34#include <seqan3/io/detail/record.hpp>
131 requires std::same_as<typename t::ref_sequences, ref_info_not_given>
133 requires alphabet<std::ranges::range_reference_t<
134 std::ranges::range_reference_t<typename t::ref_sequences>>>;
139 && (!std::same_as<typename t::ref_sequences, ref_info_not_given>
141 std::ranges::range_reference_t<std::ranges::range_reference_t<typename t::ref_ids>>>);
142 requires std::ranges::forward_range<std::ranges::range_reference_t<typename t::ref_ids>>;
143 requires std::ranges::forward_range<typename t::ref_ids>;
184template <
typename ref_sequences_t = ref_info_not_given,
typename ref_
ids_t = std::deque<std::
string>>
199 template <
typename _sequence_alphabet>
203 template <
typename _
id_alphabet>
210 template <
typename _quality_alphabet>
240template <sam_file_input_traits traits_type_ = sam_file_input_default_traits<>,
241 detail::fields_specialisation selected_field_
ids_ = fields<field::seq,
254 detail::type_list_of_sam_file_input_formats val
id_formats_ = type_list<format_sam, format_bam>>
274 using dummy_ref_type =
decltype(
views::repeat_n(
typename traits_type::sequence_alphabet{},
size_t{})
278 using ref_sequence_unsliced_type = detail::lazy_conditional_t<
279 std::ranges::range<typename traits_type::ref_sequences const>,
280 detail::lazy<std::ranges::range_reference_t, typename traits_type::ref_sequences const>,
284 using ref_sequence_sliced_type =
decltype(std::declval<ref_sequence_unsliced_type>() |
views::slice(0, 0));
295 using id_type =
typename traits_type::template id_container<char>;
306 ref_sequence_sliced_type>;
325 using quality_type =
typename traits_type::template quality_container<typename traits_type::quality_alphabet>;
398 for (
field f : selected_field_ids::as_array)
399 if (!field_ids::contains(f))
403 "You selected a field that is not valid for alignment files, please refer to the documentation "
404 "of sam_file_input::field_ids for the accepted values.");
426 using iterator = detail::in_file_iterator<sam_file_input>;
470 init_by_filename(std::move(filename));
492 template <input_stream stream_t, sam_file_input_format file_format>
493 requires std::same_as<typename std::remove_reference_t<stream_t>::char_type,
stream_char_type>
495 file_format
const & SEQAN3_DOXYGEN_ONLY(format_tag),
497 primary_stream{&stream, stream_deleter_noop}
499 init_by_format<file_format>();
503 template <input_stream stream_t, sam_file_input_format file_format>
504 requires std::same_as<typename std::remove_reference_t<stream_t>::char_type,
stream_char_type>
506 file_format
const & SEQAN3_DOXYGEN_ONLY(format_tag),
508 primary_stream{
new stream_t{std::move(stream)}, stream_deleter_default}
510 init_by_format<file_format>();
537 typename traits_type::ref_ids & ref_ids,
538 typename traits_type::ref_sequences & ref_sequences,
543 set_references(ref_ids, ref_sequences);
545 init_by_filename(std::move(filename));
573 template <input_stream stream_t, sam_file_input_format file_format>
575 typename traits_type::ref_ids & ref_ids,
576 typename traits_type::ref_sequences & ref_sequences,
577 file_format
const & SEQAN3_DOXYGEN_ONLY(format_tag),
579 primary_stream{&stream, stream_deleter_noop}
582 set_references(ref_ids, ref_sequences);
584 init_by_format<file_format>();
588 template <input_stream stream_t, sam_file_input_format file_format>
590 typename traits_type::ref_ids & ref_ids,
591 typename traits_type::ref_sequences & ref_sequences,
592 file_format
const & SEQAN3_DOXYGEN_ONLY(format_tag),
594 primary_stream{
new stream_t{std::move(stream)}, stream_deleter_default}
597 set_references(ref_ids, ref_sequences);
599 init_by_format<file_format>();
605 typename traits_type::ref_ids &&,
606 typename traits_type::ref_sequences &&,
609 template <input_stream stream_t, sam_file_input_format file_format>
611 typename traits_type::ref_ids &&,
612 typename traits_type::ref_sequences &&,
641 if (!first_record_was_read)
644 first_record_was_read =
true;
715 if (!first_record_was_read)
718 first_record_was_read =
true;
730 primary_stream->rdbuf()->pubsetbuf(stream_buffer.
data(), stream_buffer.
size());
732 ->open(filename, std::ios_base::in | std::ios::binary);
734 if (!primary_stream->good())
737 secondary_stream = detail::make_secondary_istream(*primary_stream, filename);
738 detail::set_format(format, filename);
742 template <
typename format_type>
743 void init_by_format()
745 static_assert(list_traits::contains<format_type, valid_formats>,
746 "You selected a format that is not in the valid_formats of this file.");
748 format = detail::sam_file_input_format_exposer<format_type>{};
749 secondary_stream = detail::make_secondary_istream(*primary_stream);
782 stream_ptr_t primary_stream{
nullptr, stream_deleter_noop};
784 stream_ptr_t secondary_stream{
nullptr, stream_deleter_noop};
787 bool first_record_was_read{
false};
792 using format_type =
typename detail::variant_from_tags<valid_formats, detail::sam_file_input_format_exposer>::type;
802 typename traits_type::ref_sequences
const * reference_sequences_ptr{
nullptr};
814 template <std::ranges::forward_range ref_sequences_t>
815 void set_references(
typename traits_type::ref_ids & ref_ids, ref_sequences_t && ref_sequences)
817 assert(std::ranges::distance(ref_ids) == std::ranges::distance(ref_sequences));
820 reference_sequences_ptr = &ref_sequences;
823 for (int32_t idx = 0; idx < std::ranges::distance(ref_ids); ++idx)
825 header_ptr->ref_id_info.emplace_back(std::ranges::distance(ref_sequences[idx]),
"");
827 if constexpr (std::ranges::contiguous_range<std::ranges::range_reference_t<typename traits_type::ref_ids>>
828 && std::ranges::sized_range<std::ranges::range_reference_t<typename traits_type::ref_ids>>
829 && std::ranges::borrowed_range<std::ranges::range_reference_t<typename traits_type::ref_ids>>)
831 auto &&
id = header_ptr->ref_ids()[idx];
836 header_ptr->ref_dict[header_ptr->ref_ids()[idx]] = idx;
843 void read_next_record()
846 record_buffer.clear();
847 detail::get_or_ignore<field::header_ptr>(record_buffer) = header_ptr.get();
857 auto call_read_func = [
this](
auto & ref_seq_info)
862 f.read_alignment_record(*secondary_stream,
867 detail::get_or_ignore<field::seq>(record_buffer),
868 detail::get_or_ignore<field::qual>(record_buffer),
869 detail::get_or_ignore<field::id>(record_buffer),
870 detail::get_or_ignore<field::offset>(record_buffer),
871 detail::get_or_ignore<field::ref_seq>(record_buffer),
872 detail::get_or_ignore<field::ref_id>(record_buffer),
873 detail::get_or_ignore<field::ref_offset>(record_buffer),
874 detail::get_or_ignore<field::alignment>(record_buffer),
875 detail::get_or_ignore<field::cigar>(record_buffer),
876 detail::get_or_ignore<field::flag>(record_buffer),
877 detail::get_or_ignore<field::mapq>(record_buffer),
878 detail::get_or_ignore<field::mate>(record_buffer),
879 detail::get_or_ignore<field::tags>(record_buffer),
880 detail::get_or_ignore<field::evalue>(record_buffer),
881 detail::get_or_ignore<field::bit_score>(record_buffer));
886 assert(!
format.valueless_by_exception());
888 if constexpr (!std::same_as<typename traits_type::ref_sequences, ref_info_not_given>)
889 call_read_func(*reference_sequences_ptr);
891 call_read_func(std::ignore);
903template <input_stream stream_type, sam_file_input_format file_format, detail::fields_specialisation selected_field_
ids>
910template <input_stream stream_type, sam_file_input_format file_format, detail::fields_specialisation selected_field_
ids>
917template <input_stream stream_type, sam_file_input_format file_format>
924template <input_stream stream_type, sam_file_input_format file_format>
931template <std::ranges::forward_range ref_ids_t,
932 std::ranges::forward_range ref_sequences_t,
941template <std::ranges::forward_range ref_
ids_t, std::ranges::forward_range ref_sequences_t>
948template <input_stream stream_type,
949 std::ranges::forward_range ref_ids_t,
950 std::ranges::forward_range ref_sequences_t,
960template <input_stream stream_type,
961 std::ranges::forward_range ref_ids_t,
962 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,
982template <input_stream stream_type,
983 std::ranges::forward_range ref_ids_t,
984 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.
A combined alphabet that can hold values of either of its alternatives..
Definition: alphabet_variant.hpp:120
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
A gap decorator allows the annotation of sequences with gap symbols while leaving the underlying sequ...
Definition: gap_decorator.hpp:81
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.
Provides seqan3::gap_decorator.
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: 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: traits.hpp:470
constexpr size_t size
The size of a type pack.
Definition: 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: exception.hpp:39
Type that contains multiple types.
Definition: type_list.hpp:29
Provides traits for seqan3::type_list.
Provides seqan3::tuple_like.