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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/>.
*/
#ifndef __PILEUP_ELEMENT_BASE_QUAL_H__
#define __PILEUP_ELEMENT_BASE_QUAL_H__
#include <stdint.h>
#include "PileupElement.h"
/// This class inherits from the base class and stores base and qualities.
class PileupElementBaseQual : public PileupElement
{
public:
PileupElementBaseQual();
// NOTE that this method does not actually copy, it just resets.
PileupElementBaseQual(const PileupElementBaseQual& q);
virtual ~PileupElementBaseQual();
// Add an entry to this pileup element.
virtual void addEntry(SamRecord& record);
// Perform the alalysis associated with this class. In this case, it is
// a print of the base & quality information associated with this position.
virtual void analyze();
// Resets the entry, setting the new position associated with this element.
virtual void reset(int32_t refPosition);
private:
static const char UNSET_QUAL = 0xFF;
char* myBases;
char* myQualities;
int myAllocatedSize;
int myIndex;
bool myAddDelAsBase;
};
#endif
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