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FromConfigSequenceAdapter

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

Supplies a reference sequence inline in the config, as features whose seq holds the bases for each region.

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' },
    ],
  },
}

Config slots

Adapter slots go inside the track's adapter: "adapter": { "type": "FromConfigSequenceAdapter", ... }. FromConfigSequenceAdapter 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 config holds the bases, so this suits small sequences — a plasmid, a test contig — not a genome.

Retired keys

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

KeyOn load
featureClassignored