#ifndef INDELFINDER_HH_
#define INDELFINDER_HH_

/**
 * Project     : CASAVA
 * Module      : $RCSfile: IndelFinder.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).
 *
 */

#include "applications/Application.hh"

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

namespace ca { namespace  applications {
/**
 * @class IndelFinder
 *
 * @brief Wrapper around IndelFinder functionality.
 *
 * TODO: Improve this design. Separation into IndelFinder and IndelFinderImpl is probably not necessary.
 *
 */

class IndelFinder : public Application {
public:

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

	virtual ~IndelFinder() {}

	/**
	 * Executes the first step of the indel finder workflow and identifies clusters of singleton reads.
	 *
	 * @return status
	 */
	int run();

};



}} // end namespace casava{ namespace { applications

#endif /*INDELFINDER_HH_*/