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PairedAligner.h
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PairedAligner.h
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/*++
Module Name:
SingleAligner.cpp
Abstract:
Functions 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"
struct PairedAlignerStats;
class PairedAlignerContext : public AlignerContext
{
public:
PairedAlignerContext(AlignerExtension* i_extension = NULL);
protected:
// AlignerContext
virtual AlignerOptions* parseOptions(int argc, const char **argv, const char *version);
virtual void initialize();
virtual AlignerStats* newStats();
virtual void runTask();
virtual void runIterationThread();
// for subclasses
virtual void writePair(Read* read0, Read* read1, PairedAlignmentResult* result);
virtual void updateStats(PairedAlignerStats* stats, Read* read0, Read* read1, PairedAlignmentResult* result);
protected:
int minSpacing;
int maxSpacing;
const char *fastqFile1;
bool ignoreMismatchedIDs;
};
struct PairedAlignerOptions : public AlignerOptions
{
PairedAlignerOptions(const char* i_commandLine);
virtual void usageMessage();
virtual bool parse(const char** argv, int argc, int& n);
int minSpacing;
int maxSpacing;
const char* fastqFile1;
};