read.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 IO_READ_HPP__
#define IO_READ_HPP__

#include <iostream>
#include <vector>
#include <set>

#include "shore/processing/pipeline.hpp"
#include "shore/datatype/alignment_string_ops.hpp"
#include "shore/datatype/datatypes.hpp"
#include "shore/processing/merge.hpp"
#include "shore/base/memops.hpp"

namespace shore {

class read_reader
{
 public:

        enum Sorting
        {
                SORTING_ID,
                SORTING_SEQ,
                SORTING_NONE
        };

        struct config
        {
                bool unfiltered;
                std::string sam_ref;

                config();
        };

        typedef shore::read current_type;

 private:

        config m_conf;

        shore::merge<shore::read,shore::read::compare_type> m_merger;
        shore::ptrkeeper m_cleaner;


        void open_path(const std::string& fn,const Sorting srt);

 public:

        read_reader(const std::string& fn,
                    const Sorting srt=SORTING_ID,const config &c=config());
        read_reader(const std::vector<std::string>& fn,
                    const Sorting srt=SORTING_ID,const config &c=config());

        ~read_reader();

        bool has_data() const;
        const shore::read& current() const;
        void next();

        int current_streamid() const;

        struct rltxy
        {
                std::string run;
                int lane;
                int tile;
                int x;
                int y;
        };

        static void readid2rltxy(const std::string& id,rltxy*const ret);
        //static void check_runid(const std::string& run);
        static std::string rltxy2readid(const std::string& run,int lane,int tile,
                                        int x,int y);
};

typedef shore::source<read_reader> read_source;

} // namespace

#endif // IO_READ_HPP__