Class
GffRecordRepresent a record from a GFF or GTF file.
| Implements | FormattedFileRecordConcept |
|---|---|
| All Impl'd | AssignableConcept, CopyConstructibleConcept, DefaultConstructibleConcept, FormattedFileRecordConcept |
| Defined in | <seqan/gff_io.h> |
| Signature |
class GffRecord;
|
Member Function Overview
-
static float INVALID_SCORE()Returns invalid score (NaN float value).
Member Functions Inherited From AssignableConcept
Interface Function Overview
-
void clear(record);Reset a GffRecord object.
Interface Functions Inherited From AssignableConcept
Member Variable Overview
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int32_t GffRecord::beginPosThe begin position of the record. -
int32_t GffRecord::endPosThe end position of the record. -
int32_t GffRecord::INVALID_IDXStatic member with invalid/sentinel rID value. -
char GffRecord::phaseThe phase of the record. -
CharString GffRecord::refThe sequence name of the record. -
float GffRecord::scoreThe score of the record. -
CharString GffRecord::sourceThe source of the record. -
char GffRecord::strandThe strand the record belongs to. -
TCharStringSet GffRecord::tagNamesThe names of the attributes of the record, StringSet of CharString. -
TCharStringSet GffRecord::tagValuesThe values of the attributes of the record, StringSet of CharString. -
CharString GffRecord::typeThe type of the record.
Member Functions Detail
static float INVALID_SCORE()
The term x != x (for float x is only true if x is a NaN.
Data Races
Interface Functions Detail
void clear(record);
Parameters
record
|
The GffRecord to reset. |
|---|
Data Races
Member Variables Detail
int32_t GffRecord::beginPos
int32_t GffRecord::endPos
GFF and GTF use 1-based positions in text, but they are stored as 0-based coordinates.
int32_t GffRecord::INVALID_IDX
char GffRecord::phase
For features of type "CDS", the phase indicates where the feature begins with reference to the reading frame. The phase is one of the integers 0, 1, or 2, indicating the number of bases that should be removed from the beginning of this feature to reach the first base of the next codon.
CharString GffRecord::ref
The ID of the landmark used to establish the coordinate system for the current feature, most often the contig/chromosome name.
float GffRecord::score
CharString GffRecord::source
The source is a free text qualifier intended to describe the algorithm or operating procedure that generated this feature.
char GffRecord::strand
The strand of the feature. + for positive strand (relative to the landmark), - for minus strand, and . for features that are not stranded.
TCharStringSet GffRecord::tagNames
For each value there is a name associated in tagNames.
TCharStringSet GffRecord::tagValues
Remarks
For each name there is a value associated in GffRecord::tagValues.