build_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>
 
namespace raptor
{
 
struct build_arguments
{
    // Related to k-mers
    uint8_t kmer_size{20u};
    uint32_t window_size{kmer_size};
    std::string shape_string{};
    seqan3::shape shape{seqan3::ungapped{kmer_size}};
 
    // Related to IBF
    std::filesystem::path out_path{};
    uint64_t bins{64};
    mutable uint64_t bits{4096}; // Allow to change bits for each partition
    uint64_t hash{2};
    uint8_t parts{1u};
    double fpr{0.05};
 
    // General arguments
    std::vector<std::vector<std::string>> bin_path{};
    std::filesystem::path bin_file{};
    uint8_t threads{1u};
    bool is_hibf{false};
    bool input_is_minimiser{false};
    bool quiet{false};
    std::filesystem::path timing_out{};
 
    // Timers do not copy the stored duration upon copy construction/assignment
    mutable seqan::hibf::concurrent_timer wall_clock_timer{};
    mutable seqan::hibf::concurrent_timer bin_size_timer{};
    mutable seqan::hibf::concurrent_timer index_allocation_timer{};
    mutable seqan::hibf::concurrent_timer user_bin_io_timer{};
    mutable seqan::hibf::concurrent_timer merge_kmers_timer{};
    mutable seqan::hibf::concurrent_timer fill_ibf_timer{};
    mutable seqan::hibf::concurrent_timer store_index_timer{};
 
    void print_timings() const;
    void write_timings_to_file() const;
};
struct build_arguments {…};
 
} // namespace raptor