/**
 * Project     : CASAVA
 * Module      : $RCSfile: AnomReadGroup.hh,v $
 * @author     : Tony Cox (rearranged by 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).
 *
 */

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#ifndef ANOM_READ_GROUP_HH
#define ANOM_READ_GROUP_HH

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

#include "variance/SingletonEvent.hh"
#include "variance/AnomalousRead.hh"
#include "variance/StatWidget.hh"

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

namespace ca {
namespace variance_detection {

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struct AnomReadGroup : public std::set<Singleton*>
{
    AnomReadGroup();
    AnomReadGroup(AnomalousRead::Type anomReadType);
    void print(const unsigned int minGroupSize,
               unsigned int& numGroups,
               ostream& outstr);
    AnomalousRead::Type anomReadType_;
    StatWidget positionStats_;
    StatWidget minStats_;
    StatWidget maxStats_;
  }; // ~struct AnomReadGroup: public set<int>

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

class SortAnomReadGroup
{
public:
    // TC 27.8.9 - modify to ensure forward strand groups get
    // put before reverse strand groups if the position is the same
    bool operator()(const AnomReadGroup& p1, const AnomReadGroup& p2) {
        return
            ( (p1.positionStats_.getMean()<p2.positionStats_.getMean())
              ||( (static_cast<int>(p1.positionStats_.getMean()
                                    -p2.positionStats_.getMean())==0)
                  && (p1.size()!=0)
                  && (p2.size()!=0)
                  && ((*p1.begin())->alignment_.getMatch().getStrand()
                      == Match::Forward)
                  && ((*p2.begin())->alignment_.getMatch().getStrand()
                      == Match::Reverse)));
    } // ~operator()

}; // ~ class SortAnomReadGroup

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

} // namespace variance_detection
} // namespace ca

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#endif // ! ANOM_READ_GROUP_HH

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