, 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 > | |
