index_upgrader.hpp

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// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin
// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
// SPDX-License-Identifier: BSD-3-Clause
 
#pragma once
 
#include <raptor/argument_parsing/upgrade_arguments.hpp>
#include <raptor/index.hpp>
 
namespace raptor
{
 
// class index_upgrader
// {
// public:
//     std::string index_file{};
//     std::string output_file{};
//     double fpr{};
//     size_t max_count{};
 
//     index_upgrader() = default;
//     index_upgrader(index_upgrader const &) = default;
//     index_upgrader(index_upgrader &&) = default; // GCOVR_EXCL_LINE
//     index_upgrader & operator=(index_upgrader const &) = default;
//     index_upgrader & operator=(index_upgrader &&) = default;
//     ~index_upgrader() = default;
 
//     explicit index_upgrader(upgrade_arguments const & arguments, size_t const max_count) :
//         index_file{arguments.index_file},
//         output_file{arguments.output_file},
//         fpr{arguments.fpr},
//         max_count{max_count}
//     {}
 
//     void upgrade()
//     {
//         raptor_index<index_structure::ibf> index{};
//         {
//             std::ifstream is{index_file, std::ios::binary};
//             cereal::BinaryInputArchive iarchive{is};
//             index.load_old_index(iarchive);
//         }
//         if (std::isnan(fpr))
//             fpr = compute_fpr(index.ibf().hash_function_count(), max_count, index.ibf().bin_size());
//         index.fpr_ = fpr;
//         std::cout << "FPR for " << index_file << ": " << fpr << '\n';
//         index.is_hibf_ = false;
//         std::ofstream os{output_file, std::ios::binary};
//         cereal::BinaryOutputArchive oarchive{os};
//         oarchive(index);
//     }
 
//     static double compute_fpr(size_t const hash_fun, size_t const count, size_t const bin_size)
//     {
//         double const exp_arg = (hash_fun * count) / static_cast<double>(bin_size);
//         double const log_arg = 1.0 - std::exp(-exp_arg);
//         return std::exp(hash_fun * std::log(log_arg));
//     }
// };
 
} // namespace raptor