//
// Copyright 2009 Illumina, Inc.
//
// This software is covered by the "Illumina Genome Analyzer Software
// License Agreement" and the "Illumina Source Code License Agreement",
// and certain third party copyright/licenses, and any user of this
// source file is bound by the terms therein (see accompanying files
// Illumina_Genome_Analyzer_Software_License_Agreement.pdf and
// Illumina_Source_Code_License_Agreement.pdf and third party
// copyright/license notices).
//
//

/// \file

/// \author Ivan Mikoulitch
///

#ifndef __SAMMDLIB_H
#define __SAMMDLIB_H

#include "stdafx.h"

class SamMD
{
public:
	SamMD(const string& samFile, const string& fastaFiles);
	~SamMD(void);
	bool CreateMatchDescriptors();

private:
	string samFile_;
	string fastaFiles_;
	vector<string> ReadFastFileList();
	string CreateMatchDescriptor(string& ref_seq, unsigned int ref_pos, string& sam_data);
};
#endif