27 #include <seqan3/io/detail/record.hpp>
164 template <detail::fields_specialisation selected_field_
ids_ = fields<field::seq, field::
id, field::qual>,
165 detail::type_list_of_sequence_file_output_formats val
id_formats_ =
166 type_list<format_embl, format_fasta, format_fastq, format_genbank, format_sam>>
183 #ifdef SEQAN3_DEPRECATED_310
189 static_assert([] () constexpr
191 for (
field f : selected_field_ids::as_array)
192 if (!field_ids::contains(f))
196 "You selected a field that is not valid for sequence files, please refer to the documentation "
197 "of sequence_file_output::field_ids for the accepted values.");
199 #ifdef SEQAN3_DEPRECATED_310
200 static_assert([] () constexpr
206 "You may not select field::seq_qual and either of field::seq and field::qual at the same time.");
225 using iterator = detail::out_file_iterator<sequence_file_output>;
267 primary_stream->rdbuf()->pubsetbuf(stream_buffer.
data(), stream_buffer.
size());
269 std::ios_base::out | std::ios::binary);
271 if (!primary_stream->good())
272 throw file_open_error{
"Could not open file " + filename.
string() +
" for writing."};
275 secondary_stream = detail::make_secondary_ostream(*primary_stream, filename);
278 detail::set_format(format, filename);
296 template <output_stream stream_t,
299 requires std::same_as<typename std::remove_reference_t<stream_t>::char_type,
stream_char_type>
302 file_format
const & SEQAN3_DOXYGEN_ONLY(format_tag),
304 primary_stream{&stream, stream_deleter_noop},
305 secondary_stream{&stream, stream_deleter_noop},
306 format{detail::sequence_file_output_format_exposer<file_format>{}}
308 static_assert(list_traits::contains<file_format, valid_formats>,
309 "You selected a format that is not in the valid_formats of this file.");
313 template <output_stream stream_t,
316 requires std::same_as<typename std::remove_reference_t<stream_t>::char_type,
stream_char_type>
319 file_format
const & SEQAN3_DOXYGEN_ONLY(format_tag),
321 primary_stream{
new stream_t{
std::move(stream)}, stream_deleter_default},
322 secondary_stream{&*primary_stream, stream_deleter_noop},
323 format{detail::sequence_file_output_format_exposer<file_format>{}}
325 static_assert(list_traits::contains<file_format, valid_formats>,
326 "You selected a format that is not in the valid_formats of this file.");
393 template <
typename record_t>
396 requires detail::record_like<record_t>
399 #ifdef SEQAN3_DEPRECATED_310
400 write_record(detail::get_or_ignore<field::seq>(r),
401 detail::get_or_ignore<field::id>(r),
402 detail::get_or_ignore<field::qual>(r),
403 detail::get_or_ignore<field::_seq_qual_deprecated>(r));
405 write_record(detail::get_or_ignore<field::seq>(r),
406 detail::get_or_ignore<field::id>(r),
407 detail::get_or_ignore<field::qual>(r));
432 template <
typename tuple_t>
439 #ifdef SEQAN3_DEPRECATED_310
440 write_record(detail::get_or_ignore<selected_field_ids::index_of(
field::seq)>(t),
441 detail::get_or_ignore<selected_field_ids::index_of(
field::id)>(t),
442 detail::get_or_ignore<selected_field_ids::index_of(
field::qual)>(t),
445 write_record(detail::get_or_ignore<selected_field_ids::index_of(
field::seq)>(t),
446 detail::get_or_ignore<selected_field_ids::index_of(
field::id)>(t),
447 detail::get_or_ignore<selected_field_ids::index_of(
field::qual)>(t));
474 template <
typename arg_t,
typename ...arg_types>
501 template <std::ranges::input_range rng_t>
507 for (
auto &&
record : range)
539 template <std::ranges::input_range rng_t>
550 template <std::ranges::input_range rng_t>
556 #if defined(__GNUC__) && (__GNUC__ == 9)
557 for (
auto &&
record : range)
574 return *secondary_stream;
594 stream_ptr_t primary_stream{
nullptr, stream_deleter_noop};
596 stream_ptr_t secondary_stream{
nullptr, stream_deleter_noop};
599 using format_type =
typename detail::variant_from_tags<
valid_formats,
600 detail::sequence_file_output_format_exposer>::type;
606 #ifdef SEQAN3_DEPRECATED_310
607 template <
typename seq_t,
typename id_t,
typename qual_t,
typename seq_qual_t>
608 void write_record(seq_t && seq, id_t &&
id, qual_t && qual, seq_qual_t && seq_qual)
610 template <
typename seq_t,
typename id_t,
typename qual_t>
611 void write_record(seq_t && seq, id_t &&
id, qual_t && qual)
614 #ifdef SEQAN3_DEPRECATED_310
615 static_assert(detail::decays_to_ignore_v<seq_qual_t> ||
616 (detail::decays_to_ignore_v<seq_t> && detail::decays_to_ignore_v<qual_t>),
617 "You may not select field::seq_qual and either of field::seq and field::qual at the same time.");
619 if constexpr (!detail::decays_to_ignore_v<seq_qual_t>)
620 static_assert(detail::is_type_specialisation_of_v<std::ranges::range_value_t<seq_qual_t>, qualified>,
621 "The SEQ_QUAL field must contain a range over the seqan3::qualified alphabet.");
624 assert(!
format.valueless_by_exception());
627 #ifdef SEQAN3_DEPRECATED_310
628 if constexpr (!detail::decays_to_ignore_v<seq_qual_t>)
630 f.write_sequence_record(*secondary_stream,
632 seq_qual | views::elements<0>,
634 seq_qual | views::elements<1>);
639 f.write_sequence_record(*secondary_stream,
658 template <output_stream stream_t,
666 template <output_stream stream_t,
674 template <output_stream stream_t,
684 template <output_stream stream_t,
A class for writing sequence files, e.g. FASTA, FASTQ ...
Definition: output.hpp:168
void push_back(record_t &&r)
Write a seqan3::record to the file.
Definition: output.hpp:394
sequence_file_output(std::filesystem::path filename, selected_field_ids const &fields_tag=selected_field_ids{})
Construct from filename.
Definition: output.hpp:263
void const_iterator
The const iterator type is void, because files are not const-iterable.
Definition: output.hpp:227
sequence_file_output & operator=(sequence_file_output const &)=delete
Copy assignment is explicitly deleted, because you can't have multiple access to the same file.
char stream_char_type
Character type of the stream(s).
Definition: output.hpp:179
std::default_sentinel_t sentinel
The type returned by end().
Definition: output.hpp:229
sequence_file_output(stream_t &&, file_format const &, selected_field_ids const &) -> sequence_file_output< selected_field_ids, type_list< file_format >>
Deduction guide for given stream, file format and field ids.
friend sequence_file_output operator|(rng_t &&range, sequence_file_output &&f)
This is an overloaded member function, provided for convenience. It differs from the above function o...
Definition: output.hpp:551
sequence_file_output(stream_t &&, file_format const &) -> sequence_file_output< typename sequence_file_output<>::selected_field_ids, type_list< file_format >>
This is an overloaded member function, provided for convenience. It differs from the above function o...
sequence_file_output & operator=(rng_t &&range)
Write a range of records (or tuples) to the file.
Definition: output.hpp:502
sequence_file_output(sequence_file_output &&)=default
Move construction is defaulted.
void push_back(tuple_t &&t)
Write a record in form of a std::tuple to the file.
Definition: output.hpp:433
sequence_file_output(stream_t &, file_format const &) -> sequence_file_output< typename sequence_file_output<>::selected_field_ids, type_list< file_format >>
Deduction guide for given stream and file format.
friend sequence_file_output & operator|(rng_t &&range, sequence_file_output &f)
Write a range of records (or tuples) to the file.
Definition: output.hpp:540
sequence_file_output(sequence_file_output const &)=delete
Copy construction is explicitly deleted, because you can't have multiple access to the same file.
valid_formats_ valid_formats
A seqan3::type_list with the possible formats.
Definition: output.hpp:177
sequence_file_output(stream_t &, file_format const &, selected_field_ids const &) -> sequence_file_output< selected_field_ids, type_list< file_format >>
This is an overloaded member function, provided for convenience. It differs from the above function o...
selected_field_ids_ selected_field_ids
A seqan3::fields list with the fields selected for the record.
Definition: output.hpp:175
~sequence_file_output()=default
Destructor is defaulted.
sequence_file_output_options options
The options are public and its members can be set directly.
Definition: output.hpp:567
void emplace_back(arg_t &&arg, arg_types &&... args)
Write a record to the file by passing individual fields.
Definition: output.hpp:475
void value_type
The value type (void).
Definition: output.hpp:215
sentinel end() noexcept
Returns a sentinel for comparison with iterator.
Definition: output.hpp:370
void reference
The reference type (void).
Definition: output.hpp:217
sequence_file_output & operator=(sequence_file_output &&)=default
Move assignment is defaulted.
void const_reference
The const reference type (void).
Definition: output.hpp:219
sequence_file_output()=delete
Default constructor is explicitly deleted, you need to give a stream or file name.
detail::out_file_iterator< sequence_file_output > iterator
The iterator type of this view (an output iterator).
Definition: output.hpp:225
sequence_file_output(stream_t &stream, file_format const &format_tag, selected_field_ids const &fields_tag=selected_field_ids{})
Construct from an existing stream and with specified format.
Definition: output.hpp:301
sequence_file_output(stream_t &&stream, file_format const &format_tag, selected_field_ids const &fields_tag=selected_field_ids{})
This is an overloaded member function, provided for convenience. It differs from the above function o...
Definition: output.hpp:318
iterator begin() noexcept
Returns an iterator to current position in the file.
Definition: output.hpp:351
void size_type
The size type (void).
Definition: output.hpp:221
Provides seqan3::views::elements.
This header includes C++17 filesystem support and imports it into namespace std::filesystem (independ...
field
An enumerator for the fields used in file formats.
Definition: record.hpp:63
@ _seq_qual_deprecated
[DEPRECATED] Sequence and qualities combined in one range. Use field::seq and field::qual instead.
@ id
The identifier, usually a string.
@ seq
The "sequence", usually a range of nucleotides or amino acids.
@ qual
The qualities, usually in Phred score notation.
constexpr bool contains
Whether a type occurs in a type list or not.
Definition: traits.hpp:231
auto const move
A view that turns lvalue-references into rvalue-references.
Definition: move.hpp:74
Whether a type behaves like a tuple.
Provides various utility functions.
Provides exceptions used in the I/O module.
Provides various utility functions required only for output.
The main SeqAn3 namespace.
Definition: aligned_sequence_concept.hpp:29
Provides the seqan3::detail::out_file_iterator class template.
Provides algorithms for meta programming, parameter packs and seqan3::type_list.
Adaptations of concepts from the Ranges TS.
Provides the seqan3::record template and the seqan3::field enum.
Provides seqan3::detail::record_like.
Provides seqan3::sequence_file_output_options.
A class template that holds a choice of seqan3::field.
Definition: record.hpp:172
The class template that file records are based on; behaves like an std::tuple.
Definition: record.hpp:235
The options type defines various option members that influence the behaviour of all or some formats.
Definition: output_options.hpp:22
Type that contains multiple types.
Definition: type_list.hpp:29
Provides seqan3::tuple_like.
Provides traits for seqan3::type_list.
Provides seqan3::views::convert.
Provides seqan3::views::zip.