/**
 * Project     : CASAVA
 * Module      : $RCSfile: ClusterFinder.cpp,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/ClusterFinder.hh"
#include "applications/CasavaOptions.hh"
#include "variance/SampleStats.hh"
#include "variance/SingletonEvent.hh"
#include "variance/AnomalousReadMgr.hh"
#include "variance/ClusterFinderImpl.hh"
#include "common/Alignment.hh"
#include "common/Exceptions.hh"
#include "common/PairStats.hh"



namespace ca {
namespace applications {

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



ClusterFinder::~ClusterFinder() {}

int ClusterFinder::run()
{
  Alignment alignment;
  string line, s, sampleName;

  //  static const char preamble[]="# sample=";
  map<string, OffsetInfo > sampleInfo;

  AnomalousReadMgr anomalousReadMgr(_options.clusterMaxInterBreakPtDist());

  ClusterFinderImpl clusterFinder
    ( _options.maxDistance(),
      _options.minGroupSize(),
      _options.spReadThreshold(),
      _options.inputReadsFilePath(),
      _options.summaryFilePath(),
      _options.outputFilePath(),
      _options.isQphred);

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

      clusterFinder.importSampleStats( sampleInfo );

      clusterFinder.importReads( anomalousReadMgr, sampleInfo, pairStats );

      if (anomalousReadMgr.totalNumReadsAdded() == 0)
      {
          cerr << "Warning: no reads obtained from file "
               <<  _options.inputReadsFilePath() << endl;
      } // ~if
  } catch(const casava::common::CasavaException& e) {
      cerr << "ERROR:  EXCEPTION: " << e.getContext() << ": " << e.getMessage() << std::endl;
      throw;
  }

  clusterFinder( anomalousReadMgr );


  return 0;
} // ~int IndelFinder::run()




}
} // end namespace casava{ namespace { applications