libStatGen Software
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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 |