// Copyright (c) 2011-2013, Pacific Biosciences of California, Inc.
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// Author: David Alexander

#pragma once

#include <ConsensusCore/Quiver/QuiverConfig.hpp>
#include <ConsensusCore/Types.hpp>

#include <string>

namespace ConsensusCore
{
    // A ReadScorer provides a simple but inefficient means of scoring
    // a single read against a template.  This is only to be used for
    // testing, not in production code.

    class ReadScorer
    {
    public:
        explicit ReadScorer(QuiverConfig& config);

        float Score
        (const std::string& tpl, const Read& read) const
            throw(AlphaBetaMismatchException);

        const PairwiseAlignment* Align
        (const std::string& tpl, const Read& read) const
            throw(AlphaBetaMismatchException);

        const SparseMatrix* Alpha
        (const std::string& tpl, const Read& read) const
            throw(AlphaBetaMismatchException);

        const SparseMatrix* Beta
        (const std::string& tpl, const Read& read) const
            throw(AlphaBetaMismatchException);


    private:
        QuiverConfig _quiverConfig;
    };
}
