Pileup< PILEUP_TYPE, FUNC_CLASS > Member List

This is the complete list of members for Pileup< PILEUP_TYPE, FUNC_CLASS >, including all inherited members.

addAlignmentPosition(int refPosition, SamRecord &record) (defined in Pileup< PILEUP_TYPE, FUNC_CLASS >) | Pileup< PILEUP_TYPE, FUNC_CLASS > | protected
addElement(PILEUP_TYPE &element, SamRecord &record) (defined in Pileup< PILEUP_TYPE, FUNC_CLASS >) | Pileup< PILEUP_TYPE, FUNC_CLASS > | protected virtual
analyzeElement(PILEUP_TYPE &element) (defined in Pileup< PILEUP_TYPE, FUNC_CLASS >) | Pileup< PILEUP_TYPE, FUNC_CLASS > | protected virtual
analyzeHead() (defined in Pileup< PILEUP_TYPE, FUNC_CLASS >) | Pileup< PILEUP_TYPE, FUNC_CLASS > | protected virtual
flushPileup() | Pileup< PILEUP_TYPE, FUNC_CLASS > |
flushPileup(int refID, int refPosition) (defined in Pileup< PILEUP_TYPE, FUNC_CLASS >) | Pileup< PILEUP_TYPE, FUNC_CLASS > | protected virtual
flushPileup(int refPosition) (defined in Pileup< PILEUP_TYPE, FUNC_CLASS >) | Pileup< PILEUP_TYPE, FUNC_CLASS > | protected
myAnalyzeFuncPtr (defined in Pileup< PILEUP_TYPE, FUNC_CLASS >) | Pileup< PILEUP_TYPE, FUNC_CLASS > | protected
myCurrentRefID (defined in Pileup< PILEUP_TYPE, FUNC_CLASS >) | Pileup< PILEUP_TYPE, FUNC_CLASS > | protected
myElements (defined in Pileup< PILEUP_TYPE, FUNC_CLASS >) | Pileup< PILEUP_TYPE, FUNC_CLASS > | protected
myRefPtr (defined in Pileup< PILEUP_TYPE, FUNC_CLASS >) | Pileup< PILEUP_TYPE, FUNC_CLASS > | protected
Pileup(const FUNC_CLASS &fp=FUNC_CLASS()) | Pileup< PILEUP_TYPE, FUNC_CLASS > |
Pileup(int window, const FUNC_CLASS &fp=FUNC_CLASS()) | Pileup< PILEUP_TYPE, FUNC_CLASS > |
Pileup(const std::string &refSeqFileName, const FUNC_CLASS &fp=FUNC_CLASS()) | Pileup< PILEUP_TYPE, FUNC_CLASS > |
Pileup(int window, const std::string &refSeqFileName, const FUNC_CLASS &fp=FUNC_CLASS()) | Pileup< PILEUP_TYPE, FUNC_CLASS > |
pileupHead (defined in Pileup< PILEUP_TYPE, FUNC_CLASS >) | Pileup< PILEUP_TYPE, FUNC_CLASS > | protected
pileupPosition(int refPosition) (defined in Pileup< PILEUP_TYPE, FUNC_CLASS >) | Pileup< PILEUP_TYPE, FUNC_CLASS > | protected
pileupStart (defined in Pileup< PILEUP_TYPE, FUNC_CLASS >) | Pileup< PILEUP_TYPE, FUNC_CLASS > | protected
pileupTail (defined in Pileup< PILEUP_TYPE, FUNC_CLASS >) | Pileup< PILEUP_TYPE, FUNC_CLASS > | protected
pileupWindow (defined in Pileup< PILEUP_TYPE, FUNC_CLASS >) | Pileup< PILEUP_TYPE, FUNC_CLASS > | protected
processAlignment(SamRecord &record) | Pileup< PILEUP_TYPE, FUNC_CLASS > | virtual
processAlignmentRegion(SamRecord &record, int startPos, int endPos, PosList *excludeList=NULL) | Pileup< PILEUP_TYPE, FUNC_CLASS > | virtual
processFile(const std::string &fileName, uint16_t excludeFlag=0x0704, uint16_t includeFlag=0) | Pileup< PILEUP_TYPE, FUNC_CLASS > | virtual
resetElement(PILEUP_TYPE &element, int position) (defined in Pileup< PILEUP_TYPE, FUNC_CLASS >) | Pileup< PILEUP_TYPE, FUNC_CLASS > | protected virtual
~Pileup() | Pileup< PILEUP_TYPE, FUNC_CLASS > | virtual