Loading...
Searching...
No Matches
search_arguments.hpp
Go to the documentation of this file.
// --------------------------------------------------------------------------------------------------
// 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 quiet{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 (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 << "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
std::cerr
raptor::timer
Definition timer.hpp:30
filesystem
std::fixed
T fixed(T... args)
memory_usage.hpp
Provides raptor::formatted_peak_ram.
std::filesystem::path
std::numeric_limits::quiet_NaN
T quiet_NaN(T... args)
std::setprecision
T setprecision(T... args)
raptor::search_arguments
Definition search_arguments.hpp:28
raptor::threshold::threshold_parameters
Definition threshold_parameters.hpp:23
threshold_parameters.hpp
Provides raptor::threshold::threshold_parameters.
timer.hpp
Provides raptor::timer.
vector