The IO module contains concepts, data structures and functions related to reading and writing formatted files, streams, and serialisation. More...
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... | |
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. | |
The IO module contains concepts, data structures and functions related to reading and writing formatted files, streams, and serialisation.
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An enumerator for the fields used in file formats.Some of the fields are shared between formats.
Enumerator | |
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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), |
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), |
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. |