vcf.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 IO_VCF_HPP__
#define IO_VCF_HPP__

#include <iostream>
#include <map>
#include <string>

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

namespace shore {


class vcf_writer
{
  private:
        
        shore::ostreams m_out;

        std::map<std::string,shore::sequence_record> m_refseq;

        std::string m_samplename;

        std::string m_chr;
        long m_pos;
        std::string m_refbases;
        std::string m_varbases;
        size_t m_ref_noanchorofs;
        size_t m_var_noanchorofs;
        std::vector<int> m_qual;
        std::vector<int> m_supp;

        void wbuf();

  public:

        typedef shore::local_variant append_type;

        vcf_writer(const std::string& fn,const std::string& ref);
        vcf_writer(std::ostream& os,const std::string& ref);

        void append(const shore::local_variant& f);
        void flush();
};

typedef shore::sink<vcf_writer> vcf_sink;

class qualvar_reader
{
  private:

        shore::local_variant m_current;

        shore::istreams m_in;

        bool m_hasdata;

  public:

        typedef shore::local_variant current_type;

        qualvar_reader(const std::string& qv_fn);
        qualvar_reader(std::istream& in);

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

std::istream& operator>>(std::istream& in,shore::local_variant& e);

typedef shore::source<qualvar_reader> qualvar_source;

} // namespace

#endif // IO_VCF_HPP__