libStatGen Software  1
SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType > Class Template Reference
Collaboration diagram for SmithWaterman< maxReadLengthH, maxReferenceLengthH, HCellType, Atype, Btype, QualityType, readIndexType, referenceIndexType >:

Classes

struct  weight
 

Public Member Functions

void clearAlignment ()
 
void clear ()
 
 SmithWaterman (Atype *A, QualityType *qualities, Btype *B, int m, int n, int allowedInsertDelete=INT_MAX, int direction=1, readIndexType MOffset=0, referenceIndexType NOffset=0)
 
void setRead (Atype *A)
 
void setReadQuality (QualityType *qualities)
 
void setReference (Btype *B)
 
void setReadLength (int m)
 
void setReadOffset (readIndexType MOffset)
 
void setReferenceLength (int n)
 
void setReferenceOffset (referenceIndexType NOffset)
 
void setAllowedInsertDelete (int allowedInsertDelete=INT_MAX)
 
void setDirection (int direction)
 
void clearH ()
 
void populateH ()
 
void printH (bool prettyPrint=true)
 
void debugPrint (bool doPrintH=true)
 
void populateAlignment ()
 
int getSumQ ()
 
int getSumQForward ()
 
int getSumQBackward ()
 
void rollCigarForward (CigarRoller &cigar)
 
void rollCigarBackward (CigarRoller &cigar)
 
int getSoftClipCount ()
 
void rollCigar (CigarRoller &cigar)
 
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)
 

Public Attributes

HCellType H [maxReadLengthH][maxReferenceLengthH]
 
Atype * A
 
Btype * B
 
QualityType * qualities
 
int m
 
int n
 
readIndexType MOffset
 
referenceIndexType NOffset
 
weight w
 
int allowedInsertDelete
 
int direction
 
int gapOpenCount
 
int gapCloseCount
 
int gapExtendCount
 
vector< pair< int, int > > alignment
 
HCellType maxCostValue
 
pair< int, int > maxCostPosition
 

Detailed Description

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: