130 requires std::same_as<typename t::ref_sequences, ref_info_not_given>
132 requires alphabet<std::ranges::range_reference_t<
133 std::ranges::range_reference_t<typename t::ref_sequences>>>;
138 && (!std::same_as<typename t::ref_sequences, ref_info_not_given>
140 std::ranges::range_reference_t<std::ranges::range_reference_t<typename t::ref_ids>>>);
141 requires std::ranges::forward_range<std::ranges::range_reference_t<typename t::ref_ids>>;
142 requires std::ranges::forward_range<typename t::ref_ids>;
172template <
typename ref_sequences_t = ref_info_not_given,
typename ref_
ids_t = std::deque<std::
string>>
187 template <
typename _sequence_alphabet>
191 template <
typename _
id_alphabet>
198 template <
typename _quality_alphabet>
228template <sam_file_input_traits traits_type_ = sam_file_input_default_traits<>,
229 detail::fields_specialisation selected_field_
ids_ = fields<field::seq,
240 detail::type_list_of_sam_file_input_formats val
id_formats_ = type_list<format_sam, format_bam>>
265 std::ranges::range<typename traits_type::ref_sequences const>,
281 using id_type =
typename traits_type::template id_container<char>;
309 using quality_type =
typename traits_type::template quality_container<typename traits_type::quality_alphabet>;
364 "The seqan3::field::alignment was removed from the allowed fields for seqan::sam_file_input. "
365 "Only seqan3::field::cigar is supported. Please see seqan3::alignment_from_cigar on how to get an "
366 "alignment from the cigar information.");
369 "The field::offset is deprecated. Please access field::cigar and retrieve the soft clipping (S) "
370 "value at the front of the CIGAR string (offset = 0 if there is no soft clipping at the front).");
375 for (
field f : selected_field_ids::as_array)
380 "You selected a field that is not valid for SAM files, please refer to the documentation "
381 "of sam_file_input::field_ids for the accepted values.");
469 template <input_stream stream_t, sam_file_input_format file_format>
470 requires std::same_as<typename std::remove_reference_t<stream_t>::char_type,
stream_char_type>
472 file_format
const & SEQAN3_DOXYGEN_ONLY(format_tag),
476 init_by_format<file_format>();
480 template <input_stream stream_t, sam_file_input_format file_format>
481 requires std::same_as<typename std::remove_reference_t<stream_t>::char_type,
stream_char_type>
483 file_format
const & SEQAN3_DOXYGEN_ONLY(format_tag),
487 init_by_format<file_format>();
519 typename traits_type::ref_ids & ref_ids,
520 typename traits_type::ref_sequences & ref_sequences,
560 template <input_stream stream_t, sam_file_input_format file_format>
562 typename traits_type::ref_ids & ref_ids,
563 typename traits_type::ref_sequences & ref_sequences,
564 file_format
const & SEQAN3_DOXYGEN_ONLY(format_tag),
571 init_by_format<file_format>();
575 template <input_stream stream_t, sam_file_input_format file_format>
577 typename traits_type::ref_ids & ref_ids,
578 typename traits_type::ref_sequences & ref_sequences,
579 file_format
const & SEQAN3_DOXYGEN_ONLY(format_tag),
586 init_by_format<file_format>();
592 typename traits_type::ref_ids &&,
593 typename traits_type::ref_sequences &&,
596 template <input_stream stream_t, sam_file_input_format file_format>
598 typename traits_type::ref_ids &&,
599 typename traits_type::ref_sequences &&,
719 ->open(filename, std::ios_base::in | std::ios::binary);
729 template <
typename format_type>
732 static_assert(list_traits::contains<format_type, valid_formats>,
733 "You selected a format that is not in the valid_formats of this file.");
803 template <std::ranges::forward_range ref_sequences_t>
804 void set_references(
typename traits_type::ref_ids & ref_ids, ref_sequences_t && ref_sequences)
806 assert(std::ranges::distance(ref_ids) == std::ranges::distance(ref_sequences));
812 for (int32_t idx = 0; idx < std::ranges::distance(ref_ids); ++idx)
814 header_ptr->ref_id_info.emplace_back(std::ranges::distance(ref_sequences[idx]),
"");
816 if constexpr (std::ranges::contiguous_range<std::ranges::range_reference_t<typename traits_type::ref_ids>>
817 && std::ranges::sized_range<std::ranges::range_reference_t<typename traits_type::ref_ids>>
818 && std::ranges::borrowed_range<std::ranges::range_reference_t<typename traits_type::ref_ids>>)
846 auto call_read_func = [
this](
auto & ref_seq_info)
873 assert(!
format.valueless_by_exception());
875 if constexpr (!std::same_as<typename traits_type::ref_sequences, ref_info_not_given>)
878 call_read_func(std::ignore);
890template <input_stream stream_type, sam_file_input_format file_format, detail::fields_specialisation selected_field_
ids>
897template <input_stream stream_type, sam_file_input_format file_format, detail::fields_specialisation selected_field_
ids>
904template <input_stream stream_type, sam_file_input_format file_format>
911template <input_stream stream_type, sam_file_input_format file_format>
918template <std::ranges::forward_range ref_ids_t,
919 std::ranges::forward_range ref_sequences_t,
928template <std::ranges::forward_range ref_
ids_t, std::ranges::forward_range ref_sequences_t>
935template <input_stream stream_type,
936 std::ranges::forward_range ref_ids_t,
937 std::ranges::forward_range ref_sequences_t,
947template <input_stream stream_type,
948 std::ranges::forward_range ref_ids_t,
949 std::ranges::forward_range ref_sequences_t,
959template <input_stream stream_type,
960 std::ranges::forward_range ref_ids_t,
961 std::ranges::forward_range ref_sequences_t,
969template <input_stream stream_type,
970 std::ranges::forward_range ref_ids_t,
971 std::ranges::forward_range ref_sequences_t,
Provides seqan3::aa27, container aliases and string literals.
Provides the seqan3::cigar alphabet.
Provides alphabet adaptations for standard char types.
Input iterator necessary for providing a range-like interface in input file.
Definition: in_file_iterator.hpp:41
The 15 letter DNA alphabet, containing all IUPAC smybols minus the gap..
Definition: dna15.hpp:51
The five letter DNA alphabet of A,C,G,T and the unknown character N..
Definition: dna5.hpp:51
Quality type for traditional Sanger and modern Illumina Phred scores..
Definition: phred42.hpp:47
The SAM tag dictionary class that stores all optional SAM fields.
Definition: sam_tag_dictionary.hpp:343
Auxiliary concept that checks whether a type is a specialisation of seqan3::fields.
Definition: detail/record.hpp:35
Provides auxiliary data structures and functions for seqan3::record and seqan3::fields.
Provides seqan3::dna15, container aliases and string literals.
Provides seqan3::dna5, container aliases and string literals.
sam_flag
An enum flag that describes the properties of an aligned read (given as a SAM record).
Definition: sam_flag.hpp:76
field
An enumerator for the fields used in file formats.
Definition: record.hpp:63
void set_format(format_variant_type &format, std::filesystem::path const &file_name)
Sets the file format according to the file name extension.
Definition: io/detail/misc.hpp:68
auto make_secondary_istream(std::basic_istream< char_t > &primary_stream, std::filesystem::path &filename) -> std::unique_ptr< std::basic_istream< char_t >, std::function< void(std::basic_istream< char_t > *)> >
Depending on the magic bytes of the given stream, return a decompression stream or forward the primar...
Definition: misc_input.hpp:80
@ flag
The alignment flag (bit information), uint16_t value.
@ ref_offset
Sequence (seqan3::field::ref_seq) relative start position (0-based), unsigned value.
@ alignment
The (pairwise) alignment stored in an object that models seqan3::detail::pairwise_alignment.
@ cigar
The cigar vector (std::vector<seqan3::cigar>) representing the alignment in SAM/BAM format.
@ mapq
The mapping quality of the seqan3::field::seq alignment, usually a Phred-scaled score.
@ offset
Sequence (seqan3::field::seq) relative start position (0-based), unsigned value.
@ mate
The mate pair information given as a std::tuple of reference name, offset and template length.
@ header_ptr
A pointer to the seqan3::sam_file_header object storing header information.
@ ref_id
The identifier of the (reference) sequence that seqan3::field::seq was aligned to.
@ id
The identifier, usually a string.
@ tags
The optional tags in the SAM format, stored in a dictionary.
@ 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: type_list/traits.hpp:252
decltype(detail::transform< trait_t >(list_t{})) transform
Apply a transformation trait to every type in the list and return a seqan3::type_list of the results.
Definition: type_list/traits.hpp:470
constexpr size_t size
The size of a type pack.
Definition: type_pack/traits.hpp:146
constexpr auto slice
A view adaptor that returns a half-open interval on the underlying range.
Definition: slice.hpp:178
constexpr auto repeat_n
A view factory that repeats a given value n times.
Definition: repeat_n.hpp:91
Provides the seqan3::detail::in_file_iterator class template.
The generic alphabet concept that covers most data types used in ranges.
Checks whether from can be explicitly converted to to.
A more refined container concept than seqan3::container.
Refines seqan3::alphabet and adds assignability.
A concept that indicates whether a writable alphabet represents quality scores.
Provides exceptions used in the I/O module.
The main SeqAn3 namespace.
Definition: aligned_sequence_concept.hpp:29
Provides seqan3::phred42 quality scores.
Provides quality alphabet composites.
Provides seqan3::views::repeat_n.
Provides seqan3::sam_record.
Provides helper data structures for the seqan3::sam_file_output.
Provides seqan3::views::slice.
An empty type whose only purpose is to hold an uninstantiated template plus its arguments.
Definition: lazy_conditional.hpp:33
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
Thrown if there is an unspecified filesystem or stream error while opening, e.g. permission problem.
Definition: io/exception.hpp:39
void clear() noexcept(noexcept(std::apply(expander, std::declval< record & >())))
Clears containers that provide .clear() and (re-)initialises all other elements with = {}.
Definition: record.hpp:237
Type that contains multiple types.
Definition: type_list.hpp:29
Provides traits for seqan3::type_list.
Provides seqan3::tuple_like.