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void | clearAlignment () |
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void | clear () |
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| SmithWaterman (Atype *A, QualityType *qualities, Btype *B, int m, int n, int allowedInsertDelete=INT_MAX, int direction=1, readIndexType MOffset=0, referenceIndexType NOffset=0) |
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void | setRead (Atype *A) |
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void | setReadQuality (QualityType *qualities) |
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void | setReference (Btype *B) |
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void | setReadLength (int m) |
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void | setReadOffset (readIndexType MOffset) |
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void | setReferenceLength (int n) |
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void | setReferenceOffset (referenceIndexType NOffset) |
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void | setAllowedInsertDelete (int allowedInsertDelete=INT_MAX) |
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void | setDirection (int direction) |
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void | clearH () |
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void | populateH () |
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void | printH (bool prettyPrint=true) |
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void | debugPrint (bool doPrintH=true) |
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void | populateAlignment () |
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int | getSumQ () |
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int | getSumQForward () |
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int | getSumQBackward () |
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void | rollCigarForward (CigarRoller &cigar) |
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void | rollCigarBackward (CigarRoller &cigar) |
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int | getSoftClipCount () |
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void | rollCigar (CigarRoller &cigar) |
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bool | localAlignment (uint32_t bandSize, Atype &read, readIndexType readLength, QualityType &quality, Btype &reference, referenceIndexType referenceLength, referenceIndexType referenceOffset, CigarRoller &cigarRoller, uint32_t &softClipCount, referenceIndexType &cigarStartingPoint, int &sumQ) |
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HCellType | H [maxReadLengthH][maxReferenceLengthH] |
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Atype * | A |
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Btype * | B |
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QualityType * | qualities |
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int | m |
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int | n |
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readIndexType | MOffset |
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referenceIndexType | NOffset |
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weight | w |
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int | allowedInsertDelete |
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int | direction |
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int | gapOpenCount |
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int | gapCloseCount |
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int | gapExtendCount |
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vector< pair< int, int > > | alignment |
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HCellType | maxCostValue |
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pair< int, int > | maxCostPosition |
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template<int maxReadLengthH, int maxReferenceLengthH, typename HCellType, typename Atype, typename Btype, typename QualityType, typename readIndexType, typename referenceIndexType>
class SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >
Definition at line 127 of file SmithWaterman.h.
The documentation for this class was generated from the following file: