#include "applications/CheckOrder.hh"

/**
 * Project     : CASAVA
 * Module      : $RCSfile: CheckOrder.cpp,v $
 * @author     : Lukasz Szajkowski
 * Copyright   : Copyright (c) Illumina 2008, 2009. All rights reserved.
 *
 ** 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).
 *
 */
#include <iostream>

#include <stdlib.h>
#include <stdio.h>

#include "common/Alignment.hh"

namespace ca {
namespace applications {

using namespace std;
using namespace casava::common;

int CheckOrder::run() {

	cout << "[" << "Start" << "]\n";
	const casava::common::Compression &noCompression =
			casava::common::CompressionFactory::none();

	casava::common::AlignmentReader alignmentReader(_options.inputReadsFilePath(),
			noCompression);

	if (alignmentReader && alignmentReader.good()) {
	} else {
		cout << "ERROR: failed to open. " << _options.inputReadsFilePath()
				<< "\n";
		exit(1);
	}

	casava::common::Alignment newAlignment;
	int lastPosition = -1;
	int index = 0;
	while (alignmentReader >> newAlignment) {
		if (!alignmentReader.good()){
			break;
		}

		if (newAlignment.getMatch().getPosition() < lastPosition) {
			cout << "ERROR: in file  " << _options.inputReadsFilePath() << ":"
					<< index <<" position " <<newAlignment.getMatch().getPosition() << "before "<< lastPosition <<"\n";
		} else {
			//cout << "[" << index << " " << lastPosition << "]\n";
			lastPosition = newAlignment.getMatch().getPosition();
		}
		index++;
	}
	return 0;
}

}
} // end namespace casava{ namespace { applications