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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 <raptor/argument_parsing/upgrade_arguments.hpp>
#include <raptor/build/store_index.hpp>
namespace raptor
{
template <bool compressed>
void upgrade_index(upgrade_arguments const & arguments)
{
constexpr seqan3::data_layout layout =
compressed ? seqan3::data_layout::compressed : seqan3::data_layout::uncompressed;
seqan3::interleaved_bloom_filter<layout> original_index{};
if (arguments.parts == 1u)
{
std::ifstream is{arguments.in_file, std::ios::binary};
cereal::BinaryInputArchive iarchive{is};
iarchive(original_index);
store_index(arguments.out_file, std::move(original_index), arguments);
}
else
{
for (size_t part : std::views::iota(0u, arguments.parts))
{
std::filesystem::path in_file{arguments.in_file};
in_file += "_" + std::to_string(part);
std::ifstream is{in_file, std::ios::binary};
cereal::BinaryInputArchive iarchive{is};
iarchive(original_index);
std::filesystem::path out_file{arguments.out_file};
out_file += "_" + std::to_string(part);
store_index(out_file, std::move(original_index), arguments);
}
}
}
} // namespace raptor
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