PileupElementBaseQual Class Reference

This class inherits from the base class and stores base and qualities. More...

#include <PileupElementBaseQual.h>

Inheritance diagram for PileupElementBaseQual:

Collaboration diagram for PileupElementBaseQual:

Public Member Functions
	PileupElementBaseQual (const PileupElementBaseQual &q)
virtual void	addEntry (SamRecord &record)
	Add an entry to this pileup element.
virtual void	analyze ()
	Perform the analysis associated with this class.
virtual void	reset (int32_t refPosition)
	Resets the entry, setting the new position associated with this element.
Public Member Functions inherited from PileupElement
	PileupElement ()
	Pileup element constructor.
	PileupElement (const PileupElement &q)
	Constructor that resets the pileup element, does not copy, just resets.
virtual	~PileupElement ()
	Pileup element destructor.
const char *	getChromosome () const
	Get the chromosome name stored in this element.
int32_t	getRefPosition () const
	Get the reference position stored in this element.
char	getRefBase ()
	Returns the reference base for this pileup element.

Additional Inherited Members
Static Public Member Functions inherited from PileupElement
static void	setReference (GenomeSequence *reference)
	Set the reference to use for all pilepElements.
Static Public Attributes inherited from PileupElement
static const int32_t	UNSET_POSITION = -1
Static Protected Member Functions inherited from PileupElement
static GenomeSequence *	getReference ()
	Get a pointer to the reference.

Detailed Description

This class inherits from the base class and stores base and qualities.

Definition at line 25 of file PileupElementBaseQual.h.

Constructor & Destructor Documentation

PileupElementBaseQual() [1/2]

PileupElementBaseQual::PileupElementBaseQual

(

)

Definition at line 22 of file PileupElementBaseQual.cpp.

    : PileupElement(),
      myBases(NULL),
      myQualities(NULL),
      myAllocatedSize(0),
      myIndex(-1),
      myAddDelAsBase(false)
{
    myAllocatedSize = 1024;
    myBases = (char*)malloc(myAllocatedSize + 1);
    myQualities = (char*)malloc(myAllocatedSize + 1);
    if((myBases == NULL ) || (myQualities == NULL))
    {
        // TODO, check for malloc failures.
        std::cerr << "Failed Memory Allocation\n";
    }
}

PileupElementBaseQual() [2/2]

PileupElementBaseQual::PileupElementBaseQual

(

const PileupElementBaseQual &

q

)

Definition at line 41 of file PileupElementBaseQual.cpp.

    : PileupElement(),
      myBases(NULL),
      myQualities(NULL),
      myAllocatedSize(0),
      myIndex(-1)
{
    myAllocatedSize = 1024;
    myBases = (char*)malloc(myAllocatedSize + 1);
    myQualities = (char*)malloc(myAllocatedSize + 1);
    myAddDelAsBase = q.myAddDelAsBase;
    if((myBases == NULL ) || (myQualities == NULL))
    {
        // TODO, check for malloc failures.
        std::cerr << "Failed Memory Allocation\n";
    }
}

~PileupElementBaseQual()

PileupElementBaseQual::~PileupElementBaseQual ( )

virtual

Definition at line 60 of file PileupElementBaseQual.cpp.

{
    if(myBases != NULL)
    {
        free(myBases);
        myBases = NULL;
    }
    if(myQualities != NULL)
    {
        free(myQualities);
        myQualities = NULL;
    }
}

Member Function Documentation

addEntry()

void PileupElementBaseQual::addEntry ( SamRecord & record )

virtual

Add an entry to this pileup element.

Reimplemented from PileupElement.

Definition at line 76 of file PileupElementBaseQual.cpp.

{
    // Call the base class:
    PileupElement::addEntry(record);
 
    // Increment the index
    ++myIndex;
    
    // if the index has gone beyond the allocated space, double the size.
    if(myIndex >= myAllocatedSize)
    {
        char* tempBuffer = (char*)realloc(myBases, myAllocatedSize * 2);
        if(tempBuffer == NULL)
        {
            std::cerr << "Memory Allocation Failure\n";
            // TODO
            return;
        }
        myBases = tempBuffer;
        tempBuffer = (char*)realloc(myQualities, myAllocatedSize * 2);
        if(tempBuffer == NULL)
        {
            std::cerr << "Memory Allocation Failure\n";
            // TODO
            return;
        }
        myQualities = tempBuffer;       
        myAllocatedSize = myAllocatedSize * 2;
    }
 
    Cigar* cigar = record.getCigarInfo();
    
    if(cigar == NULL)
    {
        throw std::runtime_error("Failed to retrieve cigar info from the record.");
    }
 
 
    int32_t readIndex = 
        cigar->getQueryIndex(getRefPosition(), record.get0BasedPosition());
 
    // If the readPosition is N/A, this is a deletion.
    if(readIndex != CigarRoller::INDEX_NA)
    {
        char base = record.getSequence(readIndex);
        char qual = record.getQuality(readIndex);
        if(qual == UNSET_QUAL)
        {
            qual = ' ';
        }
        myBases[myIndex] = base;
        myQualities[myIndex] = qual;
    }
    else if(myAddDelAsBase)
    {
        // This version adds deletions as bases.
        myBases[myIndex] = '-';
        myQualities[myIndex] = '0';
    }
    else
    {
        // Do not add a deletion.
        // Did not add any entries, so decrement the index counter since the
        // index was not used.
        --myIndex;
    }
}

References PileupElement::addEntry(), SamRecord::get0BasedPosition(), SamRecord::getCigarInfo(), SamRecord::getQuality(), Cigar::getQueryIndex(), PileupElement::getRefPosition(), SamRecord::getSequence(), and Cigar::INDEX_NA.

analyze()

void PileupElementBaseQual::analyze ( )

virtual

Perform the analysis associated with this class.

Reimplemented from PileupElement.

Reimplemented in TestPileupElement.

Definition at line 144 of file PileupElementBaseQual.cpp.

{
    if(getRefPosition() != UNSET_POSITION)
    {
        myBases[myIndex+1] = '\0';
        myQualities[myIndex+1] = '\0';
        std::cout << getChromosome() << "\t" << getRefPosition() << "\tN\t" << myIndex+1 << "\t";
        std::cout << myBases << "\t";
        std::cout << myQualities;
        std::cout << "\n";
    }
}

References PileupElement::getChromosome(), and PileupElement::getRefPosition().

reset()

void PileupElementBaseQual::reset ( int32_t refPosition )

virtual

Resets the entry, setting the new position associated with this element.

Reimplemented from PileupElement.

Definition at line 157 of file PileupElementBaseQual.cpp.

{
    // Call the base class.
    PileupElement::reset(refPosition);
 
    myIndex = -1;
}

References PileupElement::reset().

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

• bam/PileupElementBaseQual.h
• bam/PileupElementBaseQual.cpp