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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/strong_types.hpp>
namespace raptor
{
struct build_arguments
{
// Related to k-mers
uint8_t kmer_size{20u};
uint32_t window_size{kmer_size};
window window_size_strong{kmer_size};
std::string shape_string{};
seqan3::shape shape{seqan3::ungapped{kmer_size}};
bool compute_minimiser{false};
bool disable_cutoffs{false};
// Related to IBF
std::filesystem::path out_path{"./"};
std::string size{"1k"};
uint64_t bins{64};
uint64_t bits{4096};
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_socks{false};
bool is_hibf{false};
bool is_minimiser{false};
};
} // namespace raptor
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