//
// 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 "SamMD/stdafx.h"
#include "SamMD/fastaReader.h"
#include "SamMD/samReader.h"
#include "SamMD/samMDlib.h"
#include "SamMD/log.h"
#include "SamMD/utils.h"

const string Version="0.8.1";

const string ApplicationName="samMD";
const string description = " calculates the export match descriptor and adds this to the optional SAM field 'XD'";
const	string parameters = " [ --help ] | [ --version ] | <path to sam file> <path to text file with list of fasta files>";

//////////////////////////////////////////////////////////////////////
int main(int argc, char* argv[])
{
	if (argc==2)
	{
		string arg2(argv[1]);

		if (arg2=="--version") 
		{
			Log::Info( ApplicationName+" Version " + Version);
			return 0;
		}

		if (arg2=="--help") 
		{
			Log::Info("");
			Log::Info(ApplicationName + description);
			Log::Info("");
			Log::Info("Usage: " + ApplicationName + parameters);
			Log::Info("");
			return 0;
		}
	}

	if(argc!=3)
	{
			Log::Info("");
			Log::Info(ApplicationName + description);
			Log::Info("");
			Log::Info("Usage: " + ApplicationName + parameters);
			Log::Info("");
		return 0;
	}

	Log::Initialize();

	string samFileName(argv[1]);

	string fastaFileNames(argv[2]);

	SamMD SamMD(samFileName, fastaFileNames);

	if(SamMD.CreateMatchDescriptors())
	{
		Log::Info("");
		Log::Info("Success.");
	}
	else
	{
		Log::Info("");
		Log::Info("Failed.");
	}

	return 0;
}