SeqAn3  3.0.3
The Modern C++ library for sequence analysis.
seqan3::sam_record< field_types, field_ids > Class Template Reference

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_recordoperator= (sam_record const &)=default
 Defaulted.
 
 sam_record (sam_record &&)=default
 Defaulted.
 
sam_recordoperator= (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.
 
recordoperator= (record const &)=default
 Defaulted.
 
 record (record &&)=default
 Defaulted.
 
recordoperator= (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.
 

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_typesThe types of the fields in this record as a seqan3::type_list.
field_idsA 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 ( ) &
inline

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 ( ) &&
inline

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 &
inline

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 &&
inline

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

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 ( ) &&
inline

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 &
inline

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 &&
inline

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 ( ) &
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: