hts_file.hpp

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#ifndef GENESIS_POPULATION_FORMATS_HTS_FILE_H_
#define GENESIS_POPULATION_FORMATS_HTS_FILE_H_
 
/*
    Genesis - A toolkit for working with phylogenetic data.
    Copyright (C) 2014-2021 Lucas Czech
 
    This program 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.
 
    This program 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 this program.  If not, see <http://www.gnu.org/licenses/>.
 
    Contact:
    Lucas Czech <lczech@carnegiescience.edu>
    Department of Plant Biology, Carnegie Institution For Science
    260 Panama Street, Stanford, CA 94305, USA
*/
 
#ifdef GENESIS_HTSLIB
 
#include <string>
 
extern "C" {
    // #include <htslib/hts.h>
 
    struct htsFile;
}
 
// =================================================================================================
//     HTS File
// =================================================================================================
 
namespace genesis {
namespace population {
 
class HtsFile
{
public:
 
    // -------------------------------------------------------------------------
    //     Constructors and Rule of Five
    // -------------------------------------------------------------------------
 
    HtsFile() = default;
 
    explicit HtsFile(
        std::string const& file_name,
        std::string const& mode = "r"
    );
 
    ~HtsFile();
 
    HtsFile( HtsFile const& ) = delete;
    HtsFile( HtsFile&& other );
 
    HtsFile& operator= ( HtsFile const& ) = delete;
    HtsFile& operator= ( HtsFile&& other );
 
    // -------------------------------------------------------------------------
    //     Accessors
    // -------------------------------------------------------------------------
 
    std::string const& file_name() const
    {
        return file_name_;
    }
 
    ::htsFile* data()
    {
        return hts_file_;
    }
 
    std::string format_description() const;
 
    std::string format_extension() const;
 
    // -------------------------------------------------------------------------
    //     Data Members
    // -------------------------------------------------------------------------
 
private:
 
    std::string file_name_ = "";
    ::htsFile*  hts_file_ = nullptr;
};
 
} // namespace population
} // namespace genesis
 
#endif // htslib guard
#endif // include guard