65template <detail::fields_specialisation selected_field_
ids_ = fields<field::seq, field::
id, field::qual>,
66 detail::type_list_of_sequence_file_output_formats val
id_formats_ =
67 type_list<format_embl, format_fasta, format_fastq, format_genbank, format_sam>>
86 static_assert([] ()
constexpr
88 for (
field f : selected_field_ids::as_array)
93 "You selected a field that is not valid for sequence files, please refer to the documentation "
94 "of sequence_file_output::field_ids for the accepted values.");
156 std::ios_base::out | std::ios::binary);
159 throw file_open_error{
"Could not open file " + filename.
string() +
" for writing."};
183 template <output_stream stream_t,
186 requires std::same_as<typename std::remove_reference_t<stream_t>::char_type,
stream_char_type>
189 file_format
const & SEQAN3_DOXYGEN_ONLY(format_tag),
193 format{detail::sequence_file_output_format_exposer<file_format>{}}
195 static_assert(list_traits::contains<file_format, valid_formats>,
196 "You selected a format that is not in the valid_formats of this file.");
200 template <output_stream stream_t,
203 requires std::same_as<typename std::remove_reference_t<stream_t>::char_type,
stream_char_type>
206 file_format
const & SEQAN3_DOXYGEN_ONLY(format_tag),
210 format{detail::sequence_file_output_format_exposer<file_format>{}}
212 static_assert(list_traits::contains<file_format, valid_formats>,
213 "You selected a format that is not in the valid_formats of this file.");
280 template <
typename record_t>
283 requires detail::record_like<record_t>
287 detail::get_or_ignore<field::id>(r),
288 detail::get_or_ignore<field::qual>(r));
312 template <
typename tuple_t>
347 template <
typename arg_t,
typename ...arg_types>
374 template <std::ranges::input_range rng_t>
380 for (
auto &&
record : range)
412 template <std::ranges::input_range rng_t>
423 template <std::ranges::input_range rng_t>
429 #if defined(__GNUC__) && (__GNUC__ == 9)
430 for (
auto &&
record : range)
479 template <
typename seq_t,
typename id_t,
typename qual_t>
482 assert(!
format.valueless_by_exception());
505template <output_stream stream_t,
513template <output_stream stream_t,
521template <output_stream stream_t,
531template <output_stream stream_t,
Output iterator necessary for providing a range-like interface in output file.
Definition: out_file_iterator.hpp:47
A class for writing sequence files, e.g. FASTA, FASTQ ...
Definition: output.hpp:69
static void stream_deleter_noop(std::basic_ostream< stream_char_type > *)
Stream deleter that does nothing (no ownership assumed).
Definition: output.hpp:462
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.
void push_back(record_t &&r)
Write a seqan3::record to the file.
Definition: output.hpp:281
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...
sequence_file_output(std::filesystem::path filename, selected_field_ids const &fields_tag=selected_field_ids{})
Construct from filename.
Definition: output.hpp:150
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...
void const_iterator
The const iterator type is void, because files are not const-iterable.
Definition: output.hpp:114
char stream_char_type
Character type of the stream(s).
Definition: output.hpp:80
std::default_sentinel_t sentinel
The type returned by end().
Definition: output.hpp:116
typename detail::variant_from_tags< valid_formats, detail::sequence_file_output_format_exposer >::type format_type
Type of the format, a std::variant over the valid_formats.
Definition: output.hpp:473
friend iterator
Befriend iterator so it can access the buffers.
Definition: output.hpp:496
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:424
format_type format
The actual std::variant holding a pointer to the detected/selected format.
Definition: output.hpp:475
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:313
stream_ptr_t primary_stream
The primary stream is the user provided stream or the file stream if constructed from filename.
Definition: output.hpp:467
sequence_file_output & operator=(sequence_file_output &&)=default
Move assignment is defaulted.
sequence_file_output(sequence_file_output const &)=delete
Copy construction is explicitly deleted, because you can't have multiple access to the same file.
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:413
valid_formats_ valid_formats
A seqan3::type_list with the possible formats.
Definition: output.hpp:78
selected_field_ids_ selected_field_ids
A seqan3::fields list with the fields selected for the record.
Definition: output.hpp:76
~sequence_file_output()=default
Destructor is defaulted.
std::basic_ostream< stream_char_type > & get_stream()
Expose a reference to the secondary stream. [public, but not documented as part of the API].
Definition: output.hpp:445
sequence_file_output_options options
The options are public and its members can be set directly.
Definition: output.hpp:440
sequence_file_output & operator=(rng_t &&range)
Write a range of records (or tuples) to the file.
Definition: output.hpp:375
void emplace_back(arg_t &&arg, arg_types &&... args)
Write a record to the file by passing individual fields.
Definition: output.hpp:348
void value_type
The value type (void).
Definition: output.hpp:102
sentinel end() noexcept
Returns a sentinel for comparison with iterator.
Definition: output.hpp:257
void reference
The reference type (void).
Definition: output.hpp:104
std::vector< char > stream_buffer
A larger (compared to stl default) stream buffer to use when reading from a file.
Definition: output.hpp:453
static void stream_deleter_default(std::basic_ostream< stream_char_type > *ptr)
Stream deleter with default behaviour (ownership assumed).
Definition: output.hpp:464
stream_ptr_t secondary_stream
The secondary stream is a compression layer on the primary or just points to the primary (no compress...
Definition: output.hpp:469
void const_reference
The const reference type (void).
Definition: output.hpp:106
void write_record(seq_t &&seq, id_t &&id, qual_t &&qual)
Write record to format.
Definition: output.hpp:480
sequence_file_output()=delete
Default constructor is explicitly deleted, you need to give a stream or file name.
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:188
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:205
iterator begin() noexcept
Returns an iterator to current position in the file.
Definition: output.hpp:238
void size_type
The size type (void).
Definition: output.hpp:108
Auxiliary concept that checks whether a type is a specialisation of seqan3::fields.
Definition: record.hpp:35
Provides auxiliary data structures and functions for seqan3::record and seqan3::fields.
Provides seqan3::views::elements.
field
An enumerator for the fields used in file formats.
Definition: record.hpp:63
auto & get_or_ignore(record< field_types, field_ids > &r)
Access an element in a std::tuple or seqan3::record; return reference to std::ignore if not contained...
Definition: record.hpp:117
void set_format(format_variant_type &format, std::filesystem::path const &file_name)
Sets the file format according to the file name extension.
Definition: misc.hpp:67
auto make_secondary_ostream(std::basic_ostream< char_t > &primary_stream, std::filesystem::path &filename) -> std::unique_ptr< std::basic_ostream< char_t >, std::function< void(std::basic_ostream< char_t > *)> >
Depending on the given filename/extension, create a compression stream or just forward the primary st...
Definition: misc_output.hpp:42
@ 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.
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: cleanup.hpp:4
Provides the seqan3::detail::out_file_iterator class template.
The <ranges> header from C++20's standard library.
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:128
static constexpr bool contains(field f)
Whether a field is contained in the parameter pack.
Definition: record.hpp:149
The class template that file records are based on; behaves like a std::tuple.
Definition: record.hpp:191
The options type defines various option members that influence the behaviour of all or some formats.
Definition: output_options.hpp:26
Type that contains multiple types.
Definition: type_list.hpp:29
Provides traits for seqan3::type_list.
Provides seqan3::tuple_like.
Provides seqan3::views::convert.
Provides seqan3::views::zip.