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]