threshold_parameters.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 <filesystem>
 
#include <seqan3/search/kmer_index/shape.hpp>
 
namespace raptor::threshold
{
 
struct threshold_parameters
{
    // Basic.
    uint32_t window_size{};
    seqan3::shape shape{};
    uint64_t query_length{};
 
    // Threshold.
    uint8_t errors{};                                            // threshold_kinds::(probabilistic|lemma)
    double percentage{std::numeric_limits<double>::quiet_NaN()}; // threshold_kinds::percentage
    double p_max{};                                              // threshold_kinds::probabilistic
    double fpr{};                                                // threshold_kinds::probabilistic
    double tau{};                                                // threshold_kinds::probabilistic
 
    // Cache results.
    bool cache_thresholds{};
    std::filesystem::path output_directory{};
};
 
} // namespace raptor::threshold