bed.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_BED_HPP__
#define SHORE_IO_BED_HPP__

#include <string>

#include "shore/processing/pipeline.hpp"
#include "shore/datatype/alignment_string_ops.hpp"
#include "shore/datatype/datatypes.hpp"
#include "shore/stream/streams.hpp"

namespace shore {

class bed_writer
{
 private:

        shore::ostreams m_os;
        shore::alignment_helper m_ah;

 public:

        typedef shore::alignment append_type;

        bed_writer(const std::string &fn);

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

        void flush();
};

typedef shore::sink<bed_writer> bed_sink;

class bedgraph_writer
{
 private:

        shore::ostreams m_os;
        bool m_negate_reversescores;

 public:

        typedef shore::coverage append_type;

        bedgraph_writer(std::ostream *const os,const bool negate_rev=false);
        bedgraph_writer(const std::string &fn,const bool negate_rev=false);

        void append(const shore::coverage &f);
        void append(const shore::annotation_entry &f);

        void flush();
};

typedef shore::sink<bedgraph_writer> bedgraph_sink;

} // namespace

#endif // SHORE_IO_BED_HPP__