33#include <seqan3/io/detail/record.hpp>
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>;
173template <
typename ref_sequences_t = ref_info_not_given,
typename ref_
ids_t = std::deque<std::
string>>
188 template <
typename _sequence_alphabet>
192 template <
typename _
id_alphabet>
199 template <
typename _quality_alphabet>
229template <sam_file_input_traits traits_type_ = sam_file_input_default_traits<>,
230 detail::fields_specialisation selected_field_
ids_ = fields<field::seq,
242 detail::type_list_of_sam_file_input_formats val
id_formats_ = type_list<format_sam, format_bam>>
262 using dummy_ref_type =
decltype(
views::repeat_n(
typename traits_type::sequence_alphabet{},
size_t{})
266 using ref_sequence_unsliced_type = detail::lazy_conditional_t<
267 std::ranges::range<typename traits_type::ref_sequences const>,
268 detail::lazy<std::ranges::range_reference_t, typename traits_type::ref_sequences const>,
272 using ref_sequence_sliced_type =
decltype(std::declval<ref_sequence_unsliced_type>() |
views::slice(0, 0));
283 using id_type =
typename traits_type::template id_container<char>;
294 ref_sequence_sliced_type>;
313 using quality_type =
typename traits_type::template quality_container<typename traits_type::quality_alphabet>;
371 "The field::alignment is deprecated and only field::cigar is supported. Please see "
372 "seqan3::alignment_from_cigar on how to get an alignment from the cigar information.");
377 for (
field f : selected_field_ids::as_array)
378 if (!field_ids::contains(f))
382 "You selected a field that is not valid for SAM files, please refer to the documentation "
383 "of sam_file_input::field_ids for the accepted values.");
405 using iterator = detail::in_file_iterator<sam_file_input>;
449 init_by_filename(std::move(filename));
471 template <input_stream stream_t, sam_file_input_format file_format>
472 requires std::same_as<typename std::remove_reference_t<stream_t>::char_type,
stream_char_type>
474 file_format
const & SEQAN3_DOXYGEN_ONLY(format_tag),
476 primary_stream{&stream, stream_deleter_noop}
478 init_by_format<file_format>();
482 template <input_stream stream_t, sam_file_input_format file_format>
483 requires std::same_as<typename std::remove_reference_t<stream_t>::char_type,
stream_char_type>
485 file_format
const & SEQAN3_DOXYGEN_ONLY(format_tag),
487 primary_stream{
new stream_t{std::move(stream)}, stream_deleter_default}
489 init_by_format<file_format>();
521 typename traits_type::ref_ids & ref_ids,
522 typename traits_type::ref_sequences & ref_sequences,
527 set_references(ref_ids, ref_sequences);
529 init_by_filename(std::move(filename));
562 template <input_stream stream_t, sam_file_input_format file_format>
564 typename traits_type::ref_ids & ref_ids,
565 typename traits_type::ref_sequences & ref_sequences,
566 file_format
const & SEQAN3_DOXYGEN_ONLY(format_tag),
568 primary_stream{&stream, stream_deleter_noop}
571 set_references(ref_ids, ref_sequences);
573 init_by_format<file_format>();
577 template <input_stream stream_t, sam_file_input_format file_format>
579 typename traits_type::ref_ids & ref_ids,
580 typename traits_type::ref_sequences & ref_sequences,
581 file_format
const & SEQAN3_DOXYGEN_ONLY(format_tag),
583 primary_stream{
new stream_t{std::move(stream)}, stream_deleter_default}
586 set_references(ref_ids, ref_sequences);
588 init_by_format<file_format>();
594 typename traits_type::ref_ids &&,
595 typename traits_type::ref_sequences &&,
598 template <input_stream stream_t, sam_file_input_format file_format>
600 typename traits_type::ref_ids &&,
601 typename traits_type::ref_sequences &&,
630 if (!first_record_was_read)
633 first_record_was_read =
true;
704 if (!first_record_was_read)
707 first_record_was_read =
true;
719 primary_stream->rdbuf()->pubsetbuf(stream_buffer.
data(), stream_buffer.
size());
721 ->open(filename, std::ios_base::in | std::ios::binary);
723 if (!primary_stream->good())
726 secondary_stream = detail::make_secondary_istream(*primary_stream, filename);
727 detail::set_format(format, filename);
731 template <
typename format_type>
732 void init_by_format()
734 static_assert(list_traits::contains<format_type, valid_formats>,
735 "You selected a format that is not in the valid_formats of this file.");
737 format = detail::sam_file_input_format_exposer<format_type>{};
738 secondary_stream = detail::make_secondary_istream(*primary_stream);
771 stream_ptr_t primary_stream{
nullptr, stream_deleter_noop};
773 stream_ptr_t secondary_stream{
nullptr, stream_deleter_noop};
776 bool first_record_was_read{
false};
781 using format_type =
typename detail::variant_from_tags<valid_formats, detail::sam_file_input_format_exposer>::type;
791 typename traits_type::ref_sequences
const * reference_sequences_ptr{
nullptr};
805 template <std::ranges::forward_range ref_sequences_t>
806 void set_references(
typename traits_type::ref_ids & ref_ids, ref_sequences_t && ref_sequences)
808 assert(std::ranges::distance(ref_ids) == std::ranges::distance(ref_sequences));
811 reference_sequences_ptr = &ref_sequences;
814 for (int32_t idx = 0; idx < std::ranges::distance(ref_ids); ++idx)
816 header_ptr->ref_id_info.emplace_back(std::ranges::distance(ref_sequences[idx]),
"");
818 if constexpr (std::ranges::contiguous_range<std::ranges::range_reference_t<typename traits_type::ref_ids>>
819 && std::ranges::sized_range<std::ranges::range_reference_t<typename traits_type::ref_ids>>
820 && std::ranges::borrowed_range<std::ranges::range_reference_t<typename traits_type::ref_ids>>)
822 auto &&
id = header_ptr->ref_ids()[idx];
827 header_ptr->ref_dict[header_ptr->ref_ids()[idx]] = idx;
834 void read_next_record()
837 record_buffer.clear();
838 detail::get_or_ignore<field::header_ptr>(record_buffer) = header_ptr.get();
848 auto call_read_func = [
this](
auto & ref_seq_info)
853 f.read_alignment_record(*secondary_stream,
858 detail::get_or_ignore<field::seq>(record_buffer),
859 detail::get_or_ignore<field::qual>(record_buffer),
860 detail::get_or_ignore<field::id>(record_buffer),
861 detail::get_or_ignore<field::offset>(record_buffer),
862 detail::get_or_ignore<field::ref_seq>(record_buffer),
863 detail::get_or_ignore<field::ref_id>(record_buffer),
864 detail::get_or_ignore<field::ref_offset>(record_buffer),
865 detail::get_or_ignore<field::cigar>(record_buffer),
866 detail::get_or_ignore<field::flag>(record_buffer),
867 detail::get_or_ignore<field::mapq>(record_buffer),
868 detail::get_or_ignore<field::mate>(record_buffer),
869 detail::get_or_ignore<field::tags>(record_buffer),
870 detail::get_or_ignore<field::evalue>(record_buffer),
871 detail::get_or_ignore<field::bit_score>(record_buffer));
876 assert(!
format.valueless_by_exception());
878 if constexpr (!std::same_as<typename traits_type::ref_sequences, ref_info_not_given>)
879 call_read_func(*reference_sequences_ptr);
881 call_read_func(std::ignore);
893template <input_stream stream_type, sam_file_input_format file_format, detail::fields_specialisation selected_field_
ids>
900template <input_stream stream_type, sam_file_input_format file_format, detail::fields_specialisation selected_field_
ids>
907template <input_stream stream_type, sam_file_input_format file_format>
914template <input_stream stream_type, sam_file_input_format file_format>
921template <std::ranges::forward_range ref_ids_t,
922 std::ranges::forward_range ref_sequences_t,
931template <std::ranges::forward_range ref_
ids_t, std::ranges::forward_range ref_sequences_t>
938template <input_stream stream_type,
939 std::ranges::forward_range ref_ids_t,
940 std::ranges::forward_range ref_sequences_t,
950template <input_stream stream_type,
951 std::ranges::forward_range ref_ids_t,
952 std::ranges::forward_range ref_sequences_t,
962template <input_stream stream_type,
963 std::ranges::forward_range ref_ids_t,
964 std::ranges::forward_range ref_sequences_t,
972template <input_stream stream_type,
973 std::ranges::forward_range ref_ids_t,
974 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.
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
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
@ 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.
A class template that holds a choice of seqan3::field.
Definition: record.hpp:128
Thrown if there is an unspecified filesystem or stream error while opening, e.g. permission problem.
Definition: io/exception.hpp:39
Type that contains multiple types.
Definition: type_list.hpp:29
Provides traits for seqan3::type_list.
Provides seqan3::tuple_like.