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// --------------------------------------------------------------------------------------------------
// Copyright (c) 2006-2022, Knut Reinert & Freie Universität Berlin
// Copyright (c) 2016-2022, 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/threshold/threshold_parameters.hpp>
namespace raptor
{
// For costum default message in argparser
struct pattern_size
{
uint64_t v{};
};
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 pattern_size{};
raptor::pattern_size pattern_size_strong{};
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_socks{false};
bool is_hibf{false};
bool cache_thresholds{false};
raptor::threshold::threshold_parameters make_threshold_parameters() const noexcept
{
return {.window_size{window_size},
.shape{shape},
.pattern_size{pattern_size},
.errors{errors},
.percentage{threshold},
.p_max{p_max},
.fpr{fpr},
.tau{tau},
.cache_thresholds{cache_thresholds},
.output_directory{index_file.parent_path()}};
}
};
} // namespace raptor
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