misc_input.hpp

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// -----------------------------------------------------------------------------------------------------
// Copyright (c) 2006-2019, Knut Reinert & Freie Universität Berlin
// Copyright (c) 2016-2019, 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 <iostream>
#include <string>
#include <tuple>

#include <seqan3/core/concept/core_language.hpp>
#ifdef SEQAN3_HAS_BZIP2
    #include <seqan3/contrib/stream/bz2_istream.hpp>
#endif
#ifdef SEQAN3_HAS_ZLIB
    #include <seqan3/contrib/stream/bgzf_istream.hpp>
    #include <seqan3/contrib/stream/bgzf_stream_util.hpp>
    #include <seqan3/contrib/stream/gz_istream.hpp>
#endif
#include <seqan3/io/detail/magic_header.hpp>
#include <seqan3/std/concepts>
#include <seqan3/std/filesystem>
#include <seqan3/std/ranges>

namespace seqan3::detail
{

template <std::ranges::ForwardRange ref_t, std::ranges::ForwardRange query_t>
inline bool starts_with(ref_t && reference, query_t && query)
    requires std::EqualityComparableWith<reference_t<ref_t>, reference_t<query_t>>
{
    auto rit  = std::ranges::begin(reference);
    auto rend = std::ranges::end(reference);

    auto qit  = std::ranges::begin(query);
    auto qend = std::ranges::end(query);

    while (true)
    {
        if (qit == qend)
            return true;

        if (rit == rend)
            return false;

        if (*qit != *rit)
            return false;

        ++qit;
        ++rit;
    }
}

template <Char char_t>
inline auto make_secondary_istream(std::basic_istream<char_t> & primary_stream, std::filesystem::path & filename)
    -> std::unique_ptr<std::basic_istream<char_t>, std::function<void(std::basic_istream<char_t>*)>>
{
    assert(primary_stream.good());

    // don't assume ownership
    constexpr auto stream_deleter_noop     = [] (std::basic_istream<char_t> *) {};
    // assume ownership
    [[maybe_unused]] constexpr auto stream_deleter_default  = [] (std::basic_istream<char_t> * ptr) { delete ptr; };

    // extract "magic header"
    std::istreambuf_iterator<char_t> it{primary_stream};
    std::array<char, magic_header<bgzf_compression>.size()> magic_number{}; // Largest magic header from bgzf
    size_t read_chars = 0;
    for (; read_chars < magic_number.size(); ++read_chars)
    {
        if (it == std::istreambuf_iterator<char_t>{})
            break;

        magic_number[read_chars] = *it;
        ++it;
    }

    // unget all read chars.
    for (size_t i = 0 ; i < read_chars; ++i)
        primary_stream.unget();

    std::string const extension = filename.extension().string();

    // set return value appropriately
    if (read_chars == magic_number.size() && contrib::_bgzfCheckHeader(magic_number.data())) // BGZF
    {
    #ifdef SEQAN3_HAS_ZLIB
        if ((extension == ".bgzf"))
            filename.replace_extension();

        return {new contrib::basic_bgzf_istream<char_t>{primary_stream},
                stream_deleter_default};
        #else
            throw file_open_error{"Trying to read from a bgzf file, but no ZLIB available."};
        #endif
    }
    else if (starts_with(magic_number, magic_header<gz_compression>)) // GZIP
    {
    #ifdef SEQAN3_HAS_ZLIB
        if ((extension == ".gz") || (extension == ".bgzf"))
            filename.replace_extension();

        return {new contrib::basic_gz_istream<char_t>{primary_stream}, stream_deleter_default};
    #else
        throw file_open_error{"Trying to read from a gzipped file, but no ZLIB available."};
    #endif
    }
    else if (starts_with(magic_number, magic_header<bz2_compression>)) // BZip2
    {
    #ifdef SEQAN3_HAS_BZIP2
        if (extension == ".bz2")
            filename.replace_extension();

        return {new contrib::basic_bz2_istream<char_t>{primary_stream}, stream_deleter_default};
    #else
        throw file_open_error{"Trying to read from a bzipped file, but no libbz2 available."};
    #endif
    }
    else if (starts_with(magic_number, magic_header<zstd_compression>)) // ZStd
    {
        throw file_open_error{"Trying to read from a zst'ed file, but SeqAn does not yet support this."};
    }

    return {&primary_stream, stream_deleter_noop};
}

template <Char char_t>
inline auto make_secondary_istream(std::basic_istream<char_t> & primary_stream)
{
    std::filesystem::path p;
    return make_secondary_istream(primary_stream, p);
}

} // namespace seqan3::detail