store_index.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 <seqan3/search/dream_index/interleaved_bloom_filter.hpp>
 
#include <raptor/index.hpp>
#include <raptor/strong_types.hpp>
 
namespace raptor
{
 
// Compresion handled in chopper_build
template <index_structure::is_hibf data_t, typename arguments_t>
static inline void store_index(std::filesystem::path const & path, raptor_index<data_t> && index, arguments_t const &)
{
    std::ofstream os{path, std::ios::binary};
    cereal::BinaryOutputArchive oarchive{os};
    oarchive(index);
}
 
template <index_structure::is_ibf data_t, typename arguments_t>
static inline void
store_index(std::filesystem::path const & path, raptor_index<data_t> && index, arguments_t const & arguments)
{
    if (!arguments.compressed)
    {
        std::ofstream os{path, std::ios::binary};
        cereal::BinaryOutputArchive oarchive{os};
        oarchive(index);
    }
    else
    {
        raptor_index<index_structure::ibf_compressed> compressed_index{std::move(index)};
        std::ofstream os{path, std::ios::binary};
        cereal::BinaryOutputArchive oarchive{os};
        oarchive(compressed_index);
    }
}
 
template <seqan3::data_layout layout, typename arguments_t>
static inline void store_index(std::filesystem::path const & path,
                               seqan3::interleaved_bloom_filter<layout> && ibf,
                               arguments_t const & arguments)
{
    raptor_index<seqan3::interleaved_bloom_filter<layout>> index{window{arguments.window_size},
                                                                 arguments.shape,
                                                                 arguments.parts,
                                                                 arguments.compressed,
                                                                 arguments.bin_path,
                                                                 arguments.fpr,
                                                                 std::move(ibf)};
 
    std::ofstream os{path, std::ios::binary};
    cereal::BinaryOutputArchive oarchive{os};
    oarchive(index);
}
 
} // namespace raptor