VcfFile.h

#ifndef theplu_yat_omic_vcf_file
#define theplu_yat_omic_vcf_file

// $Id: VcfFile.h 4207 2022-08-26 04:36:28Z peter $

/*
  Copyright (C) 2018, 2019, 2020, 2021 Peter Johansson

  This file is part of the yat library, http://dev.thep.lu.se/yat

  The yat library 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.

  The yat library 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 yat. If not, see <http://www.gnu.org/licenses/>.
*/

#include "VcfHeader.h"

#include <boost/noncopyable.hpp>
#include <boost/iostreams/filtering_stream.hpp>

#include <fstream>
#include <memory>
#include <string>

namespace theplu {
namespace yat {
namespace omic {

  class VCF;

  class VcfFile : private boost::noncopyable
  {
  public:
    VcfFile(void);

    explicit VcfFile(const std::string& fn);

    void close(void);

    bool good(void) const;

    bool is_open(void) const;

    void open(const std::string& fn);

    bool read(VCF& vcf);

    VcfHeader& header(void);

    const VcfHeader& header(void) const;
  private:
    std::unique_ptr<VcfHeader> header_;
    boost::iostreams::filtering_istream fis_;
    // store here for easy garbage collection
    std::unique_ptr<std::ifstream> file_stream_;
    std::string name_;
    friend class VcfIterator;
  };

}}}

#endif