The record type of seqan3::alignment_file_input. More...

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

Inheritance diagram for seqan3::sam_record< field_types, field_ids >:

Public Types
using	base_type = detail::transfer_template_args_onto_t< field_types, std::tuple >
	A specialisation of std::tuple.

Public Member Functions
decltype(auto)	alignment () &
	The (pairwise) alignment stored in an seqan3::alignment object. More...

decltype(auto)	alignment () &&
	The (pairwise) alignment stored in an seqan3::alignment object.

decltype(auto)	alignment () const &
	The (pairwise) alignment stored in an seqan3::alignment object. More...

decltype(auto)	alignment () const &&
	The (pairwise) alignment stored in an seqan3::alignment object. More...

decltype(auto)	base_qualities () &
	The qualities, usually in phred-score notation. More...

decltype(auto)	base_qualities () &&
	The qualities, usually in phred-score notation.

decltype(auto)	base_qualities () const &
	The qualities, usually in phred-score notation. More...

decltype(auto)	base_qualities () const &&
	The qualities, usually in phred-score notation. More...

decltype(auto)	cigar_sequence () &
	The cigar vector (std::vector<seqan3::cigar>) representing the alignment in SAM/BAM format. More...

decltype(auto)	cigar_sequence () &&
	The cigar vector (std::vector<seqan3::cigar>) representing the alignment in SAM/BAM format.

decltype(auto)	cigar_sequence () const &
	The cigar vector (std::vector<seqan3::cigar>) representing the alignment in SAM/BAM format. More...

decltype(auto)	cigar_sequence () const &&
	The cigar vector (std::vector<seqan3::cigar>) representing the alignment in SAM/BAM format. More...

void	clear () noexcept(noexcept(std::apply(expander, std::declval< record & >())))
	Clears containers that provide `.clear()` and (re-)initialises all other elements with `= {}`.

decltype(auto)	flag () &
	The alignment flag (bit information), `uint16_t` value. More...

decltype(auto)	flag () &&
	The alignment flag (bit information), `uint16_t` value.

decltype(auto)	flag () const &
	The alignment flag (bit information), `uint16_t` value. More...

decltype(auto)	flag () const &&
	The alignment flag (bit information), `uint16_t` value. More...

decltype(auto)	header_ptr () &
	A pointer to the seqan3::alignment_file_header object storing header information. More...

decltype(auto)	header_ptr () &&
	A pointer to the seqan3::alignment_file_header object storing header information.

decltype(auto)	header_ptr () const &
	A pointer to the seqan3::alignment_file_header object storing header information. More...

decltype(auto)	header_ptr () const &&
	A pointer to the seqan3::alignment_file_header object storing header information. More...

decltype(auto)	id () &
	The identifier, usually a string. More...

decltype(auto)	id () &&
	The identifier, usually a string.

decltype(auto)	id () const &
	The identifier, usually a string. More...

decltype(auto)	id () const &&
	The identifier, usually a string. More...

decltype(auto)	mapping_quality () &
	The mate pair information given as a std::tuple of reference name, offset and template length. More...

decltype(auto)	mapping_quality () &&
	The mate pair information given as a std::tuple of reference name, offset and template length.

decltype(auto)	mapping_quality () const &
	The mate pair information given as a std::tuple of reference name, offset and template length. More...

decltype(auto)	mapping_quality () const &&
	The mate pair information given as a std::tuple of reference name, offset and template length. More...

decltype(auto)	mate_position () &
	The mate pair information with the position. More...

decltype(auto)	mate_position () &&
	The mate pair information with the position.

decltype(auto)	mate_position () const &
	The mate pair information with the position. More...

decltype(auto)	mate_position () const &&
	The mate pair information with the position. More...

decltype(auto)	mate_reference_id () &
	The mate pair information with the reference name. More...

decltype(auto)	mate_reference_id () &&
	The mate pair information with the reference name.

decltype(auto)	mate_reference_id () const &
	The mate pair information with the reference name. More...

decltype(auto)	mate_reference_id () const &&
	The mate pair information with the reference name. More...

decltype(auto)	reference_id () &
	The identifier of the (reference) sequence that SEQ was aligned to. More...

decltype(auto)	reference_id () &&
	The identifier of the (reference) sequence that SEQ was aligned to.

decltype(auto)	reference_id () const &
	The identifier of the (reference) sequence that SEQ was aligned to. More...

decltype(auto)	reference_id () const &&
	The identifier of the (reference) sequence that SEQ was aligned to. More...

decltype(auto)	reference_position () &
	Sequence (REF_SEQ) relative start position (0-based), unsigned value. More...

decltype(auto)	reference_position () &&
	Sequence (REF_SEQ) relative start position (0-based), unsigned value.

decltype(auto)	reference_position () const &
	Sequence (REF_SEQ) relative start position (0-based), unsigned value. More...

decltype(auto)	reference_position () const &&
	Sequence (REF_SEQ) relative start position (0-based), unsigned value. More...

decltype(auto)	reference_sequence () &
	The (reference) "sequence" information, usually a range of nucleotides or amino acids. More...

decltype(auto)	reference_sequence () &&
	The (reference) "sequence" information, usually a range of nucleotides or amino acids.

decltype(auto)	reference_sequence () const &
	The (reference) "sequence" information, usually a range of nucleotides or amino acids. More...

decltype(auto)	reference_sequence () const &&
	The (reference) "sequence" information, usually a range of nucleotides or amino acids. More...

decltype(auto)	sequence () &
	The "sequence", usually a range of nucleotides or amino acids. More...

decltype(auto)	sequence () &&
	The "sequence", usually a range of nucleotides or amino acids.

decltype(auto)	sequence () const &
	The "sequence", usually a range of nucleotides or amino acids. More...

decltype(auto)	sequence () const &&
	The "sequence", usually a range of nucleotides or amino acids. More...

decltype(auto)	sequence_position () &
	Sequence (SEQ) relative start position (0-based), unsigned value. More...

decltype(auto)	sequence_position () &&
	Sequence (SEQ) relative start position (0-based), unsigned value.

decltype(auto)	sequence_position () const &
	Sequence (SEQ) relative start position (0-based), unsigned value. More...

decltype(auto)	sequence_position () const &&
	Sequence (SEQ) relative start position (0-based), unsigned value. More...

decltype(auto)	tags () &
	The optional tags in the SAM format, stored in a dictionary. More...

decltype(auto)	tags () &&
	The optional tags in the SAM format, stored in a dictionary.

decltype(auto)	tags () const &
	The optional tags in the SAM format, stored in a dictionary. More...

decltype(auto)	tags () const &&
	The optional tags in the SAM format, stored in a dictionary. More...

decltype(auto)	template_length () &
	The mate pair information with the template length. More...

decltype(auto)	template_length () &&
	The mate pair information with the template length.

decltype(auto)	template_length () const &
	The mate pair information with the template length. More...

decltype(auto)	template_length () const &&
	The mate pair information with the template length. More...

Constructors, destructor and assignment
	sam_record ()=default
	Defaulted.

	sam_record (sam_record const &)=default
	Defaulted.

sam_record &	operator= (sam_record const &)=default
	Defaulted.

	sam_record (sam_record &&)=default
	Defaulted.

sam_record &	operator= (sam_record &&)=default
	Defaulted.

	~sam_record ()=default
	Defaulted.

Private Types
using	base_t = record< field_types, field_ids >
	The base class.

template<field f>
using	field_constant = typename base_t::template field_constant< f >
	A type alias for std::integral_constant. More...

using	tuple_base_t = typename base_t::base_type
	The underlying std::tuple class.

Static Private Member Functions
template<typename t >
static constexpr void	clear_element (t &v) noexcept(noexcept(std::declval< t & >()=t{}))
	This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

template<typename t >
static constexpr void	clear_element (t &v) noexcept(noexcept(v.clear()))
	Auxiliary functions for clear().

template<field f, typename tuple_t >
static decltype(auto)	get_impl (field_constant< f >, tuple_t &&record_as_tuple)
	This is basically the seqan3::get<f>(static_cast<tuple>(record)) implementation.

Static Private Attributes
static constexpr auto	expander = [] (auto & ...args) { (clear_element(args), ...); }
	A lambda function that expands a pack and calls `clear_element` on every argument in the pack.

Related Functions
(Note that these are not member functions.)
Free function get() interface for seqan3::record based on seqan3::field.
This is the tuple interface via seqan3::field, e.g. `seqan3::get<seqan3::field::seq>(record)`.
template<field f, typename field_types , typename field_ids >
auto &	get (record< field_types, field_ids > &r)
	Free function get() for seqan3::record based on seqan3::field.

template<field f, typename field_types , typename field_ids >
auto const &	get (record< field_types, field_ids > const &r)
	This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

template<field f, typename field_types , typename field_ids >
auto &&	get (record< field_types, field_ids > &&r)
	This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

template<field f, typename field_types , typename field_ids >
auto const &&	get (record< field_types, field_ids > const &&r)
	This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

Requirements for seqan3::tuple_like
You can expect these (meta-)functions on all types that implement seqan3::tuple_like.
auto &&	get (type &&val)
	Return the i-th element of the tuple. More...

size_t	tuple_size_v
	A unary type trait that holds the number of elements in the tuple. More...

	tuple_elment_t
	A transformation trait that holds the type of elements in the tuple. More...

Detailed Description

template<typename field_types, typename field_ids>
class seqan3::sam_record< field_types, field_ids >

The record type of seqan3::alignment_file_input.

Template Parameters

field_types	The types of the fields in this record as a seqan3::type_list.
field_ids	A seqan3::fields type with seqan3::field IDs corresponding to field_types.

Member Typedef Documentation

◆ field_constant

template<typename field_types , typename field_ids >

template<field f>

using seqan3::sam_record< field_types, field_ids >::field_constant = typename base_t::template field_constant<f>

private

A type alias for std::integral_constant.

Member Function Documentation

◆ alignment() [1/3]

template<typename field_types , typename field_ids >

decltype(auto) seqan3::sam_record< field_types, field_ids >::alignment ( ) &

inline

The (pairwise) alignment stored in an seqan3::alignment object.

◆ alignment() [2/3]

template<typename field_types , typename field_ids >

decltype(auto) seqan3::sam_record< field_types, field_ids >::alignment ( ) const &

inline

The (pairwise) alignment stored in an seqan3::alignment object.

◆ alignment() [3/3]

template<typename field_types , typename field_ids >

decltype(auto) seqan3::sam_record< field_types, field_ids >::alignment ( ) const &&

inline

The (pairwise) alignment stored in an seqan3::alignment object.

◆ base_qualities() [1/3]

template<typename field_types , typename field_ids >

decltype(auto) seqan3::sam_record< field_types, field_ids >::base_qualities ( ) &

inline

The qualities, usually in phred-score notation.

◆ base_qualities() [2/3]

template<typename field_types , typename field_ids >

decltype(auto) seqan3::sam_record< field_types, field_ids >::base_qualities ( ) const &

inline

The qualities, usually in phred-score notation.

◆ base_qualities() [3/3]

template<typename field_types , typename field_ids >

decltype(auto) seqan3::sam_record< field_types, field_ids >::base_qualities ( ) const &&

inline

The qualities, usually in phred-score notation.

◆ cigar_sequence() [1/3]

template<typename field_types , typename field_ids >

decltype(auto) seqan3::sam_record< field_types, field_ids >::cigar_sequence ( ) &

inline

The cigar vector (std::vector<seqan3::cigar>) representing the alignment in SAM/BAM format.

◆ cigar_sequence() [2/3]

template<typename field_types , typename field_ids >

decltype(auto) seqan3::sam_record< field_types, field_ids >::cigar_sequence ( ) const &

inline

The cigar vector (std::vector<seqan3::cigar>) representing the alignment in SAM/BAM format.

◆ cigar_sequence() [3/3]

template<typename field_types , typename field_ids >

decltype(auto) seqan3::sam_record< field_types, field_ids >::cigar_sequence ( ) const &&

inline

The cigar vector (std::vector<seqan3::cigar>) representing the alignment in SAM/BAM format.

◆ flag() [1/3]

template<typename field_types , typename field_ids >

decltype(auto) seqan3::sam_record< field_types, field_ids >::flag ( ) &

inline

The alignment flag (bit information), uint16_t value.

◆ flag() [2/3]

template<typename field_types , typename field_ids >

decltype(auto) seqan3::sam_record< field_types, field_ids >::flag ( ) const &

inline

The alignment flag (bit information), uint16_t value.

◆ flag() [3/3]

template<typename field_types , typename field_ids >

decltype(auto) seqan3::sam_record< field_types, field_ids >::flag ( ) const &&

inline

The alignment flag (bit information), uint16_t value.

◆ header_ptr() [1/3]

template<typename field_types , typename field_ids >

decltype(auto) seqan3::sam_record< field_types, field_ids >::header_ptr ( ) &

inline

A pointer to the seqan3::alignment_file_header object storing header information.

◆ header_ptr() [2/3]

template<typename field_types , typename field_ids >

decltype(auto) seqan3::sam_record< field_types, field_ids >::header_ptr ( ) const &

inline

A pointer to the seqan3::alignment_file_header object storing header information.

◆ header_ptr() [3/3]

template<typename field_types , typename field_ids >

decltype(auto) seqan3::sam_record< field_types, field_ids >::header_ptr ( ) const &&

inline

A pointer to the seqan3::alignment_file_header object storing header information.

◆ id() [1/3]

template<typename field_types , typename field_ids >

decltype(auto) seqan3::sam_record< field_types, field_ids >::id ( ) &

inline

The identifier, usually a string.

◆ id() [2/3]

template<typename field_types , typename field_ids >

decltype(auto) seqan3::sam_record< field_types, field_ids >::id ( ) const &

inline

The identifier, usually a string.

◆ id() [3/3]

template<typename field_types , typename field_ids >

decltype(auto) seqan3::sam_record< field_types, field_ids >::id ( ) const &&

inline

The identifier, usually a string.

◆ mapping_quality() [1/3]

template<typename field_types , typename field_ids >

decltype(auto) seqan3::sam_record< field_types, field_ids >::mapping_quality ( ) &

inline

The mate pair information given as a std::tuple of reference name, offset and template length.

◆ mapping_quality() [2/3]

template<typename field_types , typename field_ids >

decltype(auto) seqan3::sam_record< field_types, field_ids >::mapping_quality ( ) const &

inline

The mate pair information given as a std::tuple of reference name, offset and template length.

◆ mapping_quality() [3/3]

template<typename field_types , typename field_ids >

decltype(auto) seqan3::sam_record< field_types, field_ids >::mapping_quality ( ) const &&

inline

The mate pair information given as a std::tuple of reference name, offset and template length.

◆ mate_position() [1/3]

template<typename field_types , typename field_ids >

decltype(auto) seqan3::sam_record< field_types, field_ids >::mate_position ( ) &

inline

The mate pair information with the position.

◆ mate_position() [2/3]

template<typename field_types , typename field_ids >

decltype(auto) seqan3::sam_record< field_types, field_ids >::mate_position ( ) const &

inline

The mate pair information with the position.

◆ mate_position() [3/3]

template<typename field_types , typename field_ids >

decltype(auto) seqan3::sam_record< field_types, field_ids >::mate_position ( ) const &&

inline

The mate pair information with the position.

◆ mate_reference_id() [1/3]

template<typename field_types , typename field_ids >

decltype(auto) seqan3::sam_record< field_types, field_ids >::mate_reference_id ( ) &

inline

The mate pair information with the reference name.

◆ mate_reference_id() [2/3]

template<typename field_types , typename field_ids >

decltype(auto) seqan3::sam_record< field_types, field_ids >::mate_reference_id ( ) const &

inline

The mate pair information with the reference name.

◆ mate_reference_id() [3/3]

template<typename field_types , typename field_ids >

decltype(auto) seqan3::sam_record< field_types, field_ids >::mate_reference_id ( ) const &&

inline

The mate pair information with the reference name.

◆ reference_id() [1/3]

template<typename field_types , typename field_ids >

decltype(auto) seqan3::sam_record< field_types, field_ids >::reference_id ( ) &

inline

The identifier of the (reference) sequence that SEQ was aligned to.

◆ reference_id() [2/3]

template<typename field_types , typename field_ids >

decltype(auto) seqan3::sam_record< field_types, field_ids >::reference_id ( ) const &

inline

The identifier of the (reference) sequence that SEQ was aligned to.

◆ reference_id() [3/3]

template<typename field_types , typename field_ids >

decltype(auto) seqan3::sam_record< field_types, field_ids >::reference_id ( ) const &&

inline

The identifier of the (reference) sequence that SEQ was aligned to.

◆ reference_position() [1/3]

template<typename field_types , typename field_ids >

decltype(auto) seqan3::sam_record< field_types, field_ids >::reference_position ( ) &

inline

Sequence (REF_SEQ) relative start position (0-based), unsigned value.

◆ reference_position() [2/3]

template<typename field_types , typename field_ids >

decltype(auto) seqan3::sam_record< field_types, field_ids >::reference_position ( ) const &

inline

Sequence (REF_SEQ) relative start position (0-based), unsigned value.

◆ reference_position() [3/3]

template<typename field_types , typename field_ids >

decltype(auto) seqan3::sam_record< field_types, field_ids >::reference_position ( ) const &&

inline

Sequence (REF_SEQ) relative start position (0-based), unsigned value.

◆ reference_sequence() [1/3]

template<typename field_types , typename field_ids >

decltype(auto) seqan3::sam_record< field_types, field_ids >::reference_sequence ( ) &

inline

The (reference) "sequence" information, usually a range of nucleotides or amino acids.

◆ reference_sequence() [2/3]

template<typename field_types , typename field_ids >

decltype(auto) seqan3::sam_record< field_types, field_ids >::reference_sequence ( ) const &

inline

The (reference) "sequence" information, usually a range of nucleotides or amino acids.

◆ reference_sequence() [3/3]

template<typename field_types , typename field_ids >

decltype(auto) seqan3::sam_record< field_types, field_ids >::reference_sequence ( ) const &&

inline

The (reference) "sequence" information, usually a range of nucleotides or amino acids.

◆ sequence() [1/3]

template<typename field_types , typename field_ids >

decltype(auto) seqan3::sam_record< field_types, field_ids >::sequence ( ) &

inline

The "sequence", usually a range of nucleotides or amino acids.

◆ sequence() [2/3]

template<typename field_types , typename field_ids >

decltype(auto) seqan3::sam_record< field_types, field_ids >::sequence ( ) const &

inline

The "sequence", usually a range of nucleotides or amino acids.

◆ sequence() [3/3]

template<typename field_types , typename field_ids >

decltype(auto) seqan3::sam_record< field_types, field_ids >::sequence ( ) const &&

inline

The "sequence", usually a range of nucleotides or amino acids.

◆ sequence_position() [1/3]

template<typename field_types , typename field_ids >

decltype(auto) seqan3::sam_record< field_types, field_ids >::sequence_position ( ) &

inline

Sequence (SEQ) relative start position (0-based), unsigned value.

◆ sequence_position() [2/3]

template<typename field_types , typename field_ids >

decltype(auto) seqan3::sam_record< field_types, field_ids >::sequence_position ( ) const &

inline

Sequence (SEQ) relative start position (0-based), unsigned value.

◆ sequence_position() [3/3]

template<typename field_types , typename field_ids >

decltype(auto) seqan3::sam_record< field_types, field_ids >::sequence_position ( ) const &&

inline

Sequence (SEQ) relative start position (0-based), unsigned value.

◆ tags() [1/3]

template<typename field_types , typename field_ids >

decltype(auto) seqan3::sam_record< field_types, field_ids >::tags ( ) &

inline

The optional tags in the SAM format, stored in a dictionary.

◆ tags() [2/3]

template<typename field_types , typename field_ids >

decltype(auto) seqan3::sam_record< field_types, field_ids >::tags ( ) const &

inline

The optional tags in the SAM format, stored in a dictionary.

◆ tags() [3/3]

template<typename field_types , typename field_ids >

decltype(auto) seqan3::sam_record< field_types, field_ids >::tags ( ) const &&

inline

The optional tags in the SAM format, stored in a dictionary.

◆ template_length() [1/3]

template<typename field_types , typename field_ids >

decltype(auto) seqan3::sam_record< field_types, field_ids >::template_length ( ) &

inline

The mate pair information with the template length.

◆ template_length() [2/3]

template<typename field_types , typename field_ids >

decltype(auto) seqan3::sam_record< field_types, field_ids >::template_length ( ) const &

inline

The mate pair information with the template length.

◆ template_length() [3/3]

template<typename field_types , typename field_ids >

decltype(auto) seqan3::sam_record< field_types, field_ids >::template_length ( ) const &&

inline

The mate pair information with the template length.

Friends And Related Function Documentation

◆ get()

auto && get< i > ( type && val )

Template Parameters

i	The index of the element to return (of type `size_t`).

Parameters

[in,out] val The tuple-like object to operate on.

Returns: The i-th value in the tuple.

Attention: This is a concept requirement, not an actual function (however types satisfying this concept will provide an implementation).; This constraint is not enforced since empty tuples are valid.

◆ tuple_elment_t()

tuple_elment_t

Template Parameters

i	Index of the queried element type.
type	The tuple-like type.

Attention: This is a concept requirement, not an actual function (however types satisfying this concept will provide an implementation).; This constraint is not enforced since empty tuples are valid.

◆ tuple_size_v()

size_t tuple_size_v

Template Parameters

type	The tuple-like type.

Attention: This is a concept requirement, not an actual function (however types satisfying this concept will provide an implementation).

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

seqan3/io/alignment_file/record.hpp

Public Types

Public Member Functions

Private Types

Static Private Member Functions

Static Private Attributes

Related Functions

Detailed Description

template<typename field_types, typename field_ids> class seqan3::sam_record< field_types, field_ids >

Member Typedef Documentation

◆ field_constant

Member Function Documentation

◆ alignment() [1/3]

◆ alignment() [2/3]

◆ alignment() [3/3]

◆ base_qualities() [1/3]

◆ base_qualities() [2/3]

◆ base_qualities() [3/3]

◆ cigar_sequence() [1/3]

◆ cigar_sequence() [2/3]

◆ cigar_sequence() [3/3]

◆ flag() [1/3]

◆ flag() [2/3]

◆ flag() [3/3]

◆ header_ptr() [1/3]

◆ header_ptr() [2/3]

◆ header_ptr() [3/3]

◆ id() [1/3]

◆ id() [2/3]

◆ id() [3/3]

◆ mapping_quality() [1/3]

◆ mapping_quality() [2/3]

◆ mapping_quality() [3/3]

◆ mate_position() [1/3]

◆ mate_position() [2/3]

◆ mate_position() [3/3]

◆ mate_reference_id() [1/3]

◆ mate_reference_id() [2/3]

◆ mate_reference_id() [3/3]

◆ reference_id() [1/3]

◆ reference_id() [2/3]

◆ reference_id() [3/3]

◆ reference_position() [1/3]

◆ reference_position() [2/3]

◆ reference_position() [3/3]

◆ reference_sequence() [1/3]

◆ reference_sequence() [2/3]

◆ reference_sequence() [3/3]

◆ sequence() [1/3]

◆ sequence() [2/3]

◆ sequence() [3/3]

◆ sequence_position() [1/3]

◆ sequence_position() [2/3]

◆ sequence_position() [3/3]

◆ tags() [1/3]

◆ tags() [2/3]

◆ tags() [3/3]

◆ template_length() [1/3]

◆ template_length() [2/3]

◆ template_length() [3/3]

Friends And Related Function Documentation

◆ get()

◆ tuple_elment_t()

◆ tuple_size_v()

template<typename field_types, typename field_ids>
class seqan3::sam_record< field_types, field_ids >