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FromConfigSequenceAdapter

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

Example usage

Used as the adapter of an assembly's sequence (a ReferenceSequenceTrack):

{
  type: 'ReferenceSequenceTrack',
  trackId: 'my_refseq',
  adapter: {
    type: 'FromConfigSequenceAdapter',
    features: [
      { uniqueId: 'ctgA', refName: 'ctgA', start: 0, end: 10, seq: 'ATGCATGCAT' },
    ],
  },
}

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

supplies reference sequence inline in the config; each feature's seq holds the bases for its region

Config slots

These slots go inside the track's adapter: "adapter": { "type": "FromConfigSequenceAdapter", ... }. This adapter has no uri shorthand — give it the location slots below. 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
adapterId
string = ''		stable identifier used as the adapter cache key; avoids hashing the (potentially large) features array. optional — falls back to hash.
features
frozen = []		one entry per reference sequence, each with a uniqueId, refName, start, end, and a seq string holding the bases for that span. The bases live in the config, so this is for small sequences — a plasmid, a test contig — not a genome.