#ifndef ALIGNCANDINDELREADS_HH_
#define ALIGNCANDINDELREADS_HH_

/**
 * Project     : CASAVA
 * Module      : $RCSfile: AlignCandIndelReads.hh,v $
 * @author     : Tony Cox
 * 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).
 *
 */

// CASAVA Includes
#include "applications/Application.hh"
#include "applications/CasavaOptions.hh"

// c++ STL include
#include <iostream>
#include <sstream>
#include <fstream>
#include <cstdio>
#include <cassert>
#include <ctime>
#include <cstdlib>
#include <vector>
#include <cmath>
#include <string>

// remove the comment to get verbose output
//#define DEBUG_IDF

namespace ca { namespace  applications {
/**
 * @class AlignCandIndelReads
 *
 * @brief Wrapper around AlignCandIndelReads functionality.
 *
 *
 */

class AlignCandIndelReads : public ca::applications::Application {
public:

	AlignCandIndelReads(CasavaOptions &options) : Application(options){}

	virtual ~AlignCandIndelReads();

	/**
	 * Executes the align candidate indel reads of the indel finder
	 *  workflow and identifies all reads as shadow or gapped
	 *
	 * @return status
	 */
	int run();

};

}} // end namespace casava{ namespace { applications

/**


 */

#endif /*ALIGNCANDINDELREADS_HH_*/