24#if defined(SEQAN3_HAS_BZIP2)
25# include <seqan3/contrib/stream/bz2_istream.hpp>
27#if defined(SEQAN3_HAS_ZLIB)
28# include <seqan3/contrib/stream/bgzf_istream.hpp>
30# include <seqan3/contrib/stream/gz_istream.hpp>
45template <std::ranges::forward_range ref_t, std::ranges::forward_range query_t>
47 requires std::equality_comparable_with<std::ranges::range_reference_t<ref_t>,
48 std::ranges::range_reference_t<query_t>>
51 auto rend = std::ranges::end(reference);
54 auto qend = std::ranges::end(query);
79template <builtin_
character
char_t>
83 assert(primary_stream.good());
96 size_t read_chars = 0;
97 for (; read_chars < magic_number.size(); ++read_chars)
102 magic_number[read_chars] = *it;
107 for (
size_t i = 0; i < read_chars; ++i)
108 primary_stream.unget();
111 if (filename.has_extension())
112 extension = filename.extension().
string().substr(1);
115 [[maybe_unused]]
auto contains_extension = [](
auto compression_tag,
auto const & extension)
constexpr
118 != std::ranges::end(
decltype(compression_tag)::file_extensions);
124#if defined(SEQAN3_HAS_ZLIB)
126 filename.replace_extension();
128 return {
new contrib::basic_bgzf_istream<char_t>{primary_stream}, stream_deleter_default};
130 throw file_open_error{
"Trying to read from a bgzf file, but no ZLIB available."};
135#if defined(SEQAN3_HAS_ZLIB)
137 filename.replace_extension();
139 return {
new contrib::basic_gz_istream<char_t>{primary_stream}, stream_deleter_default};
141 throw file_open_error{
"Trying to read from a gzipped file, but no ZLIB available."};
146#if defined(SEQAN3_HAS_BZIP2)
148 filename.replace_extension();
150 return {
new contrib::basic_bz2_istream<char_t>{primary_stream}, stream_deleter_default};
152 throw file_open_error{
"Trying to read from a bzipped file, but no libbz2 available."};
157 throw file_open_error{
"Trying to read from a zst'ed file, but SeqAn does not yet support this."};
160 return {&primary_stream, stream_deleter_noop};
164template <builtin_
character
char_t>
Provides seqan3::contrib::bgzf_thread_count.
Provides stream compression utilities.
bool starts_with(ref_t &&reference, query_t &&query)
Check whether the query range is a prefix of the reference range.
Definition: misc_input.hpp:46
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 > *)> >
Depending on the magic bytes of the given stream, return a decompression stream or forward the primar...
Definition: misc_input.hpp:80
Provides exceptions used in the I/O module.
The internal SeqAn3 namespace.
Definition: aligned_sequence_concept.hpp:29
A tag signifying a bgzf compressed file.
Definition: magic_header.hpp:65
static bool validate_header(std::span< char_t, extend > header)
Checks if the given header is a bgzf header.
Definition: magic_header.hpp:98
static constexpr std::array< char, 18 > magic_header
The magic byte sequence to disambiguate bgzf compressed files.
Definition: magic_header.hpp:70
A tag signifying a bz2 compressed file.
Definition: magic_header.hpp:43
static constexpr std::array< char, 3 > magic_header
The magic byte sequence to disambiguate bz2 compressed files.
Definition: magic_header.hpp:48
A tag signifying a gz compressed file.
Definition: magic_header.hpp:32
static constexpr std::array< char, 3 > magic_header
The magic byte sequence to disambiguate gz compressed files.
Definition: magic_header.hpp:37
static constexpr std::array< char, 4 > magic_header
The magic byte sequence to disambiguate zstd compressed files.
Definition: magic_header.hpp:59
Thrown if there is an unspecified filesystem or stream error while opening, e.g. permission problem.
Definition: exception.hpp:39
Provides concepts that do not have equivalents in C++20.