Class to perform a pileup of all reads by position, assuming the reads are coordinate sorted.
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#include <Pileup.h>
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| Pileup (const FUNC_CLASS &fp=FUNC_CLASS()) |
| Constructor using the default maximum number of bases a read spans.
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| Pileup (int window, const FUNC_CLASS &fp=FUNC_CLASS()) |
| Constructor that sets the maximum number of bases a read spans. More...
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| Pileup (const std::string &refSeqFileName, const FUNC_CLASS &fp=FUNC_CLASS()) |
| Perform pileup with a reference.
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| Pileup (int window, const std::string &refSeqFileName, const FUNC_CLASS &fp=FUNC_CLASS()) |
| 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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void | addAlignmentPosition (int refPosition, SamRecord &record) |
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virtual void | flushPileup (int refID, int refPosition) |
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void | flushPileup (int refPosition) |
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int | pileupPosition (int refPosition) |
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virtual void | resetElement (PILEUP_TYPE &element, int position) |
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virtual void | addElement (PILEUP_TYPE &element, SamRecord &record) |
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virtual void | analyzeElement (PILEUP_TYPE &element) |
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virtual void | analyzeHead () |
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FUNC_CLASS | myAnalyzeFuncPtr |
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std::vector< PILEUP_TYPE > | myElements |
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int | pileupStart |
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int | pileupHead |
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int | pileupTail |
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int | pileupWindow |
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int | myCurrentRefID |
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GenomeSequence * | myRefPtr |
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template<class PILEUP_TYPE, class FUNC_CLASS = defaultPileup<PILEUP_TYPE>>
class Pileup< PILEUP_TYPE, FUNC_CLASS >
Class to perform a pileup of all reads by position, assuming the reads are coordinate sorted.
Definition at line 58 of file Pileup.h.
◆ Pileup()
template<class PILEUP_TYPE , class FUNC_CLASS >
Pileup< PILEUP_TYPE, FUNC_CLASS >::Pileup |
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int |
window, |
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const FUNC_CLASS & |
fp = FUNC_CLASS() |
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Constructor that sets the maximum number of bases a read spans.
This is the "window" the length of the buffer that holds the pileups for each position until the read start has moved past the position.
Definition at line 168 of file Pileup.h.
169 : myAnalyzeFuncPtr(fp),
174 pileupWindow(window),
179 myElements.resize(window);
◆ processAlignmentRegion()
template<class PILEUP_TYPE , class FUNC_CLASS >
void Pileup< PILEUP_TYPE, FUNC_CLASS >::processAlignmentRegion |
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SamRecord & |
record, |
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int |
startPos, |
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int |
endPos, |
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PosList * |
excludeList = NULL |
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Add only positions that fall within the specified region of the alignment to the pileup and outside of the specified excluded positions.
- Parameters
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record | alignment to be added to the pileup. |
startPos | 0-based start position of the bases that should be added to the pileup. |
endPos | 0-based end position of the bases that should be added to the pileup (this position is not added). Set to -1 if there is no end position to the region. |
excludeList | list of refID/positions to exclude from processing. |
Definition at line 316 of file Pileup.h.
330 if(startPos > refPosition)
332 refPosition = startPos;
343 if((endPos != -1) && (refPosition >= endPos))
350 if(excludeList != NULL)
361 addAlignmentPosition(refPosition, record);
◆ processFile()
template<class PILEUP_TYPE , class FUNC_CLASS >
int Pileup< PILEUP_TYPE, FUNC_CLASS >::processFile |
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const std::string & |
fileName, |
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uint16_t |
excludeFlag = 0x0704 , |
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uint16_t |
includeFlag = 0 |
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Performs a pileup on the specified file.
- Parameters
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excludeFlag | if specified, if any bit set in the exclude flag is set in the record's flag, it will be dropped. Defaulted to exclude:
- unmapped,
- not primary alignment
- failed platform/vendor quality check
- PCR or optical duplicate
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includeFlag | if specified, every bit must be set in the record's flag for it to be included - defaulted to 0, no bits are required to be set. |
- Returns
- 0 for success and non-zero for failure.
Definition at line 235 of file Pileup.h.
266 uint16_t flag = record.
getFlag();
267 if(flag & excludeFlag)
273 if((flag & includeFlag) != includeFlag)
The documentation for this class was generated from the following file: