misc_input.hpp

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// SPDX-FileCopyrightText: 2006-2025 Knut Reinert & Freie Universität Berlin
// SPDX-FileCopyrightText: 2016-2025 Knut Reinert & MPI für molekulare Genetik
// SPDX-License-Identifier: BSD-3-Clause
 
#pragma once
 
#include <algorithm>
#include <concepts>
#include <filesystem>
#include <iostream>
#include <ranges>
#include <span>
#include <string>
#include <tuple>
 
#include <seqan3/contrib/stream/bgzf.hpp>
#include <seqan3/contrib/stream/bgzf_istream.hpp>
#include <seqan3/contrib/stream/bgzf_stream_util.hpp>
#include <seqan3/contrib/stream/bz2_istream.hpp>
#include <seqan3/contrib/stream/gz_istream.hpp>
#include <seqan3/io/detail/magic_header.hpp>
#include <seqan3/io/exception.hpp>
#include <seqan3/utility/concept.hpp>
 
namespace seqan3::detail
{
 
template <std::ranges::forward_range ref_t, std::ranges::forward_range query_t>
inline bool starts_with(ref_t && reference, query_t && query)
    requires std::equality_comparable_with<std::ranges::range_reference_t<ref_t>,
                                           std::ranges::range_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 <builtin_character 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, bgzf_compression::magic_header.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(); // If you unget() more characters than are present in the get area, badbit is set.
 
    assert(primary_stream.good() && "`unget()` was called too many times on primary_stream.");
 
    std::string extension{};
    if (filename.has_extension())
        extension = filename.extension().string().substr(1);
 
    // tests whether the given extension matches with one of the given compression tags.
    [[maybe_unused]] auto contains_extension = [](auto compression_tag, auto const & extension) constexpr
    {
        return std::ranges::find(decltype(compression_tag)::file_extensions, extension)
            != std::ranges::end(decltype(compression_tag)::file_extensions);
    };
 
    // set return value appropriately
    if (read_chars == magic_number.size() && bgzf_compression::validate_header(std::span{magic_number})) // BGZF
    {
#if SEQAN3_HAS_ZLIB
        if (contains_extension(gz_compression{}, extension) || contains_extension(bgzf_compression{}, extension))
            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 // SEQAN3_HAS_ZLIB
    }
    else if (starts_with(magic_number, gz_compression::magic_header)) // GZIP
    {
#if SEQAN3_HAS_ZLIB
        if (contains_extension(gz_compression{}, extension) || contains_extension(bgzf_compression{}, extension))
            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 // SEQAN3_HAS_ZLIB
    }
    else if (starts_with(magic_number, bz2_compression::magic_header)) // BZip2
    {
#if SEQAN3_HAS_BZIP2
        if (contains_extension(bz2_compression{}, extension))
            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 // SEQAN3_HAS_BZIP2
    }
    else if (starts_with(magic_number, zstd_compression::magic_header)) // 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 <builtin_character 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