sample_counts_filter_numerical.hpp

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#ifndef GENESIS_POPULATION_FILTER_SAMPLE_COUNTS_FILTER_NUMERICAL_H_
#define GENESIS_POPULATION_FILTER_SAMPLE_COUNTS_FILTER_NUMERICAL_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/sample_counts.hpp"
#include "genesis/population/filter/sample_counts_filter.hpp"
#include "genesis/population/filter/variant_filter.hpp"
 
#include <functional>
#include <iosfwd>
#include <memory>
#include <stdexcept>
#include <string>
#include <utility>
#include <vector>
 
namespace genesis {
namespace population {
 
// =================================================================================================
//     Transform by Count
// =================================================================================================
 
void transform_zero_out_by_min_count(
    SampleCounts& sample,
    size_t min_count,
    bool also_n_and_d_counts = true
);
 
void transform_zero_out_by_min_count(
    Variant& variant,
    size_t min_count,
    bool also_n_and_d_counts = true
);
 
void transform_zero_out_by_max_count(
    SampleCounts& sample,
    size_t max_count,
    bool also_n_and_d_counts = true
);
 
void transform_zero_out_by_max_count(
    Variant& variant,
    size_t max_count,
    bool also_n_and_d_counts = true
);
 
// =================================================================================================
//     Sample Counts Filter Numerical Params
// =================================================================================================
 
struct SampleCountsFilterNumericalParams
{
    // -------------------------------------------
    //     Numeric
    // -------------------------------------------
 
    size_t min_count = 0;
 
    size_t max_count = 0;
 
    size_t deletions_count_limit = 0;
 
    size_t min_read_depth = 0;
 
    size_t max_read_depth = 0;
 
    // -------------------------------------------
    //     SNP vs Invariant
    // -------------------------------------------
 
    bool only_snps = false;
 
    bool only_biallelic_snps = false;
};
 
// =================================================================================================
//     Sample Counts Filter Numerical Functions
// =================================================================================================
 
// --------------------------------------------------------------------------------------
//     apply_sample_counts_filter_numerical
// --------------------------------------------------------------------------------------
 
bool apply_sample_counts_filter_numerical(
    SampleCounts& sample,
    SampleCountsFilterNumericalParams const& params,
    SampleCountsFilterStats& stats
);
 
bool apply_sample_counts_filter_numerical(
    SampleCounts& sample,
    SampleCountsFilterNumericalParams const& params
);
 
bool apply_sample_counts_filter_numerical(
    Variant& variant,
    SampleCountsFilterNumericalParams const& params,
    VariantFilterStats& variant_stats,
    SampleCountsFilterStats& sample_count_stats,
    bool all_need_pass = false
);
 
bool apply_sample_counts_filter_numerical(
    Variant& variant,
    SampleCountsFilterNumericalParams const& params,
    bool all_need_pass = false
);
 
// --------------------------------------------------------------------------------------
//     make_sample_counts_filter_numerical
// --------------------------------------------------------------------------------------
 
inline std::function<void(Variant&)> make_sample_counts_filter_numerical_tagging(
    SampleCountsFilterNumericalParams const& params,
    bool all_need_pass = false
) {
    return [params, all_need_pass]( Variant& variant ){
        apply_sample_counts_filter_numerical( variant, params, all_need_pass );
    };
}
 
inline std::function<void(Variant&)> make_sample_counts_filter_numerical_tagging(
    SampleCountsFilterNumericalParams const& params,
    VariantFilterStats& variant_stats,
    SampleCountsFilterStats& sample_count_stats,
    bool all_need_pass = false
) {
    return [params, &variant_stats, &sample_count_stats, all_need_pass]( Variant& variant ){
        apply_sample_counts_filter_numerical(
            variant, params, variant_stats, sample_count_stats, all_need_pass
        );
    };
}
 
} // namespace population
} // namespace genesis
 
#endif // include guard