 |
SeqAn3
3.0.2
The Modern C++ library for sequence analysis.
|
|
Go to the documentation of this file.
100 template <
typename stream_type,
101 typename seq_legal_alph_type,
bool seq_qual_combined,
109 qual_type & qualities)
112 auto stream_it = begin(stream_view);
115 size_t sequence_size_before = 0;
116 size_t sequence_size_after = 0;
117 if constexpr (!detail::decays_to_ignore_v<seq_type>)
121 if (*stream_it !=
'@')
124 detail::make_printable(*stream_it)};
128 if constexpr (!detail::decays_to_ignore_v<id_type>)
134 std::cpp20::back_inserter(
id));
141 std::cpp20::back_inserter(
id));
152 if constexpr (!detail::decays_to_ignore_v<seq_type>)
154 auto constexpr is_legal_alph = is_in_alphabet<seq_legal_alph_type>;
157 if (!is_legal_alph(c))
161 " evaluated to false on " +
162 detail::make_printable(c)};
167 std::cpp20::back_inserter(
sequence));
172 auto it = begin(seq_view);
173 auto it_end = end(seq_view);
177 ++sequence_size_after;
182 if (*stream_it !=
'+')
185 detail::make_printable(*stream_it)};
190 auto qview = stream_view | std::views::filter(!
is_space)
192 if constexpr (seq_qual_combined)
196 std::ranges::copy(qview |
views::char_to<
typename std::ranges::range_value_t<qual_type>::quality_alphabet_type>,
197 begin(qualities) + sequence_size_before);
199 else if constexpr (!detail::decays_to_ignore_v<qual_type>)
201 std::ranges::copy(qview |
views::char_to<std::ranges::range_value_t<qual_type>>,
202 std::cpp20::back_inserter(qualities));
206 detail::consume(qview);
211 template <
typename stream_type,
219 qual_type && qualities)
221 seqan3::detail::fast_ostreambuf_iterator stream_it{*stream.rdbuf()};
224 if constexpr (detail::decays_to_ignore_v<id_type>)
226 throw std::logic_error{
"The ID field may not be set to ignore when writing FASTQ files."};
230 if (std::ranges::empty(
id))
234 stream_it.write_range(
id);
239 if constexpr (detail::decays_to_ignore_v<seq_type>)
241 throw std::logic_error{
"The SEQ and SEQ_QUAL fields may not both be set to ignore when writing FASTQ files."};
253 if constexpr (!detail::decays_to_ignore_v<id_type>)
258 stream_it.write_range(
id);
264 if constexpr (detail::decays_to_ignore_v<qual_type>)
266 throw std::logic_error{
"The QUAL and SEQ_QUAL fields may not both be set to ignore when writing FASTQ files."};
270 if (std::ranges::empty(qualities))
273 if constexpr (std::ranges::sized_range<seq_type> && std::ranges::sized_range<qual_type>)
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.hpp:91
Provides seqan3::views::take_until and seqan3::views::take_until_or_throw.
auto const char_to
A view over an alphabet, given a range of characters.
Definition: char_to.hpp:69
bool fastq_double_id
Whether to write the ID only '@' or also after '+' line.
Definition: output_options.hpp:34
constexpr auto is_space
Checks whether c is a space character.
Definition: predicate.hpp:146
Adaptations of algorithms from the Ranges TS.
Thrown if there is a parse error, such as reading an unexpected character from an input stream.
Definition: exception.hpp:48
Provides various transformation traits used by the range module.
Provides seqan3::dna5, container aliases and string literals.
The main SeqAn3 namespace.
Definition: aligned_sequence_concept.hpp:29
The options type defines various option members that influence the behaviour of all or some formats.
Definition: output_options.hpp:22
bool add_carriage_return
The default plain text line-ending is "\n", but on Windows an additional carriage return is recommend...
Definition: output_options.hpp:39
Provides seqan3::sequence_file_output_options.
constexpr auto is_cntrl
Checks whether c is a control character.
Definition: predicate.hpp:110
constexpr size_t size
The size of a type pack.
Definition: traits.hpp:116
Provides alphabet adaptations for standard char types.
Provides seqan3::views::to_char.
Provides seqan3::views::take.
Adaptations of concepts from the Ranges TS.
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.hpp:90
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.hpp:624
Provides seqan3::views::take_exactly and seqan3::views::take_exactly_or_throw.
Provides character predicates for tokenisation.
SeqAn specific customisations in the standard namespace.
auto const to_char
A view that calls seqan3::to_char() on each element in the input range.
Definition: to_char.hpp:65
Provides seqan3::detail::ignore_output_iterator for writing to null stream.
Provides aliases for qualified.
Provides seqan3::views::istreambuf.
seqan3::type_list< trait_t< pack_t >... > transform
Apply a transformation trait to every type in the pack and return a seqan3::type_list of the results.
Definition: traits.hpp:307
Provides seqan3::views::take_line and seqan3::views::take_line_or_throw.
Provides seqan3::fast_istreambuf_iterator and seqan3::fast_ostreambuf_iterator, as well as,...
Provides various utility functions.
constexpr auto is_blank
Checks whether c is a blank character.
Definition: predicate.hpp:163
Provides various utility functions.
The generic concept for a sequence.
Provides seqan3::views::char_to.
constexpr auto istreambuf
A view factory that returns a view over the stream buffer of an input stream.
Definition: istreambuf.hpp:113