Pileup< PILEUP_TYPE, FUNC_CLASS > Class Template Reference

Collaboration diagram for Pileup< PILEUP_TYPE, FUNC_CLASS >:

[legend]

List of all members.

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)
	Add an alignment to the pileup.
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.
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 49 of file Pileup.h.

---

Member Function Documentation

template<class PILEUP_TYPE , class FUNC_CLASS >

void Pileup< PILEUP_TYPE, FUNC_CLASS >::processAlignmentRegion	(	SamRecord &	record,
		int	startPos,
		int	endPos,
		PosList *	excludeList = NULL
	)			[inline, virtual]

Add only positions that fall within the specified region of the alignment to the pileup and outside of the specified excluded positions.

Parameters:

	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 299 of file Pileup.h.

References SamRecord::get0BasedAlignmentEnd(), SamRecord::get0BasedPosition(), SamRecord::getReferenceID(), and PosList::hasPosition().

{
    int refPosition = record.get0BasedPosition();
    int refID = record.getReferenceID();

    // Flush any elements from the pileup that are prior to this record
    // since the file is sorted, we are done with those positions.
    flushPileup(refID, refPosition);
    
    // Check if the region starts after this reference starts.  If so,
    // we only want to start adding at the region start position.
    if(startPos > refPosition)
    {
        refPosition = startPos;
    }

    // Loop through for each reference position covered by the record.
    // It is up to the PILEUP_TYPE to handle insertions/deletions, etc
    // that are related with the given reference position.
    for(; refPosition <= record.get0BasedAlignmentEnd(); ++refPosition)
    {
        // Check to see if we have gone past the end of the region, in which
        // case we can stop processing this record.  Check >= since the
        // end position is not in the region.
        if((endPos != -1) && (refPosition >= endPos))
        {
            break;
        }

        // Check to see if this position is in the exclude list.
        bool addPos = true;
        if(excludeList != NULL)
        {
            // There is an exclude list, so lookup the position.
            if(excludeList->hasPosition(refID, refPosition))
            {
                // This position is in the exclude list, so don't add it.
                addPos = false;
            }
        }
        if(addPos)
        {
            addAlignmentPosition(refPosition, record);
        }
    }
}

---

The documentation for this class was generated from the following file:

• bam/Pileup.h