24 #ifdef SEQAN3_HAS_BZIP2
25 #include <seqan3/contrib/stream/bz2_istream.hpp>
27 #ifdef SEQAN3_HAS_ZLIB
28 #include <seqan3/contrib/stream/bgzf_istream.hpp>
30 #include <seqan3/contrib/stream/gz_istream.hpp>
43 template <std::ranges::forward_range ref_t, std::ranges::forward_range query_t>
46 requires std::equality_comparable_with<std::ranges::range_reference_t<ref_t>,
47 std::ranges::range_reference_t<query_t>>
53 auto qit = std::ranges::begin(query);
54 auto qend = std::ranges::end(query);
78 template <builtin_
character
char_t>
82 assert(primary_stream.good());
92 size_t read_chars = 0;
93 for (; read_chars < magic_number.size(); ++read_chars)
98 magic_number[read_chars] = *it;
103 for (
size_t i = 0 ; i < read_chars; ++i)
104 primary_stream.unget();
107 if (filename.has_extension())
108 extension = filename.extension().
string().substr(1);
111 [[maybe_unused]]
auto contains_extension = [] (
auto compression_tag,
auto const & extension) constexpr
113 return std::ranges::find(decltype(compression_tag)::file_extensions, extension) !=
114 std::ranges::end(decltype(compression_tag)::file_extensions);
120 #ifdef SEQAN3_HAS_ZLIB
122 filename.replace_extension();
124 return {
new contrib::basic_bgzf_istream<char_t>{primary_stream},
125 stream_deleter_default};
127 throw file_open_error{
"Trying to read from a bgzf file, but no ZLIB available."};
132 #ifdef SEQAN3_HAS_ZLIB
134 filename.replace_extension();
136 return {
new contrib::basic_gz_istream<char_t>{primary_stream}, stream_deleter_default};
138 throw file_open_error{
"Trying to read from a gzipped file, but no ZLIB available."};
143 #ifdef SEQAN3_HAS_BZIP2
145 filename.replace_extension();
147 return {
new contrib::basic_bz2_istream<char_t>{primary_stream}, stream_deleter_default};
149 throw file_open_error{
"Trying to read from a bzipped file, but no libbz2 available."};
154 throw file_open_error{
"Trying to read from a zst'ed file, but SeqAn does not yet support this."};
157 return {&primary_stream, stream_deleter_noop};
161 template <builtin_
character
char_t>
Adaptations of algorithms from the Ranges TS.
Provides stream compression utilities.
Provides concepts for core language types and relations that don't have concepts in C++20 (yet).
This header includes C++17 filesystem support and imports it into namespace std::filesystem (independ...
constexpr ptrdiff_t find
Get the index of the first occurrence of a type in a pack.
Definition: traits.hpp:186
Provides exceptions used in the I/O module.
The internal SeqAn3 namespace.
Definition: aligned_sequence_concept.hpp:29
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:79
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:44
Adaptations of concepts from the Ranges TS.
Provides std::span from the C++20 standard library.
A tag signifying a bgzf compressed file.
Definition: magic_header.hpp:74
static bool validate_header(std::span< char_t, extend > header)
Checks if the given header is a bgzf header.
Definition: magic_header.hpp:97
static constexpr std::array< char, 18 > magic_header
The magic byte sequence to disambiguate bgzf compressed files.
Definition: magic_header.hpp:83
A tag signifying a bz2 compressed file.
Definition: magic_header.hpp:46
static constexpr std::array< char, 3 > magic_header
The magic byte sequence to disambiguate bz2 compressed files.
Definition: magic_header.hpp:54
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:40
This is helper structure to deprecate seqan3::reference and will be removed before SeqAn 3....
Definition: pre.hpp:81
static constexpr std::array< char, 4 > magic_header
The magic byte sequence to disambiguate zstd compressed files.
Definition: magic_header.hpp:68
Thrown if there is an unspecified filesystem or stream error while opening, e.g. permission problem.
Definition: exception.hpp:40