upgrade_arguments.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 <vector>
 
#include <seqan3/search/kmer_index/shape.hpp>
 
namespace raptor
{
 
struct upgrade_arguments
{
    uint32_t window_size{};
    seqan3::shape shape{};
    bool compressed{};
    bool input_is_minimiser{};
    uint8_t parts{1u};
    uint8_t threads{1u};
    double fpr{std::numeric_limits<double>::quiet_NaN()};
 
    std::filesystem::path bin_file{};
    std::filesystem::path index_file{};
    std::filesystem::path output_file{};
 
    std::vector<std::vector<std::string>> bin_path{};
};
 
} // namespace raptor