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

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

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

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

decltype(auto)	alignment () &&
	The (pairwise) alignment stored in an object that models seqan3::detail::pairwise_alignment. More...

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

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

decltype(auto)	base_qualities () &
	The qualities, usually in Phred score notation. (SAM Column ID: QUAL) More...

decltype(auto)	base_qualities () &&
	The qualities, usually in Phred score notation. (SAM Column ID: QUAL) More...

decltype(auto)	base_qualities () const &
	The qualities, usually in Phred score notation. (SAM Column ID: QUAL) More...

decltype(auto)	base_qualities () const &&
	The qualities, usually in Phred score notation. (SAM Column ID: QUAL) More...

decltype(auto)	cigar_sequence () &
	The cigar vector representing the alignment. (SAM Column ID: CIGAR) More...

decltype(auto)	cigar_sequence () &&
	The cigar vector representing the alignment. (SAM Column ID: CIGAR) More...

decltype(auto)	cigar_sequence () const &
	The cigar vector representing the alignment. (SAM Column ID: CIGAR) More...

decltype(auto)	cigar_sequence () const &&
	The cigar vector representing the alignment. (SAM Column ID: CIGAR) More...

decltype(auto)	flag () &
	The alignment flag (bit information), `uint16_t` value. (SAM Column ID: FLAG) More...

decltype(auto)	flag () &&
	The alignment flag (bit information), `uint16_t` value. (SAM Column ID: FLAG) More...

decltype(auto)	flag () const &
	The alignment flag (bit information), `uint16_t` value. (SAM Column ID: FLAG) More...

decltype(auto)	flag () const &&
	The alignment flag (bit information), `uint16_t` value. (SAM Column ID: FLAG) More...

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

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

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

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

decltype(auto)	id () &
	The identifier, usually a string. (SAM Column ID: QNAME) More...

decltype(auto)	id () &&
	The identifier, usually a string. (SAM Column ID: QNAME) More...

decltype(auto)	id () const &
	The identifier, usually a string. (SAM Column ID: QNAME) More...

decltype(auto)	id () const &&
	The identifier, usually a string. (SAM Column ID: QNAME) More...

decltype(auto)	mapping_quality () &
	The mapping quality of the alignment, usually a Phred-scaled score. (SAM Column ID: MAPQ) More...

decltype(auto)	mapping_quality () &&
	The mapping quality of the alignment, usually a Phred-scaled score. (SAM Column ID: MAPQ) More...

decltype(auto)	mapping_quality () const &
	The mapping quality of the alignment, usually a Phred-scaled score. (SAM Column ID: MAPQ) More...

decltype(auto)	mapping_quality () const &&
	The mapping quality of the alignment, usually a Phred-scaled score. (SAM Column ID: MAPQ) More...

decltype(auto)	mate_position () &
	(Reference) Sequence relative start position (0-based) of the mate. (SAM Column ID: PNEXT) More...

decltype(auto)	mate_position () &&
	(Reference) Sequence relative start position (0-based) of the mate. (SAM Column ID: PNEXT) More...

decltype(auto)	mate_position () const &
	(Reference) Sequence relative start position (0-based) of the mate. (SAM Column ID: PNEXT) More...

decltype(auto)	mate_position () const &&
	(Reference) Sequence relative start position (0-based) of the mate. (SAM Column ID: PNEXT) More...

decltype(auto)	mate_reference_id () &
	The identifier of the (reference) sequence of the mate. (SAM Column ID: RNEXT) More...

decltype(auto)	mate_reference_id () &&
	The identifier of the (reference) sequence of the mate. (SAM Column ID: RNEXT) More...

decltype(auto)	mate_reference_id () const &
	The identifier of the (reference) sequence of the mate. (SAM Column ID: RNEXT) More...

decltype(auto)	mate_reference_id () const &&
	The identifier of the (reference) sequence of the mate. (SAM Column ID: RNEXT) More...

decltype(auto)	reference_id () &
	The identifier of the (reference) sequence that seqan3::sam_record::sequence was aligned to. (SAM Column ID: RNAME) More...

decltype(auto)	reference_id () &&
	The identifier of the (reference) sequence that seqan3::sam_record::sequence was aligned to. (SAM Column ID: RNAME) More...

decltype(auto)	reference_id () const &
	The identifier of the (reference) sequence that seqan3::sam_record::sequence was aligned to. (SAM Column ID: RNAME) More...

decltype(auto)	reference_id () const &&
	The identifier of the (reference) sequence that seqan3::sam_record::sequence was aligned to. (SAM Column ID: RNAME) More...

decltype(auto)	reference_position () &
	(Reference) Sequence (seqan3::sam_record::reference_sequence) relative start position (0-based), unsigned value. (SAM Column ID: POS) More...

decltype(auto)	reference_position () &&
	(Reference) Sequence (seqan3::sam_record::reference_sequence) relative start position (0-based), unsigned value. (SAM Column ID: POS) More...

decltype(auto)	reference_position () const &
	(Reference) Sequence (seqan3::sam_record::reference_sequence) relative start position (0-based), unsigned value. (SAM Column ID: POS) More...

decltype(auto)	reference_position () const &&
	(Reference) Sequence (seqan3::sam_record::reference_sequence) relative start position (0-based), unsigned value. (SAM Column ID: POS) More...

decltype(auto)	reference_sequence ()=delete
	The (reference) "sequence" information, usually a range of nucleotides or amino acids. (Currently not implemented!)

decltype(auto)	sequence () &
	The "sequence", usually a range of nucleotides or amino acids. (SAM Column ID: SEQ) More...

decltype(auto)	sequence () &&
	The "sequence", usually a range of nucleotides or amino acids. (SAM Column ID: SEQ) More...

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

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

decltype(auto)	sequence_position () &
	Sequence (seqan3::sam_record::sequence) relative start position (0-based), unsigned value. (SAM Column ID: POS) More...

decltype(auto)	sequence_position () &&
	Sequence (seqan3::sam_record::sequence) relative start position (0-based), unsigned value. (SAM Column ID: POS) More...

decltype(auto)	sequence_position () const &
	Sequence (seqan3::sam_record::sequence) relative start position (0-based), unsigned value. (SAM Column ID: POS) More...

decltype(auto)	sequence_position () const &&
	Sequence (seqan3::sam_record::sequence) relative start position (0-based), unsigned value. (SAM Column ID: POS) More...

decltype(auto)	tags () &
	The optional tags in the SAM format. More...

decltype(auto)	tags () &&
	The optional tags in the SAM format. More...

decltype(auto)	tags () const &
	The optional tags in the SAM format. More...

decltype(auto)	tags () const &&
	The optional tags in the SAM format. More...

decltype(auto)	template_length () &
	The observed template length. (SAM Column ID: TLEN) More...

decltype(auto)	template_length () &&
	The observed template length. (SAM Column ID: TLEN) More...

decltype(auto)	template_length () const &
	The observed template length. (SAM Column ID: TLEN) More...

decltype(auto)	template_length () const &&
	The observed template length. (SAM Column ID: TLEN) 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.

Public Member Functions inherited from seqan3::record< field_types, field_ids >
void	clear () noexcept(noexcept(std::apply(expander, std::declval< record & >())))
	Clears containers that provide `.clear()` and (re-)initialises all other elements with `= {}`.

	record ()=default
	Defaulted.

	record (record const &)=default
	Defaulted.

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

	record (record &&)=default
	Defaulted.

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

	~record ()=default
	Defaulted.

Additional Inherited Members
Public Types inherited from seqan3::record< field_types, field_ids >
using	base_type = detail::transfer_template_args_onto_t< field_types, std::tuple >
	A specialisation of std::tuple.

Related Functions inherited from seqan3::record< field_types, field_ids >
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.

Related Functions inherited from tuple_like
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...

auto &&	get (type &&val)
	Return the i-th element of the tuple. More...

Detailed Descriptionno-api

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 Function Documentation

◆ alignment() [1/4]

template<typename field_types , typename field_ids >

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

no-apiinline

The (pairwise) alignment stored in an object that models seqan3::detail::pairwise_alignment.

Returns: seqan3::sam_file_input::alignment_type per default

◆ alignment() [2/4]

template<typename field_types , typename field_ids >

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

no-apiinline

The (pairwise) alignment stored in an object that models seqan3::detail::pairwise_alignment.

Returns: seqan3::sam_file_input::alignment_type per default

◆ alignment() [3/4]

template<typename field_types , typename field_ids >

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

no-apiinline

The (pairwise) alignment stored in an object that models seqan3::detail::pairwise_alignment.

Returns: seqan3::sam_file_input::alignment_type per default

◆ alignment() [4/4]

template<typename field_types , typename field_ids >

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

no-apiinline

The (pairwise) alignment stored in an object that models seqan3::detail::pairwise_alignment.

Returns: seqan3::sam_file_input::alignment_type per default

◆ base_qualities() [1/4]

template<typename field_types , typename field_ids >

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

no-apiinline

The qualities, usually in Phred score notation. (SAM Column ID: QUAL)

Returns: seqan3::sam_file_input::quality_type per default

◆ base_qualities() [2/4]

template<typename field_types , typename field_ids >

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

no-apiinline

The qualities, usually in Phred score notation. (SAM Column ID: QUAL)

Returns: seqan3::sam_file_input::quality_type per default

◆ base_qualities() [3/4]

template<typename field_types , typename field_ids >

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

no-apiinline

The qualities, usually in Phred score notation. (SAM Column ID: QUAL)

Returns: seqan3::sam_file_input::quality_type per default

◆ base_qualities() [4/4]

template<typename field_types , typename field_ids >

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

no-apiinline

The qualities, usually in Phred score notation. (SAM Column ID: QUAL)

Returns: seqan3::sam_file_input::quality_type per default

◆ cigar_sequence() [1/4]

template<typename field_types , typename field_ids >

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

no-apiinline

The cigar vector representing the alignment. (SAM Column ID: CIGAR)

Returns: std::vector<seqan3::cigar> per default

◆ cigar_sequence() [2/4]

template<typename field_types , typename field_ids >

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

no-apiinline

The cigar vector representing the alignment. (SAM Column ID: CIGAR)

Returns: std::vector<seqan3::cigar> per default

◆ cigar_sequence() [3/4]

template<typename field_types , typename field_ids >

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

no-apiinline

The cigar vector representing the alignment. (SAM Column ID: CIGAR)

Returns: std::vector<seqan3::cigar> per default

◆ cigar_sequence() [4/4]

template<typename field_types , typename field_ids >

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

no-apiinline

The cigar vector representing the alignment. (SAM Column ID: CIGAR)

Returns: std::vector<seqan3::cigar> per default

◆ flag() [1/4]

template<typename field_types , typename field_ids >

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

no-apiinline

The alignment flag (bit information), uint16_t value. (SAM Column ID: FLAG)

Returns: seqan3::sam_file_input::flag_type per default

◆ flag() [2/4]

template<typename field_types , typename field_ids >

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

no-apiinline

The alignment flag (bit information), uint16_t value. (SAM Column ID: FLAG)

Returns: seqan3::sam_file_input::flag_type per default

◆ flag() [3/4]

template<typename field_types , typename field_ids >

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

no-apiinline

The alignment flag (bit information), uint16_t value. (SAM Column ID: FLAG)

Returns: seqan3::sam_file_input::flag_type per default

◆ flag() [4/4]

template<typename field_types , typename field_ids >

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

no-apiinline

The alignment flag (bit information), uint16_t value. (SAM Column ID: FLAG)

Returns: seqan3::sam_file_input::flag_type per default

◆ header_ptr() [1/4]

template<typename field_types , typename field_ids >

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

no-apiinline

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

Returns: seqan3::sam_file_input::header_type* per default

See also: Please see the seqan3::sam_file_output::header member function for details on how to access the seqan3::sam_file_header of the file

◆ header_ptr() [2/4]

template<typename field_types , typename field_ids >

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

no-apiinline

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

Returns: seqan3::sam_file_input::header_type* per default

See also: Please see the seqan3::sam_file_output::header member function for details on how to access the seqan3::sam_file_header of the file

◆ header_ptr() [3/4]

template<typename field_types , typename field_ids >

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

no-apiinline

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

Returns: seqan3::sam_file_input::header_type* per default

See also: Please see the seqan3::sam_file_output::header member function for details on how to access the seqan3::sam_file_header of the file

◆ header_ptr() [4/4]

template<typename field_types , typename field_ids >

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

no-apiinline

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

Returns: seqan3::sam_file_input::header_type* per default

See also: Please see the seqan3::sam_file_output::header member function for details on how to access the seqan3::sam_file_header of the file

◆ id() [1/4]

template<typename field_types , typename field_ids >

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

no-apiinline

The identifier, usually a string. (SAM Column ID: QNAME)

Returns: seqan3::sam_file_input::id_type per default

◆ id() [2/4]

template<typename field_types , typename field_ids >

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

no-apiinline

The identifier, usually a string. (SAM Column ID: QNAME)

Returns: seqan3::sam_file_input::id_type per default

◆ id() [3/4]

template<typename field_types , typename field_ids >

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

no-apiinline

The identifier, usually a string. (SAM Column ID: QNAME)

Returns: seqan3::sam_file_input::id_type per default

◆ id() [4/4]

template<typename field_types , typename field_ids >

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

no-apiinline

The identifier, usually a string. (SAM Column ID: QNAME)

Returns: seqan3::sam_file_input::id_type per default

◆ mapping_quality() [1/4]

template<typename field_types , typename field_ids >

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

no-apiinline

The mapping quality of the alignment, usually a Phred-scaled score. (SAM Column ID: MAPQ)

Returns: seqan3::sam_file_input::mapq_type per default

◆ mapping_quality() [2/4]

template<typename field_types , typename field_ids >

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

no-apiinline

The mapping quality of the alignment, usually a Phred-scaled score. (SAM Column ID: MAPQ)

Returns: seqan3::sam_file_input::mapq_type per default

◆ mapping_quality() [3/4]

template<typename field_types , typename field_ids >

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

no-apiinline

The mapping quality of the alignment, usually a Phred-scaled score. (SAM Column ID: MAPQ)

Returns: seqan3::sam_file_input::mapq_type per default

◆ mapping_quality() [4/4]

template<typename field_types , typename field_ids >

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

no-apiinline

The mapping quality of the alignment, usually a Phred-scaled score. (SAM Column ID: MAPQ)

Returns: seqan3::sam_file_input::mapq_type per default

◆ mate_position() [1/4]

template<typename field_types , typename field_ids >

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

no-apiinline

(Reference) Sequence relative start position (0-based) of the mate. (SAM Column ID: PNEXT)

Returns: seqan3::sam_file_input::ref_offset_type per default

◆ mate_position() [2/4]

template<typename field_types , typename field_ids >

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

no-apiinline

(Reference) Sequence relative start position (0-based) of the mate. (SAM Column ID: PNEXT)

Returns: seqan3::sam_file_input::ref_offset_type per default

◆ mate_position() [3/4]

template<typename field_types , typename field_ids >

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

no-apiinline

(Reference) Sequence relative start position (0-based) of the mate. (SAM Column ID: PNEXT)

Returns: seqan3::sam_file_input::ref_offset_type per default

◆ mate_position() [4/4]

template<typename field_types , typename field_ids >

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

no-apiinline

(Reference) Sequence relative start position (0-based) of the mate. (SAM Column ID: PNEXT)

Returns: seqan3::sam_file_input::ref_offset_type per default

◆ mate_reference_id() [1/4]

template<typename field_types , typename field_ids >

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

no-apiinline

The identifier of the (reference) sequence of the mate. (SAM Column ID: RNEXT)

Returns: seqan3::sam_file_input::ref_id_type per default

If RNEXT is =, it returns the same as seqan3::sam_record::reference_id.

◆ mate_reference_id() [2/4]

template<typename field_types , typename field_ids >

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

no-apiinline

The identifier of the (reference) sequence of the mate. (SAM Column ID: RNEXT)

Returns: seqan3::sam_file_input::ref_id_type per default

If RNEXT is =, it returns the same as seqan3::sam_record::reference_id.

◆ mate_reference_id() [3/4]

template<typename field_types , typename field_ids >

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

no-apiinline

The identifier of the (reference) sequence of the mate. (SAM Column ID: RNEXT)

Returns: seqan3::sam_file_input::ref_id_type per default

If RNEXT is =, it returns the same as seqan3::sam_record::reference_id.

◆ mate_reference_id() [4/4]

template<typename field_types , typename field_ids >

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

no-apiinline

The identifier of the (reference) sequence of the mate. (SAM Column ID: RNEXT)

Returns: seqan3::sam_file_input::ref_id_type per default

If RNEXT is =, it returns the same as seqan3::sam_record::reference_id.

◆ reference_id() [1/4]

template<typename field_types , typename field_ids >

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

no-apiinline

The identifier of the (reference) sequence that seqan3::sam_record::sequence was aligned to. (SAM Column ID: RNAME)

Returns: seqan3::sam_file_input::ref_id_type per default

◆ reference_id() [2/4]

template<typename field_types , typename field_ids >

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

no-apiinline

The identifier of the (reference) sequence that seqan3::sam_record::sequence was aligned to. (SAM Column ID: RNAME)

Returns: seqan3::sam_file_input::ref_id_type per default

◆ reference_id() [3/4]

template<typename field_types , typename field_ids >

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

no-apiinline

The identifier of the (reference) sequence that seqan3::sam_record::sequence was aligned to. (SAM Column ID: RNAME)

Returns: seqan3::sam_file_input::ref_id_type per default

◆ reference_id() [4/4]

template<typename field_types , typename field_ids >

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

no-apiinline

The identifier of the (reference) sequence that seqan3::sam_record::sequence was aligned to. (SAM Column ID: RNAME)

Returns: seqan3::sam_file_input::ref_id_type per default

◆ reference_position() [1/4]

template<typename field_types , typename field_ids >

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

no-apiinline

(Reference) Sequence (seqan3::sam_record::reference_sequence) relative start position (0-based), unsigned value. (SAM Column ID: POS)

Returns: seqan3::sam_file_input::ref_offset_type per default

◆ reference_position() [2/4]

template<typename field_types , typename field_ids >

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

no-apiinline

(Reference) Sequence (seqan3::sam_record::reference_sequence) relative start position (0-based), unsigned value. (SAM Column ID: POS)

Returns: seqan3::sam_file_input::ref_offset_type per default

◆ reference_position() [3/4]

template<typename field_types , typename field_ids >

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

no-apiinline

(Reference) Sequence (seqan3::sam_record::reference_sequence) relative start position (0-based), unsigned value. (SAM Column ID: POS)

Returns: seqan3::sam_file_input::ref_offset_type per default

◆ reference_position() [4/4]

template<typename field_types , typename field_ids >

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

no-apiinline

(Reference) Sequence (seqan3::sam_record::reference_sequence) relative start position (0-based), unsigned value. (SAM Column ID: POS)

Returns: seqan3::sam_file_input::ref_offset_type per default

◆ sequence() [1/4]

template<typename field_types , typename field_ids >

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

no-apiinline

The "sequence", usually a range of nucleotides or amino acids. (SAM Column ID: SEQ)

Returns: seqan3::sam_file_input::sequence_type per default

◆ sequence() [2/4]

template<typename field_types , typename field_ids >

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

no-apiinline

The "sequence", usually a range of nucleotides or amino acids. (SAM Column ID: SEQ)

Returns: seqan3::sam_file_input::sequence_type per default

◆ sequence() [3/4]

template<typename field_types , typename field_ids >

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

no-apiinline

The "sequence", usually a range of nucleotides or amino acids. (SAM Column ID: SEQ)

Returns: seqan3::sam_file_input::sequence_type per default

◆ sequence() [4/4]

template<typename field_types , typename field_ids >

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

no-apiinline

The "sequence", usually a range of nucleotides or amino acids. (SAM Column ID: SEQ)

Returns: seqan3::sam_file_input::sequence_type per default

◆ sequence_position() [1/4]

template<typename field_types , typename field_ids >

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

no-apiinline

Sequence (seqan3::sam_record::sequence) relative start position (0-based), unsigned value. (SAM Column ID: POS)

Returns: seqan3::sam_file_input::offset_type per default

The position is the length of the soft-clipping at the start of the seqan3::sam_record::cigar_sequence if a soft-clipping is present and 0 otherwise.

◆ sequence_position() [2/4]

template<typename field_types , typename field_ids >

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

no-apiinline

Sequence (seqan3::sam_record::sequence) relative start position (0-based), unsigned value. (SAM Column ID: POS)

Returns: seqan3::sam_file_input::offset_type per default

The position is the length of the soft-clipping at the start of the seqan3::sam_record::cigar_sequence if a soft-clipping is present and 0 otherwise.

◆ sequence_position() [3/4]

template<typename field_types , typename field_ids >

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

no-apiinline

Sequence (seqan3::sam_record::sequence) relative start position (0-based), unsigned value. (SAM Column ID: POS)

Returns: seqan3::sam_file_input::offset_type per default

The position is the length of the soft-clipping at the start of the seqan3::sam_record::cigar_sequence if a soft-clipping is present and 0 otherwise.

◆ sequence_position() [4/4]

template<typename field_types , typename field_ids >

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

no-apiinline

Sequence (seqan3::sam_record::sequence) relative start position (0-based), unsigned value. (SAM Column ID: POS)

Returns: seqan3::sam_file_input::offset_type per default

The position is the length of the soft-clipping at the start of the seqan3::sam_record::cigar_sequence if a soft-clipping is present and 0 otherwise.

◆ tags() [1/4]

template<typename field_types , typename field_ids >

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

no-apiinline

The optional tags in the SAM format.

Returns: seqan3::sam_tag_dictionary per default

◆ tags() [2/4]

template<typename field_types , typename field_ids >

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

no-apiinline

The optional tags in the SAM format.

Returns: seqan3::sam_tag_dictionary per default

◆ tags() [3/4]

template<typename field_types , typename field_ids >

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

no-apiinline

The optional tags in the SAM format.

Returns: seqan3::sam_tag_dictionary per default

◆ tags() [4/4]

template<typename field_types , typename field_ids >

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

no-apiinline

The optional tags in the SAM format.

Returns: seqan3::sam_tag_dictionary per default

◆ template_length() [1/4]

template<typename field_types , typename field_ids >

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

no-apiinline

The observed template length. (SAM Column ID: TLEN)

Returns: int32_t per default

◆ template_length() [2/4]

template<typename field_types , typename field_ids >

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

no-apiinline

The observed template length. (SAM Column ID: TLEN)

Returns: int32_t per default

◆ template_length() [3/4]

template<typename field_types , typename field_ids >

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

no-apiinline

The observed template length. (SAM Column ID: TLEN)

Returns: int32_t per default

◆ template_length() [4/4]

template<typename field_types , typename field_ids >

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

no-apiinline

The observed template length. (SAM Column ID: TLEN)

Returns: int32_t per default

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

seqan3/io/sam_file/record.hpp

Public Member Functions

Additional Inherited Members

Detailed Descriptionno-api

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

Member Function Documentation

◆ alignment() [1/4]

◆ alignment() [2/4]

◆ alignment() [3/4]

◆ alignment() [4/4]

◆ base_qualities() [1/4]

◆ base_qualities() [2/4]

◆ base_qualities() [3/4]

◆ base_qualities() [4/4]

◆ cigar_sequence() [1/4]

◆ cigar_sequence() [2/4]

◆ cigar_sequence() [3/4]

◆ cigar_sequence() [4/4]

◆ flag() [1/4]

◆ flag() [2/4]

◆ flag() [3/4]

◆ flag() [4/4]

◆ header_ptr() [1/4]

◆ header_ptr() [2/4]

◆ header_ptr() [3/4]

◆ header_ptr() [4/4]

◆ id() [1/4]

◆ id() [2/4]

◆ id() [3/4]

◆ id() [4/4]

◆ mapping_quality() [1/4]

◆ mapping_quality() [2/4]

◆ mapping_quality() [3/4]

◆ mapping_quality() [4/4]

◆ mate_position() [1/4]

◆ mate_position() [2/4]

◆ mate_position() [3/4]

◆ mate_position() [4/4]

◆ mate_reference_id() [1/4]

◆ mate_reference_id() [2/4]

◆ mate_reference_id() [3/4]

◆ mate_reference_id() [4/4]

◆ reference_id() [1/4]

◆ reference_id() [2/4]

◆ reference_id() [3/4]

◆ reference_id() [4/4]

◆ reference_position() [1/4]

◆ reference_position() [2/4]

◆ reference_position() [3/4]

◆ reference_position() [4/4]

◆ sequence() [1/4]

◆ sequence() [2/4]

◆ sequence() [3/4]

◆ sequence() [4/4]

◆ sequence_position() [1/4]

◆ sequence_position() [2/4]

◆ sequence_position() [3/4]

◆ sequence_position() [4/4]

◆ tags() [1/4]

◆ tags() [2/4]

◆ tags() [3/4]

◆ tags() [4/4]

◆ template_length() [1/4]

◆ template_length() [2/4]

◆ template_length() [3/4]

◆ template_length() [4/4]

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