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Gff3Adapter

Auto-generated from the config schema in the source — see the config guide for concepts. Provided by the gff3 plugin. View source.

Reads plain-text GFF3 files. The adapter loads the whole file into memory, so use Gff3TabixAdapter for large files.

Example usage

{
  type: 'FeatureTrack',
  trackId: 'my_track',
  name: 'My track',
  assemblyNames: ['hg38'],
  adapter: {
    type: 'Gff3Adapter',
    uri: 'https://example.com/genes.gff3',
  },
}

JBrowse infers Gff3Adapter and FeatureTrack from genes.gff3, and name defaults to the file name. In a config declaring one assembly, assemblyNames comes from there too — see the shortest track.

{
  trackId: 'my_track',
  uri: 'https://example.com/genes.gff3',
  assemblyNames: ['hg38'],
}

Config slots

Adapter slots go inside the track's adapter: "adapter": { "type": "Gff3Adapter", ... }. It also accepts the shorthand keys uri, baseUri in place of writing a location slot out. Slot types (fileLocation, frozen, ...) are explained in the config slot types reference. Slots a base configuration contributes are listed here too, so this table is the whole surface.

SlotDescription
gffLocation
fileLocation = { uri: '/path/to/my.gff', locationType: 'UriLocation' }		location of the GFF3 file. May be gzipped; it is decompressed and parsed in full on first use, so the file has to fit in memory.