//
// 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 __SAMREADER_H
#define __SAMREADER_H

#include "SamMD2Export/stdafx.h"
#include "export.h"

class SamReader
{
public:
	SamReader(const string& fileName);
	~SamReader(void);
	bool Open();
	void Close();
	bool GetNextSamLine();
	bool WriteExportLine(const Export& ex);
	void WriteInfo(const string& str);
	void WriteWarning(const string& str);
	void WriteError(const string& str);
	bool WriteWarningErrorSummary();
	void WriteFailedRead(const string& message, const string& read);
	
	char* BUFFER;

private:
	string sam_file_name_;
	string export_file_name_;
	string export_log_file_name_;
	ifstream sam_ifs_;
	ofstream export_ofs_;
	ofstream export_log_;

	static const int BUFFER_SIZE = 1024;
	
	bool has_data_;

	static const int MAX_EXPORT_LINE_COUNT=100000;
	int export_line_count;
	string export_buffer;
	int num_invalid_reads_;

	void ReadHeader();
	void Flush();
};
#endif