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BedGraphAdapter

Auto-generated config schema for the current JBrowse release — see the config guide for concepts. Provided by the bed plugin. View source.

Example usage

{
  type: 'QuantitativeTrack',
  trackId: 'my_track',
  name: 'My track',
  assemblyNames: ['hg38'],
  adapter: {
    type: 'BedGraphAdapter',
    uri: 'https://example.com/signal.bedGraph',
  },
}

signal.bedGraph infers BedGraphAdapter and QuantitativeTrack on its own, 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/signal.bedGraph',
  assemblyNames: ['hg38'],
}

See the Config slots section below for all available configuration fields.

used to load plain-text bedGraph signal files. Loads the whole file into memory, so prefer the BedGraphTabixAdapter for large files.

Config slots

These slots go inside the track's adapter: "adapter": { "type": "BedGraphAdapter", ... }. 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
bedGraphLocation
fileLocation = { uri: '/path/to/my.bedgraph', locationType: 'UriLocation' }		location of the plain-text bedGraph (chrom start end value, one line per interval). May be gzipped.
columnNames
stringArray = []		List of column names