/**
 ** 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 Bcl2FastqRecordConverter.hh
 **
 ** \brief Converts between a composite BCL record and a Fastq record.
 **
 ** \author Roman Petrovski
 **/

#ifndef CASAVA_DEMULTIPLEX_BCL_2_FASTQ_RECORD_CONVERTER_HH
#define CASAVA_DEMULTIPLEX_BCL_2_FASTQ_RECORD_CONVERTER_HH

#include <string>
#include "io/FastqWriter.hh"
#include "demultiplex/CompositeBclReader.hh"
#include "demultiplex/MaskQvalsByEamss.hh"

namespace casava
{
namespace demultiplex
{
/**
 * @brief Converts CompositeBclReader::RecordType object into FastqWriter::RecordType one.
 * Tries to reduce the memory management by reusing an object across multiple conversion
 * calls. Therefore - not thread-safe.
 */
struct Bcl2FastqRecordConverter
{
    // converts the Illumina BQ offset (64) to the FASTQ BQ offset (33)
    struct IlluminaToFastqOffset {
        char operator()(char c) {
            return c - 31;
        }
    };

    Bcl2FastqRecordConverter(const std::string &instrumentName,
                             const unsigned int runNumber,
                             const std::string &flowCellId,
                             const unsigned int lane, const unsigned int tile,
                             const unsigned int readNumber,
                             const bool withEamss,
                             const bool unified,
                             const unsigned barcodeCycles)
    : buffer_(instrumentName, runNumber, flowCellId, lane, tile,
                         std::make_pair(0,0), "", readNumber, false, 0, std::make_pair("", ""))
    , unifiedFilterControl(unified)
    , withEamss(withEamss)
    , maskQvalsByEamss()
    , barcodeCycles_(barcodeCycles)
    {}

    const cio::FastqWriter::RecordType &operator()(const CompositeBclReader::RecordType &bclRecord) const
    {
        buffer_.position_.first = static_cast<int>(roundf(1000.0f + 10.0f * bclRecord.position_.first));
        buffer_.position_.second = static_cast<int>(roundf(1000.0f + 10.0f * bclRecord.position_.second));
        buffer_.barcode_ = bclRecord.cluster_.first.substr(bclRecord.cluster_.first.size() - barcodeCycles_);;
        buffer_.filter_ = static_cast<bool>(0x01 & bclRecord.filter_);
        buffer_.control_ = static_cast<unsigned short int>(0xFFFE &
                                                 (unifiedFilterControl ? bclRecord.filter_ : bclRecord.control_) );
        buffer_.cluster_.first = bclRecord.cluster_.first.substr(0, bclRecord.cluster_.first.size() - barcodeCycles_);
        buffer_.cluster_.second.clear();
        const std::string::const_iterator dataCyclesEnd =
            bclRecord.cluster_.second.begin() + bclRecord.cluster_.second.size() - barcodeCycles_;
        if (withEamss)
        {
            std::copy(bclRecord.cluster_.second.begin(), dataCyclesEnd,
                      std::back_inserter(buffer_.cluster_.second));
            maskQvalsByEamss(buffer_.cluster_.second, bclRecord.cluster_.first);

            std::transform(buffer_.cluster_.second.begin(), buffer_.cluster_.second.end(),
                           buffer_.cluster_.second.begin(), IlluminaToFastqOffset());
        }
        else
        {
            std::transform(bclRecord.cluster_.second.begin(), dataCyclesEnd,
                           std::back_inserter(buffer_.cluster_.second), IlluminaToFastqOffset());
        }

        return buffer_;
    }
private:
    mutable cio::FastqWriter::RecordType buffer_;
    const bool unifiedFilterControl;
    const bool withEamss;
    const MaskQvalsByEamss maskQvalsByEamss;
    const unsigned barcodeCycles_;
};

} // namespce demultiplex
} // namespace casava

#endif // CASAVA_DEMULTIPLEX_BCL_2_FASTQ_RECORD_CONVERTER_HH