libStatGen Software  1
TestPileup Member List

This is the complete list of members for TestPileup, including all inherited members.

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