SeqAn3
IO

The IO module contains concepts, data structures and functions related to reading and writing formatted files, streams, and serialisation. More...

Collaboration diagram for IO:

Modules

 Alignment File
 
 Sequence File
 
 Stream
 The stream sub-module contains data structures and functions for streaming and tokenization.
 
 Structure File
 Provides reading and writing of files that contain structured sequences in various formats.
 

Classes

struct  seqan3::fields< fs >
 A class template that holds a choice of seqan3::field. More...
 
struct  seqan3::record< field_types, field_ids >
 The class template that file records are based on; behaves like an std::tuple. More...
 

Enumerations

enum  seqan3::field {
  seqan3::field::SEQ, seqan3::field::ID, seqan3::field::QUAL, seqan3::field::SEQ_QUAL,
  seqan3::field::OFFSET, seqan3::field::BPP, seqan3::field::STRUCTURE, seqan3::field::STRUCTURED_SEQ,
  seqan3::field::ENERGY, seqan3::field::REACT, seqan3::field::REACT_ERR, seqan3::field::COMMENT,
  seqan3::field::ALIGNMENT, seqan3::field::REF_ID, seqan3::field::REF_SEQ, seqan3::field::REF_OFFSET,
  seqan3::field::HEADER_PTR, seqan3::field::FLAG, seqan3::field::MATE, seqan3::field::MAPQ,
  seqan3::field::TAGS, seqan3::field::BIT_SCORE, seqan3::field::EVALUE, seqan3::field::USER_DEFINED_0,
  seqan3::field::USER_DEFINED_1, seqan3::field::USER_DEFINED_2, seqan3::field::USER_DEFINED_3, seqan3::field::USER_DEFINED_4,
  seqan3::field::USER_DEFINED_5, seqan3::field::USER_DEFINED_6, seqan3::field::USER_DEFINED_7, seqan3::field::USER_DEFINED_8,
  seqan3::field::USER_DEFINED_9
}
 An enumerator for the fields used in file formats.Some of the fields are shared between formats. More...
 

Variables

template<typename t >
concept fields_concept = is_value_specialisation_of_v<t, fields>
 Auxiliary concept that checks whether a type is a specialisation of seqan3::fields.
 

Detailed Description

The IO module contains concepts, data structures and functions related to reading and writing formatted files, streams, and serialisation.

Todo:
write me!

!

Enumeration Type Documentation

◆ field

enum seqan3::field
strong

An enumerator for the fields used in file formats.Some of the fields are shared between formats.

Todo:
Table which files take which fields
Enumerator
SEQ 

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

ID 

The identifier, usually a string.

QUAL 

The qualities, usually in phred-score notation.

SEQ_QUAL 

Sequence and qualities combined in one range.

OFFSET 

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

BPP 

Base pair probability matrix of interactions, usually a matrix of float numbers.

STRUCTURE 

Fixed interactions, usually a string of structure alphabet characters.

STRUCTURED_SEQ 

Sequence and fixed interactions combined in one range.

ENERGY 

Energy of a folded sequence, represented by one float number.

REACT 

Reactivity values of the sequence characters given in a vector of float numbers.

REACT_ERR 

Reactivity error values given in a vector corresponding to REACT.

COMMENT 

Comment field of arbitrary content, usually a string.

ALIGNMENT 

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

REF_ID 

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

REF_SEQ 

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

REF_OFFSET 

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

HEADER_PTR 

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

FLAG 

The alignment flag (bit information), uint16_t value.

MATE 

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

MAPQ 

The mapping quality of the SEQ alignment, usually a ohred-scaled score.

TAGS 

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

BIT_SCORE 

The bit score (statistical significance indicator), unsigned value.

EVALUE 

The e-value (length normalized bit score), double value.

USER_DEFINED_0 

Identifier for user defined file formats and specialisations.

USER_DEFINED_1 

Identifier for user defined file formats and specialisations.

USER_DEFINED_2 

Identifier for user defined file formats and specialisations.

USER_DEFINED_3 

Identifier for user defined file formats and specialisations.

USER_DEFINED_4 

Identifier for user defined file formats and specialisations.

USER_DEFINED_5 

Identifier for user defined file formats and specialisations.

USER_DEFINED_6 

Identifier for user defined file formats and specialisations.

USER_DEFINED_7 

Identifier for user defined file formats and specialisations.

USER_DEFINED_8 

Identifier for user defined file formats and specialisations.

USER_DEFINED_9 

Identifier for user defined file formats and specialisations.