read_processing.hpp

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/*
 * Copyright 2008,2009,2010,2011,2012 Stephan Ossowski, Korbinian Schneeberger,
 * Felix Ott, Joerg Hagmann, Alf Scotland, Sebastian Bender
 * 
 * This file is part of SHORE.
 * 
 * SHORE is free software: you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation, either version 3 of the License, or
 * (at your option) any later version.
 * 
 * SHORE is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU General Public License for more details.
 * 
 * You should have received a copy of the GNU General Public License
 * along with SHORE.  If not, see <http://www.gnu.org/licenses/>.
 */


#ifndef SHORE_READ_PROCESSING_HPP__
#define SHORE_READ_PROCESSING_HPP__

#include "shore/datatype/datatypes.hpp"

namespace shore {

class color2seq
{
 private:

        shore::read m_current;
        bool m_hasdata;
        char m_lut[256];

 public:

        typedef shore::read append_type;
        typedef shore::read current_type;


        color2seq();

        const shore::read &current();
        bool has_data() const;
        void next();
        void append(const shore::read &r);
        void flush();
};

class pefilter
{
 private:

        shore::read m_current;
        bool m_hasdata;
        const int m_pe;

 public:

        typedef shore::read append_type;
        typedef shore::read current_type;


        pefilter(const int pe);

        const shore::read &current();
        bool has_data() const;
        void next();
        void append(const shore::read &r);
        void flush();
};

} // namespace

#endif // SHORE_READ_PROCESSING_HPP__