21#if defined(SEQAN3_HAS_BZIP2)
22# include <seqan3/contrib/stream/bz2_istream.hpp>
24#if defined(SEQAN3_HAS_ZLIB)
25# include <seqan3/contrib/stream/bgzf_istream.hpp>
27# include <seqan3/contrib/stream/gz_istream.hpp>
34namespace seqan3::detail
42template <std::ranges::forward_range ref_t, std::ranges::forward_range query_t>
43inline bool starts_with(ref_t && reference, query_t && query)
44 requires std::equality_comparable_with<std::ranges::range_reference_t<ref_t>,
45 std::ranges::range_reference_t<query_t>>
48 auto rend = std::ranges::end(reference);
51 auto qend = std::ranges::end(query);
76template <builtin_
character
char_t>
80 assert(primary_stream.good());
92 std::array<char, bgzf_compression::magic_header.
size()> magic_number{};
93 size_t read_chars = 0;
94 for (; read_chars < magic_number.size(); ++read_chars)
99 magic_number[read_chars] = *it;
104 for (
size_t i = 0; i < read_chars; ++i)
105 primary_stream.unget();
107 assert(primary_stream.good() &&
"`unget()` was called too many times on primary_stream.");
110 if (filename.has_extension())
111 extension = filename.extension().
string().substr(1);
114 [[maybe_unused]]
auto contains_extension = [](
auto compression_tag,
auto const & extension)
constexpr
117 != std::ranges::end(
decltype(compression_tag)::file_extensions);
121 if (read_chars == magic_number.size() && bgzf_compression::validate_header(
std::span{magic_number}))
123#if defined(SEQAN3_HAS_ZLIB)
124 if (contains_extension(gz_compression{}, extension) || contains_extension(bgzf_compression{}, extension))
125 filename.replace_extension();
127 return {
new contrib::basic_bgzf_istream<char_t>{primary_stream}, stream_deleter_default};
129 throw file_open_error{
"Trying to read from a bgzf file, but no ZLIB available."};
132 else if (starts_with(magic_number, gz_compression::magic_header))
134#if defined(SEQAN3_HAS_ZLIB)
135 if (contains_extension(gz_compression{}, extension) || contains_extension(bgzf_compression{}, extension))
136 filename.replace_extension();
138 return {
new contrib::basic_gz_istream<char_t>{primary_stream}, stream_deleter_default};
140 throw file_open_error{
"Trying to read from a gzipped file, but no ZLIB available."};
143 else if (starts_with(magic_number, bz2_compression::magic_header))
145#if defined(SEQAN3_HAS_BZIP2)
146 if (contains_extension(bz2_compression{}, extension))
147 filename.replace_extension();
149 return {
new contrib::basic_bz2_istream<char_t>{primary_stream}, stream_deleter_default};
151 throw file_open_error{
"Trying to read from a bzipped file, but no libbz2 available."};
154 else if (starts_with(magic_number, zstd_compression::magic_header))
156 throw file_open_error{
"Trying to read from a zst'ed file, but SeqAn does not yet support this."};
159 return {&primary_stream, stream_deleter_noop};
163template <builtin_
character
char_t>
167 return make_secondary_istream(primary_stream, p);
Provides seqan3::contrib::bgzf_thread_count.
Provides stream compression utilities.
Provides exceptions used in the I/O module.
Provides concepts that do not have equivalents in C++20.