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void | testPileupPosition () |
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| Pileup (const defaultPileup< TestPileupElement > &fp=defaultPileup< TestPileupElement >()) |
| Constructor using the default maximum number of bases a read spans.
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| Pileup (int window, const defaultPileup< TestPileupElement > &fp=defaultPileup< TestPileupElement >()) |
| Constructor that sets the maximum number of bases a read spans. More...
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| Pileup (const std::string &refSeqFileName, const defaultPileup< TestPileupElement > &fp=defaultPileup< TestPileupElement >()) |
| Perform pileup with a reference.
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| Pileup (int window, const std::string &refSeqFileName, const defaultPileup< TestPileupElement > &fp=defaultPileup< TestPileupElement >()) |
| Perform pileup with a reference and a specified window size.
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virtual | ~Pileup () |
| Destructor.
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virtual int | processFile (const std::string &fileName, uint16_t excludeFlag=0x0704, uint16_t includeFlag=0) |
| Performs a pileup on the specified file. More...
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virtual void | processAlignment (SamRecord &record) |
| Add an alignment to the pileup.
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virtual void | processAlignmentRegion (SamRecord &record, int startPos, int endPos, PosList *excludeList=NULL) |
| Add only positions that fall within the specified region of the alignment to the pileup and outside of the specified excluded positions. More...
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void | flushPileup () |
| Done processing, flush every position that is currently being stored in the pileup.
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Definition at line 32 of file TestPileup.h.
The documentation for this class was generated from the following files: