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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 >protectedvirtual
analyzeElement(PILEUP_TYPE &element) (defined in Pileup< PILEUP_TYPE, FUNC_CLASS >)Pileup< PILEUP_TYPE, FUNC_CLASS >protectedvirtual
analyzeHead() (defined in Pileup< PILEUP_TYPE, FUNC_CLASS >)Pileup< PILEUP_TYPE, FUNC_CLASS >protectedvirtual
flushPileup()Pileup< PILEUP_TYPE, FUNC_CLASS >
flushPileup(int refID, int refPosition) (defined in Pileup< PILEUP_TYPE, FUNC_CLASS >)Pileup< PILEUP_TYPE, FUNC_CLASS >protectedvirtual
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 >protectedvirtual
~Pileup()Pileup< PILEUP_TYPE, FUNC_CLASS >virtual