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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_H__
#define __PILEUP_ELEMENT_H__
#include "SamRecord.h"
/// This is a base class pileup component, representing the information
/// for one reference position. Child classes will be defined to detail more
/// information that needs to be saved and how it should be analyzed.
class PileupElement
{
public:
static const int32_t UNSET_POSITION = -1;
/// Pileup element constructor.
PileupElement();
/// Constructor that resets the pileup element, does not copy, just resets.
PileupElement(const PileupElement& q);
/// Pileup element destructor.
virtual ~PileupElement();
/// Add an entry to this pileup element.
virtual void addEntry(SamRecord& record);
/// Perform the analysis associated with this class.
virtual void analyze();
/// Resets the entry, setting the new position associated with this element.
virtual void reset(int32_t refPosition);
/// Get the chromosome name stored in this element.
const char* getChromosome() const { return(myChromosome.c_str()); }
/// Get the reference position stored in this element.
int32_t getRefPosition() const { return(myRefPosition); }
/// Returns the reference base for this pileup element.
/// Only works if a reference has been set, otherwise, 'N' is returned.
char getRefBase();
/// Set the reference to use for all pilepElements.
static void setReference(GenomeSequence* reference);
protected:
/// Get a pointer to the reference.
static GenomeSequence* getReference() { return(myRefPtr); }
private:
int32_t myRefPosition;
std::string myChromosome;
static GenomeSequence* myRefPtr;
};
#endif
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