configuration.hpp

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// ---------------------------------------------------------------------------------------------------
// Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin
// Copyright (c) 2016-2023, Knut Reinert & MPI für molekulare Genetik
// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License
// shipped with this file and also available at: https://github.com/seqan/chopper/blob/main/LICENSE.md
// ---------------------------------------------------------------------------------------------------
 
#pragma once
 
#include <cinttypes>
#include <filesystem>
#include <iosfwd>
 
#include <cereal/cereal.hpp>
 
#include <hibf/cereal/path.hpp> // IWYU pragma: keep
#include <hibf/config.hpp>
#include <hibf/misc/timer.hpp>
 
namespace chopper
{
 
struct configuration
{
    std::filesystem::path data_file;
 
    bool debug{false};
 
    std::filesystem::path output_filename{"layout.txt"};
 
    std::filesystem::path output_timings{};
 
    uint8_t k{19};
 
    uint8_t window_size{k};
 
    bool precomputed_files{false};
 
    std::filesystem::path sketch_directory{};
 
    bool disable_sketch_output{false};
 
    bool determine_best_tmax{false};
 
    bool force_all_binnings{false};
 
    bool output_verbose_statistics{false};
 
    seqan::hibf::config hibf_config;
 
    mutable seqan::hibf::concurrent_timer compute_sketches_timer{};
    mutable seqan::hibf::concurrent_timer union_estimation_timer{};
    mutable seqan::hibf::concurrent_timer rearrangement_timer{};
    mutable seqan::hibf::concurrent_timer dp_algorithm_timer{};
 
    void read_from(std::istream & stream);
 
    void write_to(std::ostream & stream) const;
 
private:
    friend class cereal::access;
 
    template <typename archive_t>
    void serialize(archive_t & archive)
    {
        uint32_t version{2};
        archive(CEREAL_NVP(version));
 
        archive(CEREAL_NVP(data_file));
        archive(CEREAL_NVP(debug));
        archive(CEREAL_NVP(sketch_directory));
        archive(CEREAL_NVP(k));
        archive(CEREAL_NVP(window_size));
        archive(CEREAL_NVP(disable_sketch_output));
        archive(CEREAL_NVP(precomputed_files));
 
        archive(CEREAL_NVP(output_filename));
        archive(CEREAL_NVP(determine_best_tmax));
        archive(CEREAL_NVP(force_all_binnings));
    }
};
 
} // namespace chopper