Inheritance diagram for TestPileup:

Collaboration diagram for TestPileup:

Public Member Functions
void	testPileupPosition ()

Public Member Functions inherited from Pileup< TestPileupElement >
	Pileup (const defaultPileup< TestPileupElement > &fp=defaultPileup< TestPileupElement >())
	Constructor using the default maximum number of bases a read spans.

	Pileup (int window, const defaultPileup< TestPileupElement > &fp=defaultPileup< TestPileupElement >())
	Constructor that sets the maximum number of bases a read spans. More...

	Pileup (const std::string &refSeqFileName, const defaultPileup< TestPileupElement > &fp=defaultPileup< TestPileupElement >())
	Perform pileup with a reference.

	Pileup (int window, const std::string &refSeqFileName, const defaultPileup< TestPileupElement > &fp=defaultPileup< TestPileupElement >())
	Perform pileup with a reference and a specified window size.

virtual	~Pileup ()
	Destructor.

virtual int	processFile (const std::string &fileName, uint16_t excludeFlag=0x0704, uint16_t includeFlag=0)
	Performs a pileup on the specified file. More...

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. More...

void	flushPileup ()
	Done processing, flush every position that is currently being stored in the pileup.

Additional Inherited Members
Protected Member Functions inherited from Pileup< TestPileupElement >
virtual void	flushPileup (int refID, int refPosition)

void	flushPileup (int refPosition)

void	addAlignmentPosition (int refPosition, SamRecord &record)

int	pileupPosition (int refPosition)

virtual void	resetElement (TestPileupElement &element, int position)

virtual void	addElement (TestPileupElement &element, SamRecord &record)

virtual void	analyzeElement (TestPileupElement &element)

virtual void	analyzeHead ()

Protected Attributes inherited from Pileup< TestPileupElement >
defaultPileup< TestPileupElement >	myAnalyzeFuncPtr

std::vector< TestPileupElement >	myElements

int	pileupStart

int	pileupHead

int	pileupTail

int	pileupWindow

int	myCurrentRefID

GenomeSequence *	myRefPtr

Detailed Description

Definition at line 32 of file TestPileup.h.

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

Public Member Functions