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

Inheritance diagram for seqan3::alignment_file_output< selected_field_ids_, valid_formats_, ref_ids_type >:

Additional Inherited Members
Public Types inherited from seqan3::sam_file_output< fields< field::seq, field::id, field::offset, field::ref_id, field::ref_offset, field::alignment, field::cigar, field::mapq, field::qual, field::flag, field::mate, field::tags, field::header_ptr >, type_list< format_sam, format_bam >, ref_info_not_given >
using	field_ids = fields< field::seq, field::id, field::offset, field::ref_id, field::ref_offset, field::alignment, field::cigar, field::mapq, field::flag, field::qual, field::mate, field::tags, field::header_ptr >
	The subset of seqan3::field IDs that are valid for this file.

using	value_type = void
	The value type (void).

using	reference = void
	The reference type (void).

using	const_reference = void
	The const reference type (void).

using	size_type = void
	The size type (void).

using	difference_type = std::ptrdiff_t
	A signed integer type, usually std::ptrdiff_t.

using	iterator = detail::out_file_iterator< sam_file_output >
	The iterator type of this view (an output 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	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).

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

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

	sam_file_output (sam_file_output const &)=delete
	Copy construction is explicitly deleted, because you can't have multiple access to the same file.

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

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

	sam_file_output (stream_type &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_output (stream_type &&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_output (std::filesystem::path const &filename, ref_ids_type_ &&ref_ids, ref_lengths_type &&ref_lengths, selected_field_ids const &fields_tag=selected_field_ids{})
	Construct from filename. More...

	sam_file_output (stream_type &&stream, ref_ids_type_ &&ref_ids, ref_lengths_type &&ref_lengths, 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_output &	operator= (sam_file_output const &)=delete
	Copy assignment is explicitly deleted, because you can't have multiple access to the same file.

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

	~sam_file_output ()=default
	Destructor is defaulted.

sam_file_output &	operator= (rng_t &&range)
	Write a range of records (or tuples) to the file. More...

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

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

void	push_back (record_t &&r)
	Write a seqan3::record to the file. More...

void	push_back (tuple_t &&t)
	Write a record in form of a std::tuple to the file. More...

void	emplace_back (arg_t &&arg, arg_types &&... args) requires(!is_default_selected_field_ids)
	Write a record to the file by passing individual fields. More...

Public Attributes inherited from seqan3::sam_file_output< fields< field::seq, field::id, field::offset, field::ref_id, field::ref_offset, field::alignment, field::cigar, field::mapq, field::qual, field::flag, field::mate, field::tags, field::header_ptr >, type_list< format_sam, format_bam >, ref_info_not_given >
sam_file_output_options	options
	The options are public and its members can be set directly.

Static Public Attributes inherited from seqan3::sam_file_output< fields< field::seq, field::id, field::offset, field::ref_id, field::ref_offset, field::alignment, field::cigar, field::mapq, field::qual, field::flag, field::mate, field::tags, field::header_ptr >, type_list< format_sam, format_bam >, ref_info_not_given >
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_output< fields< field::seq, field::id, field::offset, field::ref_id, field::ref_offset, field::alignment, field::cigar, field::mapq, field::qual, field::flag, field::mate, field::tags, field::header_ptr >, type_list< format_sam, format_bam >, ref_info_not_given >
	sam_file_output (std::filesystem::path, selected_field_ids const &) -> sam_file_output< selected_field_ids, typename sam_file_output<>::valid_formats, ref_info_not_given >
	Deduces selected_field_ids from input and sets sam_file_output::ref_ids_type to seqan3::detail::ref_info_not_given. valid_formats is set to the default.

	sam_file_output (stream_type &&, file_format const &, selected_field_ids const &) -> sam_file_output< selected_field_ids, type_list< file_format >, ref_info_not_given >
	Deduces selected_field_ids, and the valid format from input and sets sam_file_output::ref_ids_type to seqan3::detail::ref_info_not_given.

	sam_file_output (stream_type &, file_format const &, selected_field_ids const &) -> sam_file_output< selected_field_ids, type_list< file_format >, ref_info_not_given >
	Deduces selected_field_ids, and the valid format from input and sets sam_file_output::ref_ids_type to seqan3::detail::ref_info_not_given.

	sam_file_output (stream_type &&, file_format const &) -> sam_file_output< typename sam_file_output<>::selected_field_ids, type_list< file_format >, ref_info_not_given >
	Deduces the valid format from input and sets sam_file_output::ref_ids_type to seqan3::detail::ref_info_not_given. selected_field_ids is set to the default.

	sam_file_output (stream_type &, file_format const &) -> sam_file_output< typename sam_file_output<>::selected_field_ids, type_list< file_format >, ref_info_not_given >
	Deduces the valid format from input and sets sam_file_output::ref_ids_type to seqan3::detail::ref_info_not_given. selected_field_ids is set to the default.

	sam_file_output (std::filesystem::path const &, ref_info_not_given &&, ref_lengths_type &&, selected_field_ids const &) -> sam_file_output< selected_field_ids, typename sam_file_output<>::valid_formats, std::remove_reference_t< ref_info_not_given >>
	Deduces selected_field_ids and ref_ids_type from input. valid_formats is set to the default.

	sam_file_output (std::filesystem::path const &, ref_info_not_given &&, ref_lengths_type &&) -> sam_file_output< typename sam_file_output<>::selected_field_ids, typename sam_file_output<>::valid_formats, std::remove_reference_t< ref_info_not_given >>
	Deduces ref_ids_type from input. Valid formats, and selected_field_ids are set to the default.

	sam_file_output (stream_type &&, ref_info_not_given &&, ref_lengths_type &&, file_format const &, selected_field_ids const &) -> sam_file_output< selected_field_ids, type_list< file_format >, std::remove_reference_t< ref_info_not_given >>
	Deduces selected_field_ids, the valid format, and the ref_ids_type from input.

	sam_file_output (stream_type &, ref_info_not_given &&, ref_lengths_type &&, file_format const &, selected_field_ids const &) -> sam_file_output< selected_field_ids, type_list< file_format >, std::remove_reference_t< ref_info_not_given >>
	Deduces selected_field_ids, the valid format, and the ref_ids_type from input.

	sam_file_output (stream_type &&, ref_info_not_given &&, ref_lengths_type &&, file_format const &) -> sam_file_output< typename sam_file_output<>::selected_field_ids, type_list< file_format >, std::remove_reference_t< ref_info_not_given >>
	Deduces the valid format, and the ref_ids_type from input. selected_field_ids set to the default.

	sam_file_output (stream_type &, ref_info_not_given &&, ref_lengths_type &&, file_format const &) -> sam_file_output< typename sam_file_output<>::selected_field_ids, type_list< file_format >, std::remove_reference_t< ref_info_not_given >>
	Deduces the valid format, and the ref_ids_type from input. selected_field_ids set to the default.

Detailed Description

template<detail::fields_specialisation selected_field_ids_ = fields<field::seq, field::id, field::offset, field::ref_id, field::ref_offset, field::alignment, field::cigar, field::mapq, field::qual, field::flag, field::mate, field::tags, field::header_ptr>, detail::type_list_of_sam_file_output_formats valid_formats_ = type_list<format_sam, format_bam>, typename ref_ids_type = ref_info_not_given>
struct seqan3::alignment_file_output< selected_field_ids_, valid_formats_, ref_ids_type >

Deprecated:: Use seqan3::sam_file_output instead.

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

seqan3/io/alignment_file/output.hpp

Additional Inherited Members

Detailed Description