#include <seqan3/io/alignment_file/input.hpp>

Inheritance diagram for seqan3::alignment_file_input< traits_type_, selected_field_ids_, valid_formats_ >:

Additional Inherited Members
Public Types inherited from seqan3::sam_file_input< sam_file_input_default_traits<>, fields< field::seq, field::id, field::offset, field::ref_seq, field::ref_id, field::ref_offset, field::alignment, field::cigar, field::mapq, field::qual, field::flag, field::mate, field::tags, field::evalue, field::bit_score, field::header_ptr >, type_list< format_sam, format_bam > >
using	traits_type = traits_type_
	A traits type that defines aliases and template for storage of the fields.

using	selected_field_ids = selected_field_ids_
	A seqan3::fields list with the fields selected for the record.

using	valid_formats = valid_formats_
	A seqan3::type_list with the possible formats.

using	stream_char_type = char
	Character type of the stream(s).

using	value_type = record_type
	The value_type is the record_type.

using	reference = record_type &
	The reference type.

using	const_reference = void
	The const_reference type is void because files are not const-iterable.

using	size_type = size_t
	An unsigned integer type, usually std::size_t.

using	difference_type = std::make_signed_t< size_t >
	A signed integer type, usually std::ptrdiff_t.

using	iterator = detail::in_file_iterator< sam_file_input >
	The iterator type of this view (an input iterator).

using	const_iterator = void
	The const iterator type is void because files are not const-iterable.

using	sentinel = std::default_sentinel_t
	The type returned by end().

using	sequence_type = typename traits_type::template sequence_container< typename traits_type::sequence_alphabet >
	The type of field::seq (default std::vector<seqan3::dna5>).

using	id_type = typename traits_type::template id_container< char >
	The type of field::id (default std::string by default).

using	offset_type = int32_t
	The type of field::offset is fixed to int32_t.

using	ref_sequence_type = std::conditional_t< std::same_as< typename traits_type::ref_sequences, ref_info_not_given >, dummy_ref_type, ref_sequence_sliced_type >
	The type of field::ref_seq (default depends on construction). More...

using	ref_id_type = std::optional< int32_t >
	The type of field::ref_id is fixed to std::optional<int32_t>. More...

using	ref_offset_type = std::optional< int32_t >
	The type of field::ref_offset is fixed to an std::optional<int32_t>. More...

using	mapq_type = uint8_t
	The type of field::mapq is fixed to uint8_t.

using	quality_type = typename traits_type::template quality_container< typename traits_type::quality_alphabet >
	The type of field::qual (default std::vector<seqan3::phred42>).

using	flag_type = sam_flag
	The type of field::flag is fixed to seqan3::sam_flag.

using	cigar_type = std::vector< cigar >
	The type of field::cigar is fixed to std::vector<cigar>.

using	mate_type = std::tuple< ref_id_type, ref_offset_type, int32_t >
	The type of field::mate is fixed to std::tuple<ref_id_type, ref_offset_type, int32_t>).

using	e_value_type = double
	The type of field::evalue is fixed to double.

using	bitscore_type = double
	The type of field::bitscore is fixed to double.

using	header_type = sam_file_header< typename traits_type::ref_ids >
	The type of field::header_ptr (default: sam_file_header<typename traits_type::ref_ids>).

using	alignment_type = std::tuple< gap_decorator< ref_sequence_type >, alignment_query_type >
	The type of field::alignment (default: std::pair<std::vector<gapped<dna5>>, std::vector<gapped<dna5>>>).

using	field_types = type_list< sequence_type, id_type, offset_type, ref_sequence_type, ref_id_type, ref_offset_type, alignment_type, std::vector< cigar >, mapq_type, quality_type, flag_type, mate_type, sam_tag_dictionary, e_value_type, bitscore_type, header_type * >
	The previously defined types aggregated in a seqan3::type_list.

using	field_ids = fields< field::seq, field::id, field::offset, field::ref_seq, field::ref_id, field::ref_offset, field::alignment, field::cigar, field::mapq, field::qual, field::flag, field::mate, field::tags, field::evalue, field::bit_score, field::header_ptr >
	The subset of seqan3::field tags valid for this file; order corresponds to the types in field_types. More...

using	record_type = sam_record< detail::select_types_with_ids_t< field_types, field_ids, selected_field_ids >, selected_field_ids >
	The type of the record, a specialisation of seqan3::record; acts as a tuple of the selected field types.

Public Member Functions inherited from seqan3::sam_file_input< sam_file_input_default_traits<>, fields< field::seq, field::id, field::offset, field::ref_seq, field::ref_id, field::ref_offset, field::alignment, field::cigar, field::mapq, field::qual, field::flag, field::mate, field::tags, field::evalue, field::bit_score, field::header_ptr >, type_list< format_sam, format_bam > >
header_type &	header ()
	Access the file's header. More...

	sam_file_input ()=delete
	Default constructor is explicitly deleted, you need to give a stream or file name.

	sam_file_input (sam_file_input const &)=delete
	Copy construction is explicitly deleted because you cannot have multiple access to the same file.

	sam_file_input (sam_file_input &&)=default
	Move construction is defaulted.

	sam_file_input (std::filesystem::path filename, selected_field_ids const &fields_tag=selected_field_ids{})
	Construct from filename. More...

	sam_file_input (stream_t &stream, file_format const &format_tag, selected_field_ids const &fields_tag=selected_field_ids{})
	Construct from an existing stream and with specified format. More...

	sam_file_input (stream_t &&stream, file_format const &format_tag, selected_field_ids const &fields_tag=selected_field_ids{})
	This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

	sam_file_input (std::filesystem::path filename, typename traits_type::ref_ids &ref_ids, typename traits_type::ref_sequences &ref_sequences, selected_field_ids const &fields_tag=selected_field_ids{})
	Construct from filename and given additional reference information. More...

	sam_file_input (stream_t &stream, typename traits_type::ref_ids &ref_ids, typename traits_type::ref_sequences &ref_sequences, file_format const &format_tag, selected_field_ids const &fields_tag=selected_field_ids{})
	Construct from an existing stream and with specified format. More...

	sam_file_input (stream_t &&stream, typename traits_type::ref_ids &ref_ids, typename traits_type::ref_sequences &ref_sequences, file_format const &format_tag, selected_field_ids const &fields_tag=selected_field_ids{})
	This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

sam_file_input &	operator= (sam_file_input const &)=delete
	Copy assignment is explicitly deleted because you cannot have multiple access to the same file.

sam_file_input &	operator= (sam_file_input &&)=default
	Move assignment is defaulted.

	~sam_file_input ()=default
	Destructor is defaulted.

iterator	begin ()
	Returns an iterator to current position in the file. More...

sentinel	end () noexcept
	Returns a sentinel for comparison with iterator. More...

reference	front () noexcept
	Return the record we are currently at in the file. More...

Public Attributes inherited from seqan3::sam_file_input< sam_file_input_default_traits<>, fields< field::seq, field::id, field::offset, field::ref_seq, field::ref_id, field::ref_offset, field::alignment, field::cigar, field::mapq, field::qual, field::flag, field::mate, field::tags, field::evalue, field::bit_score, field::header_ptr >, type_list< format_sam, format_bam > >
sam_file_input_options< typename traits_type::sequence_legal_alphabet >	options
	The options are public and its members can be set directly.

Static Public Attributes inherited from seqan3::sam_file_input< sam_file_input_default_traits<>, fields< field::seq, field::id, field::offset, field::ref_seq, field::ref_id, field::ref_offset, field::alignment, field::cigar, field::mapq, field::qual, field::flag, field::mate, field::tags, field::evalue, field::bit_score, field::header_ptr >, type_list< format_sam, format_bam > >
static constexpr bool	is_default_selected_field_ids
	brief Does selected_field_ids contain all fields like in the default case?

Related Functions inherited from seqan3::sam_file_input< sam_file_input_default_traits<>, fields< field::seq, field::id, field::offset, field::ref_seq, field::ref_id, field::ref_offset, field::alignment, field::cigar, field::mapq, field::qual, field::flag, field::mate, field::tags, field::evalue, field::bit_score, field::header_ptr >, type_list< format_sam, format_bam > >
	sam_file_input (stream_type &&stream, file_format const &, selected_field_ids const &) -> sam_file_input< typename sam_file_input<>::traits_type, selected_field_ids, type_list< file_format >>
	Deduce selected fields, file_format, and default the rest.

	sam_file_input (stream_type &stream, file_format const &, selected_field_ids const &) -> sam_file_input< typename sam_file_input<>::traits_type, selected_field_ids, type_list< file_format >>
	Deduce selected fields, file_format, and default the rest.

	sam_file_input (stream_type &&stream, file_format const &) -> sam_file_input< typename sam_file_input<>::traits_type, typename sam_file_input<>::selected_field_ids, type_list< file_format >>
	Deduce file_format, and default the rest.

	sam_file_input (stream_type &stream, file_format const &) -> sam_file_input< typename sam_file_input<>::traits_type, typename sam_file_input<>::selected_field_ids, type_list< file_format >>
	Deduce file_format, and default the rest.

	sam_file_input (std::filesystem::path path, ref_ids_t &, ref_sequences_t &, selected_field_ids const &) -> sam_file_input< sam_file_input_default_traits< std::remove_reference_t< ref_sequences_t >, std::remove_reference_t< ref_ids_t >>, selected_field_ids, typename sam_file_input<>::valid_formats >
	Deduce selected fields, ref_sequences_t and ref_ids_t, default the rest.

	sam_file_input (std::filesystem::path path, ref_ids_t &, ref_sequences_t &) -> sam_file_input< sam_file_input_default_traits< std::remove_reference_t< ref_sequences_t >, std::remove_reference_t< ref_ids_t >>, typename sam_file_input<>::selected_field_ids, typename sam_file_input<>::valid_formats >
	Deduce ref_sequences_t and ref_ids_t, default the rest.

	sam_file_input (stream_type &&stream, ref_ids_t &, ref_sequences_t &, file_format const &, selected_field_ids const &) -> sam_file_input< sam_file_input_default_traits< std::remove_reference_t< ref_sequences_t >, std::remove_reference_t< ref_ids_t >>, selected_field_ids, type_list< file_format >>
	Deduce selected fields, ref_sequences_t and ref_ids_t, and file format.

	sam_file_input (stream_type &stream, ref_ids_t &, ref_sequences_t &, file_format const &, selected_field_ids const &) -> sam_file_input< sam_file_input_default_traits< std::remove_reference_t< ref_sequences_t >, std::remove_reference_t< ref_ids_t >>, selected_field_ids, type_list< file_format >>
	Deduce selected fields, ref_sequences_t and ref_ids_t, and file format.

	sam_file_input (stream_type &&stream, ref_ids_t &, ref_sequences_t &, file_format const &) -> sam_file_input< sam_file_input_default_traits< std::remove_reference_t< ref_sequences_t >, std::remove_reference_t< ref_ids_t >>, typename sam_file_input<>::selected_field_ids, type_list< file_format >>
	Deduce ref_sequences_t and ref_ids_t, and file format.

	sam_file_input (stream_type &stream, ref_ids_t &, ref_sequences_t &, file_format const &) -> sam_file_input< sam_file_input_default_traits< std::remove_reference_t< ref_sequences_t >, std::remove_reference_t< ref_ids_t >>, typename sam_file_input<>::selected_field_ids, type_list< file_format >>
	Deduce selected fields, ref_sequences_t and ref_ids_t, and file format.

Detailed Description

template<sam_file_input_traits traits_type_ = sam_file_input_default_traits<>, detail::fields_specialisation selected_field_ids_ = fields<field::seq, field::id, field::offset, field::ref_seq, field::ref_id, field::ref_offset, field::alignment, field::cigar, field::mapq, field::qual, field::flag, field::mate, field::tags, field::evalue, field::bit_score, field::header_ptr>, detail::type_list_of_sam_file_input_formats valid_formats_ = type_list<format_sam, format_bam>>
struct seqan3::alignment_file_input< traits_type_, selected_field_ids_, valid_formats_ >

Deprecated:: Use seqan3::sam_file_input instead.

The documentation for this struct was generated from the following file:

seqan3/io/alignment_file/input.hpp

Additional Inherited Members

Detailed Description