search_arguments.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/raptor/blob/main/LICENSE.md
// --------------------------------------------------------------------------------------------------
 
#pragma once
 
#include <filesystem>
#include <vector>
 
#include <seqan3/search/kmer_index/shape.hpp>
 
#include <raptor/argument_parsing/memory_usage.hpp>
#include <raptor/argument_parsing/timer.hpp>
#include <raptor/threshold/threshold_parameters.hpp>
 
namespace raptor
{
 
struct search_arguments
{
    // Related to k-mers
    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 threads{1u};
    uint8_t parts{1u};
 
    // Related to thresholding
    double tau{0.9999};
    double threshold{std::numeric_limits<double>::quiet_NaN()};
    double p_max{0.15};
    double fpr{0.05};
    uint64_t query_length{};
    uint8_t errors{0};
 
    // Related to IBF
    std::filesystem::path index_file{};
    bool compressed{false};
 
    // General arguments
    std::vector<std::vector<std::string>> bin_path{};
    std::filesystem::path query_file{};
    std::filesystem::path out_file{"search.out"};
    bool write_time{false};
    bool is_hibf{false};
    bool cache_thresholds{false};
    bool verbose{false};
 
    // Timers do not copy the stored duration upon copy construction/assignment
    mutable timer<concurrent::yes> wall_clock_timer{};
    mutable timer<concurrent::yes> query_length_timer{};
    mutable timer<concurrent::yes> query_file_io_timer{};
    mutable timer<concurrent::yes> load_index_timer{};
    mutable timer<concurrent::yes> compute_minimiser_timer{};
    mutable timer<concurrent::yes> query_ibf_timer{};
    mutable timer<concurrent::yes> generate_results_timer{};
 
    void print_timings() const
    {
        if (!verbose)
            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 << "Determine query length [s]: " << query_length_timer.in_seconds() << '\n';
        std::cerr << "Query file I/O [s]: " << query_file_io_timer.in_seconds() << '\n';
        std::cerr << "Load index [s]: " << load_index_timer.in_seconds() << '\n';
        std::cerr << "Compute minimiser [s]: " << compute_minimiser_timer.in_seconds() / threads << '\n';
        std::cerr << "Query IBF [s]: " << query_ibf_timer.in_seconds() / threads << '\n';
        std::cerr << "Generate results [s]: " << generate_results_timer.in_seconds() / threads << '\n';
    }
 
    raptor::threshold::threshold_parameters make_threshold_parameters() const noexcept
    {
        return {.window_size{window_size},
                .shape{shape},
                .query_length{query_length},
                .errors{errors},
                .percentage{threshold},
                .p_max{p_max},
                .tau{tau},
                .cache_thresholds{cache_thresholds},
                .output_directory{index_file.parent_path()}};
    }
};
 
} // namespace raptor