30#include <seqan3/io/detail/record.hpp>
146 template <
typename _sequence_alphabet>
153 template <
typename _
id_alphabet>
160 template <
typename _quality_alphabet>
206 detail::type_list_of_sequence_file_input_formats valid_formats_ =
232 for (
field f : selected_field_ids::as_array)
233 if (!field_ids::contains(f))
237 "You selected a field that is not valid for sequence files, please refer to the documentation "
238 "of sequence_file_input::field_ids for the accepted values.");
248 using id_type =
typename traits_type::template id_container<typename traits_type::id_alphabet>;
250 using quality_type =
typename traits_type::template quality_container<typename traits_type::quality_alphabet>;
274 using iterator = detail::in_file_iterator<sequence_file_input>;
317 primary_stream->rdbuf()->pubsetbuf(stream_buffer.
data(), stream_buffer.
size());
319 ->open(filename, std::ios_base::in | std::ios::binary);
321 if (!primary_stream->good())
322 throw file_open_error{
"Could not open file " + filename.
string() +
" for reading."};
325 secondary_stream = detail::make_secondary_istream(*primary_stream, filename);
328 using format_variant_t =
329 typename detail::variant_from_tags<valid_formats, detail::sequence_file_input_format_exposer>::type;
330 format_variant_t format_variant{};
331 detail::set_format(format_variant, filename);
334 [&](
auto && selected_format)
337 format = std::make_unique<selected_sequence_format<format_t>>();
362 template <input_stream stream_t, sequence_file_input_format file_format>
363 requires std::same_as<typename std::remove_reference_t<stream_t>::char_type,
stream_char_type>
365 file_format
const & SEQAN3_DOXYGEN_ONLY(format_tag),
367 primary_stream{&stream, stream_deleter_noop},
368 format{std::make_unique<selected_sequence_format<file_format>>()}
370 static_assert(list_traits::contains<file_format, valid_formats>,
371 "You selected a format that is not in the valid_formats of this file.");
374 secondary_stream = detail::make_secondary_istream(*primary_stream);
378 template <input_stream stream_t, sequence_file_input_format file_format>
379 requires std::same_as<typename std::remove_reference_t<stream_t>::char_type,
stream_char_type>
381 file_format
const & SEQAN3_DOXYGEN_ONLY(format_tag),
383 primary_stream{
new stream_t{std::move(stream)}, stream_deleter_default},
384 format{std::make_unique<selected_sequence_format<file_format>>()}
386 static_assert(list_traits::contains<file_format, valid_formats>,
387 "You selected a format that is not in the valid_formats of this file.");
390 secondary_stream = detail::make_secondary_istream(*primary_stream);
415 if (!first_record_was_read)
418 first_record_was_read =
true;
505 stream_ptr_t primary_stream{
nullptr, stream_deleter_noop};
507 stream_ptr_t secondary_stream{
nullptr, stream_deleter_noop};
510 bool first_record_was_read{
false};
517 void read_next_record()
520 record_buffer.clear();
530 format->read_sequence_record(*secondary_stream, record_buffer, position_buffer,
options);
543 struct sequence_format_base
548 sequence_format_base() =
default;
549 sequence_format_base(sequence_format_base
const &) =
default;
550 sequence_format_base(sequence_format_base &&) =
default;
551 sequence_format_base &
operator=(sequence_format_base
const &) =
default;
552 sequence_format_base &
operator=(sequence_format_base &&) =
default;
553 virtual ~sequence_format_base() =
default;
567 virtual void read_sequence_record(
std::istream & instream,
584 template <
typename format_t>
585 struct selected_sequence_format final :
public sequence_format_base
590 selected_sequence_format() =
default;
591 selected_sequence_format(selected_sequence_format
const &) =
default;
592 selected_sequence_format(selected_sequence_format &&) =
default;
593 selected_sequence_format &
operator=(selected_sequence_format
const &) =
default;
594 selected_sequence_format &
operator=(selected_sequence_format &&) =
default;
595 ~selected_sequence_format() =
default;
606 _format.read_sequence_record(instream,
609 detail::get_or_ignore<field::seq>(record_buffer),
610 detail::get_or_ignore<field::id>(record_buffer),
611 detail::get_or_ignore<field::qual>(record_buffer));
616 detail::sequence_file_input_format_exposer<format_t> _format{};
632template <input_stream stream_type, sequence_file_input_format file_format>
640template <input_stream stream_type, sequence_file_input_format file_format>
648template <input_stream stream_type,
659template <input_stream stream_type,
Provides seqan3::aa27, container aliases and string literals.
Provides alphabet adaptations for standard char types.
The twenty-seven letter amino acid alphabet..
Definition: aa27.hpp:46
The 15 letter DNA alphabet, containing all IUPAC smybols minus the gap..
Definition: dna15.hpp:51
The five letter DNA alphabet of A,C,G,T and the unknown character N..
Definition: dna5.hpp:51
Quality type for traditional Sanger and modern Illumina Phred scores..
Definition: phred42.hpp:47
Provides seqan3::dna15, container aliases and string literals.
Provides seqan3::dna5, container aliases and string literals.
field
An enumerator for the fields used in file formats.
Definition: record.hpp:63
Provides the seqan3::detail::in_file_iterator class template.
Checks whether from can be explicitly converted to to.
A more refined container concept than seqan3::container.
Refines seqan3::alphabet and adds assignability.
A concept that indicates whether a writable alphabet represents quality scores.
Provides exceptions used in the I/O module.
The main SeqAn3 namespace.
Definition: aligned_sequence_concept.hpp:29
Provides seqan3::phred42 quality scores.
Provides quality alphabet composites.
Provides seqan3::sequence_record.
A class template that holds a choice of seqan3::field.
Definition: record.hpp:128
Type that contains multiple types.
Definition: type_list.hpp:29
Provides traits for seqan3::type_list.