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SeqAn3
3.0.1
The Modern C++ library for sequence analysis.
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Go to the documentation of this file.
22 #pragma GCC diagnostic push
23 #pragma GCC diagnostic ignored "-Wdeprecated-declarations"
35 #include <seqan3/io/detail/record.hpp>
169 template <detail::fields_specialisation selected_field_
ids_ = fields<field::seq, field::
id, field::qual>,
170 detail::type_list_of_sequence_file_output_formats val
id_formats_ =
171 type_list<format_embl, format_fasta, format_fastq, format_genbank, format_sam>>
190 static_assert([] () constexpr
192 for (
field f : selected_field_ids::as_array)
193 if (!field_ids::contains(f))
197 "You selected a field that is not valid for sequence files, please refer to the documentation "
198 "of sequence_file_output::field_ids for the accepted values.");
200 static_assert([] () constexpr
206 "You may not select field::seq_qual and either of field::seq and field::qual at the same time.");
224 using iterator = detail::out_file_iterator<sequence_file_output>;
264 primary_stream{
new std::ofstream{filename, std::ios_base::out | std::ios::binary}, stream_deleter_default}
266 if (!primary_stream->good())
267 throw file_open_error{
"Could not open file " + filename.
string() +
" for writing."};
270 secondary_stream = detail::make_secondary_ostream(*primary_stream, filename);
273 detail::set_format(format, filename);
291 template <output_stream stream_t,
297 file_format
const & SEQAN3_DOXYGEN_ONLY(format_tag),
299 primary_stream{&stream, stream_deleter_noop},
300 secondary_stream{&stream, stream_deleter_noop},
301 format{detail::sequence_file_output_format_exposer<file_format>{}}
303 static_assert(list_traits::contains<file_format, valid_formats>,
304 "You selected a format that is not in the valid_formats of this file.");
308 template <output_stream stream_t,
314 file_format
const & SEQAN3_DOXYGEN_ONLY(format_tag),
316 primary_stream{
new stream_t{
std::move(stream)}, stream_deleter_default},
317 secondary_stream{&*primary_stream, stream_deleter_noop},
318 format{detail::sequence_file_output_format_exposer<file_format>{}}
320 static_assert(list_traits::contains<file_format, valid_formats>,
321 "You selected a format that is not in the valid_formats of this file.");
388 template <
typename record_t>
391 requires { requires detail::is_type_specialisation_of_v<remove_cvref_t<record_t>,
record>; }
393 write_record(detail::get_or_ignore<field::seq>(r),
394 detail::get_or_ignore<field::id>(r),
395 detail::get_or_ignore<field::qual>(r),
396 detail::get_or_ignore<field::seq_qual>(r));
421 template <
typename tuple_t>
426 write_record(detail::get_or_ignore<selected_field_ids::index_of(
field::seq)>(t),
427 detail::get_or_ignore<selected_field_ids::index_of(
field::id)>(t),
428 detail::get_or_ignore<selected_field_ids::index_of(
field::qual)>(t),
429 detail::get_or_ignore<selected_field_ids::index_of(
field::seq_qual)>(t));
455 template <
typename arg_t,
typename ...arg_types>
482 template <std::ranges::input_range rng_t>
486 for (
auto &&
record : range)
518 template <std::ranges::input_range rng_t>
527 template <std::ranges::input_range rng_t>
531 #if defined(__GNUC__) && (__GNUC__ == 9) // an unreported build problem of GCC9
532 for (
auto &&
record : range)
534 #else // ^^^ workaround | regular solution ↓↓↓
549 return *secondary_stream;
567 stream_ptr_t primary_stream{
nullptr, stream_deleter_noop};
569 stream_ptr_t secondary_stream{
nullptr, stream_deleter_noop};
572 using format_type =
typename detail::variant_from_tags<
valid_formats,
573 detail::sequence_file_output_format_exposer>::type;
579 template <
typename seq_t,
typename id_t,
typename qual_t,
typename seq_qual_t>
580 void write_record(seq_t &&
seq, id_t &&
id, qual_t &&
qual, seq_qual_t &&
seq_qual)
582 static_assert(detail::decays_to_ignore_v<seq_qual_t> ||
583 (detail::decays_to_ignore_v<seq_t> && detail::decays_to_ignore_v<qual_t>),
584 "You may not select field::seq_qual and either of field::seq and field::qual at the same time.");
586 if constexpr (!detail::decays_to_ignore_v<seq_qual_t>)
587 static_assert(detail::is_type_specialisation_of_v<value_type_t<seq_qual_t>, qualified>,
588 "The SEQ_QUAL field must contain a range over the seqan3::qualified alphabet.");
590 assert(!format.valueless_by_exception());
593 if constexpr (!detail::decays_to_ignore_v<seq_qual_t>)
595 f.write_sequence_record(*secondary_stream,
603 f.write_sequence_record(*secondary_stream,
621 template <output_stream stream_t,
624 sequence_file_output(stream_t &,
627 type_list<file_format>>;
630 template <output_stream stream_t,
632 sequence_file_output(stream_t &&,
635 type_list<file_format>>;
638 template <output_stream stream_t,
640 detail::fields_specialisation selected_field_ids>
641 sequence_file_output(stream_t &&,
643 selected_field_ids
const &)
644 -> sequence_file_output<selected_field_ids,
645 type_list<file_format>>;
648 template <output_stream stream_t,
650 detail::fields_specialisation selected_field_ids>
651 sequence_file_output(stream_t &,
653 selected_field_ids
const &)
654 -> sequence_file_output<selected_field_ids,
655 type_list<file_format>>;
659 #pragma GCC diagnostic pop
std::ranges::default_sentinel_t sentinel
The type returned by end().
Definition: output.hpp:228
Sequence and qualities combined in one range.
void reference
The reference type (void).
Definition: output.hpp:216
Provides seqan3::views::zip.
The "sequence", usually a range of nucleotides or amino acids.
void push_back(tuple_t &&t) requires tuple_like< tuple_t >
Write a record in form of a std::tuple to the file.
Definition: output.hpp:422
sequence_file_output_options options
The options are public and its members can be set directly.
Definition: output.hpp:542
Provides algorithms for meta programming, parameter packs and seqan3::type_list.
Provides various utility functions required only for output.
Provides seqan3::tuple_like.
void value_type
The value type (void).
Definition: output.hpp:214
Provides seqan3::views::convert.
The identifier, usually a string.
const auto move
A view that turns lvalue-references into rvalue-references.
Definition: move.hpp:68
iterator begin() noexcept
Returns an iterator to current position in the file.
Definition: output.hpp:346
Provides the seqan3::record template and the seqan3::field enum.
sequence_file_output & operator=(rng_t &&range) requires tuple_like< reference_t< rng_t >>
Write a range of records (or tuples) to the file.
Definition: output.hpp:483
This header includes C++17 filesystem support and imports it into namespace seqan3::filesystem (indep...
friend sequence_file_output & operator|(rng_t &&range, sequence_file_output &f) requires tuple_like< reference_t< rng_t >>
Write a range of records (or tuples) to the file.
Definition: output.hpp:519
valid_formats_ valid_formats
A seqan3::type_list with the possible formats.
Definition: output.hpp:182
constexpr bool contains
Whether a type occurs in a pack or not.
Definition: traits.hpp:193
friend sequence_file_output operator|(rng_t &&range, sequence_file_output &&f) requires tuple_like< reference_t< rng_t >>
This is an overloaded member function, provided for convenience. It differs from the above function o...
Definition: output.hpp:528
A class template that holds a choice of seqan3::field.
Definition: record.hpp:165
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.
The concept std::same_as<T, U> is satisfied if and only if T and U denote the same type.
sentinel end() noexcept
Returns a sentinel for comparison with iterator.
Definition: output.hpp:365
selected_field_ids_ selected_field_ids
A seqan3::fields list with the fields selected for the record.
Definition: output.hpp:180
void push_back(record_t &&r) requires tuple_like< record_t > &&requires
Write a seqan3::record to the file.
Definition: output.hpp:389
Provides exceptions used in the I/O module.
The main SeqAn3 namespace.
Definition: aligned_sequence_concept.hpp:36
A class for writing sequence files, e.g. FASTA, FASTQ ...
Definition: output.hpp:172
The options type defines various option members that influence the behaviour of all or some formats.
Definition: output_options.hpp:21
Provides seqan3::sequence_file_output_options.
void const_reference
The const reference type (void).
Definition: output.hpp:218
Whether a type behaves like a tuple.
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:296
Adaptations of concepts from the Ranges TS.
void emplace_back(arg_t &&arg, arg_types &&... args)
Write a record to the file by passing individual fields.
Definition: output.hpp:456
void const_iterator
The const iterator type is void, because files are not const-iterable.
Definition: output.hpp:226
detail::out_file_iterator< sequence_file_output > iterator
The iterator type of this view (an output iterator).
Definition: output.hpp:224
~sequence_file_output()=default
Destructor is defaulted.
void size_type
The size type (void).
Definition: output.hpp:220
field
An enumerator for the fields used in file formats.
Definition: record.hpp:64
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:313
The class template that file records are based on; behaves like an std::tuple.
Definition: record.hpp:225
sequence_file_output()=delete
Default constructor is explicitly deleted, you need to give a stream or file name.
The qualities, usually in phred-score notation.
char stream_char_type
Character type of the stream(s).
Definition: output.hpp:184
Provides the seqan3::detail::out_file_iterator class template.
sequence_file_output(std::filesystem::path filename, selected_field_ids const &fields_tag=selected_field_ids{})
Construct from filename.
Definition: output.hpp:262
Provides various utility functions.
Provides traits for seqan3::type_list.
Provides seqan3::views::get.