/**
 ** Copyright (c) 2007-2009 Illumina, Inc.
 **
 ** This source file is covered by the "Illumina Public Source License"
 ** agreement and bound by the terms therein.
 **
 ** This file is part of the Off Line Base-caller (OLB)
 **
 ** \file StatsToSignalMeansConverter.hh
 **
 ** Top level application to convert a set of stats files - and their associated
 ** filter - for a single tile into the corresponding SignalMeans files
 **
 ** \author Come Raczy
 **/

#ifndef CASAVA_STATS_TO_SIGNAL_MEANS_CONVERTER_HH
#define CASAVA_STATS_TO_SIGNAL_MEANS_CONVERTER_HH

#include <string>
#include <boost/filesystem.hpp>

namespace casava
{
namespace basecalling
{

namespace fs = boost::filesystem;

class StatsToSignalMeansConverter
{
public:
    StatsToSignalMeansConverter(unsigned int laneIdentifier,
                                unsigned int repeatIdentifier,
                                const std::vector<unsigned int> &cycleList,
                                const fs::path &inputDirectory,
                                const std::string statsfileName,
                                const fs::path &filterFilePath,
                                const fs::path &signalMeansFilePath,
                                const bool checkCycles,
                                const bool ignoreMissingStats,
                                const bool ctrlIncluded);
    void run();
private:
    const unsigned int laneIdentifier_;
    const unsigned int repeatIdentifier_;
    const std::vector<unsigned int> cycleList_;
    const fs::path inputDirectory_;
    const std::string statsFileName_;
    const fs::path filterFilePath_;
    const fs::path signalMeansFilePath_;
    const bool checkCycles_;
    const bool ignoreMissingStats_;
    const bool ctrlIncluded_;
};

} // namespace basecalling
} // namespace casava

#endif // #ifndef CASAVA_STATS_TO_SIGNAL_MEANS_CONVERTER_HH