flatread.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_FLATREAD_HPP__
#define SHORE_IO_FLATREAD_HPP__

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

#include "shore/processing/pipeline.hpp"
#include "shore/datatype/alignment_processing.hpp"
#include "shore/datatype/datatypes.hpp"
#include "shore/algo/sort_file.hpp"
#include "shore/fmtio/text.hpp"
#include "shore/fmtio/sff.hpp"

namespace shore {

class flatread_tags_parser
{
 private:

        typedef boost::function<void ()> tagfun_t;
        tagfun_t *m_tagfuns;

        const char *m_tagbeg;
        const char *m_tagend;

        static size_t th(const char *const s);

 protected:

        static const size_t MAXTAGS=128*128;

        shore::read::accessory *m_readtags;

        flatread_tags_parser();
        ~flatread_tags_parser();

        void parse_tags(std::string &s);

        void tagfun_invalid();
        void tagfun_BAx();
        void tagfun_DST();
        void tagfun_CLx();
        void tagfun_RGR();
        void tagfun_ORI();
        void tagfun_NUM();
};

class basic_flatread_reader
:public flatread_tags_parser
{
 private:

        shore::basic_line_reader m_reader;
        std::string m_linebuf;
        std::string m_tagbuf;
        shore::read::InsertState m_insstate_conv[256];

        std::string m_readgroup_default;
        size_t m_cliplen_default;
        shore::read::InsertState m_pestate_default;


        void set_default_tags(shore::read &r);

 public:

        typedef shore::read current_type;

        basic_flatread_reader(const std::string& fn);
        basic_flatread_reader(std::istream *const is);
        
        bool next(shore::read &r);

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

typedef shore::monolithic<basic_flatread_reader,
                          shore::read,shore::read::compare_type> flatread_reader;

typedef shore::source<flatread_reader> flatread_source;

class flatread_writer
{
 public:

        typedef shore::read append_type;

 private:

        shore::ostreams m_os;
        shore::read m_readbuf;

        shore::feed<shore::alignment> m_alfeed;
        shore::flatten_alignment_pipe m_fa;
        shore::sink<flatread_writer> m_thissink;

        shore::feed<shore::sff_read> m_sfffeed;
        shore::sff_flatten_pipe m_sffflatten;

        bool m_writetags;

        bool m_applytags;

        bool m_discard_qual_aux;

 public:

        flatread_writer(const std::string& fn);
        flatread_writer(std::ostream*const os);

        void set_writetags(const bool w);

        void set_applytags(const bool a);

        void set_discard_qual_aux(const bool b);

        void append(const shore::read& f);
        void append(const shore::alignment& f);
        void append(const shore::sff_read& f);

        void flush();

        static std::ostream &write_read(std::ostream &out,
                                        const shore::read &e,
                                        const bool discard_qual_aux=false);
};

std::ostream& operator<<(std::ostream& out,const shore::read &e);

typedef shore::sink<flatread_writer> flatread_sink;

} // namespace

#endif // SHORE_IO_FLATREAD_HPP__