seqan3::sam_record< field_types, field_ids > Class Template Reference

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

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

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

Public Member Functions
SEQAN3_DEPRECATED_340 decltype(auto)	alignment () &
	[DEPRECATED] The (pairwise) alignment stored in an object that models seqan3::detail::pairwise_alignment.
SEQAN3_DEPRECATED_340 decltype(auto)	alignment () &&
	[DEPRECATED] The (pairwise) alignment stored in an object that models seqan3::detail::pairwise_alignment.
SEQAN3_DEPRECATED_340 decltype(auto)	alignment () const &
	[DEPRECATED] The (pairwise) alignment stored in an object that models seqan3::detail::pairwise_alignment.
SEQAN3_DEPRECATED_340 decltype(auto)	alignment () const &&
	[DEPRECATED] The (pairwise) alignment stored in an object that models seqan3::detail::pairwise_alignment.
decltype(auto)	base_qualities () &
	The qualities, usually in Phred score notation. (SAM Column ID: QUAL)
decltype(auto)	base_qualities () &&
	The qualities, usually in Phred score notation. (SAM Column ID: QUAL)
decltype(auto)	base_qualities () const &
	The qualities, usually in Phred score notation. (SAM Column ID: QUAL)
decltype(auto)	base_qualities () const &&
	The qualities, usually in Phred score notation. (SAM Column ID: QUAL)
decltype(auto)	cigar_sequence () &
	The cigar vector representing the alignment. (SAM Column ID: CIGAR)
decltype(auto)	cigar_sequence () &&
	The cigar vector representing the alignment. (SAM Column ID: CIGAR)
decltype(auto)	cigar_sequence () const &
	The cigar vector representing the alignment. (SAM Column ID: CIGAR)
decltype(auto)	cigar_sequence () const &&
	The cigar vector representing the alignment. (SAM Column ID: CIGAR)
decltype(auto)	flag () &
	The alignment flag (bit information), uint16_t value. (SAM Column ID: FLAG)
decltype(auto)	flag () &&
	The alignment flag (bit information), uint16_t value. (SAM Column ID: FLAG)
decltype(auto)	flag () const &
	The alignment flag (bit information), uint16_t value. (SAM Column ID: FLAG)
decltype(auto)	flag () const &&
	The alignment flag (bit information), uint16_t value. (SAM Column ID: FLAG)
decltype(auto)	header_ptr () &
	A pointer to the seqan3::sam_file_header object storing header information.
decltype(auto)	header_ptr () &&
	A pointer to the seqan3::sam_file_header object storing header information.
decltype(auto)	header_ptr () const &
	A pointer to the seqan3::sam_file_header object storing header information.
decltype(auto)	header_ptr () const &&
	A pointer to the seqan3::sam_file_header object storing header information.
decltype(auto)	id () &
	The identifier, usually a string. (SAM Column ID: QNAME)
decltype(auto)	id () &&
	The identifier, usually a string. (SAM Column ID: QNAME)
decltype(auto)	id () const &
	The identifier, usually a string. (SAM Column ID: QNAME)
decltype(auto)	id () const &&
	The identifier, usually a string. (SAM Column ID: QNAME)
decltype(auto)	mapping_quality () &
	The mapping quality of the alignment, usually a Phred-scaled score. (SAM Column ID: MAPQ)
decltype(auto)	mapping_quality () &&
	The mapping quality of the alignment, usually a Phred-scaled score. (SAM Column ID: MAPQ)
decltype(auto)	mapping_quality () const &
	The mapping quality of the alignment, usually a Phred-scaled score. (SAM Column ID: MAPQ)
decltype(auto)	mapping_quality () const &&
	The mapping quality of the alignment, usually a Phred-scaled score. (SAM Column ID: MAPQ)
decltype(auto)	mate_position () &
	(Reference) Sequence relative start position (0-based) of the mate. (SAM Column ID: PNEXT)
decltype(auto)	mate_position () &&
	(Reference) Sequence relative start position (0-based) of the mate. (SAM Column ID: PNEXT)
decltype(auto)	mate_position () const &
	(Reference) Sequence relative start position (0-based) of the mate. (SAM Column ID: PNEXT)
decltype(auto)	mate_position () const &&
	(Reference) Sequence relative start position (0-based) of the mate. (SAM Column ID: PNEXT)
decltype(auto)	mate_reference_id () &
	The identifier of the (reference) sequence of the mate. (SAM Column ID: RNEXT)
decltype(auto)	mate_reference_id () &&
	The identifier of the (reference) sequence of the mate. (SAM Column ID: RNEXT)
decltype(auto)	mate_reference_id () const &
	The identifier of the (reference) sequence of the mate. (SAM Column ID: RNEXT)
decltype(auto)	mate_reference_id () const &&
	The identifier of the (reference) sequence of the mate. (SAM Column ID: RNEXT)
decltype(auto)	reference_id () &
	The identifier of the (reference) sequence that seqan3::sam_record::sequence was aligned to. (SAM Column ID: RNAME)
decltype(auto)	reference_id () &&
	The identifier of the (reference) sequence that seqan3::sam_record::sequence was aligned to. (SAM Column ID: RNAME)
decltype(auto)	reference_id () const &
	The identifier of the (reference) sequence that seqan3::sam_record::sequence was aligned to. (SAM Column ID: RNAME)
decltype(auto)	reference_id () const &&
	The identifier of the (reference) sequence that seqan3::sam_record::sequence was aligned to. (SAM Column ID: RNAME)
decltype(auto)	reference_position () &
	(Reference) Sequence (seqan3::sam_record::reference_sequence) relative start position (0-based), unsigned value. (SAM Column ID: POS)
decltype(auto)	reference_position () &&
	(Reference) Sequence (seqan3::sam_record::reference_sequence) relative start position (0-based), unsigned value. (SAM Column ID: POS)
decltype(auto)	reference_position () const &
	(Reference) Sequence (seqan3::sam_record::reference_sequence) relative start position (0-based), unsigned value. (SAM Column ID: POS)
decltype(auto)	reference_position () const &&
	(Reference) Sequence (seqan3::sam_record::reference_sequence) relative start position (0-based), unsigned value. (SAM Column ID: POS)
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)
decltype(auto)	sequence () &&
	The "sequence", usually a range of nucleotides or amino acids. (SAM Column ID: SEQ)
decltype(auto)	sequence () const &
	The "sequence", usually a range of nucleotides or amino acids. (SAM Column ID: SEQ)
decltype(auto)	sequence () const &&
	The "sequence", usually a range of nucleotides or amino acids. (SAM Column ID: SEQ)
SEQAN3_DEPRECATED_340 decltype(auto)	sequence_position () &
	[DEPRECATED] Sequence (seqan3::sam_record::sequence) relative start position (0-based), unsigned value.
SEQAN3_DEPRECATED_340 decltype(auto)	sequence_position () &&
	[DEPRECATED] Sequence (seqan3::sam_record::sequence) relative start position (0-based), unsigned value.
SEQAN3_DEPRECATED_340 decltype(auto)	sequence_position () const &
	[DEPRECATED] Sequence (seqan3::sam_record::sequence) relative start position (0-based), unsigned value.
SEQAN3_DEPRECATED_340 decltype(auto)	sequence_position () const &&
	[DEPRECATED] Sequence (seqan3::sam_record::sequence) relative start position (0-based), unsigned value.
decltype(auto)	tags () &
	The optional tags in the SAM format.
decltype(auto)	tags () &&
	The optional tags in the SAM format.
decltype(auto)	tags () const &
	The optional tags in the SAM format.
decltype(auto)	tags () const &&
	The optional tags in the SAM format.
decltype(auto)	template_length () &
	The observed template length. (SAM Column ID: TLEN)
decltype(auto)	template_length () &&
	The observed template length. (SAM Column ID: TLEN)
decltype(auto)	template_length () const &
	The observed template length. (SAM Column ID: TLEN)
decltype(auto)	template_length () const &&
	The observed template length. (SAM Column ID: TLEN)
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 & >().as_base())))
	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 Symbols inherited from tuple_like
size_t	tuple_size_v
	A unary type trait that holds the number of elements in the tuple.
	tuple_elment_t
	A transformation trait that holds the type of elements in the tuple.
auto &&	get (type &&val)
	Return the i-th element of the tuple.

Detailed Description

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

The record type of seqan3::sam_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.

Remarks

For a complete overview, take a look at SAM File

Member Function Documentation

alignment() [1/4]

template<typename field_types , typename field_ids >

SEQAN3_DEPRECATED_340 decltype(auto) seqan3::sam_record< field_types, field_ids >::alignment ( ) &

inline

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

Deprecated:

Please access cigar() and then use seqan3::alignment_from_cigar to retrieve the alignment.

alignment() [2/4]

template<typename field_types , typename field_ids >

SEQAN3_DEPRECATED_340 decltype(auto) seqan3::sam_record< field_types, field_ids >::alignment ( ) &&

inline

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

Deprecated:

Please access cigar() and then use seqan3::alignment_from_cigar to retrieve the alignment.

alignment() [3/4]

template<typename field_types , typename field_ids >

SEQAN3_DEPRECATED_340 decltype(auto) seqan3::sam_record< field_types, field_ids >::alignment ( ) const &

inline

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

Deprecated:

Please access cigar() and then use seqan3::alignment_from_cigar to retrieve the alignment.

alignment() [4/4]

template<typename field_types , typename field_ids >

SEQAN3_DEPRECATED_340 decltype(auto) seqan3::sam_record< field_types, field_ids >::alignment ( ) const &&

inline

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

Deprecated:

Please access cigar() and then use seqan3::alignment_from_cigar to retrieve the alignment.

base_qualities() [1/4]

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. (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 ( ) &&

inline

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 &

inline

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 &&

inline

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 ( ) &

inline

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 ( ) &&

inline

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 &

inline

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 &&

inline

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 ( ) &

inline

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 ( ) &&

inline

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 &

inline

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 &&

inline

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 ( ) &

inline

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 ( ) &&

inline

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 &

inline

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 &&

inline

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 ( ) &

inline

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 ( ) &&

inline

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 &

inline

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 &&

inline

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 ( ) &

inline

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 ( ) &&

inline

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 &

inline

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 &&

inline

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 ( ) &

inline

(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 ( ) &&

inline

(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 &

inline

(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 &&

inline

(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 ( ) &

inline

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 ( ) &&

inline

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 &

inline

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 &&

inline

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 ( ) &

inline

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 ( ) &&

inline

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 &

inline

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 &&

inline

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 ( ) &

inline

(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 ( ) &&

inline

(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 &

inline

(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 &&

inline

(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 ( ) &

inline

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 ( ) &&

inline

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 &

inline

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 &&

inline

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 >

SEQAN3_DEPRECATED_340 decltype(auto) seqan3::sam_record< field_types, field_ids >::sequence_position ( ) &

inline

[DEPRECATED] Sequence (seqan3::sam_record::sequence) relative start position (0-based), unsigned value.

Returns

0

Deprecated:

This member is deprecated please access the seqan3::sam_record::cigar() information directly and check the value for soft clipping (S) at the front of the CIGAR string. It is synonym to the offset. If not soft clipping is present at the front, the offset is zero.

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 >

SEQAN3_DEPRECATED_340 decltype(auto) seqan3::sam_record< field_types, field_ids >::sequence_position ( ) &&

inline

[DEPRECATED] Sequence (seqan3::sam_record::sequence) relative start position (0-based), unsigned value.

Returns

0

Deprecated:

This member is deprecated please access the seqan3::sam_record::cigar() information directly and check the value for soft clipping (S) at the front of the CIGAR string. It is synonym to the offset. If not soft clipping is present at the front, the offset is zero.

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 >

SEQAN3_DEPRECATED_340 decltype(auto) seqan3::sam_record< field_types, field_ids >::sequence_position ( ) const &

inline

[DEPRECATED] Sequence (seqan3::sam_record::sequence) relative start position (0-based), unsigned value.

Returns

0

Deprecated:

This member is deprecated please access the seqan3::sam_record::cigar() information directly and check the value for soft clipping (S) at the front of the CIGAR string. It is synonym to the offset. If not soft clipping is present at the front, the offset is zero.

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 >

SEQAN3_DEPRECATED_340 decltype(auto) seqan3::sam_record< field_types, field_ids >::sequence_position ( ) const &&

inline

[DEPRECATED] Sequence (seqan3::sam_record::sequence) relative start position (0-based), unsigned value.

Returns

0

Deprecated:

This member is deprecated please access the seqan3::sam_record::cigar() information directly and check the value for soft clipping (S) at the front of the CIGAR string. It is synonym to the offset. If not soft clipping is present at the front, the offset is zero.

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 ( ) &

inline

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 ( ) &&

inline

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 &

inline

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 &&

inline

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 ( ) &

inline

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 ( ) &&

inline

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 &

inline

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 &&

inline

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

Returns

int32_t per default

---

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

• sam_file/record.hpp