//
// 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
///

#include "SamMD2Export/stdafx.h"
#include "SamMD2Export/sam2Export.h"
#include "SamMD2Export/utils.h"

const string ApplicationName = "samMD2Export";
const string ApplicationVersion="version 0.8.1";
const string ParameterHelp = "--help";
const string ParameterVersion = "--version";
const string ParameterPrefix = "--reference_prefix=prefix";
const string ParameterSuffix = "--reference_suffix=suffix";
const string ReferencePrefix = "--reference_prefix";
const string ReferenceSuffix = "--reference_suffix";

//////////////////////////////////////////////////////////////////////
void PrintVersion()
{
	cout << ApplicationName << " " << ApplicationVersion << endl;
}

//////////////////////////////////////////////////////////////////////
void PrintUsage()
{
	cout << endl;
	cout << ApplicationName << " converts SAM files to export files. Each SAM record must contain the export" << endl;
	cout << "match descriptor in the optional 'XD' field to be converted to an export record." << endl;
	cout << endl;
	cout << "Usage:  " << ApplicationName << " ["<< ParameterHelp <<"] | [" << ParameterVersion << "] | [" << ParameterPrefix << "] [" << ParameterSuffix << "] path_to_sam_file" << endl;
	cout << endl;
	cout << "Options:" << endl;
	cout << "    " << ParameterHelp   << "                        Show help info."<<endl;
	cout << "    " << ParameterVersion<< "                     Show version number."<<endl;
	cout << "    " << ParameterPrefix << "   Add the prefix characters to a chromosome match." << endl;
	cout << "    " << ParameterSuffix << "   Add the suffix characters to a chromosome match." << endl;
	cout << endl;
}

//////////////////////////////////////////////////////////////////////
string GetPrefixSuffixFromParameter(const string& param, const string& paramHeader)
{
	if (param.size()== 0) return "";

	if (param.size() <= paramHeader.size()) return "";

	if(0==param.compare(0, paramHeader.size(), paramHeader))
	{
		std::size_t index1 = param.find_first_of("=");

		if (index1==string::npos) return "";
		
		string str = param.substr(index1+1);
		return str;
	}
	else return "";
}

//////////////////////////////////////////////////////////////////////
int main(int argc, char* argv[])
{
	string param1, param2, param3, sam_file_name;

	switch(argc)
	{
	case 2: // help or version or file name
		{
			string param(argv[1]);
			if (param=="--help")
			{
				PrintUsage();
				return 0;
			}
			else if (param=="--version")
			{
				PrintVersion();
				return 0;
			}
			else 
			{
				sam_file_name.assign(argv[1]);
			}
			break;
		}
	case 3: // prefix or suffix and file name
		param1.assign(argv[1]);
		sam_file_name.assign(argv[2]);
		break;
	case 4: // prefix and suffix and file name
		param1.assign(argv[1]);
		param2.assign(argv[2]);
		sam_file_name.assign(argv[3]);
		break;
	default:
		PrintUsage();
		return 0;
	}

	string prefix, suffix;
	string prefix1, suffix1;
	string prefix2, suffix2;
	bool parameter_error=false;

	if(param1.size()!=0)
	{
		prefix1 = GetPrefixSuffixFromParameter(param1, ReferencePrefix);
		suffix1 = GetPrefixSuffixFromParameter(param1, ReferenceSuffix);
		if(prefix1.size()==0 && suffix1.size()==0)
		{
			parameter_error=true;
			cout << "Error!!! " << "Invalid parameter: "+param1 << endl;
		}
	}

	if(param2.size()!=0)
	{
		prefix2 = GetPrefixSuffixFromParameter(param2, ReferencePrefix);
		suffix2 = GetPrefixSuffixFromParameter(param2, ReferenceSuffix);
		if(prefix2.size()==0 && suffix2.size()==0)
		{
			parameter_error=true;
			cout << "Error!!! " << "Invalid parameter: "+param2 << endl;
		}
	}

	if (parameter_error) return 0;

	if (prefix1.size()>0) prefix=prefix1;
	if (prefix2.size()>0) prefix=prefix2;
	if (suffix1.size()>0) suffix=suffix1;
	if (suffix2.size()>0) suffix=suffix2;

	PrintVersion();

	Sam2Export sam2Export(sam_file_name, prefix, suffix);

	if(sam2Export.CreateExportFile())
	{
		cout << endl << "Success." << endl;
	}
//	else
//	{
//		cout << endl << "Failed." << endl;
//	}

	return 0;
}