/**
 ** 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 CountingBclWriter.hh
 **
 ** \brief BCL writer that also collects statistics about written bases.
 **
 ** \author Roman Petrovski
 **/

#ifndef CASAVA_DEMULTIPLEX_COUNTING_BCL_WRITER_HH
#define CASAVA_DEMULTIPLEX_COUNTING_BCL_WRITER_HH

#include "io/BclWriter.hh"

namespace casava
{
namespace demultiplex
{

namespace fs = boost::filesystem;
namespace cc = casava::common;
namespace cio = casava::io;

/**
 ** @brief Same as casava::common::BclWriter but knows how many of which bases has been written.
 **/
class CountingBclWriter: protected cio::BclWriter
{
public:
    typedef std::pair<std::string, std::string> Cluster;
    CountingBclWriter(const fs::path &cyclePath, const unsigned int expectedClusters)
        : BclWriter(cyclePath, expectedClusters)
        , baseCounts_('T' + 1){;}

    void put(const Cluster& cluster) {
        cio::BclWriter::put(cluster);
        ++baseCounts_.at(cluster.first[0]);
    }

    void close(){cio::BclWriter::close();}
    int getBaseCount(char base){
        return baseCounts_[base];
    }
private:
    std::vector<int> baseCounts_;

    CountingBclWriter();
    CountingBclWriter(const CountingBclWriter &);
    CountingBclWriter &operator=(const CountingBclWriter &);
};

} // namespace demultiplex
} // namespace casava

#endif // CASAVA_DEMULTIPLEX_COUNTING_BCL_WRITER_HH