, including all inherited members.
addAlignmentPosition(int refPosition, SamRecord &record) (defined in Pileup< PileupElementBaseQual >) | Pileup< PileupElementBaseQual > | [protected] |
addElement(PileupElementBaseQual &element, SamRecord &record) (defined in Pileup< PileupElementBaseQual >) | Pileup< PileupElementBaseQual > | [protected, virtual] |
analyzeElement(PileupElementBaseQual &element) (defined in Pileup< PileupElementBaseQual >) | Pileup< PileupElementBaseQual > | [protected, virtual] |
analyzeHead() (defined in Pileup< PileupElementBaseQual >) | Pileup< PileupElementBaseQual > | [protected, virtual] |
flushPileup() (defined in Pileup< PileupElementBaseQual >) | Pileup< PileupElementBaseQual > | |
flushPileup(int refID, int refPosition) (defined in Pileup< PileupElementBaseQual >) | Pileup< PileupElementBaseQual > | [protected, virtual] |
flushPileup(int refPosition) (defined in Pileup< PileupElementBaseQual >) | Pileup< PileupElementBaseQual > | [protected] |
myAnalyzeFuncPtr (defined in Pileup< PileupElementBaseQual >) | Pileup< PileupElementBaseQual > | [protected] |
myCurrentRefID (defined in Pileup< PileupElementBaseQual >) | Pileup< PileupElementBaseQual > | [protected] |
myElements (defined in Pileup< PileupElementBaseQual >) | Pileup< PileupElementBaseQual > | [protected] |
myRefPtr (defined in Pileup< PileupElementBaseQual >) | Pileup< PileupElementBaseQual > | [protected] |
Pileup(const defaultPileup< PileupElementBaseQual > &fp=defaultPileup< PileupElementBaseQual >()) (defined in Pileup< PileupElementBaseQual >) | Pileup< PileupElementBaseQual > | |
Pileup(int window, const defaultPileup< PileupElementBaseQual > &fp=defaultPileup< PileupElementBaseQual >()) (defined in Pileup< PileupElementBaseQual >) | Pileup< PileupElementBaseQual > | |
Pileup(const std::string &refSeqFileName, const defaultPileup< PileupElementBaseQual > &fp=defaultPileup< PileupElementBaseQual >()) (defined in Pileup< PileupElementBaseQual >) | Pileup< PileupElementBaseQual > | |
Pileup(int window, const std::string &refSeqFileName, const defaultPileup< PileupElementBaseQual > &fp=defaultPileup< PileupElementBaseQual >()) (defined in Pileup< PileupElementBaseQual >) | Pileup< PileupElementBaseQual > | |
pileupHead (defined in Pileup< PileupElementBaseQual >) | Pileup< PileupElementBaseQual > | [protected] |
pileupPosition(int refPosition) (defined in Pileup< PileupElementBaseQual >) | Pileup< PileupElementBaseQual > | [protected] |
pileupStart (defined in Pileup< PileupElementBaseQual >) | Pileup< PileupElementBaseQual > | [protected] |
pileupTail (defined in Pileup< PileupElementBaseQual >) | Pileup< PileupElementBaseQual > | [protected] |
pileupWindow (defined in Pileup< PileupElementBaseQual >) | Pileup< PileupElementBaseQual > | [protected] |
processAlignment(SamRecord &record) (defined in Pileup< PileupElementBaseQual >) | Pileup< PileupElementBaseQual > | [virtual] |
processFile(const std::string &fileName, uint16_t excludeFlag=0x0704, uint16_t includeFlag=0) (defined in Pileup< PileupElementBaseQual >) | Pileup< PileupElementBaseQual > | [virtual] |
resetElement(PileupElementBaseQual &element, int position) (defined in Pileup< PileupElementBaseQual >) | Pileup< PileupElementBaseQual > | [protected, virtual] |
testPileupPosition() (defined in TestPileup) | TestPileup | |
~Pileup() (defined in Pileup< PileupElementBaseQual >) | Pileup< PileupElementBaseQual > | |