function/variant_input_stream.hpp

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#ifndef GENESIS_POPULATION_FUNCTION_VARIANT_INPUT_STREAM_H_
#define GENESIS_POPULATION_FUNCTION_VARIANT_INPUT_STREAM_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 <lucas.czech@sund.ku.dk>
    University of Copenhagen, Globe Institute, Section for GeoGenetics
    Oster Voldgade 5-7, 1350 Copenhagen K, Denmark
*/
 
#include "genesis/population/stream/variant_input_stream.hpp"
#include "genesis/population/function/genome_locus.hpp"
#include "genesis/population/genome_locus.hpp"
#include "genesis/population/variant.hpp"
#include "genesis/sequence/functions/dict.hpp"
#include "genesis/sequence/sequence_dict.hpp"
 
#include <functional>
#include <memory>
#include <stdexcept>
#include <string>
#include <vector>
 
namespace genesis {
namespace population {
 
// =================================================================================================
//     Sample Name Filter
// =================================================================================================
 
std::vector<bool> make_sample_name_filter(
    std::vector<std::string> const& sample_names,
    std::vector<std::string> const& names_filter,
    bool inverse_filter = false
);
 
std::function<void(Variant&)> make_variant_input_stream_sample_name_filter_transform(
    std::vector<bool> const& sample_filter
);
 
// =================================================================================================
//     Sample Subsetting / Subsampling
// =================================================================================================
 
enum class SubsamplingMethod
{
    kSubscale,
 
    kSubsampleWithReplacement,
 
    kSubsampleWithoutReplacement
};
 
std::function<void(Variant&)> make_variant_input_stream_sample_subsampling_transform(
    size_t max_depth,
    SubsamplingMethod method = SubsamplingMethod::kSubscale
);
 
// =================================================================================================
//     Observers
// =================================================================================================
 
std::function<void(Variant const&)> make_variant_input_stream_sequence_order_observer(
    std::shared_ptr<genesis::sequence::SequenceDict> sequence_dict = {},
    bool check_sequence_lengths = true
);
 
std::function<void(Variant const&)> make_variant_input_stream_sequence_length_observer(
    std::shared_ptr<genesis::sequence::SequenceDict> sequence_dict
);
 
} // namespace population
} // namespace genesis
 
#endif // include guard