TestPileup Class Reference

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

Additional Inherited Members
Protected Member Functions inherited from Pileup< TestPileupElement >
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.

Member Function Documentation

testPileupPosition()

void TestPileup::testPileupPosition

(

)

Definition at line 32 of file TestPileup.cpp.

{
    assert(pileupPosition(14000) == 0);
    assert(pileupHead == 14000);
    assert(pileupStart == 14000);
    assert(pileupTail == 14000);
 
    bool caught = false;
    try
    {
        pileupPosition(13999);
    }
    catch(std::exception& e)
    {
        caught = true;
        assert(strcmp(e.what(), "Overflow on the pileup buffer: specifiedPosition = 13999, pileup buffer start position: 14000, pileup buffer end position: 15024") == 0);
    }
    assert(caught);
 
    caught = false;
    try
    {
        pileupPosition(15025);
    }
    catch(std::exception& e)
    {
        caught = true;
        assert(strcmp(e.what(), "Overflow on the pileup buffer: specifiedPosition = 15025, pileup buffer start position: 14000, pileup buffer end position: 15024") == 0);
    }
    assert(caught);
}

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

• bam/test/TestPileup.h
• bam/test/TestPileup.cpp