Pileup< PILEUP_TYPE, FUNC_CLASS > Class Template Reference
Collaboration diagram for Pileup< PILEUP_TYPE, FUNC_CLASS >:
Public Member Functions | |
| Pileup (const FUNC_CLASS &fp=FUNC_CLASS()) | |
| Pileup (int window, const FUNC_CLASS &fp=FUNC_CLASS()) | |
| Pileup (const std::string &refSeqFileName, const FUNC_CLASS &fp=FUNC_CLASS()) | |
| Pileup (int window, const std::string &refSeqFileName, const FUNC_CLASS &fp=FUNC_CLASS()) | |
| virtual int | processFile (const std::string &fileName, uint16_t excludeFlag=0x0704, uint16_t includeFlag=0) |
| virtual void | processAlignment (SamRecord &record) |
| void | flushPileup () |
Protected Member Functions | |
| void | addAlignmentPosition (int refPosition, SamRecord &record) |
| virtual void | flushPileup (int refID, int refPosition) |
| void | flushPileup (int refPosition) |
| int | pileupPosition (int refPosition) |
| virtual void | resetElement (PILEUP_TYPE &element, int position) |
| virtual void | addElement (PILEUP_TYPE &element, SamRecord &record) |
| virtual void | analyzeElement (PILEUP_TYPE &element) |
| virtual void | analyzeHead () |
Protected Attributes | |
| FUNC_CLASS | myAnalyzeFuncPtr |
| std::vector< PILEUP_TYPE > | myElements |
| int | pileupStart |
| int | pileupHead |
| int | pileupTail |
| int | pileupWindow |
| int | myCurrentRefID |
| GenomeSequence * | myRefPtr |
Detailed Description
template<class PILEUP_TYPE, class FUNC_CLASS = defaultPileup<PILEUP_TYPE>>
class Pileup< PILEUP_TYPE, FUNC_CLASS >
Definition at line 48 of file Pileup.h.
The documentation for this class was generated from the following file:
- bam/Pileup.h
