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/*
* Copyright (C) 2010 Regents of the University of Michigan
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
#include <stdexcept>
#include "PileupElementBaseQual.h"
PileupElementBaseQual::PileupElementBaseQual()
: 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";
}
}
// NOTE that this method does not actually copy, it just resets.
PileupElementBaseQual::PileupElementBaseQual(const PileupElementBaseQual& q)
: 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()
{
if(myBases != NULL)
{
free(myBases);
myBases = NULL;
}
if(myQualities != NULL)
{
free(myQualities);
myQualities = NULL;
}
}
// Add an entry to this pileup element.
void PileupElementBaseQual::addEntry(SamRecord& record)
{
// 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;
}
}
void PileupElementBaseQual::analyze()
{
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";
}
}
void PileupElementBaseQual::reset(int refPosition)
{
// Call the base class.
PileupElement::reset(refPosition);
myIndex = -1;
}
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