qseq.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_IO_QSEQ_HPP__
#define SHORE_IO_QSEQ_HPP__

#include <string>

#include "shore/datatype/datatypes.hpp"
#include "shore/fmtio/text.hpp"
#include "shore/processing/monolithic_source.hpp"

namespace shore {

class basic_qseq_reader
{
 private:

        static const std::string QSEQ_COLUMNS;

        shore::row_reader m_in;
        std::string m_fn;

        bool m_rawreads;

 public:

        typedef shore::read current_type;

        basic_qseq_reader(const std::string &fn,const bool rawreads=true);

        bool next(shore::read & buf);

        const std::string &get_name() const;
};

typedef shore::monolithic<basic_qseq_reader,
                          shore::read,shore::read::compare_type> qseq_reader;

typedef shore::source<qseq_reader> qseq_source;

} // namespace

#endif // SHORE_IO_QSEQ_HPP__