libStatGen Software 1
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Public Member Functions | |
void | testPileupPosition () |
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Pileup (const defaultPileup< TestPileupElement > &fp=defaultPileup< TestPileupElement >()) | |
Constructor using the default maximum number of bases a read spans. | |
Pileup (int window, const defaultPileup< TestPileupElement > &fp=defaultPileup< TestPileupElement >()) | |
Constructor that sets the maximum number of bases a read spans. | |
Pileup (const std::string &refSeqFileName, const defaultPileup< TestPileupElement > &fp=defaultPileup< TestPileupElement >()) | |
Perform pileup with a reference. | |
Pileup (int window, const std::string &refSeqFileName, const defaultPileup< TestPileupElement > &fp=defaultPileup< TestPileupElement >()) | |
Perform pileup with a reference and a specified window size. | |
virtual | ~Pileup () |
Destructor. | |
virtual int | processFile (const std::string &fileName, uint16_t excludeFlag=0x0704, uint16_t includeFlag=0) |
Performs a pileup on the specified file. | |
virtual void | processAlignment (SamRecord &record) |
Add an alignment to the pileup. | |
virtual void | processAlignmentRegion (SamRecord &record, int startPos, int endPos, PosList *excludeList=NULL) |
Add only positions that fall within the specified region of the alignment to the pileup and outside of the specified excluded positions. | |
void | flushPileup () |
Done processing, flush every position that is currently being stored in the pileup. | |
Additional Inherited Members | |
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virtual void | flushPileup (int refID, int refPosition) |
void | flushPileup (int refPosition) |
void | addAlignmentPosition (int refPosition, SamRecord &record) |
int | pileupPosition (int refPosition) |
virtual void | resetElement (TestPileupElement &element, int position) |
virtual void | addElement (TestPileupElement &element, SamRecord &record) |
virtual void | analyzeElement (TestPileupElement &element) |
virtual void | analyzeHead () |
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defaultPileup< TestPileupElement > | myAnalyzeFuncPtr |
std::vector< TestPileupElement > | myElements |
int | pileupStart |
int | pileupHead |
int | pileupTail |
int | pileupWindow |
int | myCurrentRefID |
GenomeSequence * | myRefPtr |
Definition at line 32 of file TestPileup.h.
void TestPileup::testPileupPosition | ( | ) |
Definition at line 32 of file TestPileup.cpp.