map_bim_reader.hpp

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#ifndef GENESIS_POPULATION_FORMAT_MAP_BIM_READER_H_
#define GENESIS_POPULATION_FORMAT_MAP_BIM_READER_H_
 
/*
    Genesis - A toolkit for working with phylogenetic data.
    Copyright (C) 2014-2024 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
*/
 
#include "genesis/population/genome_locus_set.hpp"
#include "genesis/population/genome_region.hpp"
#include "genesis/population/genome_region_list.hpp"
#include "genesis/utils/io/input_source.hpp"
#include "genesis/utils/io/input_stream.hpp"
 
#include <cstdint>
#include <functional>
#include <string>
#include <utility>
#include <vector>
 
namespace genesis {
namespace population {
 
// =================================================================================================
//     MAP/BIM Reader
// =================================================================================================
 
class MapBimReader
{
public:
 
    // -------------------------------------------------------------------------
    //     Typedefs and Enums
    // -------------------------------------------------------------------------
 
    struct Feature
    {
        std::string chromosome;
        std::string variant_id;
        double position;
        int64_t coordinate;
        char allele_1;
        char allele_2;
    };
 
    // -------------------------------------------------------------------------
    //     Constructors and Rule of Five
    // -------------------------------------------------------------------------
 
    MapBimReader() = default;
    ~MapBimReader() = default;
 
    MapBimReader( MapBimReader const& ) = default;
    MapBimReader( MapBimReader&& )      = default;
 
    MapBimReader& operator= ( MapBimReader const& ) = default;
    MapBimReader& operator= ( MapBimReader&& )      = default;
 
    // ---------------------------------------------------------------------
    //     Reading
    // ---------------------------------------------------------------------
 
    std::vector<Feature> read(
        std::shared_ptr< utils::BaseInputSource > source
    ) const;
 
    GenomeLocusSet read_as_genome_locus_set(
        std::shared_ptr< utils::BaseInputSource > source
    ) const;
 
    GenomeRegionList read_as_genome_region_list(
        std::shared_ptr< utils::BaseInputSource > source,
        bool merge = true
    ) const;
 
    void read_as_genome_region_list(
        std::shared_ptr< utils::BaseInputSource > source,
        GenomeRegionList& target,
        bool merge = true
    ) const;
 
    // -------------------------------------------------------------------------
    //     Settings
    // -------------------------------------------------------------------------
 
    bool skip_negative_coordinates() const
    {
        return skip_negative_coordinates_;
    }
 
    MapBimReader& skip_negative_coordinates( bool value )
    {
        skip_negative_coordinates_ = value;
        return *this;
    }
 
    // -------------------------------------------------------------------------
    //     Internal Helpers
    // -------------------------------------------------------------------------
 
private:
 
    void read_(
        std::shared_ptr< utils::BaseInputSource > source,
        std::function<void(Feature&&)> callback
    ) const;
 
    size_t parse_line_(
        utils::InputStream&       input_stream,
        Feature&                  feature,
        std::vector<std::string>& buffer
    ) const;
 
    // -------------------------------------------------------------------------
    //     Member Variables
    // -------------------------------------------------------------------------
 
    bool skip_negative_coordinates_ = true;
 
};
 
} // namespace population
} // namespace genesis
 
#endif // include guard