//
// 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 "stdafx.h"

//typedef multimap<unsigned int,string> multimap_type;
// map<reference<line_number, sam_data> > 
typedef map<string, map<unsigned int,string> > map_type;

class FastaReader;

class SamReader
{
public:
	SamReader(string fileName);
	~SamReader(void);

	bool ReadSamFile();
	bool ProcessReferenceData(FastaReader& fr);
	bool CreateModifiedSamFile();
	void Close();

	unsigned int num_reads;

private:
	string fileName_;
	string out_file_name_;
	string out_file_name_not_found_;
	string out_file_name_excluded_;

	// maps RNAME -> map <line_number, data> 
	map_type ref_map_;

	ifstream fs_;
	ifstream ifs_;
	ofstream ofs_;
	ofstream ofs_not_found_;
	ofstream ofs_excluded_;

	unsigned int total_reads_processed_;
	
	unsigned int GetInMemoryData(const char* pchar, string& rname, string& data);
	string ModifySamLine(string& line_string, char* line_buffer, const unsigned int line_number);
};
#endif