misc_output.hpp

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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/seqan3/blob/master/LICENSE.md
// -----------------------------------------------------------------------------------------------------
 
#pragma once
 
#include <filesystem>
#include <functional>
#include <iostream>
#include <string>
#include <tuple>
 
#if defined(SEQAN3_HAS_BZIP2)
#    include <seqan3/contrib/stream/bz2_ostream.hpp>
#endif
#if defined(SEQAN3_HAS_ZLIB)
#    include <seqan3/contrib/stream/bgzf_ostream.hpp>
#    include <seqan3/contrib/stream/gz_ostream.hpp>
#endif
#include <seqan3/contrib/stream/bgzf.hpp>
#include <seqan3/io/exception.hpp>
#include <seqan3/utility/concept.hpp>
 
namespace seqan3::detail
{
 
template <builtin_character char_t>
inline auto make_secondary_ostream(std::basic_ostream<char_t> & primary_stream, std::filesystem::path & filename)
    -> std::unique_ptr<std::basic_ostream<char_t>, std::function<void(std::basic_ostream<char_t> *)>>
{
    // don't assume ownership
    constexpr auto stream_deleter_noop = [](std::basic_ostream<char_t> *) {};
    // assume ownership
    [[maybe_unused]] constexpr auto stream_deleter_default = [](std::basic_ostream<char_t> * ptr)
    {
        delete ptr;
    };
 
    std::string extension = filename.extension().string();
 
    if (extension == ".gz")
    {
#if defined(SEQAN3_HAS_ZLIB)
        filename.replace_extension("");
        return {new contrib::basic_gz_ostream<char_t>{primary_stream}, stream_deleter_default};
#else
        throw file_open_error{"Trying to write a gzipped file, but no ZLIB available."};
#endif
    }
    else if ((extension == ".bgzf") || (extension == ".bam"))
    {
#if defined(SEQAN3_HAS_ZLIB)
        if (extension != ".bam") // remove extension except for bam
            filename.replace_extension("");
 
        return {new contrib::basic_bgzf_ostream<char_t>{primary_stream}, stream_deleter_default};
#else
        throw file_open_error{"Trying to write a bgzf'ed file, but no ZLIB available."};
#endif
    }
    else if (extension == ".bz2")
    {
#if defined(SEQAN3_HAS_BZIP2)
        filename.replace_extension("");
        return {new contrib::basic_bz2_ostream<char_t>{primary_stream}, stream_deleter_default};
#else
        throw file_open_error{"Trying to write a bzipped file, but no libbz2 available."};
#endif
    }
    else if (extension == ".zst")
    {
        throw file_open_error{"Trying to write a zst'ed file, but SeqAn does not yet support this."};
    }
 
    return {&primary_stream, stream_deleter_noop};
}
 
} // namespace seqan3::detail