/**
 * Project     : CASAVA
 * Module      : $RCSfile: ClusterMerger.hh,v $
 * @author     : Tony Cox
 * Copyright   : Copyright (c) Illumina 2010. 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).
 *
 */
/*****************************************************************************/

#ifndef CLUSTER_MERGER_HH
#define CLUSTER_MERGER_HH

/*****************************************************************************/

#include "applications/Application.hh"

/*****************************************************************************/

namespace ca { 
namespace applications {

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/**
 * @class ClusterMerger
 *
 * @brief Wrapper around ClusterMerger functionality.
 */

class ClusterMerger : public Application {
public:

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

	virtual ~ClusterMerger();

	/**
	 * Step within the indel finder workflow that merges compatible clusters 
     * of different types of anomalous reads.
	 *
	 * @return status
	 */
	int run();
};

/*****************************************************************************/

} // end namespace applications
} // end namespace ca

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#endif // ! CLUSTER_MERGER_HH

/*****************************************************************************/