ else {
+ cout << "Please specify a lookup table length." << endl;
+ exit(1);
+ }
+ }
+ else if (strcmp(argv[argi], "-mamy") == 0) {
+ saBuildType = manmy;
+ }
+ else if (strcmp(argv[argi], "-larsson") == 0) {
+ saBuildType = larsson;
+ }
+ else if (strcmp(argv[argi], "-mcilroy") == 0) {
+ saBuildType = mcilroy;
+ }
+ else if (strcmp(argv[argi], "-slow") == 0) {
+ saBuildType = slow;
+ }
+ else if (strcmp(argv[argi], "-kark") == 0) {
+ saBuildType = kark;
+ }
+ else if (strcmp(argv[argi], "-mafe") == 0) {
+ saBuildType = mafe;
+ }
+ else if (strcmp(argv[argi], "-welter") == 0) {
+ saBuildType = welter;
+ }
+ else if (strcmp(argv[argi], "-welterweight") == 0) {
+ if (argi < argc-1) {
+ diffCoverSize = atoi(argv[++argi]);
+ }
+ else {
+ cout << "Please specify a difference cover size. Valid values are 7,32,64,111, and 2281. Larger values use less memory but may be slower." << endl;
+ exit(1);
+ }
+ if ( ! (diffCoverSize == 7 or
+ diffCoverSize == 32 or
+ diffCoverSize == 64 or
+ diffCoverSize == 111 or
+ diffCoverSize == 2281) ) {
+ cout << "The difference cover size must be one of 7,32,64,111, or 2281." << endl;
+ cout << "Larger numbers use less space but are more slow." << endl;
+ exit(1);
+ }
+ }
+ else if (strcmp(argv[argi], "-4bit") == 0) {
+ read4BitCompressed = 1;
+ }
+ else {
+ PrintUsage();
+ cout << "ERROR, bad option: " << argv[argi] << endl;
+ exit(1);
+ }
+ }
+ ++argi;
+ }
+
+ if (inFiles.size() == 0) {
+ //
+ // Special use case: the input file is a fasta file. Write to that file + .sa
+ //
+ inFiles.push_back(saFile);
+ saFile = saFile + ".sa";
+ }
+
+ VectorIndex inFileIndex;
+ FASTASequence seq;
+ CompressedSequence<FASTASequence> compSeq;
+
+ if (read4BitCompressed == 0) {
+ for (inFileIndex = 0; inFileIndex < inFiles.size(); ++inFileIndex) {
+ FASTAReader reader;
+ reader.Init(inFiles[inFileIndex]);
+ reader.SetSpacePadding(111);
+ if (saBuildType == kark) {
+ //
+ // The Karkkainen sa building method requires a little extra
+ // space at the end of the dna sequence so that counting may
+ // be done mod 3 without adding extra logic for boundaries.
+ //
+ }
+
+ if (inFileIndex == 0) {
+ reader.ReadAllSequencesIntoOne(seq);
+ reader.Close();
+ }
+ else {
+ while(reader.ConcatenateNext(seq)) {
+ cout << "added " << seq.title << endl;
+ }
+ }
+ }
+ seq.ToThreeBit();
+ //seq.ToUpper();
+ }
+ else {
+ assert(inFiles.size() == 1);
+ cout << "reading compressed sequence." << endl;
+ compSeq.Read(inFiles[0]);
+ seq.seq = compSeq.seq;
+ seq.length = compSeq.length;
+ compSeq.RemoveCompressionCounts();
+ cout << "done." << endl;
+ }
+
+ //
+ // For now, do not allow creation of suffix arrays on sequences > 4G.
+ //
+ if (seq.length >= UINT_MAX) {
+ cout << "ERROR, references greater than " << UINT_MAX << " bases are not supported." << endl;
+ cout << "Consider breaking the reference into multiple files, running alignment. " << endl;
+ cout << "against each file, and merging the result." << endl;
+ exit(1);
+ }
+ vector<int> alphabet;
+
+ SuffixArray<Nucleotide, vector<int> > sa;
+ // sa.InitTwoBitDNAAlphabet(alphabet);
+ // sa.InitAsciiCharDNAAlphabet(alphabet);
+ sa.InitThreeBitDNAAlphabet(alphabet);
+
+ if (saBuildType == manmy) {
+ sa.MMBuildSuffixArray(seq.seq, seq.length, alphabet);
+ }
+ else if (saBuildType == mcilroy) {
+ sa.index = new SAIndex[seq.length+1];
+ DNALength i;
+ for (i = 0; i < seq.length; i++) { sa.index[i] = seq.seq[i] + 1;}
+ sa.index[seq.length] = 0;
+ ssort(sa.index, NULL);
+ for (i = 1; i < seq.length+1; i++ ){ sa.index[i-1] = sa.index[i];};
+ sa.length = seq.length;
+ }
+ else if (saBuildType == larsson) {
+ sa.LarssonBuildSuffixArray(seq.seq, seq.length, alphabet);
+ }
+ else if (saBuildType == kark) {
+ sa.index = new SAIndex[seq.length];
+ seq.ToThreeBit();
+ DNALength p;
+ for (p = 0; p < seq.length; p++ ){ seq.seq[p]++; }
+ KarkkainenBuildSuffixArray<Nucleotide>(seq.seq, sa.index, seq.length, 5);
+ sa.length = seq.length;
+ }
+ else if (saBuildType == mafe) {
+ // sa.MaFeBuildSuffixArray(seq.seq, seq.length);
+
+ }
+ else if (saBuildType == welter) {
+ if (diffCoverSize == 0) {
+ sa.LightweightBuildSuffixArray(seq.seq, seq.length);
+ }
+ else {
+ sa.LightweightBuildSuffixArray(seq.seq, seq.length, diffCoverSize);
+ }
+ }
+ if (doBLT) {
+ sa.BuildLookupTable(seq.seq, seq.length, bltPrefixLength);
+ }
+ sa.Write(saFile);
+
+ return 0;
+
+}
diff --git a/utils/SDPMatcher.cpp b/utils/SDPMatcher.cpp
new file mode 100644
index 0000000..d35a7d6
--- /dev/null
+++ b/utils/SDPMatcher.cpp
@@ -0,0 +1,166 @@
+#include <string>
+#include <iostream>
+#include <assert.h>
+#include <math.h>
+
+#include "defs.h"
+#include "FASTAReader.hpp"
+#include "FASTASequence.hpp"
+#include "tuples/DNATuple.hpp"
+#include "tuples/TupleMetrics.hpp"
+#include "datastructures/alignment/Path.h"
+#include "datastructures/alignment/Alignment.hpp"
+#include "algorithms/alignment/AlignmentUtils.hpp"
+#include "format/StickAlignmentPrinter.hpp"
+#include "algorithms/alignment/SWAlign.hpp"
+#include "algorithms/alignment/SDPAlign.hpp"
+
+/*
+ * Performs sparse dynamic programming (SDP) between pairs of sequences as they
+ * are given in two FASTA files, one called for convenience query, the other
+ * target. k is the size of the k-mer used for the SDP algorithm.
+ */
+
+void PrintUsage() {
+ cout << "usage: sdpMatcher query target k [-indelRate delta] "
+ "[-showalign] [-printsw] [-noRefine] [-indel i] [ -local ] "
+ "[-match m] [-sdpIndel i]" << endl;
+}
+
+int main(int argc, char* argv[]) {
+ if (argc < 4) {
+ PrintUsage();
+ exit(1);
+ }
+
+ string queryName, targetName;
+ queryName = argv[1];
+ targetName = argv[2];
+ TupleMetrics tm;
+ tm.Initialize(atoi(argv[3]));
+ int argi = 4;
+ float indelRate = 0.25;
+ int indel = 3;
+ int match = 0;
+ int printSW = 0;
+ int refineAlignments = 1;
+ int showalign = 0;
+ int fixedTarget = 0;
+ int sdpIndel = indel;
+ int sdpIns = 5;
+ int sdpDel = 5;
+ AlignmentType alignType = Global;
+ while (argi < argc) {
+ if (strcmp(argv[argi], "-indelRate") == 0) {
+ ++argi;
+ indelRate = atof(argv[argi]);
+ }
+ else if (strcmp(argv[argi], "-printsw") == 0) {
+ printSW = 1;
+ }
+ else if (strcmp(argv[argi], "-noRefine") == 0) {
+ refineAlignments = 0;
+ }
+ else if (strcmp(argv[argi], "-indel") == 0) {
+ indel = atoi(argv[++argi]);
+ }
+ else if (strcmp(argv[argi], "-sdpIndel") == 0) {
+ sdpIndel = atoi(argv[++argi]);
+ }
+ else if (strcmp(argv[argi], "-sdpIns") == 0) {
+ sdpIns = atoi(argv[++argi]);
+ }
+ else if (strcmp(argv[argi], "-sdpDel") == 0) {
+ sdpDel = atoi(argv[++argi]);
+ }
+ else if (strcmp(argv[argi], "-showalign") == 0) {
+ showalign = 1;
+ }
+ else if (strcmp(argv[argi], "-local") == 0) {
+ alignType = Local;
+ }
+ else if (strcmp(argv[argi], "-match") == 0) {
+ match = atoi(argv[++argi]);
+ }
+ else if (strcmp(argv[argi], "-fixedtarget") == 0) {
+ fixedTarget = 1;
+ }
+ else {
+ PrintUsage();
+ cout << "Bad option: " << argv[argi] << endl;
+ exit(1);
+ }
+ ++argi;
+ }
+
+ FASTASequence query, target;
+ FASTAReader queryReader, targetReader;
+ queryReader.Init(queryName);
+
+ targetReader.Init(targetName);
+
+ if (match != 0) {
+ int i;
+ for (i = 0; i < 4; i++ ){
+ LocalAlignLowMutationMatrix[i][i] = match;
+ }
+ }
+
+ int seqIndex = 0;
+ Alignment alignment;
+ vector<int> scoreMat;
+ vector<Arrow> pathMat;
+ DistanceMatrixScoreFunction<DNASequence, DNASequence> distScoreFn;
+ distScoreFn.del = indel;
+ distScoreFn.ins = indel;
+ distScoreFn.InitializeScoreMatrix(SMRTDistanceMatrix);
+
+ if (fixedTarget) {
+ targetReader.GetNext(target);
+ }
+
+ cout << "qid,tid,qstart,qend,qlen,tstart,tend,tlen,score" << endl;
+ while (queryReader.GetNext(query) and
+ (fixedTarget or targetReader.GetNext(target))) {
+
+ if (query.length == 0 or target.length == 0)
+ continue;
+ alignment.blocks.clear();
+
+ int alignScore;
+ alignScore = SDPAlign(query, target,
+ distScoreFn, tm.tupleSize,
+ sdpIndel, sdpIndel, indelRate,
+ alignment,
+ alignType,
+ refineAlignments,
+ false,
+ 0);
+
+ if (alignScore > 0){ // in rare cases the SDP returns positive.
+ alignScore = 0; // this makes it more like a true local alignment
+ }
+
+ if (showalign) {
+ StickPrintAlignment(alignment, query, target, cout);
+ }
+
+ if (printSW) {
+ MatchedAlignment swAlignment;
+ vector<int> scoreMat;
+ vector<Arrow> pathMat;
+ SWAlign(query, target, scoreMat, pathMat, swAlignment, distScoreFn);
+ StickPrintAlignment(swAlignment, query, target, cout);
+ }
+
+ cout << query.GetName() << "," << target.GetName() << ","
+ << alignment.qPos << "," << alignment.QEnd() << ","
+ << query.length << "," << alignment.tPos << ","
+ << alignment.TEnd() << "," << target.length << ","
+ << alignScore << endl;
+
+ ++seqIndex;
+ }
+
+ return 0;
+}
diff --git a/utils/SamFilter.cpp b/utils/SamFilter.cpp
new file mode 100644
index 0000000..dccf586
--- /dev/null
+++ b/utils/SamFilter.cpp
@@ -0,0 +1,544 @@
+/*
+ * =====================================================================================
+ *
+ * Filename: SAMFilter.cpp
+ *
+ * Description: Filter SAM Hits according to
+ * filteration criteria
+ * minPctSimilarity, minAccuracy,
+ * minLength, holeNumbers
+ * and multiple-hit policy
+ * random : a random hit
+ * all : all hits
+ * allbest : all hits with the best score
+ * randombest: a random hit selected from all the hits
+ * that have the best score
+ *
+ * Version: 1.0
+ * Created: 03/19/2013 01:19:43 PM
+ * Revision: none
+ * Compiler: gcc
+ *
+ * Author: Yuan Li (yli), yli at pacificbiosciences.com
+ * Company: Pacific Biosciences
+ *
+ * =====================================================================================
+ */
+#include <climits>
+
+#include <iostream>
+
+#include "FASTASequence.hpp"
+#include "FASTAReader.hpp"
+#include "CommandLineParser.hpp"
+#include "ChangeListID.hpp"
+#include "utils/TimeUtils.hpp"
+#include "utils/RangeUtils.hpp"
+#include "utils/SMRTReadUtils.hpp"
+#include "algorithms/alignment/DistanceMatrixScoreFunction.hpp"
+#include "algorithms/alignment/AlignmentUtils.hpp"
+#include "algorithms/alignment/StringToScoreMatrix.hpp"
+#include "sam/SAMReader.hpp"
+#include "format/SAMPrinter.hpp"
+#include "datastructures/alignment/AlignmentCandidate.hpp"
+#include "datastructures/alignment/FilterCriteria.hpp"
+#include "metagenome/TitleTable.hpp"
+#include "datastructures/alignment/SAMToAlignmentCandidateAdapter.hpp"
+#include "GFFFile.hpp"
+#include "defs.h"
+#include "../RegisterFilterOptions.h"
+
+//#define USE_GOOGLE_PROFILER
+#ifdef USE_GOOGLE_PROFILER
+#include "gperftools/profiler.h"
+#endif
+
+char VERSION[] = "v0.1.0";
+char PERFORCE_VERSION_STRING[] = "$Change: 134995 $";
+// By default negative score is better.
+ScoreSign scoreSign = ScoreSign::NEGATIVE;
+
+// Compare SAMAlignment objects by qName, score and
+// target positions.
+bool byQNameScoreTStart(const SAMAlignment & a,
+ const SAMAlignment & b) {
+ if (a.qName == b.qName) {
+ if (a.score == b.score)
+ return a.pos < b.pos;
+ return Score(a.score, scoreSign).WorseThan(Score(b.score, scoreSign));
+ }
+ return (a.qName < b.qName);
+}
+
+// Compare SAMAlignment objects by rName and qName
+bool byRNameQName(const SAMAlignment & a,
+ const SAMAlignment & b) {
+ if (a.rName == b.rName) {
+ return a.qName < b.qName;
+ }
+ return (a.rName < b.rName);
+}
+
+// Get the next group of SAM alignments that have the same qName from
+// allSAMAlignments[groupBegin ... groupEnd)
+// Note that allSAMAlignments is already sorted by qName, score and tPos.
+void GetNextSAMAlignmentGroup(vector<SAMAlignment> & allSAMAlignments,
+ unsigned int groupBegin,
+ unsigned int & groupEnd) {
+ assert(groupBegin < allSAMAlignments.size());
+ groupEnd = groupBegin + 1;
+ string queryName = allSAMAlignments[groupBegin].qName;
+ while(groupEnd < allSAMAlignments.size()) {
+ if (allSAMAlignments[groupEnd].qName == queryName)
+ groupEnd ++;
+ else break;
+ }
+}
+
+// Get the best SAM alignments whose alignment score are the best.
+// Assume that alignments in allSAMAlignments[groupBegin, groupEnd)
+// all have the same queryName and are sorted by score and tPos
+// asscendingly: worst, ...., best
+void GetBestSAMAlignmentsInGroup(vector<SAMAlignment> & allSAMAlignments,
+ const unsigned int & groupBegin,
+ const unsigned int & groupEnd,
+ unsigned int & bestBegin,
+ unsigned int & bestEnd) {
+ assert(groupEnd <= allSAMAlignments.size() and
+ groupBegin < groupEnd);
+
+ bestEnd = groupEnd;
+ bestBegin = groupEnd - 1;
+ int groupBestScore = allSAMAlignments[bestBegin].score;
+ string queryName = allSAMAlignments[bestBegin].qName;
+ while (bestBegin >= groupBegin and bestBegin < groupEnd) {
+ assert(allSAMAlignments[bestBegin].qName == queryName);
+ if (allSAMAlignments[bestBegin].score == groupBestScore)
+ bestBegin -= 1;
+ else break;
+ }
+ bestBegin += 1;
+}
+
+
+// Apply hit policy to a group of SAM alignments and return indices
+// of the selected alignments.
+vector<unsigned int> ApplyHitPolicy(HitPolicy & hitPolicy,
+ vector<SAMAlignment> & allSAMAlignments,
+ const unsigned int & groupBegin,
+ const unsigned int & groupEnd) {
+ vector<unsigned int> hitIndices;
+ if (hitPolicy.IsAll()) {
+ for(unsigned int i = groupBegin; i < groupEnd; i++){
+ hitIndices.push_back(i);
+ }
+ } else if (hitPolicy.IsRandom()) {
+ hitIndices.push_back(rand()%(groupEnd - groupBegin) + groupBegin);
+ } else {
+ unsigned int bestBegin, bestEnd;
+ GetBestSAMAlignmentsInGroup(allSAMAlignments, groupBegin, groupEnd,
+ bestBegin, bestEnd);
+ if (hitPolicy.IsAllbest()) {
+ for(unsigned int i = bestBegin; i < bestEnd; i++){
+ hitIndices.push_back(i);
+ }
+ } else if (hitPolicy.IsRandombest()) {
+ hitIndices.push_back(rand()%(bestEnd-bestBegin) + bestBegin);
+ } else if (hitPolicy.IsLeftmost()) {
+ hitIndices.push_back(bestBegin);
+ } else {
+ assert(false);
+ }
+ }
+ return hitIndices;
+}
+
+// Convert references[...].title in reference.fasta to their corresponding
+// indices in the title table.
+void ConvertTitlesToTitleTableIndices(vector<FASTASequence> & references,
+ string & titleTableName) {
+ TitleTable tt;
+ tt.Read(titleTableName);
+ for(int i = 0; i < references.size(); i++) {
+ string title = references[i].GetTitle();
+ int idx = -1;
+ if (tt.Lookup(title, idx)) {
+ stringstream ss;
+ ss << idx;
+ references[i].CopyTitle(ss.str());
+ } else {
+ cout << "ERROR, reference " << title << " does not exist "
+ << " in the title table " << titleTableName << ". The "
+ << "reference fasta and the title table do not match."
+ << endl;
+ exit(1);
+ }
+ }
+ tt.Free();
+}
+
+// Return true if the alignment can only map to an adapter specified
+// in the adapter GFF file.
+// A sample record in adapter GFF file:
+// ref000001 . adapter 10955 10999 0.00 + . xxxx
+// ref000001 . adapter 32886 32930 0.00 + . xxxx
+// Note that the first field (e.g., 'ref000001') is id of sequence
+// in a reference repository, not sequence name, so we need to
+// reconstruct the mapping between sequence id and sequence name.
+bool CheckAdapterOnly(GFFFile & adapterGffFile, //Adapter gff file
+ AlignmentCandidate<> & alignment, // An alignment
+ map<string, int> & refNameToIndex) {
+ // Map target sequence name to its index in reference repository.
+ if (refNameToIndex.find(alignment.tName) == refNameToIndex.end()) {
+ // This should not happen ...
+ cout << "ERROR, could not find alignment target name "
+ << alignment.tName << " in the reference file." << endl;
+ exit(1);
+ }
+ int refNameIndex = refNameToIndex[alignment.tName];
+ char buf [16];
+ sprintf(buf, "ref%06d", refNameIndex + 1);
+ // Reconstruct ref id in the format "ref00000?".
+ string refNameId(buf);
+ int FUZZY_OVERLAP = 20;
+ for(int eindex = 0; eindex < adapterGffFile.entries.size();
+ eindex++) {
+ GFFEntry & entry = adapterGffFile.entries[eindex];
+ // Convert each GFF record from 1-based inclusive to
+ // 0-based exclusive.
+ if (entry.type == "adapter" and
+ (entry.name == alignment.tName or
+ entry.name == refNameId)) {
+ UInt estart = entry.start - 1;
+ UInt eend = entry.end;
+ if (entry.strand == '-') {
+ UInt tmp = estart;
+ estart = alignment.tLength - 1 - eend;
+ eend = alignment.tLength - 1 - tmp;
+ }
+ if (not (eend < alignment.GenomicTBegin() or
+ estart > alignment.GenomicTEnd())) {
+ int lengthUnion = max(eend, alignment.GenomicTEnd()) -
+ min(estart, alignment.GenomicTBegin());
+ if (lengthUnion < eend - estart + FUZZY_OVERLAP) {
+ return true;
+ }
+ }
+ }
+ }
+ return false;
+}
+
+int main(int argc, char* argv[]) {
+#ifdef USE_GOOGLE_PROFILER
+ char *profileFileName = getenv("CPUPROFILE");
+ if (profileFileName != NULL) {
+ ProfilerStart(profileFileName);
+ }
+ else {
+ ProfilerStart("google_profile.txt");
+ }
+#endif
+
+ // Register inputs and outputs.
+ string samFileName, refFileName, outFileName;
+
+ CommandLineParser clp;
+ clp.RegisterStringOption("file.sam", &samFileName,
+ "Input SAM file.");
+ clp.RegisterStringOption("reference.fasta", &refFileName,
+ "Reference used to generate reads.");
+ clp.RegisterStringOption("out.sam", &outFileName,
+ "Output SAM file.");
+ clp.RegisterPreviousFlagsAsHidden();
+
+ // Register filter criteria options.
+ int minAlnLength = 50;
+ float minPctSimilarity = 70, minPctAccuracy = 70;
+ string hitPolicyStr = "randombest";
+ bool useScoreCutoff = false;
+ int scoreCutoff = INF_INT;
+ int scoreSignInt = -1;
+ RegisterFilterOptions(clp, minAlnLength, minPctSimilarity,
+ minPctAccuracy, hitPolicyStr, useScoreCutoff,
+ scoreSignInt, scoreCutoff);
+
+ int seed = 1;
+ clp.RegisterIntOption("seed", &seed,
+ "(1) Seed for random number generator.\n"
+ "If seed is 0, then use current time as seed.",
+ CommandLineParser::Integer);
+
+ string holeNumberStr;
+ Ranges holeNumberRanges;
+ clp.RegisterStringOption("holeNumbers", &holeNumberStr,
+ "A string of comma-delimited hole number ranges to output hits, "
+ "such as '1,2,10-12'. "
+ "This requires hit titles to be in SMRT read title format.");
+
+ bool parseSmrtTitle = false;
+ clp.RegisterFlagOption("smrtTitle", &parseSmrtTitle,
+ "Use this option when filtering alignments generated by "
+ "programs other than blasr, e.g. bwa-sw or gmap. "
+ " Parse read coordinates from the SMRT read title. "
+ "The title is in the format /name/hole/coordinates, where"
+ " coordinates are in the format \\d+_\\d+, and represent "
+ "the interval of the read that was aligned.");
+ /* This experimental option can be useful for metagenomics, in which case
+ * there are hundreds of sequences in the target, of which many titles are
+ * long and may contain white spaces (e.g., ' ', '\t').
+ * In order to save disc space and avoid the (possibly) none unique mapping
+ * between full and short reference names, one may call blasr with
+ * -titleTable option to represent all target sequences in the output
+ * by their indices in the title table.*/
+
+ string titleTableName = "";
+ clp.RegisterStringOption("titleTable", &titleTableName,
+ "Use this experimental option when filtering alignments generated by "
+ "blasr with -titleTable titleTableName, in which case "
+ "reference titles in SAM are represented by their "
+ "indices (e.g., 0, 1, 2, ...) in the title table.");
+
+ string adapterGffFileName = "";
+ clp.RegisterStringOption("filterAdapterOnly", &adapterGffFileName,
+ "Use this option to remove reads which can only map to adapters "
+ "specified in the GFF file.");
+
+ bool verbose = false;
+ clp.RegisterFlagOption("v", &verbose, "Be verbose.");
+
+ clp.SetExamples(
+ "Because SAM has optional tags that have different meanings"
+ " in different programs, careful usage is required in order "
+ "to have proper output. The \"xs\" tag in bwa-sw is used to "
+ "show the suboptimal score, but in PacBio SAM (blasr) it is "
+ "defined as the start in the query sequence of the alignment.\n"
+ "When \"-smrtTitle\" is specified, the xs tag is ignored, but "
+ "when it is not specified, the coordinates given by the xs and "
+ "xe tags are used to define the interval of a read that is "
+ "aligned. The CIGAR string is relative to this interval.");
+
+ clp.ParseCommandLine(argc, argv);
+
+ // Set random number seed.
+ if (seed == 0) {
+ srand(time(NULL));
+ } else {
+ srand(seed);
+ }
+
+ scoreSign = (scoreSignInt == -1)?ScoreSign::NEGATIVE:ScoreSign::POSITIVE;
+ Score s(static_cast<float>(scoreCutoff), scoreSign);
+ FilterCriteria filterCriteria(minAlnLength, minPctSimilarity,
+ minPctAccuracy, true, s);
+ filterCriteria.Verbose(verbose);
+ HitPolicy hitPolicy(hitPolicyStr, scoreSign);
+
+ string errMsg;
+ if (not filterCriteria.MakeSane(errMsg)) {
+ cout << errMsg << endl;
+ exit(1);
+ }
+
+ // Parse hole number ranges.
+ if (holeNumberStr.size() != 0) {
+ if (not holeNumberRanges.setRanges(holeNumberStr)) {
+ cout << "Could not parse hole number ranges: "
+ << holeNumberStr << "." << endl;
+ exit(1);
+ }
+ }
+
+ // Open output file.
+ ostream * outFilePtr = &cout;
+ ofstream outFileStrm;
+ if (outFileName != "") {
+ CrucialOpen(outFileName, outFileStrm, std::ios::out);
+ outFilePtr = &outFileStrm;
+ }
+
+ GFFFile adapterGffFile;
+ if (adapterGffFileName != "")
+ adapterGffFile.ReadAll(adapterGffFileName);
+
+ SAMReader<SAMFullReferenceSequence, SAMReadGroup, SAMAlignment> samReader;
+ FASTAReader fastaReader;
+
+ //
+ // Initialize samReader and fastaReader.
+ //
+ samReader.Initialize(samFileName);
+ fastaReader.Initialize(refFileName);
+
+ //
+ // Configure the file log.
+ //
+ string command;
+ CommandLineParser::CommandLineToString(argc, argv, command);
+ string log = "Filter sam hits.";
+ string program = "samFilter";
+ string versionString = VERSION;
+ AppendPerforceChangelist(PERFORCE_VERSION_STRING, versionString);
+
+ //
+ // Read necessary input.
+ //
+ vector<FASTASequence> references;
+ fastaReader.ReadAllSequences(references);
+
+ // If the SAM file is generated by blasr with -titleTable,
+ // then references in the SAM are represented by
+ // their corresponding indices in the title table.
+ // In that case, we need to convert reference titles in fasta file
+ // to their corresponding indices in the title table, such that
+ // references in both SAM and fasta files are represented
+ // by title table indices and therefore can match.
+ if (titleTableName != "") {
+ ConvertTitlesToTitleTableIndices(references, titleTableName);
+ }
+
+ AlignmentSet<SAMFullReferenceSequence, SAMReadGroup, SAMAlignment> alignmentSet;
+ vector<string> allHeaders = samReader.ReadHeader(alignmentSet);
+
+ // Process SAM Header.
+ string commandLineString;
+ clp.CommandLineToString(argc, argv, commandLineString);
+ allHeaders.push_back("@PG\tID:SAMFILTER\tVN:" + versionString + \
+ "\tCL:" + program + " " + commandLineString);
+ for (int i = 0; i < allHeaders.size(); i++) {
+ outFileStrm << allHeaders[i] << endl;
+ }
+
+ //
+ // The order of references in vector<FASTASequence> references and
+ // AlignmentSet<, , >alignmentSet.references can be different.
+ // Rearrange alignmentSet.references such that they are ordered in
+ // exactly the same way as vector<FASTASequence> references.
+ //
+ alignmentSet.RearrangeReferences(references);
+
+ // Map reference name obtained from SAM file to indices
+ map<string, int> refNameToIndex;
+ for (int i = 0; i < references.size(); i++) {
+ string refName = alignmentSet.references[i].GetSequenceName();
+ refNameToIndex[refName] = i;
+ }
+
+ //
+ // Store the alignments.
+ //
+ SAMAlignment samAlignment;
+ int alignIndex = 0;
+
+ //
+ // For 150K, each chip produces about 300M sequences
+ // (not including quality values and etc.).
+ // Let's assume that the sam file and reference data can
+ // fit in the memory.
+ // Need to scale for larger sequal data in the future.
+ //
+ vector<SAMAlignment> allSAMAlignments;
+ while (samReader.GetNextAlignment(samAlignment)) {
+ if (samAlignment.rName == "*") {
+ continue;
+ }
+
+ if (parseSmrtTitle and holeNumberStr.size() != 0) {
+ string movieName;
+ int thisHoleNumber;
+ if (not ParsePBIReadName(samAlignment.qName,
+ movieName,
+ thisHoleNumber)) {
+ cout << "ERROR, could not parse SMRT title: "
+ << samAlignment.qName << "." << endl;
+ exit(1);
+ }
+ if (not holeNumberRanges.contains(UInt(thisHoleNumber))) {
+ if (verbose)
+ cout << thisHoleNumber << " is not in range." << endl;
+ continue;
+ }
+ }
+
+ if (samAlignment.cigar.find('P') != string::npos) {
+ cout << "WARNING. Could not process SAM record with 'P' in "
+ << "its cigar string." << endl;
+ continue;
+ }
+
+ vector<AlignmentCandidate<> > convertedAlignments;
+ SAMAlignmentsToCandidates(samAlignment,
+ references, refNameToIndex,
+ convertedAlignments, parseSmrtTitle, false);
+
+ if (convertedAlignments.size() > 1) {
+ cout << "WARNING. Ignore multiple segments." << endl;
+ continue;
+ }
+
+ for (int i = 0; i < 1; i++) {
+ AlignmentCandidate<> & alignment = convertedAlignments[i];
+
+ //score func does not matter
+ DistanceMatrixScoreFunction<DNASequence, DNASequence> distFunc;
+ ComputeAlignmentStats(alignment, alignment.qAlignedSeq.seq,
+ alignment.tAlignedSeq.seq, distFunc);
+
+ // Check whether this alignment can only map to adapters in
+ // the adapter GFF file.
+ if (adapterGffFileName != "" and
+ CheckAdapterOnly(adapterGffFile, alignment, refNameToIndex)) {
+ if (verbose)
+ cout << alignment.qName << " filter adapter only."
+ << endl;
+ continue;
+ }
+
+ // Assign score to samAlignment.
+ samAlignment.score = samAlignment.as;
+
+ if (not filterCriteria.Satisfy(static_cast<AlignmentCandidate<> *>(&alignment))) {
+ continue;
+ }
+ allSAMAlignments.push_back( samAlignment );
+
+ alignment.FreeSubsequences();
+ }
+ ++alignIndex;
+ }
+
+ // Sort all SAM alignments by qName, score and target position.
+ sort(allSAMAlignments.begin(), allSAMAlignments.end(),
+ byQNameScoreTStart);
+
+ unsigned int groupBegin = 0;
+ unsigned int groupEnd = -1;
+ vector<SAMAlignment> filteredSAMAlignments;
+ while(groupBegin < allSAMAlignments.size()) {
+ // Get the next group of SAM alignments which have the same qName
+ // from allSAMAlignments[groupBegin ... groupEnd)
+ GetNextSAMAlignmentGroup(allSAMAlignments, groupBegin, groupEnd);
+ vector<unsigned int> hitIndices = ApplyHitPolicy(
+ hitPolicy, allSAMAlignments, groupBegin, groupEnd);
+ for(unsigned int i = 0; i < hitIndices.size(); i++) {
+ filteredSAMAlignments.push_back(allSAMAlignments[hitIndices[i]]);
+ }
+ groupBegin = groupEnd;
+ }
+
+ // Sort all SAM alignments by reference name and query name
+ sort(filteredSAMAlignments.begin(), filteredSAMAlignments.end(),
+ byRNameQName);
+
+ for(unsigned int i = 0; i < filteredSAMAlignments.size(); i++) {
+ filteredSAMAlignments[i].PrintSAMAlignment(outFileStrm);
+ }
+
+ if (outFileName != "") {
+ outFileStrm.close();
+ }
+#ifdef USE_GOOGLE_PROFILER
+ ProfilerStop();
+#endif
+ return 0;
+}
diff --git a/utils/SamToCmpH5.cpp b/utils/SamToCmpH5.cpp
new file mode 100644
index 0000000..e6219e0
--- /dev/null
+++ b/utils/SamToCmpH5.cpp
@@ -0,0 +1,209 @@
+#include <iostream>
+
+#include "datastructures/alignment/AlignmentCandidate.hpp"
+#include "sam/SAMReader.hpp"
+#include "format/StickAlignmentPrinter.hpp"
+#include "HDFCmpFile.hpp"
+#include "FASTASequence.hpp"
+#include "FASTAReader.hpp"
+#include "CommandLineParser.hpp"
+#include "datastructures/alignmentset/AlignmentSetToCmpH5Adapter.hpp"
+#include "datastructures/alignment/SAMToAlignmentCandidateAdapter.hpp"
+#include "ChangeListID.hpp"
+#include "utils/TimeUtils.hpp"
+
+char VERSION[] = "v1.0.0";
+char PERFORCE_VERSION_STRING[] = "$Change: 141782 $";
+
+int main(int argc, char* argv[]) {
+ string program = "samtoh5";
+ string versionString = VERSION;
+ AppendPerforceChangelist(PERFORCE_VERSION_STRING, versionString);
+ string samFileName, cmpFileName, refFileName;
+ bool parseSmrtTitle = false;
+ bool useShortRefName = false;
+ bool copyQVs = false;
+ CommandLineParser clp;
+ string readType = "standard";
+ int verbosity = 0;
+
+ clp.SetProgramName(program);
+ clp.SetProgramSummary("Converts in.sam file to out.cmp.h5 file.");
+ clp.SetVersion(versionString);
+
+ clp.RegisterStringOption("in.sam", &samFileName,
+ "Input SAM file.", true);
+ clp.RegisterStringOption("reference.fasta", &refFileName,
+ "Reference used to generate reads.", true);
+ clp.RegisterStringOption("out.cmp.h5", &cmpFileName,
+ "Output cmp.h5 file.", true);
+ clp.RegisterPreviousFlagsAsHidden();
+ clp.RegisterFlagOption("smrtTitle", &parseSmrtTitle,
+ "Use this option when converting alignments "
+ "generated from reads produced by the "
+ "pls2fasta from bas.h5 files by parsing read "
+ "coordinates from the SMRT read title. The title "
+ "is in the format /name/hole/coordinates, where "
+ "coordinates are in the format \\d+_\\d+, and "
+ "represent the interval of the read that was "
+ "aligned.");
+ clp.RegisterStringOption("readType", &readType,
+ "Set the read type: 'standard', 'strobe', 'CCS', "
+ "or 'cDNA'");
+ clp.RegisterIntOption("verbosity", &verbosity,
+ "Set desired verbosity.",
+ CommandLineParser::PositiveInteger);
+ clp.RegisterFlagOption("useShortRefName", &useShortRefName,
+ "Use abbreviated reference names obtained "
+ "from file.sam instead of using full names "
+ "from reference.fasta.");
+ clp.RegisterFlagOption("copyQVs", ©QVs,
+ "Copy all QVs available in the SAM file into the "
+ "cmp.h5 file. This includes things like InsertionQV "
+ "and DeletionTag.");
+ string description = ("Because SAM has optional tags that have different "
+ "meanings in different programs, careful usage is required in order to "
+ "have proper output. The \"xs\" tag in bwa-sw is used to show the "
+ "suboptimal score, but in PacBio SAM (blasr) it is defined as the start "
+ "in the query sequence of the alignment.\nWhen \"-smrtTitle\" is "
+ "specified, the xs tag is ignored, but when it is not specified, the "
+ "coordinates given by the xs and xe tags are used to define the interval "
+ "of a read that is aligned. The CIGAR string is relative to this interval.");
+ clp.SetExamples(description);
+
+ clp.ParseCommandLine(argc, argv);
+
+ if (readType != "standard" and readType != "strobe" and
+ readType != "cDNA" and readType != "CCS") {
+ cout << "ERROR. Read type '" << readType
+ << "' must be one of either 'standard', 'strobe', 'cDNA' or 'CCS'."
+ << endl;
+ exit(1);
+ }
+
+ cerr << "[INFO] " << GetTimestamp() << " [" << program << "] started." << endl;
+
+ SAMReader<SAMFullReferenceSequence, SAMReadGroup, SAMPosAlignment> samReader;
+ FASTAReader fastaReader;
+ HDFCmpFile<AlignmentCandidate<FASTASequence, FASTASequence> > cmpFile;
+
+ //
+ // Initialize input/output files.
+ //
+ samReader.Initialize(samFileName);
+ fastaReader.Initialize(refFileName);
+ cmpFile.Create(cmpFileName);
+
+ //
+ // Configure the file log.
+ //
+ string command;
+ CommandLineParser::CommandLineToString(argc, argv, command);
+ string log = "Convert sam to cmp.h5";
+ cmpFile.fileLogGroup.AddEntry(command, log, program, GetTimestamp(), versionString);
+
+ //
+ // Set the readType
+ //
+ cmpFile.SetReadType(readType);
+
+ //
+ // Read necessary input.
+ //
+
+ vector<FASTASequence> references;
+ fastaReader.ReadAllSequences(references);
+
+ //
+ // This should probably be handled by the alignmentSetAdapter, but
+ // time constraints...
+ //
+ AlignmentSet<SAMFullReferenceSequence, SAMReadGroup, SAMPosAlignment> alignmentSet;
+ samReader.ReadHeader(alignmentSet);
+
+ //
+ // The order of references in vector<FASTASequence> references and
+ // AlignmentSet<, , >alignmentSet.references can be different.
+ // Rearrange alignmentSet.references such that it is ordered in
+ // exactly the same way as vector<FASTASequence> references.
+ //
+ alignmentSet.RearrangeReferences(references);
+
+ //
+ // Always recompute the MD5 values even if they exist in the input
+ // sam file. Because MD5 is defined differently in sam and cmp.h5 files.
+ // The SAM convention uppercases and normalizes before computing the MD5.
+ // For cmp.h5, we compute the MD5 on the sequence 'as is'.
+ //
+ for(int i = 0; i < alignmentSet.references.size(); i++) {
+ MakeMD5((const char*)&references[i].seq[0],
+ (unsigned int)references[i].length, alignmentSet.references[i].md5);
+ }
+
+ //
+ // Map short names for references obtained from file.sam to full names obtained from reference.fasta
+ //
+ map<string, string> shortRefNameToFull;
+ map<string, string>::iterator it;
+ assert(references.size() == alignmentSet.references.size());
+ if (!useShortRefName) {
+ for (int i = 0; i < references.size(); i++) {
+ string shortRefName = alignmentSet.references[i].GetSequenceName();
+ string fullRefName(references[i].title);
+ if (shortRefNameToFull.find(shortRefName) != shortRefNameToFull.end()) {
+ cout << "ERROR, Found more than one reference " << shortRefName << "in sam header" << endl;
+ exit(1);
+ }
+ shortRefNameToFull[shortRefName] = fullRefName;
+ alignmentSet.references[i].sequenceName = fullRefName;
+ }
+ }
+
+ //
+ // Start setting up the cmp.h5 file.
+ //
+ AlignmentSetToCmpH5Adapter<HDFCmpFile<AlignmentCandidate<FASTASequence, FASTASequence> > > alignmentSetAdapter;
+ alignmentSetAdapter.Initialize();
+ alignmentSetAdapter.StoreReferenceInfo(alignmentSet.references, cmpFile);
+
+ //
+ // Store the alignments.
+ //
+ SAMAlignment samAlignment;
+ while (samReader.GetNextAlignment(samAlignment)) {
+ if (samAlignment.rName == "*") {
+ continue;
+ }
+ if (!useShortRefName) {
+ //convert shortRefName to fullRefName
+ it = shortRefNameToFull.find(samAlignment.rName);
+ if (it == shortRefNameToFull.end()) {
+ cout << "ERROR, Could not find " << samAlignment.rName << " in the reference repository." << endl;
+ exit(1);
+ }
+ samAlignment.rName = (*it).second;
+ }
+ vector<AlignmentCandidate<> > convertedAlignments;
+ if (verbosity > 0) {
+ cout << "Storing alignment for " << samAlignment.qName << endl;
+ }
+ SAMAlignmentsToCandidates(samAlignment,
+ // Order of references and alignmentSetAdapter.RefInfoGroup
+ // should be exactly the same.
+ references, alignmentSetAdapter.refNameToRefInfoIndex,
+ convertedAlignments, parseSmrtTitle, false,
+ copyQVs);
+
+ // -1: moleculeID will be computed dynamically.
+ // o.w., the value will be assigned as moleculeID.
+ alignmentSetAdapter.StoreAlignmentCandidateList(convertedAlignments, cmpFile, -1, copyQVs);
+
+ int a;
+ for (a = 0; a < convertedAlignments.size(); a++) {
+ convertedAlignments[a].FreeSubsequences();
+ }
+ }
+
+ cerr << "[INFO] " << GetTimestamp() << " [" << program << "] ended." << endl;
+ return 0;
+}
diff --git a/utils/SamToM4.cpp b/utils/SamToM4.cpp
new file mode 100644
index 0000000..6933688
--- /dev/null
+++ b/utils/SamToM4.cpp
@@ -0,0 +1,222 @@
+/*
+ * =====================================================================================
+ *
+ * Filename: SamToM4.cpp
+ *
+ * Description: Convert a sam file to a blasr m4 file.
+ *
+ * Version: 1.0
+ * Created: 04/03/2013 01:19:43 PM
+ * Revision: none
+ * Compiler: gcc
+ *
+ * Author: Yuan Li (yli), yli at pacificbiosciences.com
+ * Company: Pacific Biosciences
+ *
+ * =====================================================================================
+ */
+#include <iostream>
+#include "FASTASequence.hpp"
+#include "FASTAReader.hpp"
+#include "CommandLineParser.hpp"
+#include "ChangeListID.hpp"
+#include "algorithms/alignment/DistanceMatrixScoreFunction.hpp"
+#include "algorithms/alignment/AlignmentUtils.hpp"
+#include "sam/SAMReader.hpp"
+#include "format/IntervalPrinter.hpp"
+#include "datastructures/alignment/AlignmentCandidate.hpp"
+#include "datastructures/alignment/SAMToAlignmentCandidateAdapter.hpp"
+
+char VERSION[] = "v0.1.0";
+char PERFORCE_VERSION_STRING[] = "$Change: 126414 $";
+
+int main(int argc, char* argv[]) {
+ string program = "samtom4";
+ string versionString = VERSION;
+ AppendPerforceChangelist(PERFORCE_VERSION_STRING, versionString);
+
+ string samFileName, refFileName, outFileName;
+ bool printHeader = false;
+ bool parseSmrtTitle = false;
+ bool useShortRefName = false;
+
+ CommandLineParser clp;
+ clp.SetProgramName(program);
+ clp.SetVersion(versionString);
+ clp.SetProgramSummary("Converts a SAM file generated by blasr to M4 format.");
+ clp.RegisterStringOption("in.sam", &samFileName,
+ "Input SAM file, which is produced by blasr.");
+ clp.RegisterStringOption("reference.fasta", &refFileName,
+ "Reference used to generate file.sam.");
+ clp.RegisterStringOption("out.m4", &outFileName,
+ "Output in blasr M4 format.");
+ clp.RegisterPreviousFlagsAsHidden();
+ clp.RegisterFlagOption("header", &printHeader,
+ "Print M4 header.");
+ clp.RegisterFlagOption("useShortRefName", &useShortRefName,
+ "Use abbreviated reference names obtained "
+ "from file.sam instead of using full names "
+ "from reference.fasta.");
+ //clp.SetExamples(program + " file.sam reference.fasta out.m4");
+
+ clp.ParseCommandLine(argc, argv);
+
+ ostream * outFilePtr = &cout;
+ ofstream outFileStrm;
+ if (outFileName != "") {
+ CrucialOpen(outFileName, outFileStrm, std::ios::out);
+ outFilePtr = &outFileStrm;
+ }
+
+ SAMReader<SAMFullReferenceSequence, SAMReadGroup, SAMAlignment> samReader;
+ FASTAReader fastaReader;
+
+ //
+ // Initialize samReader and fastaReader.
+ //
+ samReader.Initialize(samFileName);
+ fastaReader.Initialize(refFileName);
+
+ //
+ // Configure the file log.
+ //
+ string command;
+ CommandLineParser::CommandLineToString(argc, argv, command);
+
+ //
+ // Read necessary input.
+ //
+ vector<FASTASequence> references;
+ fastaReader.ReadAllSequences(references);
+
+ AlignmentSet<SAMFullReferenceSequence, SAMReadGroup, SAMAlignment> alignmentSet;
+ samReader.ReadHeader(alignmentSet);
+
+ //
+ // The order of references in vector<FASTASequence> references and
+ // AlignmentSet<, , >alignmentSet.references can be different.
+ // Rearrange alignmentSet.references such that it is ordered in
+ // exactly the same way as vector<FASTASequence> references.
+ //
+ alignmentSet.RearrangeReferences(references);
+
+ //
+ // Map short names for references obtained from file.sam to
+ // full names obtained from reference.fasta
+ //
+ map<string, string> shortRefNameToFull;
+ map<string, string>::iterator it;
+ assert(references.size() == alignmentSet.references.size());
+ if (!useShortRefName) {
+ for (int i = 0; i < references.size(); i++) {
+ string shortRefName = alignmentSet.references[i].GetSequenceName();
+ string fullRefName(references[i].title);
+ if (shortRefNameToFull.find(shortRefName) != shortRefNameToFull.end()) {
+ cout << "ERROR, Found more than one reference " << shortRefName << "in sam header" << endl;
+ exit(1);
+ }
+ shortRefNameToFull[shortRefName] = fullRefName;
+ alignmentSet.references[i].sequenceName = fullRefName;
+ }
+ }
+
+ // Map reference name obtained from SAM file to indices
+ map<string, int> refNameToIndex;
+ for (int i = 0; i < references.size(); i++) {
+ string refName = alignmentSet.references[i].GetSequenceName();
+ refNameToIndex[refName] = i;
+ }
+
+ //
+ // Store the alignments.
+ //
+ SAMAlignment samAlignment;
+ int alignIndex = 0;
+
+ //
+ // For 150K, each chip produces about 300M sequences
+ // (not including quality values and etc.).
+ // Let's assume that the sam file and reference data can
+ // fit in the memory.
+ // Need to scale for larger sequal data in the future.
+ //
+ if (printHeader)
+ IntervalOutput::PrintHeader(*outFilePtr);
+
+ // The socre matrix does not matter because we will use the
+ // aligner's score from SAM file anyway.
+ DistanceMatrixScoreFunction<DNASequence, DNASequence> distScoreFn;
+
+ while (samReader.GetNextAlignment(samAlignment)) {
+ if (samAlignment.rName == "*") {
+ continue;
+ }
+
+ if (!useShortRefName) {
+ //convert shortRefName to fullRefName
+ it = shortRefNameToFull.find(samAlignment.rName);
+ if (it == shortRefNameToFull.end()) {
+ cout << "ERROR, Could not find " << samAlignment.rName << " in the reference repository." << endl;
+ exit(1);
+ }
+ samAlignment.rName = (*it).second;
+ }
+
+ // The padding character 'P' is not supported
+ if (samAlignment.cigar.find('P') != string::npos) {
+ cout << "WARNING. Could not process sam record with 'P' in its cigar string."
+ << endl;
+ continue;
+ }
+
+ vector<AlignmentCandidate<> > convertedAlignments;
+
+ //
+ // Keep reference as forward.
+ // So if IsReverseComplement(sam.flag)==true, then qStrand is reverse
+ // and tStrand is forward.
+ //
+ bool keepRefAsForward = false;
+
+ SAMAlignmentsToCandidates(samAlignment, references, refNameToIndex,
+ convertedAlignments, parseSmrtTitle,
+ keepRefAsForward);
+
+ if (convertedAlignments.size() > 1) {
+ cout << "WARNING. Ignore an alignment which has multiple segments." << endl;
+ continue;
+ }
+
+ //all alignments are unique single-ended alignments.
+ for (int i = 0; i < 1; i++) {
+ AlignmentCandidate<> & alignment = convertedAlignments[i];
+
+ ComputeAlignmentStats(alignment, alignment.qAlignedSeq.seq,
+ alignment.tAlignedSeq.seq, distScoreFn);
+
+ // Use aligner's score from SAM file anyway.
+ alignment.score = samAlignment.as;
+ alignment.mapQV = samAlignment.mapQV;
+
+ // Since SAM only has the aligned sequence, many info of the
+ // original query (e.g. the full length) is missing.
+ // Overwrite alignment.qLength (which is length of the query
+ // in the SAM alignment) with xq (which is the length of the
+ // original query sequence saved by blasr) right before printing
+ // the output so that one can reconstruct a blasr m4 record from
+ // a blasr sam alignment.
+ if (samAlignment.xq!=0)
+ alignment.qLength = samAlignment.xq;
+
+ IntervalOutput::PrintFromSAM(alignment, *outFilePtr);
+
+ alignment.FreeSubsequences();
+ }
+ ++alignIndex;
+ }
+
+ if (outFileName != "") {
+ outFileStrm.close();
+ }
+ return 0;
+}
diff --git a/utils/ToAfg.cpp b/utils/ToAfg.cpp
new file mode 100644
index 0000000..2d0a82f
--- /dev/null
+++ b/utils/ToAfg.cpp
@@ -0,0 +1,178 @@
+#include <algorithm>
+#include <iostream>
+#include <string>
+#include <vector>
+
+#include "HDFPlsReader.hpp"
+#include "amos/AfgBasWriter.hpp"
+#include "HDFRegionTableReader.hpp"
+#include "reads/RegionTable.hpp"
+#include "reads/ReadInterval.hpp"
+#include "files/ReaderAgglomerate.hpp"
+#include "utils/FileOfFileNames.hpp"
+#include "utils/RegionUtils.hpp"
+#include "SMRTSequence.hpp"
+#include "utils.hpp"
+
+using namespace std;
+void PrintUsage() {
+ cout << "usage: toAfg input.filetype output.filetype" << endl
+ << " [-minSubreadLength l] " << endl
+ << " [-regionTable regions_file] " << endl
+ << " [-noSplitSubreads]" << endl
+ << " [-useccsdenovo]" << endl
+ << " [-uniformQV QV]" << endl
+ << "Print reads stored in a file (pls|fasta|fastq) as an afg." << endl;
+}
+int main(int argc, char* argv[]) {
+
+ string inputFileName, outputFileName;
+
+ if (argc < 2) {
+ PrintUsage();
+ exit(1);
+ }
+ vector<string> inputFileNames;
+ inputFileName = argv[1];
+ outputFileName = argv[2];
+ int argi = 3;
+ RegionTable regionTable;
+ string regionsFOFNName = "";
+ vector<string> regionFileNames;
+ bool splitSubreads = true;
+ bool useCCS = false;
+ bool useUniformQV = false;
+ int uniformQV = 7;
+ int minSubreadLength = 1;
+ while (argi < argc) {
+ if (strcmp(argv[argi], "-regionTable") == 0) {
+ regionsFOFNName = argv[++argi];
+ }
+ else if (strcmp(argv[argi], "-noSplitSubreads") == 0) {
+ splitSubreads = false;
+ }
+ else if (strcmp(argv[argi], "-minSubreadLength") == 0) {
+ minSubreadLength = atoi(argv[++argi]);
+ }
+ else if (strcmp(argv[argi], "-useccsdenovo") == 0) {
+ useCCS = true;
+ }
+ else if (strcmp(argv[argi], "-uniformQV") == 0) {
+ useUniformQV = true;
+ uniformQV = atoi(argv[++argi]);
+ }
+ else {
+ PrintUsage();
+ cout << "ERROR! Option " << argv[argi] << " is not supported." << endl;
+ }
+ argi++;
+ }
+
+ if (FileOfFileNames::IsFOFN(inputFileName)) {
+ FileOfFileNames::FOFNToList(inputFileName, inputFileNames);
+ }
+ else {
+ inputFileNames.push_back(inputFileName);
+ }
+ if (regionsFOFNName == "") {
+ regionFileNames = inputFileNames;
+ }
+ else {
+ if (FileOfFileNames::IsFOFN(regionsFOFNName)) {
+ FileOfFileNames::FOFNToList(regionsFOFNName, regionFileNames);
+ }
+ else {
+ regionFileNames.push_back(regionsFOFNName);
+ }
+ }
+
+ ofstream fastaOut;
+ CrucialOpen(outputFileName, fastaOut);
+ int plsFileIndex;
+ HDFRegionTableReader hdfRegionReader;
+ AfgBasWriter afgWriter;
+ if (useUniformQV){
+ afgWriter.SetDefaultQuality(uniformQV);
+ }
+
+ afgWriter.Initialize(outputFileName);
+
+ for (plsFileIndex = 0; plsFileIndex < inputFileNames.size(); plsFileIndex++) {
+ if (splitSubreads) {
+ hdfRegionReader.Initialize(regionFileNames[plsFileIndex]);
+ hdfRegionReader.ReadTable(regionTable);
+ regionTable.SortTableByHoleNumber();
+ }
+
+ ReaderAgglomerate reader;
+ // reader.SkipReadQuality(); // should have been taken care of by *Filter modules
+ if (useCCS){
+ reader.UseCCS();
+ } else {
+ reader.IgnoreCCS();
+ }
+ reader.Initialize(inputFileNames[plsFileIndex]);
+ CCSSequence seq;
+ int seqIndex = 0;
+ int numRecords = 0;
+ vector<ReadInterval> subreadIntervals;
+ while (reader.GetNext(seq)){
+ ++seqIndex;
+
+ if (useUniformQV && seq.qual.data != NULL){
+ for (int qvIndex = 0; qvIndex < seq.length; qvIndex++){
+ seq.qual[qvIndex] = uniformQV;
+ }
+ }
+
+ if (splitSubreads == false) {
+ if (seq.length >= minSubreadLength) {
+ afgWriter.Write(seq);
+ }
+ seq.Free();
+ continue;
+ }
+
+
+ DNALength hqReadStart, hqReadEnd;
+ int score;
+ GetReadTrimCoordinates(seq, seq.zmwData, regionTable, hqReadStart, hqReadEnd, score);
+ subreadIntervals.clear(); // clear old, new intervals are appended.
+ CollectSubreadIntervals(seq,®ionTable, subreadIntervals);
+
+ if (seq.length == 0 and subreadIntervals.size() > 0) {
+ cout << "WARNING! A high quality interval region exists for a read of length 0." <<endl;
+ cout << " The offending ZMW number is " << seq.zmwData.holeNumber << endl;
+ seq.Free();
+ continue;
+ }
+
+
+ for (int intvIndex = 0; intvIndex < subreadIntervals.size(); intvIndex++) {
+ SMRTSequence subreadSequence;
+
+ int subreadStart = subreadIntervals[intvIndex].start > hqReadStart ?
+ subreadIntervals[intvIndex].start : hqReadStart;
+ int subreadEnd = subreadIntervals[intvIndex].end < hqReadEnd ?
+ subreadIntervals[intvIndex].end : hqReadEnd;
+ int subreadLength = subreadEnd - subreadStart;
+
+ if (subreadLength < minSubreadLength) continue;
+
+ subreadSequence.subreadStart = subreadStart;
+ subreadSequence.subreadEnd = subreadEnd;
+ subreadSequence.ReferenceSubstring(seq, subreadStart, subreadLength);
+
+
+ stringstream titleStream;
+ titleStream << seq.title << "/" << subreadIntervals[intvIndex].start
+ << "_" << subreadIntervals[intvIndex].end;
+ subreadSequence.CopyTitle(titleStream.str());
+ afgWriter.Write(subreadSequence);
+ }
+ seq.Free();
+ }
+ reader.Close();
+ hdfRegionReader.Close();
+ }
+}
diff --git a/utils/ctest/loadPulses.t b/utils/ctest/loadPulses.t
new file mode 100644
index 0000000..8b07e2f
--- /dev/null
+++ b/utils/ctest/loadPulses.t
@@ -0,0 +1,193 @@
+Set up directories
+ $ . $TESTDIR/setup.sh
+
+Set up the executable: loadPulses.
+ $ EXEC=$TESTDIR/../loadPulses
+
+#Test loadPulses: input is a pls.h5 file
+#Test -byread and -bymetric
+ $ PLS_IN=$DATDIR/ecoli_lp.fofn
+ $ CMP_IN_2=$DATDIR/ecoli_lp_tiny.cmp.h5
+ $ CMP_STDOUT_2=$STDDIR/ecoli_lp_tiny.cmp.h5
+ $ CMP_OUT_byread_2=$OUTDIR/ecoli_lp_tiny.byread.cmp.h5
+ $ CMP_OUT_bymetric_2=$OUTDIR/ecoli_lp_tiny.bymetric.cmp.h5
+ $ METRICS=StartFrame,PulseWidth,WidthInFrames,pkmid,IPD,Light
+
+ $ rm -f $CMP_OUT_byread_2
+ $ cp $CMP_IN_2 $CMP_OUT_byread_2
+ $ $EXEC $PLS_IN $CMP_OUT_byread_2 -metrics $METRICS -byread
+ [INFO] * [loadPulses] started. (glob)
+ loading 2 alignments for movie 1
+ loading 2 alignments for movie 2
+ [INFO] * [loadPulses] ended. (glob)
+
+ $ h5diff -c $CMP_OUT_byread_2 $CMP_STDOUT_2
+ dataset: </FileLog/CommandLine> and </FileLog/CommandLine>
+ \d+ differences found (re)
+ dataset: </FileLog/Timestamp> and </FileLog/Timestamp>
+ \d+ differences found (re)
+ [1]
+
+ $ rm -f $CMP_OUT_bymetric_2
+ $ cp $CMP_IN_2 $CMP_OUT_bymetric_2
+ $ $EXEC $PLS_IN $CMP_OUT_bymetric_2 -metrics $METRICS -bymetric
+ [INFO] * [loadPulses] started. (glob)
+ loading 2 alignments for movie 1
+ loading 2 alignments for movie 2
+ [INFO] * [loadPulses] ended. (glob)
+
+ $ h5diff -c $CMP_OUT_bymetric_2 $CMP_STDOUT_2
+ dataset: </FileLog/CommandLine> and </FileLog/CommandLine>
+ \d+ differences found (re)
+ dataset: </FileLog/Timestamp> and </FileLog/Timestamp>
+ \d+ differences found (re)
+ [1]
+
+#Test loadPulses for deep sorted cmp.h5
+ $ FOFN_IN=$DATDIR/ecoli_lp.fofn
+ $ CMP_IN_SORTED=$DATDIR/ecoli_lp_tiny_sorted.cmp.h5
+ $ CMP_STDOUT_SORTED=$STDDIR/ecoli_lp_tiny_sorted.cmp.h5
+ $ CMP_OUT_SORTED_bymetric=$OUTDIR/ecoli_lp_tiny_sorted_bymetric.cmp.h5
+ $ CMP_OUT_SORTED_byread=$OUTDIR/ecoli_lp_tiny_sorted_byread.cmp.h5
+ $ METRICS=StartFrame,PulseWidth,WidthInFrames,pkmid,IPD,Light,DeletionQV,InsertionQV,SubstitutionQV,MergeQV,QualityValue,DeletionTag,SubstitutionTag,ClassifierQV,PreBaseFrames,PulseIndex
+
+ $ rm -f $CMP_OUT_SORTED_bymetric
+ $ cp $CMP_IN_SORTED $CMP_OUT_SORTED_bymetric
+ $ $EXEC $FOFN_IN $CMP_OUT_SORTED_bymetric -bymetric -metrics $METRICS > $OUTDIR/tmp.log
+ [INFO] * [loadPulses] started. (glob)
+ [INFO] * [loadPulses] ended. (glob)
+
+ $ h5diff -c $CMP_OUT_SORTED_bymetric $CMP_STDOUT_SORTED
+ dataset: </FileLog/CommandLine> and </FileLog/CommandLine>
+ \d+ differences found (re)
+ dataset: </FileLog/Timestamp> and </FileLog/Timestamp>
+ \d+ differences found (re)
+ [1]
+
+
+ $ rm -f $CMP_OUT_SORTED_byread
+ $ cp $CMP_IN_SORTED $CMP_OUT_SORTED_byread
+ $ $EXEC $FOFN_IN $CMP_OUT_SORTED_byread -byread -metrics $METRICS > $OUTDIR/tmp.log
+ [INFO] * [loadPulses] started. (glob)
+ [INFO] * [loadPulses] ended. (glob)
+
+ $ h5diff -c $CMP_OUT_SORTED_bymetric $CMP_STDOUT_SORTED
+ dataset: </FileLog/CommandLine> and </FileLog/CommandLine>
+ \d+ differences found (re)
+ dataset: </FileLog/Timestamp> and </FileLog/Timestamp>
+ \d+ differences found (re)
+ [1]
+
+#Test loadPulses for a zero-alignment cmp.h5 file.
+ $ FOFN_IN=$DATDIR/ecoli_lp.fofn
+ $ CMP_IN_NOALN=$DATDIR/noaln_lp.cmp.h5
+ $ $EXEC $FOFN_IN $CMP_IN_NOALN -byread -metrics $METRICS
+ [INFO] * [loadPulses] started. (glob)
+ WARNING, there is no alignment in the cmp file.
+ [INFO] * [loadPulses] ended. (glob)
+
+#Test loadPulses -byMetric with a 'large' bas.h5 file of which the dataset size is greater than maxElements.
+ $ FOFN_IN=$DATDIR/ecoli_lp.fofn
+ $ CMP_IN=$DATDIR/ecoli_lp_tiny_sorted.cmp.h5
+ $ CMP_OUT=$OUTDIR/ecoli_lp_maxEle.cmp.h5
+ $ CMP_STDOUT=$STDDIR/ecoli_lp_maxEle.cmp.h5
+ $ METRICS=QualityValue,MergeQV,InsertionQV,DeletionQV,DeletionTag,PulseWidth,SubstitutionQV,SubstitutionTag
+ $ MAX_ELEMENTS=140000000
+
+ $ rm -f $CMP_OUT
+ $ cp $CMP_IN $CMP_OUT
+ $ $EXEC $FOFN_IN $CMP_OUT -bymetric -metrics $METRICS -maxElements $MAX_ELEMENTS
+ [INFO] * [loadPulses] started. (glob)
+ Either the number of elements exceeds maxElement (140000000). Or the estimated memory
+ consumption exceeds maxMemory (4 GB).
+ Loading pulses from .+ by read. (re)
+ loading 2 alignments for movie 1
+ loading 2 alignments for movie 2
+ [INFO] * [loadPulses] ended. (glob)
+
+ $ h5diff -c $CMP_OUT $CMP_STDOUT
+ dataset: </FileLog/CommandLine> and </FileLog/CommandLine>
+ \d+ differences found (re)
+ dataset: </FileLog/Timestamp> and </FileLog/Timestamp>
+ \d+ differences found (re)
+ dataset: </FileLog/Version> and </FileLog/Version>
+ \d+ differences found (re)
+ [1]
+
+#Test loadPulses -byMetric on a multi-streaming job.
+ $ FOFN_IN=$DATDIR/lambda_bax.fofn
+ $ CMP_IN=$DATDIR/lambda_bax.cmp.h5
+ $ CMP_OUT=$OUTDIR/lambda_bax.cmp.h5
+ $ CMP_STDOUT=$STDDIR/lambda_bax.cmp.h5
+ $ METRICS=QualityValue,MergeQV,InsertionQV,DeletionQV,DeletionTag,PulseWidth,SubstitutionQV,SubstitutionTag
+
+ $ rm -f $CMP_OUT
+ $ cp $CMP_IN $CMP_OUT
+ $ $EXEC $FOFN_IN $CMP_OUT -bymetric -metrics $METRICS
+ [INFO] * [loadPulses] started. (glob)
+ WARNING: There is insufficient data to compute metric: MergeQV in the file .+ It will be ignored. (re)
+ loading 2 alignments for movie 1
+ loading 2 alignments for movie 1
+ [INFO] * [loadPulses] ended. (glob)
+
+ $ h5diff -c $CMP_OUT $CMP_STDOUT
+ dataset: </FileLog/CommandLine> and </FileLog/CommandLine>
+ \d+ differences found (re)
+ dataset: </FileLog/Timestamp> and </FileLog/Timestamp>
+ \d+ differences found (re)
+ dataset: </FileLog/Version> and </FileLog/Version>
+ \d+ differences found (re)
+ [1]
+
+
+#Test loadPulses -bymetric for a ccs cmp.h5 file generated from multiple movies.
+ $ FOFN_IN=$DATDIR/ccs_lp.fofn
+ $ CMP_IN=$DATDIR/ccs_lp.cmp.h5
+ $ CMP_OUT=$OUTDIR/ccs_lp.cmp.h5
+
+# The original pls.h5 files disappeared, to use another dataset instead.
+ $ rm -f CMP_OUT
+ $ cp $CMP_IN $CMP_OUT
+ $ $EXEC $FOFN_IN $CMP_OUT -bymetric -metrics QualityValue
+ [INFO] * [loadPulses] started. (glob)
+ loading 100 alignments for movie 1
+ loading 45 alignments for movie 2
+ [INFO] * [loadPulses] ended. (glob)
+
+ $ h5ls -r $CMP_OUT | grep "AlnInfo"
+ /AlnInfo Group
+ /AlnInfo/AlnIndex Dataset {145/Inf, 22}
+ /AlnInfo/NumPasses Dataset {145/Inf}
+
+
+#Test loadPulses *.fofn cmp.h5 where *.fofn can either contain ccs.h5 or bas.h5
+# and the cmp.h5 s readType is CCS
+ $ CCS_FOFN=$DATDIR/test_ccs.fofn
+ $ BAS_FOFN=$DATDIR/test_bas.fofn
+
+ $ CMP_IN=$DATDIR/test_ccs_bas.cmp.h5
+ $ CCS_OUT=$OUTDIR/test_ccs_bas_ccs.cmp.h5
+ $ BAS_OUT=$OUTDIR/test_ccs_bas_bas.cmp.h5
+
+ $ cp $CMP_IN $CCS_OUT
+ $ cp $CMP_IN $BAS_OUT
+
+ $ $EXEC $CCS_FOFN $CCS_OUT -metrics QualityValue,DeletionQV,DeletionTag,InsertionQV,SubstitutionQV
+ [INFO] * [loadPulses] started. (glob)
+ loading 11 alignments for movie 1
+ [INFO] * [loadPulses] ended. (glob)
+
+ $ sleep 1
+
+ $ $EXEC $BAS_FOFN $BAS_OUT -metrics QualityValue,DeletionQV,DeletionTag,InsertionQV,SubstitutionQV
+ [INFO] * [loadPulses] started. (glob)
+ loading 11 alignments for movie 1
+ [INFO] * [loadPulses] ended. (glob)
+
+ $ h5diff $CCS_OUT $BAS_OUT
+ dataset: </FileLog/CommandLine> and </FileLog/CommandLine> (glob)
+ * differences found (glob)
+ dataset: </FileLog/Timestamp> and </FileLog/Timestamp>
+ * differences found (glob)
+ [1]
+
diff --git a/utils/ctest/loadPulses_fast.t b/utils/ctest/loadPulses_fast.t
new file mode 100644
index 0000000..d7999a1
--- /dev/null
+++ b/utils/ctest/loadPulses_fast.t
@@ -0,0 +1,41 @@
+Set up directories
+ $ . $TESTDIR/setup.sh
+
+Set up the executable: loadPulses.
+ $ EXEC=$TESTDIR/../loadPulses
+
+#Test loadPulses: input is a bas.h5 file
+#Test -byread and -bymetric
+ $ BAS_IN_1=$DATDIR/lambda_lp.fofn
+ $ CMP_IN_1=$DATDIR/lambda_lp.cmp.h5
+ $ CMP_STDOUT_1=$STDDIR/lambda_lp.cmp.h5
+ $ CMP_OUT_byread_1=$OUTDIR/lambda.byread.cmp.h5
+ $ CMP_OUT_bymetric_1=$OUTDIR/lambda.bymetric.cmp.h5
+ $ METRICS=QualityValue,MergeQV,InsertionQV,DeletionQV,DeletionTag,PulseWidth,SubstitutionQV,SubstitutionTag
+
+ $ rm -f $CMP_OUT_byread_1
+ $ cp $CMP_IN_1 $CMP_OUT_byread_1
+ $ $EXEC $BAS_IN_1 $CMP_OUT_byread_1 -metrics $METRICS -byread > $OUTDIR/tmp.log
+ [INFO] * [loadPulses] started. (glob)
+ [INFO] * [loadPulses] ended. (glob)
+
+ $ h5diff -c $CMP_OUT_byread_1 $CMP_STDOUT_1
+ dataset: </FileLog/CommandLine> and </FileLog/CommandLine>
+ \d+ differences found (re)
+ dataset: </FileLog/Timestamp> and </FileLog/Timestamp>
+ \d+ differences found (re)
+ [1]
+
+ $ rm -f $CMP_OUT_bymetric_1
+ $ cp $CMP_IN_1 $CMP_OUT_bymetric_1
+ $ $EXEC $BAS_IN_1 $CMP_OUT_bymetric_1 -metrics $METRICS -bymetric > $OUTDIR/tmp.log
+ [INFO] * [loadPulses] started. (glob)
+ [INFO] * [loadPulses] ended. (glob)
+ $ h5diff -c $CMP_OUT_bymetric_1 $CMP_STDOUT_1
+ dataset: </FileLog/CommandLine> and </FileLog/CommandLine>
+ \d+ differences found (re)
+ dataset: </FileLog/Timestamp> and </FileLog/Timestamp>
+ \d+ differences found (re)
+ [1]
+
+
diff --git a/utils/ctest/pls2fasta.t b/utils/ctest/pls2fasta.t
new file mode 100644
index 0000000..124ae35
--- /dev/null
+++ b/utils/ctest/pls2fasta.t
@@ -0,0 +1,20 @@
+Set up
+ $ . $TESTDIR/setup.sh
+
+Set up the executable: pls2fasta.
+ $ EXEC=$TESTDIR/../pls2fasta
+
+Test pls2fasta
+Condition: the order of region tables do not match the order bax.h5 files.
+ $ $EXEC $DATDIR/test_pls2fasta.fofn $OUTDIR/test_pls2fasta.fa -regionTable $DATDIR/test_pls2fasta_rgn.fofn -trimByRegion
+ [INFO] * [pls2fasta] started. (glob)
+ [INFO] * [pls2fasta] ended. (glob)
+
+
+Test pls2fasta output fastq
+ $ $EXEC $DATDIR/ecoli_lp.fofn $OUTDIR/test_pls2fasta_ecoli.fq -trimByRegion -fastq
+ [INFO] * [pls2fasta] started. (glob)
+ [INFO] * [pls2fasta] ended. (glob)
+ $ echo $?
+ 0
+ $ diff $OUTDIR/test_pls2fasta_ecoli.fq $STDDIR/test_pls2fasta_ecoli.fq
diff --git a/utils/ctest/pls2fasta_fast.t b/utils/ctest/pls2fasta_fast.t
new file mode 100644
index 0000000..d2cd862
--- /dev/null
+++ b/utils/ctest/pls2fasta_fast.t
@@ -0,0 +1,15 @@
+Set up
+ $ . $TESTDIR/setup.sh
+
+Set up the executable: pls2fasta.
+ $ EXEC=$TESTDIR/../pls2fasta
+
+Test pls2fasta output fasta
+ $ $EXEC $DATDIR/ecoli_lp.fofn $OUTDIR/test_pls2fasta_ecoli.fa -trimByRegion
+ [INFO] * [pls2fasta] started. (glob)
+ [INFO] * [pls2fasta] ended. (glob)
+ $ echo $?
+ 0
+ $ diff $OUTDIR/test_pls2fasta_ecoli.fa $STDDIR/test_pls2fasta_ecoli.fa
+
+
diff --git a/utils/ctest/samFilter.t b/utils/ctest/samFilter.t
new file mode 100644
index 0000000..9dfed3b
--- /dev/null
+++ b/utils/ctest/samFilter.t
@@ -0,0 +1,95 @@
+Set up
+ $ . $TESTDIR/setup.sh
+
+Set up the executable: samFilter.
+ $ EXEC=$TESTDIR/../samFilter
+
+#Test samFilter with a *.sam file generated by blasr
+ $ OUTFILE=$OUTDIR/lambda_bax_filter_1.sam
+ $ STDFILE=$STDDIR/lambda_bax_filter_1.sam
+ $ TMP1=$OUTDIR/$$.tmp.out
+ $ TMP2=$OUTDIR/$$.tmp.stdout
+
+ $ rm -f $OUTFILE
+ $ $EXEC $DATDIR/lambda_bax.sam $DATDIR/lambda_ref.fasta $OUTFILE -minAccuracy 70 -minPctSimilarity 30 -hitPolicy all
+ $ tail -n+7 $OUTFILE |sort > $TMP1
+ $ tail -n+7 $STDFILE |sort > $TMP2
+ $ diff $TMP1 $TMP2
+ $ rm $TMP1 $TMP2
+
+#Test whether minAccuracy and minPctSimilarity can be float.
+# $ rm -f $OUTFILE
+# $ $EXEC $DATDIR/lambda_bax.sam $DATDIR/lambda_ref.fasta $OUTFILE -minAccuracy 70.0 -minPctSimilarity 30.0 -hitPolicy all
+# $ tail -n+7 $OUTFILE | sort > $TMP1
+# $ tail -n+7 $STDFILE | sort > $TMP2
+# $ diff $TMP1 $TMP2
+# $ rm $TMP1 $TMP2
+
+#Test samFilter with -hitPolicy allbest
+ $ OUTFILE=$OUTDIR/lambda_bax_filter_2.sam
+ $ STDFILE=$STDDIR/lambda_bax_filter_2.sam
+
+ $ rm -f $OUTFILE
+ $ $EXEC $DATDIR/lambda_bax.sam $DATDIR/lambda_ref.fasta $OUTFILE -hitPolicy allbest
+ $ tail -n+7 $OUTFILE > $TMP1
+ $ tail -n+7 $STDFILE > $TMP2
+ $ diff $TMP1 $TMP2
+ $ rm $TMP1 $TMP2
+
+#Test samFilter with -hitPolicy random
+ $ OUTFILE=$OUTDIR/lambda_bax_filter_3.sam
+ $ STDFILE=$STDDIR/lambda_bax_filter_3.sam
+
+ $ rm -f $OUTFILE
+ $ $EXEC $DATDIR/lambda_bax.sam $DATDIR/lambda_ref.fasta $OUTFILE -hitPolicy random
+ $ tail -n+7 $OUTFILE > $TMP1
+ $ tail -n+7 $STDFILE > $TMP2
+ $ diff $TMP1 $TMP2
+ $ rm $TMP1 $TMP2
+
+#Test samFilter with -hitPolicy randombest
+ $ OUTFILE=$OUTDIR/lambda_bax_filter_4.sam
+ $ STDFILE=$STDDIR/lambda_bax_filter_4.sam
+
+ $ rm -f $OUTFILE
+ $ $EXEC $DATDIR/lambda_bax.sam $DATDIR/lambda_ref.fasta $OUTFILE -hitPolicy randombest
+ $ tail -n+7 $OUTFILE > $TMP1
+ $ tail -n+7 $STDFILE > $TMP2
+ $ diff $TMP1 $TMP2
+ $ rm $TMP1 $TMP2
+
+
+# Test samFilter with -hitPolicy leftmost
+ $ OUTFILE=$OUTDIR/test_leftmost_out.sam
+
+ $ rm -f $OUTFILE
+ $ $EXEC $DATDIR/test_leftmost.sam $DATDIR/test_leftmost_target.fasta $OUTFILE -hitPolicy leftmost
+ $ tail -n+6 $OUTFILE |cut -f 4
+ 1
+
+ $ OUTFILE=$OUTDIR/lambda_bax_filter_5.sam
+ $ STDFILE=$STDDIR/lambda_bax_filter_5.sam
+
+ $ rm -f $OUTFILE
+ $ $EXEC $DATDIR/lambda_bax.sam $DATDIR/lambda_ref.fasta $OUTFILE
+ $ tail -n+7 $OUTFILE > $TMP1
+ $ tail -n+7 $STDFILE > $TMP2
+ $ diff $TMP1 $TMP2
+ $ rm $TMP1 $TMP2
+
+#Test samFilter with -holeNumbers
+ $ OUTFILE=$OUTDIR/lambda_bax_filter_6.sam
+ $ STDFILE=$STDDIR/lambda_bax_filter_6.sam
+
+ $ rm -f $OUTFILE
+ $ $EXEC $DATDIR/lambda_bax.sam $DATDIR/lambda_ref.fasta $OUTFILE -holeNumbers 101350-105000,21494
+ $ tail -n+7 $OUTFILE > $TMP1
+ $ tail -n+7 $STDFILE > $TMP2
+ $ diff $TMP1 $TMP2
+ $ rm $TMP1 $TMP2
+
+#Test samFilter with -filterAdapterOnly
+ $ $EXEC $DATDIR/filterAdapterOnly.sam $DATDIR/references/H1_6_Scal_6x/sequence/H1_6_Scal_6x.fasta $OUTDIR/filterAdapterOnly.sam -filterAdapterOnly $DATDIR/references/H1_6_Scal_6x/annotations/H1_6_Scal_6x_adapters.gff
+ $ tail -n+6 $OUTDIR/filterAdapterOnly.sam |cut -f 1,2,3,4
+ m130302_124313_42130_c100502672550000001523078308081365_s1_p0/10817\t16\t11k_plasmidbell_H1_6_Scal_6x\t29466 (esc)
+
diff --git a/utils/ctest/samtoh5.t b/utils/ctest/samtoh5.t
new file mode 100644
index 0000000..acfd689
--- /dev/null
+++ b/utils/ctest/samtoh5.t
@@ -0,0 +1,141 @@
+Set up directories
+ $ . $TESTDIR/setup.sh
+
+Set up the executable: samtoh5.
+ $ EXEC=$TESTDIR/../samtoh5
+
+
+#2014_06_05, changed cmp.h5 /version and /primaryversion from 1.3.1* to 2.0.0
+#2014_10_30, changelist 141782, make cmp.h5 column 10 (0 based) moleculeID unique for zmws.
+
+#Test samtoh5 with *.sam files generated by blasr.
+ $ rm -f $OUTDIR/ecoli.cmp.h5
+ $ $EXEC -useShortRefName $DATDIR/ecoli.sam $DATDIR/ecoli_reference.fasta $OUTDIR/ecoli.cmp.h5
+ [INFO] * [samtoh5] started. (glob)
+ [INFO] * [samtoh5] ended. (glob)
+ $ h5diff $OUTDIR/ecoli.cmp.h5 $STDDIR/ecoli_2014_10_30.cmp.h5
+ dataset: </FileLog/CommandLine> and </FileLog/CommandLine>
+ \d+ differences found (re)
+ dataset: </FileLog/Timestamp> and </FileLog/Timestamp>
+ \d+ differences found (re)
+ [1]
+# dataset: </FileLog/Version> and </FileLog/Version>
+# \d+ differences found (re)
+
+#Verify bug 21794 has been fixed.
+#samtoh5 should print the following error message.
+ $ rm -f $OUTDIR/bug21794.cmp.h5
+ $ $EXEC $DATDIR/bug21794.sam $DATDIR/bug21794_reference.fasta $OUTDIR/bug21794.cmp.h5
+ [INFO] * [samtoh5] started. (glob)
+ WARNING. The mapping of read m120504_033026_sherri_c100311672550000001523012508061292_s1_p0/71092/3721_4845 to reference chr4_ctg9_hap1 is out of bounds.
+ StartPos (4294967288) + AlnLength (614) > RefLength (590426) + 2
+ [INFO] * [samtoh5] ended. (glob)
+
+
+#Test boundary case where a read exactly maps to the end of reference.
+ $ rm -f $OUTDIR/bad.cmp.h5
+ $ $EXEC -useShortRefName $DATDIR/bad.sam $DATDIR/ecoli_mutated.fasta $OUTDIR/bad.cmp.h5
+ [INFO] * [samtoh5] started. (glob)
+ [INFO] * [samtoh5] ended. (glob)
+
+ $ h5diff $OUTDIR/bad.cmp.h5 $STDDIR/bad_2014_10_30.cmp.h5
+ dataset: </FileLog/CommandLine> and </FileLog/CommandLine>
+ \d+ differences found (re)
+ dataset: </FileLog/Timestamp> and </FileLog/Timestamp>
+ \d+ differences found (re)
+ [1]
+# dataset: </FileLog/Version> and </FileLog/Version>
+# \d+ differences found (re)
+
+#Test more out-of-boundary cases. samtoh5 prints warnings.
+ $ rm -f $OUTDIR/bad2.cmp.h5
+ $ $EXEC $DATDIR/bad2.sam $DATDIR/ecoli_mutated.fasta $OUTDIR/bad2.cmp.h5
+ [INFO] * [samtoh5] started. (glob)
+ WARNING. The mapping of read m120724_232507_ethan_c100384812550000001523033110171290_s1_p0/21020/11218_12655 to reference ecoliK12_mutated is out of bounds.
+ StartPos (4638237) + AlnLength (1327) > RefLength (4639560) + 2
+ WARNING. The mapping of read m120724_232507_ethan_c100384812550000001523033110171290_s1_p0/60189/0_4202 to reference ecoliK12_mutated is out of bounds.
+ StartPos (4639141) + AlnLength (431) > RefLength (4639560) + 2
+ [INFO] * [samtoh5] ended. (glob)
+
+#Test samtoh5 uses full reference names instead of short reference names, if -useShortRefName is not specified
+ $ rm -f $OUTDIR/ecoli_fullRefName.cmp.h5
+ $ $EXEC $DATDIR/ecoli.sam $DATDIR/ecoli_reference.fasta $OUTDIR/ecoli_fullRefName.cmp.h5
+ [INFO] * [samtoh5] started. (glob)
+ [INFO] * [samtoh5] ended. (glob)
+ $ h5diff $OUTDIR/ecoli_fullRefName.cmp.h5 $STDDIR/ecoli_fullRefName_2014_10_30.cmp.h5
+ dataset: </FileLog/CommandLine> and </FileLog/CommandLine>
+ \d+ differences found (re)
+ dataset: </FileLog/Timestamp> and </FileLog/Timestamp>
+ \d+ differences found (re)
+ [1]
+# dataset: </FileLog/Version> and </FileLog/Version>
+# \d+ differences found (re)
+
+ $ h5dump --dataset /RefInfo/FullName $OUTDIR/ecoli_fullRefName.cmp.h5 | sed -n '11p'
+ (0): "ref000001|gi|49175990|ref|NC_000913.2| Escherichia coli str. K-12 substr. MG1655 chromosome, complete genome"
+
+#Compare the generated reference names with option -useShortRefName is set
+ $ h5dump --dataset /RefInfo/FullName $OUTDIR/ecoli.cmp.h5 |sed -n '11p'
+ (0): "ref000001|gi|49175990|ref|NC_000913.2|"
+
+#Test whether samtoh5 generates correct MD5 for the output cmp.h5 files
+#even if there are invalid MD5 values in the input sam file. bug 22578.
+ $ rm -f $OUTDIR/test_MD5.cmp.h5
+ $ $EXEC $DATDIR/test_MD5.sam $DATDIR/test_MD5MultiContigsRef.fasta $OUTDIR/test_MD5.cmp.h5
+ [INFO] * [samtoh5] started. (glob)
+ [INFO] * [samtoh5] ended. (glob)
+ $ h5dump -d /RefInfo/MD5 $OUTDIR/test_MD5.cmp.h5 |tail -7 |head -4
+ (0): "3cba630ed67592e8e11fb94ef99a122a",
+ (1): "a687c808a666ea90e0a273c4ac2591c3",
+ (2): "81cf96e23ab1392d898a697c9c4c3acd",
+ (3): "4f4bff70a6ac5ae926e5ed6165684dd3"
+
+
+#Test whether samtoh5 accepts smrtTitle movie/zmw/start_end/start2_end2
+ $ rm -f $OUTDIR/test_smrtTitle.cmp.h5
+ $ $EXEC $DATDIR/fns.sam $DATDIR/ecoli_reference.fasta $OUTDIR/test_smrtTitle.cmp.h5
+ [INFO] * [samtoh5] started. (glob)
+ [INFO] * [samtoh5] ended. (glob)
+ $ h5dump -d /AlnInfo/AlnIndex $OUTDIR/test_smrtTitle.cmp.h5 | sed -n '6,25p'
+ (0,0): 1, 1, 1, 1, 4407727, 4407871, 0, 6, 0, 0, 6, 18, 165, 254, 137, 3,
+ (0,16): 7, 4, 0, 151, 0, 0,
+ (1,0): 2, 1, 1, 1, 4407311, 4407788, 1, 6, 0, 0, 6, 109, 657, 254, 460, 4,
+ (1,16): 84, 13, 152, 713, 0, 0,
+ (2,0): 3, 1, 1, 1, 4407314, 4407871, 0, 6, 0, 0, 6, 5, 641, 254, 547, 2,
+ (2,16): 87, 8, 714, 1358, 0, 0,
+ (3,0): 4, 1, 1, 1, 4407372, 4407876, 1, 6, 0, 0, 6, 0, 586, 254, 494, 2,
+ (3,16): 90, 8, 1359, 1953, 0, 0,
+ (4,0): 5, 1, 1, 1, 4407316, 4407877, 0, 6, 0, 0, 6, 7, 640, 254, 545, 4,
+ (4,16): 84, 12, 1954, 2599, 0, 0,
+ (5,0): 6, 1, 1, 1, 4407334, 4407870, 1, 6, 0, 0, 6, 6, 632, 254, 521, 6,
+ (5,16): 99, 9, 2600, 3235, 0, 0,
+ (6,0): 7, 1, 1, 1, 4407310, 4407868, 0, 6, 0, 0, 6, 3, 639, 254, 542, 8,
+ (6,16): 86, 8, 3236, 3880, 0, 0,
+ (7,0): 8, 1, 1, 1, 4407311, 4407815, 0, 6, 0, 0, 6, 0, 601, 254, 484, 5,
+ (7,16): 112, 15, 3881, 4497, 0, 0,
+ (8,0): 9, 1, 1, 1, 4407319, 4407806, 1, 6, 0, 0, 6, 87, 681, 254, 473, 6,
+ (8,16): 115, 8, 4498, 5100, 0, 0,
+ (9,0): 10, 1, 1, 1, 4407381, 4407592, 0, 6, 0, 0, 6, 93, 345, 254, 205, 3,
+ (9,16): 44, 3, 5101, 5356, 0, 0
+
+
+
+#Test whether samtoh5 mimic the behaviour of compareSequences.py and remove
+#reference groups which have no alignments to any movie.
+# $ NAME=test_rm_empty_refGroup
+# $ rm -f $OUTDIR/$NAME.cmp.h5
+# $ $EXEC $DATDIR/$NAME.sam $DATDIR/$NAME.fasta $OUTDIR/$NAME.cmp.h5
+# [INFO] * [samtoh5] started. (glob)
+# [INFO] * [samtoh5] ended. (glob)
+# $ h5dump -d /RefGroup/ID $OUTDIR/$NAME.cmp.h5 | sed -n '6,6p'
+# (0): 1, 2
+#
+# $ h5dump -d /RefGroup/Path $OUTDIR/$NAME.cmp.h5 | sed -n '11,11p'
+# (0): "/ref000003", "/ref000005"
+
+#Test whether samtoh5 accepts PBI reads in format "movie/holeNumber"
+ $ NAME=test_pbiname
+ $ rm -f $OUTDIR/$NAME.cmp.h5
+ $ $EXEC $DATDIR/$NAME.sam $DATDIR/ecoli_reference.fasta $OUTDIR/$NAME.cmp.h5
+ [INFO] * [samtoh5] started. (glob)
+ [INFO] * [samtoh5] ended. (glob)
diff --git a/utils/ctest/samtom4.t b/utils/ctest/samtom4.t
new file mode 100644
index 0000000..2f589ff
--- /dev/null
+++ b/utils/ctest/samtom4.t
@@ -0,0 +1,44 @@
+Set up directories
+ $ . $TESTDIR/setup.sh
+
+Set up the executable: samtom4.
+ $ EXEC=$TESTDIR/../samtom4
+
+#Test samtom4 with a *.sam file generated by blasr from a fofn
+ $ OUTFILE=$OUTDIR/lambda_bax.m4
+#STDFILE has been generated by blasr -m 4 && sort
+ $ STDFILE=$STDDIR/lambda_bax.m4
+ $ TMPFILE=test_samtom4_2.tmp
+
+ $ rm -rf $OUTFILE $TMPFILE
+ $ $EXEC $DATDIR/lambda_bax.sam $DATDIR/lambda_ref.fasta $TMPFILE
+ $ sort $TMPFILE > $OUTFILE
+ $ diff $OUTFILE $STDFILE
+
+ $ rm $TMPFILE
+
+
+#Test samtom4 with a *.sam file generated by blasr with -noSplitSubreads from a fofn
+ $ OUTFILE=$OUTDIR/lambda_bax_noSplitSubreads.m4
+#STDFILE has been generated by blasr -m 4 && sort
+ $ STDFILE=$STDDIR/lambda_bax_noSplitSubreads.m4
+ $ TMPFILE=test_samtom4_3.tmp
+
+ $ rm -rf $OUTFILE $TMPFILE
+ $ $EXEC $DATDIR/lambda_bax_noSplitSubreads.sam $DATDIR/lambda_ref.fasta $TMPFILE
+ $ sort $TMPFILE > $OUTFILE
+ $ diff $OUTFILE $STDFILE
+
+ $ rm $TMPFILE
+
+#Test samtom4 with a *.sam file generated by blasr.
+ $ OUTFILE=$OUTDIR/ecoli_samtom4.m4
+#STDFILE has been generated by blasr -m 4 && sort
+ $ STDFILE=$STDDIR/ecoli_sorted.m4
+ $ TMPFILE=$OUTDIR/test_samtom4_4.tmp
+
+ $ rm -rf $OUTFILE $TMPFILE
+ $ $EXEC $DATDIR/ecoli.sam $DATDIR/ecoli_reference.fasta $OUTFILE -useShortRefName
+ $ sort -n $OUTFILE > $TMPFILE
+ $ diff $TMPFILE $STDFILE
+
diff --git a/utils/ctest/sawriter.t b/utils/ctest/sawriter.t
new file mode 100644
index 0000000..791d581
--- /dev/null
+++ b/utils/ctest/sawriter.t
@@ -0,0 +1,30 @@
+Set up directories
+ $ CURDIR=$TESTDIR
+ $ REMOTEDIR=/mnt/secondary-siv/testdata/BlasrTestData/ctest
+ $ DATDIR=$REMOTEDIR/data
+ $ OUTDIR=$CURDIR/out
+ $ STDDIR=$REMOTEDIR/stdout
+
+Set up the executable: sawriter.
+ $ EXEC=$TESTDIR/../sawriter
+
+Define tmporary files
+ $ TMP1=$OUTDIR/$$.tmp.out
+ $ TMP2=$OUTDIR/$$.tmp.stdout
+
+Make OUTDIR
+ $ mkdir -p $OUTDIR
+
+ $ $EXEC $OUTDIR/ecoli_larsson.sa $DATDIR/ecoli_reference.fasta -blt 11 -larsson
+ $ echo $?
+ 0
+
+ $ $EXEC $OUTDIR/ecoli_welter.sa $DATDIR/ecoli_reference.fasta -blt 11 -welter 2>$OUTDIR/sawriter.log
+ $ echo $?
+ 0
+
+ $ md5sum $OUTDIR/ecoli_larsson.sa |cut -f 1 -d ' '
+ e23b6afe6ddd74b2656e36bf93f6840c
+
+ $ md5sum $OUTDIR/ecoli_welter.sa |cut -f 1 -d ' '
+ e23b6afe6ddd74b2656e36bf93f6840c
diff --git a/utils/ctest/sdpMatcher.t b/utils/ctest/sdpMatcher.t
new file mode 100644
index 0000000..efe69f7
--- /dev/null
+++ b/utils/ctest/sdpMatcher.t
@@ -0,0 +1,24 @@
+Set up directories
+ $ CURDIR=$TESTDIR
+ $ REMOTEDIR=/mnt/secondary-siv/testdata/BlasrTestData/ctest
+ $ DATDIR=$REMOTEDIR/data
+ $ OUTDIR=$CURDIR/out
+ $ STDDIR=$REMOTEDIR/stdout
+
+Set up the executable: sdpMatcher.
+ $ EXEC=$TESTDIR/../sdpMatcher
+
+Define tmporary files
+ $ TMP1=$OUTDIR/$$.tmp.out
+ $ TMP2=$OUTDIR/$$.tmp.stdout
+
+Make OUTDIR
+ $ mkdir -p $OUTDIR
+
+ $ FA=$DATDIR/ecoli_subset.fasta
+ $ $EXEC $FA $FA 10 -local > $OUTDIR/sdpMatcher.out
+ $ echo $?
+ 0
+ $ diff $OUTDIR/sdpMatcher.out $STDDIR/sdpMatcher.stdout
+
+
diff --git a/utils/ctest/setup.sh b/utils/ctest/setup.sh
new file mode 100755
index 0000000..0365beb
--- /dev/null
+++ b/utils/ctest/setup.sh
@@ -0,0 +1,14 @@
+# Set up directories
+CURDIR=$TESTDIR
+REMOTEDIR=/mnt/secondary-siv/testdata/BlasrTestData/ctest
+DATDIR=$REMOTEDIR/data
+OUTDIR=$CURDIR/out
+STDDIR=$REMOTEDIR/stdout
+
+# Define tmporary files
+TMP1=$OUTDIR/$$.tmp.out
+TMP2=$OUTDIR/$$.tmp.stdout
+
+# Make OUTDIR
+mkdir -p $OUTDIR
+
diff --git a/utils/ctest/toAfg.t b/utils/ctest/toAfg.t
new file mode 100644
index 0000000..491304c
--- /dev/null
+++ b/utils/ctest/toAfg.t
@@ -0,0 +1,70 @@
+Set up directories
+ $ . $TESTDIR/setup.sh
+
+Set up the executable: toAfg.
+ $ EXEC=$TESTDIR/../toAfg
+
+test basic FASTA use case
+ $ $EXEC $DATDIR/read.fasta output.afg -noSplitSubreads
+ $ head output.afg
+ {UNV
+ iid:1
+ com:
+ generated by AfgBasWriter
+ Mon Jun 28 14:43:52 2010
+ .
+ }
+ {LIB
+ iid:1
+ {DST
+ $ tail output.afg
+ qlt:
+ 55555555555555555555555555555555555555555555555555555555555555555555555555555555
+ 55555555555555555555
+ .
+ }
+ {FRG
+ iid:24
+ lib:1
+ typ:I
+ }
+
+test uniform QV use case
+ $ $EXEC $DATDIR/test_toafg.fastq output.afg -noSplitSubreads -uniformQV 3
+ $ head output.afg
+ {UNV
+ iid:1
+ com:
+ generated by AfgBasWriter
+ Mon Jun 28 14:43:52 2010
+ .
+ }
+ {LIB
+ iid:1
+ {DST
+
+test uniform QV FASTA use case
+ $ $EXEC $DATDIR/read.fasta output.afg -noSplitSubreads -uniformQV 7
+ $ head output.afg
+ {UNV
+ iid:1
+ com:
+ generated by AfgBasWriter
+ Mon Jun 28 14:43:52 2010
+ .
+ }
+ {LIB
+ iid:1
+ {DST
+ $ tail output.afg
+ qlt:
+ 77777777777777777777777777777777777777777777777777777777777777777777777777777777
+ 77777777777777777777
+ .
+ }
+ {FRG
+ iid:24
+ lib:1
+ typ:I
+ }
+
diff --git a/utils/p4.mk b/utils/p4.mk
new file mode 100644
index 0000000..34a5e6f
--- /dev/null
+++ b/utils/p4.mk
@@ -0,0 +1,65 @@
+# 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
new file mode 100644
index 0000000..f33276b
--- /dev/null
+++ b/yli.common.mk
@@ -0,0 +1,94 @@
+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
new file mode 100644
index 0000000..bc8af98
--- /dev/null
+++ b/yli.makefile
@@ -0,0 +1,80 @@
+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)
--
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