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BigBedAdapter

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

Reads BigBed files, the indexed binary form of BED.

Example usage

{
  type: 'FeatureTrack',
  trackId: 'my_track',
  name: 'My track',
  assemblyNames: ['hg38'],
  adapter: {
    type: 'BigBedAdapter',
    uri: 'https://example.com/features.bb',
  },
}

JBrowse infers BigBedAdapter and FeatureTrack from features.bb, 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/features.bb',
  assemblyNames: ['hg38'],
}

Config slots

Adapter slots go inside the track's adapter: "adapter": { "type": "BigBedAdapter", ... }. 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
bigBedLocation
fileLocation = { uri: '/path/to/my.bb', locationType: 'UriLocation' }		location of the BigBed file. The file has an index and summary zoom levels built in, so there is no separate index to configure.
scoreColumn
string = ''		The column to use as a "score" attribute
aggregateField
string = 'geneName2'		An attribute to aggregate features with
disableGeneHeuristic
boolean = false		Disable the heuristic that auto-detects BED12 features as gene/transcript structures. Useful for files that have BED12-like structure but are not genes (e.g. tandem duplications)