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build_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/strong_types.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};
bool compressed{false};
// 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};
// Timers do not copy the stored duration upon copy construction/assignment
mutable timer<concurrent::yes> wall_clock_timer{};
mutable timer<concurrent::yes> bin_size_timer{};
mutable timer<concurrent::yes> index_allocation_timer{};
mutable timer<concurrent::yes> user_bin_io_timer{};
mutable timer<concurrent::yes> merge_kmers_timer{};
mutable timer<concurrent::yes> fill_ibf_timer{};
mutable timer<concurrent::yes> store_index_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';
if (!is_hibf)
std::cerr << "Determine IBF size [s]: " << bin_size_timer.in_seconds() << '\n';
std::cerr << "Index allocation [s]: " << index_allocation_timer.in_seconds() << '\n';
std::cerr << "User bin I/O avg per thread [s]: " << user_bin_io_timer.in_seconds() / threads << '\n';
std::cerr << "User bin I/O sum [s]: " << user_bin_io_timer.in_seconds() << '\n';
if (is_hibf)
{
std::cerr << "Merge kmer sets avg per thread [s]: " << merge_kmers_timer.in_seconds() / threads << '\n';
std::cerr << "Merge kmer sets sum [s]: " << merge_kmers_timer.in_seconds() << '\n';
}
std::cerr << "Fill IBF avg per thread [s]: " << fill_ibf_timer.in_seconds() / threads << '\n';
std::cerr << "Fill IBF sum [s]: " << fill_ibf_timer.in_seconds() << '\n';
std::cerr << "Store index [s]: " << store_index_timer.in_seconds() << '\n';
}
};
} // namespace raptor
std::string
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::setprecision
T setprecision(T... args)
strong_types.hpp
Provides raptor::window.
raptor::build_arguments
Definition build_arguments.hpp:28
timer.hpp
Provides raptor::timer.
vector