99 template <
typename stream_type,
100 typename seq_legal_alph_type,
101 typename stream_pos_type,
107 stream_pos_type & position_buffer,
110 qual_type & qualities)
116 size_t sequence_size_before = 0;
117 size_t sequence_size_after = 0;
118 if constexpr (!detail::decays_to_ignore_v<seq_type>)
119 sequence_size_before = size(
sequence);
120 position_buffer = stream.tellg();
123 if (*stream_it !=
'@')
130#if SEQAN3_WORKAROUND_VIEW_PERFORMANCE
131 auto e = std::ranges::end(stream_view);
132 if constexpr (!detail::decays_to_ignore_v<id_type>)
136 for (; (stream_it != e) && (!(
is_cntrl ||
is_blank))(*stream_it); ++stream_it)
139 id.push_back(*stream_it);
141 id.push_back(
assign_char_to(*stream_it, std::ranges::range_value_t<id_type>{}));
143 for (; (stream_it != e) && (!
is_char<
'\n'>)(*stream_it); ++stream_it)
148 for (; (stream_it != e) && (!
is_char<
'\n'>)(*stream_it); ++stream_it)
151 id.push_back(*stream_it);
153 id.push_back(
assign_char_to(*stream_it, std::ranges::range_value_t<id_type>{}));
159 for (; (stream_it != e) && (!
is_char<
'\n'>)(*stream_it); ++stream_it)
170 if constexpr (!detail::decays_to_ignore_v<seq_type>)
172 for (; (stream_it != e) && (!
is_char<
'+'>)(*stream_it); ++stream_it)
182 if (!char_is_valid_for<seq_legal_alph_type>(*stream_it))
191 sequence_size_after = size(
sequence);
195 for (; (stream_it != e) && (!
is_char<
'+'>)(*stream_it); ++stream_it)
197 ++sequence_size_after;
204 if (*stream_it !=
'+')
210 for (; (stream_it != e) && (!
is_char<
'\n'>)(*stream_it); ++stream_it)
219 if constexpr (!detail::decays_to_ignore_v<qual_type>)
221 while (sequence_size_after > sequence_size_before)
228 --sequence_size_after;
231 qualities.push_back(*stream_it);
248 while (sequence_size_after > sequence_size_before)
254 --sequence_size_after;
261 if ((!
is_char<
'\n'>)(*stream_it))
262 throw parse_error{
"Qualitites longer than sequence."};
269 if constexpr (!detail::decays_to_ignore_v<id_type>)
293 if constexpr (!detail::decays_to_ignore_v<seq_type>)
295 constexpr auto is_legal_alph = char_is_valid_for<seq_legal_alph_type>;
298 | std::views::transform(
299 [is_legal_alph](
char const c)
301 if (!is_legal_alph(c))
304 +
"char_is_valid_for<"
305 + detail::type_name_as_string<seq_legal_alph_type>
312 sequence_size_after = size(
sequence);
316 auto it = begin(seq_view);
317 auto it_end = end(seq_view);
321 ++sequence_size_after;
328 auto qview = stream_view | std::views::filter(!
is_space)
330 if constexpr (!detail::decays_to_ignore_v<qual_type>)
343 template <
typename stream_type,
351 qual_type && qualities)
356 if constexpr (detail::decays_to_ignore_v<id_type>)
358 throw std::logic_error{
"The ID field may not be set to ignore when writing FASTQ files."};
362 if (std::ranges::empty(
id))
366 stream_it.write_range(
id);
371 if constexpr (detail::decays_to_ignore_v<seq_type>)
374 "The SEQ and SEQ_QUAL fields may not both be set to ignore when writing FASTQ files."};
386 if constexpr (!detail::decays_to_ignore_v<id_type>)
391 stream_it.write_range(
id);
397 if constexpr (detail::decays_to_ignore_v<qual_type>)
400 "The QUAL and SEQ_QUAL fields may not both be set to ignore when writing FASTQ files."};
404 if (std::ranges::empty(qualities))
407 if constexpr (std::ranges::sized_range<seq_type> && std::ranges::sized_range<qual_type>)
409 assert(std::ranges::size(
sequence) == std::ranges::size(qualities));
Provides aliases for qualified.
Core alphabet concept and free function/type trait wrappers.
T back_inserter(T... args)
Provides alphabet adaptations for standard char types.
Provides seqan3::views::char_to.
Functionally the same as std::ostreambuf_iterator, but offers writing a range more efficiently.
Definition: fast_ostreambuf_iterator.hpp:40
Provides various utility functions.
Provides various transformation traits used by the range module.
Provides seqan3::dna5, container aliases and string literals.
Provides seqan3::detail::fast_ostreambuf_iterator.
auto const to_char
A view that calls seqan3::to_char() on each element in the input range.
Definition: to_char.hpp:63
auto const char_to
A view over an alphabet, given a range of characters.
Definition: char_to.hpp:67
constexpr auto assign_char_to
Assign a character to an alphabet object.
Definition: alphabet/concept.hpp:524
constexpr auto char_is_valid_for
Returns whether a character is in the valid set of a seqan3::alphabet (usually implies a bijective ma...
Definition: alphabet/concept.hpp:670
constexpr void consume(rng_t &&rng)
Iterate over a range (consumes single-pass input ranges).
Definition: core/range/detail/misc.hpp:28
constexpr auto take_exactly_or_throw
A view adaptor that returns the first size elements from the underlying range and also exposes size i...
Definition: take_exactly_view.hpp:590
constexpr auto take_until_or_throw
A view adaptor that returns elements from the underlying range until the functor evaluates to true (t...
Definition: take_until_view.hpp:574
constexpr auto istreambuf
A view factory that returns a view over the stream buffer of an input stream.
Definition: istreambuf_view.hpp:107
constexpr auto take_line_or_throw
A view adaptor that returns a single line from the underlying range (throws if there is no end-of-lin...
Definition: take_line_view.hpp:85
constexpr auto is_blank
Checks whether c is a blank character.
Definition: predicate.hpp:142
std::string make_printable(char const c)
Returns a printable value for the given character c.
Definition: pretty_print.hpp:48
constexpr auto is_char
Checks whether a given letter is the same as the template non-type argument.
Definition: predicate.hpp:63
constexpr auto is_space
Checks whether c is a space character.
Definition: predicate.hpp:125
constexpr auto is_cntrl
Checks whether c is a control character.
Definition: predicate.hpp:90
Provides seqan3::detail::ignore_output_iterator for writing to null stream.
This concept encompasses exactly the types char, signed char, unsigned char, wchar_t,...
The generic concept for a (biological) sequence.
Provides various utility functions.
Provides seqan3::detail::istreambuf.
The main SeqAn3 namespace.
Definition: aligned_sequence_concept.hpp:29
SeqAn specific customisations in the standard namespace.
Provides character predicates for tokenisation.
Provides seqan3::sequence_file_output_options.
Thrown if there is a parse error, such as reading an unexpected character from an input stream.
Definition: io/exception.hpp:48
The options type defines various option members that influence the behaviour of all or some formats.
Definition: sequence_file/output_options.hpp:26
bool add_carriage_return
The default plain text line-ending is "\n", but on Windows an additional carriage return is recommend...
Definition: sequence_file/output_options.hpp:42
bool fastq_double_id
Whether to write the ID only '@' or also after '+' line.
Definition: sequence_file/output_options.hpp:37
Provides seqan3::views::take_exactly and seqan3::views::take_exactly_or_throw.
Provides seqan3::detail::take_line and seqan3::detail::take_line_or_throw.
Provides seqan3::views::take_until and seqan3::views::take_until_or_throw.
Provides seqan3::views::to_char.
Provides traits to inspect some information of a type, for example its name.
Provides concepts that do not have equivalents in C++20.