/**
 ** Copyright (c) 2007-2009 Illumina, Inc.
 **
 ** 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).
 **
 ** This file is part of the Consensus Assessment of Sequence And VAriation
 ** (CASAVA) software package.
 **
 ** \file StatsFileRecord.hh
 **
 ** \brief Defines RTA stats file io exchange helpers.
 **
 ** \author Roman Petrovski
 **/

#ifndef CASAVA_IO_STATS_FILE_RECORD_HH
#define CASAVA_IO_STATS_FILE_RECORD_HH

#include <string>
#include <iostream>
#include "common/FastIo.hh"

namespace casava
{
namespace io
{

namespace cc = casava::common;

struct StatsFileRecord
{
    StatsFileRecord(): cycle_(0), clusterIntensity_(0),
        allA_(0.0), allC_(0.0), allG_(0.0), allT_(0.0),
        callA_(0.0), callC_(0.0), callG_(0.0), callT_(0.0),
        numA_(0), numC_(0), numG_(0), numT_(0), numX_(0),
        numAllA_(0), numAllC_(0), numAllG_(0), numAllT_(0){;}

    int cycle_;                     //cycle number zero-based.
    double clusterIntensity_;       // average cycle intensity
    double allA_;
    double allC_;
    double allG_;
    double allT_;
    double callA_;
    double callC_;
    double callG_;
    double callT_;
    int numA_;                      //Number of A bases in the tile cycle.
    int numC_;                      //Number of C bases in the tile cycle.
    int numG_;                      //Number of G bases in the tile cycle.
    int numT_;                      //Number of T bases in the tile cycle.
    int numX_;                      //Number of unknown bases in the tile cycle.
    int numAllA_;
    int numAllC_;
    int numAllG_;
    int numAllT_;

};

inline std::istream &operator>>(std::istream &is, StatsFileRecord &sfr)
{
    !is || (sfr.cycle_ = cc::readInteger<4>(is));
    !is || (sfr.clusterIntensity_ = cc::readDouble(is));
    !is || (sfr.allA_ = cc::readDouble(is));
    !is || (sfr.allC_ = cc::readDouble(is));
    !is || (sfr.allG_ = cc::readDouble(is));
    !is || (sfr.allT_ = cc::readDouble(is));
    !is || (sfr.callA_ = cc::readDouble(is));
    !is || (sfr.callC_ = cc::readDouble(is));
    !is || (sfr.callG_ = cc::readDouble(is));
    !is || (sfr.callT_ = cc::readDouble(is));
    !is || (sfr.numA_ = cc::readInteger<4>(is));
    !is || (sfr.numC_ = cc::readInteger<4>(is));
    !is || (sfr.numG_ = cc::readInteger<4>(is));
    !is || (sfr.numT_ = cc::readInteger<4>(is));
    !is || (sfr.numX_ = cc::readInteger<4>(is));
    !is || (sfr.numAllA_ = cc::readInteger<4>(is));
    !is || (sfr.numAllC_ = cc::readInteger<4>(is));
    !is || (sfr.numAllG_ = cc::readInteger<4>(is));
    !is || (sfr.numAllT_ = cc::readInteger<4>(is));
    return is;
}

inline std::ostream &operator<<(std::ostream &os, const StatsFileRecord &sfr)
{
    !os || cc::writeInteger<4>(os, sfr.cycle_);
    !os || cc::writeDouble(os, sfr.clusterIntensity_);
    !os || cc::writeDouble(os, sfr.allA_);
    !os || cc::writeDouble(os, sfr.allC_);
    !os || cc::writeDouble(os, sfr.allG_);
    !os || cc::writeDouble(os, sfr.allT_);
    !os || cc::writeDouble(os, sfr.callA_);
    !os || cc::writeDouble(os, sfr.callC_);
    !os || cc::writeDouble(os, sfr.callG_);
    !os || cc::writeDouble(os, sfr.callT_);
    !os || cc::writeInteger<4>(os, sfr.numA_);
    !os || cc::writeInteger<4>(os, sfr.numC_);
    !os || cc::writeInteger<4>(os, sfr.numG_);
    !os || cc::writeInteger<4>(os, sfr.numT_);
    !os || cc::writeInteger<4>(os, sfr.numX_);
    !os || cc::writeInteger<4>(os, sfr.numAllA_);
    !os || cc::writeInteger<4>(os, sfr.numAllC_);
    !os || cc::writeInteger<4>(os, sfr.numAllG_);
    !os || cc::writeInteger<4>(os, sfr.numAllT_);
    return os;
}

} // namespace io
} // namespace casava

#endif // CASAVA_IO_STATS_FILE_RECORD_HH