sync_out.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 <fstream>
#include <mutex>
 
#include <seqan3/utility/views/join_with.hpp>
 
#include <raptor/argument_parsing/search_arguments.hpp>
 
namespace raptor
{
 
class sync_out
{
public:
    sync_out() = default;
    sync_out(sync_out const &) = default;
    sync_out & operator=(sync_out const &) = default;
    sync_out(sync_out &&) = default;
    sync_out & operator=(sync_out &&) = default;
    ~sync_out() = default;
 
    sync_out(search_arguments const & arguments) : file{arguments.out_file}
    {
        write_header(arguments);
    }
 
    template <typename t>
    void write(t && data)
    {
        std::lock_guard<std::mutex> lock{write_mutex};
        file << std::forward<t>(data);
    }
 
private:
    void write_header(search_arguments const & arguments)
    {
        file << "### Minimiser parameters\n";
        file << "## Window size = " << arguments.window_size << '\n';
        file << "## Shape = " << arguments.shape.to_string() << '\n';
        file << "## Shape size (length) = " << static_cast<uint16_t>(arguments.shape_size) << '\n';
        file << "## Shape count (number of 1s) = " << static_cast<uint16_t>(arguments.shape_weight) << '\n';
        file << "### Search parameters\n";
        file << "## Query file = " << arguments.query_file << '\n';
        file << "## Pattern size = " << arguments.query_length << '\n';
        file << "## Output file = " << arguments.out_file << '\n';
        file << "## Threads = " << static_cast<uint16_t>(arguments.threads) << '\n';
        file << "## tau = " << arguments.tau << '\n';
        file << "## p_max = " << arguments.p_max << '\n';
        file << "## Percentage threshold = " << arguments.threshold << '\n';
        file << "## Errors = " << static_cast<uint16_t>(arguments.errors) << '\n';
        file << "## Cache thresholds = " << std::boolalpha << arguments.cache_thresholds << '\n';
        file << "### Index parameters\n";
        file << "## Index = " << arguments.index_file << '\n';
        file << "## Index parts = " << static_cast<uint16_t>(arguments.parts) << '\n';
        file << "## False positive rate = " << arguments.fpr << '\n';
        file << "## Index is compressed = " << std::boolalpha << arguments.compressed << '\n';
        file << "## Index is HIBF = " << std::boolalpha << arguments.is_hibf << '\n';
 
        size_t user_bin_id{};
        for (auto const & file_list : arguments.bin_path)
        {
            file << '#' << user_bin_id << '\t';
            for (auto const elem : seqan3::views::join_with(file_list, ','))
                file << elem;
            file << '\n';
            ++user_bin_id;
        }
 
        file << "#QUERY_NAME\tUSER_BINS\n";
    }
 
    std::ofstream file;
    std::mutex write_mutex;
};
 
} // namespace raptor