eland.hpp

Go to the documentation of this file.

/*
 * 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_ELAND_HPP__
#define SHORE_IO_ELAND_HPP__

#include <string>
#include <deque>

#include "shore/datatype/alignment_processing.hpp"
#include "shore/processing/pipeline.hpp"
#include "shore/datatype/datatypes.hpp"
#include "shore/fmtio/read.hpp"
#include "shore/fmtio/text.hpp"

namespace shore {

class eland_reader
{
 private:

        shore::line_reader m_rfile;
        shore::read_reader m_rread;
        int m_max_mm;
        int m_firstread_len;

        shore::alignment_queue m_queue;
        shore::alignment m_template;
        size_t m_currenthits;

        std::vector<shore::sequence_record> m_ref;

        shore::feed<shore::read> m_leftovers;


        void parse();

 public:

        typedef shore::alignment current_type;

        eland_reader(const std::string &fn,
                     const std::string &ref_fn,const std::string &reads_fn,
                     const int max_mm);

        const shore::alignment &current() const;

        bool has_data();

        void next();

        shore::feed<shore::read> &leftovers();
};

typedef shore::source<eland_reader> eland_source;

} // namespace

#endif // SHORE_IO_ELAND_HPP__