sync_reader.hpp

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#ifndef GENESIS_POPULATION_FORMAT_SYNC_READER_H_
#define GENESIS_POPULATION_FORMAT_SYNC_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/variant.hpp"
#include "genesis/utils/io/input_source.hpp"
#include "genesis/utils/io/input_stream.hpp"
 
#include <string>
#include <vector>
 
namespace genesis {
namespace population {
 
// =================================================================================================
//     PoPoolation2 Synchronized File Reader
// =================================================================================================
 
class SyncReader
{
public:
 
    // -------------------------------------------------------------------------
    //     Constructors and Rule of Five
    // -------------------------------------------------------------------------
 
    SyncReader() = default;
    ~SyncReader() = default;
 
    SyncReader( SyncReader const& ) = default;
    SyncReader( SyncReader&& )      = default;
 
    SyncReader& operator= ( SyncReader const& ) = default;
    SyncReader& operator= ( SyncReader&& )      = default;
 
    // ---------------------------------------------------------------------
    //     Read Header
    // ---------------------------------------------------------------------
 
    std::vector<std::string> read_header(
        utils::InputStream& input_stream
    ) const;
 
    std::vector<std::string> read_header(
        utils::InputStream& input_stream,
        std::vector<bool> const& sample_filter
    ) const;
 
    // ---------------------------------------------------------------------
    //     Reading
    // ---------------------------------------------------------------------
 
    std::vector<Variant> read(
        std::shared_ptr< utils::BaseInputSource > source
    ) const;
 
    std::vector<Variant> read(
        std::shared_ptr< utils::BaseInputSource > source,
        std::vector<bool> const&                  sample_filter
    ) const;
 
    // -------------------------------------------------------------------------
    //     Parsing
    // -------------------------------------------------------------------------
 
    bool parse_line(
        utils::InputStream& input_stream,
        Variant&            sample_set
    ) const;
 
    bool parse_line(
        utils::InputStream&      input_stream,
        Variant&                 sample_set,
        std::vector<bool> const& sample_filter
    ) const;
 
    // -------------------------------------------------------------------------
    //     Settings
    // -------------------------------------------------------------------------
 
    bool guess_alt_base() const
    {
        return guess_alt_base_;
    }
 
    SyncReader& guess_alt_base( bool value )
    {
        guess_alt_base_ = value;
        return *this;
    }
 
    bool allow_missing() const
    {
        return allow_missing_;
    }
 
    SyncReader& allow_missing( bool value )
    {
        allow_missing_ = value;
        return *this;
    }
 
    // -------------------------------------------------------------------------
    //     Internal Members
    // -------------------------------------------------------------------------
 
private:
 
    bool parse_line_(
        utils::InputStream&      input_stream,
        Variant&                 sample_set,
        std::vector<bool> const& sample_filter,
        bool                     use_sample_filter
    ) const;
 
    // Only use intrinsics version for the compilers that support them!
    #if defined(__GNUC__) || defined(__GNUG__) || defined(__clang__)
 
        void parse_sample_gcc_intrinsic_(
            utils::InputStream& input_stream,
            SampleCounts&       sample
        ) const;
 
    #endif
 
    void parse_sample_simple_(
        utils::InputStream& input_stream,
        SampleCounts&       sample
    ) const;
 
    void parse_sample_(
        utils::InputStream& input_stream,
        SampleCounts&       sample
    ) const;
 
    void skip_sample_(
        utils::InputStream& input_stream
    ) const;
 
    // -------------------------------------------------------------------------
    //     Member Varables
    // -------------------------------------------------------------------------
 
private:
 
    bool guess_alt_base_ = false;
    bool allow_missing_ = true;
 
};
 
} // namespace population
} // namespace genesis
 
#endif // include guard