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BedGraphTabixAdapter

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

Reads bgzip-compressed, tabix-indexed bedGraph signal files.

Several signals in one file are a MultiQuantitativeTrack's subtracks: one value column each, named by the header, or a source column naming each row's, which is the form Save track data writes.

Example usage

The uri shorthand auto-resolves the .tbi index:

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

JBrowse infers BedGraphTabixAdapter and QuantitativeTrack from signal.bedGraph.gz, 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.gz',
  assemblyNames: ['hg38'],
}

Config slots

Adapter slots go inside the track's adapter: "adapter": { "type": "BedGraphTabixAdapter", ... }. It also accepts the shorthand keys uri, baseUri, csi 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
bedGraphGzLocation
fileLocation = { uri: '/path/to/my.bedgraph', locationType: 'UriLocation' }		location of the bgzip-compressed bedGraph (chrom start end value, sorted by position). Must be bgzip rather than plain gzip, which tabix cannot index.
index
TabixIndex		The tabix index location and its kind. The uri shorthand derives both, so a config using it states neither.
columnNames
stringArray = []		List of column names