threshold.hpp

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// SPDX-FileCopyrightText: 2006-2026 Knut Reinert & Freie Universität Berlin
// SPDX-FileCopyrightText: 2016-2026 Knut Reinert & MPI für molekulare Genetik
// SPDX-License-Identifier: BSD-3-Clause
 
#pragma once
 
#include <raptor/threshold/precompute_correction.hpp>
#include <raptor/threshold/precompute_threshold.hpp>
 
namespace raptor::threshold
{
 
class threshold
{
public:
    threshold() = default;
    threshold(threshold const &) = default;
    threshold & operator=(threshold const &) = default;
    threshold(threshold &&) = default;
    threshold & operator=(threshold &&) = default;
    ~threshold() = default;
 
    threshold(threshold_parameters const & arguments);
 
    size_t get(size_t const minimiser_count) const noexcept;
 
protected:
    enum class threshold_kinds : uint8_t
    {
        probabilistic,
        lemma,
        percentage
    };
 
    threshold_kinds threshold_kind{threshold_kinds::probabilistic};
    std::vector<size_t> precomp_correction{};
    std::vector<size_t> precomp_thresholds{};
    size_t kmer_lemma{};
    size_t minimal_number_of_minimizers{};
    size_t maximal_number_of_minimizers{};
    double threshold_percentage{};
    uint8_t errors{};
};
 
} // namespace raptor::threshold