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/*++
Module Name:
SingleAligner.h
Abstract:
Headers for running the single end aligner sub-program.
Authors:
Matei Zaharia, February, 2012
Environment:
User mode service.
Revision History:
Adapted from cSNAP, which was in turn adapted from the scala prototype
--*/
#pragma once
#include "stdafx.h"
#include "AlignerContext.h"
#include "AlignerStats.h"
#include "ReadSupplierQueue.h"
#include "AlignmentResult.h"
class SingleAlignerContext : public AlignerContext
{
public:
SingleAlignerContext(AlignerExtension* i_extension = NULL);
protected:
// AlignerContext overrides
virtual AlignerStats* newStats();
virtual void runTask();
virtual void runIterationThread();
virtual void typeSpecificBeginIteration();
virtual void typeSpecificNextIteration();
// for subclasses
virtual void updateStats(AlignerStats* stats, Read* read, AlignmentResult result, int score, int mapq);
//RangeSplittingReadSupplierGenerator *readSupplierGenerator;
ReadSupplierGenerator *readSupplierGenerator;
friend class AlignerContext2;
bool isPaired() {return false;}
};
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