prepare_arguments.hpp

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// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin
// SPDX-FileCopyrightText: 2016-2024 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>
 
#include <hibf/misc/timer.hpp>
 
#include <raptor/argument_parsing/memory_usage.hpp>
#include <raptor/strong_types.hpp>
 
namespace raptor
{
 
struct prepare_arguments
{
    uint8_t kmer_size{20u};
    uint32_t window_size{kmer_size};
    std::string shape_string{};
    seqan3::shape shape{seqan3::ungapped{kmer_size}};
    bool use_filesize_dependent_cutoff{false};
    uint8_t kmer_count_cutoff{1u};
 
    std::filesystem::path out_dir{"./"};
 
    std::vector<std::vector<std::string>> bin_path{};
    std::filesystem::path bin_file{};
    uint8_t threads{1u};
    bool quiet{false};
 
    // Timers do not copy the stored duration upon copy construction/assignment
    mutable seqan::hibf::concurrent_timer wall_clock_timer{};
    mutable seqan::hibf::concurrent_timer compute_minimiser_timer{};
    mutable seqan::hibf::concurrent_timer write_minimiser_timer{};
    mutable seqan::hibf::concurrent_timer write_header_timer{};
 
    void print_timings() const
    {
        if (quiet)
            return;
        std::cerr << std::fixed << std::setprecision(2) << "============= Timings =============\n";
        std::cerr << "Wall clock time [s]: " << wall_clock_timer.in_seconds() << '\n';
        std::cerr << "Peak memory usage " << formatted_peak_ram() << '\n';
        std::cerr << "Compute minimiser [s]: " << compute_minimiser_timer.in_seconds() / threads << '\n';
        std::cerr << "Write minimiser files [s]: " << write_minimiser_timer.in_seconds() / threads << '\n';
        std::cerr << "Write header files [s]: " << write_header_timer.in_seconds() / threads << '\n';
    }
};
struct prepare_arguments {…};
 
} // namespace raptor