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TwoBitAdapter

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

Reads a UCSC .2bit reference sequence, optionally with a chrom.sizes file to speed up loading.

Example usage

A .2bit file is self-contained; add chromSizes to skip an initial full-file scan on genomes with many contigs:

{
  type: 'ReferenceSequenceTrack',
  trackId: 'my_assembly-ReferenceSequenceTrack',
  adapter: {
    type: 'TwoBitAdapter',
    uri: 'https://example.com/genome.2bit',
  },
}

Config slots

Adapter slots go inside the track's adapter: "adapter": { "type": "TwoBitAdapter", ... }. It also accepts the shorthand keys uri, baseUri, chromSizes 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
twoBitLocation
fileLocation = { uri: '/path/to/my.2bit', locationType: 'UriLocation' }		location of the UCSC .2bit file. It is self-contained — sequence and index in one file — but its per-sequence header is spread through the file, so a genome with many contigs benefits from chromSizesLocation.
chromSizesLocation
maybeFileLocation		An optional chrom.sizes file can be supplied to speed up loading since parsing the twobit file can take time