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#pragma once
#include "stdafx.h"
// #include "ProgramOptions.h"
class CReadsMappingFlags
{
public:
CReadsMappingFlags(void);
~CReadsMappingFlags(void);
protected:
// int ptr_initialization(CProgramOptions *_param);
int set_Default_Opt(void);
//unsigned int uiSubThreshold;
bool bSaveTable;
bool bPrintUnMappedReads;
bool bPrintAlignment;
bool bPrintGeneName;
// search not only the best in terms of mismatches, but all within the criteria.
bool bSearchAllAlignment; // Currently set to be false by default
char cOutputFormat;
};
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