/**
 * Project     : CASAVA
 * Module      : $RCSfile: ClusterMerger.cpp,v $
 * @author     : Richard Shaw
 * 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).
 *
 */
/*****************************************************************************/

#include "applications/ClusterMerger.hh"

#include "applications/CasavaOptions.hh"
#include "common/Exceptions.hh"
#include "common/PairStats.hh"

#include "variance/ClusterMergerImpl.hh"

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

namespace ca {
namespace applications {

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

using namespace casava::common;
using namespace ca::variance_detection;

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

ClusterMerger::~ClusterMerger() {}

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

int ClusterMerger::run()
{
    try {
        // Load PairStats.
        const boost::filesystem::path
            rawClustersFilePath(_options.rawClustersFilePath());
        const boost::filesystem::path
          projDirPath(rawClustersFilePath.parent_path().parent_path().
                      parent_path().parent_path());
        PairStats pairStats(projDirPath);
        pairStats.setNumSds(_options.numLowInsertSizeSds(),
                            _options.numHighInsertSizeSds());

        const unsigned int maxLinksPerCluster(10);

        ClusterMergerImpl 
            clusterMerger(_options.rawClustersFilePath(),
                          _options.outputFilePath(),
                          _options.doAdjMerge(),
                          _options.clusterMaxAdjMergeInterBreakPtDist(),
                          maxLinksPerCluster);

        clusterMerger.importClusters(pairStats);
        clusterMerger.mergeClusters();
        clusterMerger.generateOutputFile();
    } catch(const casava::common::CasavaException& e) {
        cerr << "ERROR:  EXCEPTION: " << e.getContext() << ": " << e.getMessage() << std::endl;
        throw;
    }

    return 0;
}

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

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

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