update_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 update_arguments
{
    std::filesystem::path index_file{};
    std::filesystem::path out_path{};
 
    std::vector<std::vector<std::string>> bin_path{};
    std::filesystem::path bin_file{};
    uint8_t threads{1u};
 
    // Read from the index, not from the command line.
    uint32_t window_size{20u};
    seqan3::shape shape{seqan3::ungapped{20u}};
    uint8_t shape_size{shape.size()};
    uint8_t shape_weight{shape.count()};
    uint8_t parts{1u};
    bool is_hibf{false};
    double fpr{0.05};
 
    bool disable_partial_rebuild{false};
    bool stats{false};
 
    std::vector<size_t> user_bins_to_delete{};
    std::vector<std::vector<std::string>> user_bins_to_insert{};
 
    mutable size_t partial_rebuilds{};
    mutable size_t full_rebuilds{};
 
    void print_stats() const;
};
 
} // namespace raptor