Package htsjdk.tribble.gff
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Interface Summary Interface Description Gff3Feature Gff3 format spec is defined at https://github.com/The-Sequence-Ontology/Specifications/blob/31f62ad469b31769b43af42e0903448db1826925/gff3.md Discontinuous features which are split between multiple lines in the gff files are implemented as separate features linked as "co-features" -
Class Summary Class Description Gff3BaseData Gff3Codec Codec for parsing Gff3 files, as defined in https://github.com/The-Sequence-Ontology/Specifications/blob/31f62ad469b31769b43af42e0903448db1826925/gff3.md Note that while spec states that all feature types must be defined in sequence ontology, this implementation makes no check on feature types, and allows any string as feature type Each feature line in the Gff3 file will be emitted as a separate feature.Gff3Constants Gff3FeatureImpl Gff3 format spec is defined at https://github.com/The-Sequence-Ontology/Specifications/blob/31f62ad469b31769b43af42e0903448db1826925/gff3.md Discontinuous features which are split between multiple lines in the gff files are implemented as separate features linked as "co-features"Gff3Writer A class to write out gff3 files.SequenceRegion Represents a sequence region feature in a gff3 file. -
Enum Summary Enum Description Gff3Codec.DecodeDepth Gff3Codec.Gff3Directive Enum for parsing directive lines.