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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>
namespace raptor
{
struct upgrade_arguments
{
uint32_t window_size{};
uint8_t kmer_size{};
seqan3::shape shape{};
uint8_t parts{1u};
bool compressed{false};
std::filesystem::path bin_file{};
std::filesystem::path in_file{};
std::filesystem::path out_file{};
std::vector<std::vector<std::string>> bin_path{};
};
} // namespace raptor
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