ChromSizesAdapter

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

Reads the chromosome names and lengths in a UCSC-style .chrom.sizes file (tab-separated name<TAB>length), for an assembly with no sequence. Use it for karyotype, whole-genome or synteny views that need no base-level sequence.

Example usage#

{
  type: 'ReferenceSequenceTrack',
  trackId: 'my_assembly-ReferenceSequenceTrack',
  adapter: {
    type: 'ChromSizesAdapter',
    uri: 'https://example.com/species.chrom.sizes',
  },
}

Related links#

• Track: ReferenceSequenceTrack
• Display: LinearReferenceSequenceDisplay
• Tutorial: Synteny visualization (OrthoFinder orthogroups)
• Config guide: FromConfig adapters
• Config guide: Supported file types

Config slots#

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

{ uri: '/path/to/species.chrom.sizes', locationType: 'UriLocation' }