//
// 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 __FASTA_READER_H
#define __FASTA_READER_H

#include "stdafx.h"

class FastaReader
{
public:
	FastaReader(void);
	FastaReader(string fileName);
	~FastaReader(void);
	bool Open();
	void Close();
	bool ReadNextReference();
//	string GetNextFastaReference();
	string GetMatchDescriptorInfo(const string& sam_data);
//	string GetMatchDescriptor(const string& read, const string& reference, long position, const string& cigar);
	const string& GetRefHeader() { return ref_header_; }
private:
	string fileName_;
	ifstream fs_;
	string ref_header_;
	string ref_header_next_;
	string ref_sequence_;
//	string line_;
//	map<string, string> sequences_;
//	void ReadSequences();
//	void ReadSequences(ifstream&);
	bool inline IsHeaderLine(string& line);
	string inline GetHeaderId(string& header);
//	string GetSequence(const string& reference);
//	string GetCigarReferenceSequence(long position, const string& cigar);
};

#endif