CytobandAdapter

Auto-generated from the config schema in the source — see the config guide for concepts. Built into JBrowse core. View source.

Reads an assembly's cytoband file, which the linear genome view draws as ideogram banding in its overview bar.

Example usage#

Goes on an ASSEMBLY, under cytobands — not on a track. It draws the ideogram banding in the linear genome view's overview bar:

{
  name: 'hg38',
  sequence: {
    type: 'ReferenceSequenceTrack',
    trackId: 'hg38-ReferenceSequenceTrack',
    adapter: {
      type: 'BgzipFastaAdapter',
      uri: 'https://example.com/hg38.fa.gz',
    },
  },
  cytobands: {
    adapter: {
      type: 'CytobandAdapter',
      uri: 'https://example.com/hg38.cytoBand.txt.gz',
    },
  },
}

Config slots#

Adapter slots go inside the track's adapter: "adapter": { "type": "CytobandAdapter", ... }. 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.

Retired keys#

An older config may still write these. Each loads without an error, and jbrowse validate reports it as stale.