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IndexedFastaAdapter

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

Example usage

The uri shorthand auto-resolves the .fai index:

{
  type: 'ReferenceSequenceTrack',
  trackId: 'my_assembly-ReferenceSequenceTrack',
  adapter: {
    type: 'IndexedFastaAdapter',
    uri: 'https://example.com/genome.fa',
  },
}

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

Config slots

These slots go inside the track's adapter: "adapter": { "type": "IndexedFastaAdapter", ... }. 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.

SlotDescription
fastaLocation
fileLocation = { uri: '/path/to/seq.fa', locationType: 'UriLocation' }		location of the FASTA file. Only the visible bases are fetched, as byte ranges resolved through the .fai, so the file itself is never downloaded whole.
faiLocation
fileLocation = { uri: '/path/to/seq.fa.fai', locationType: 'UriLocation' }		location of the samtools faidx index (.fai). It supplies the reference names and lengths as well as the byte offsets, so the assembly cannot load without it.
metadataLocation
fileLocation = 
{ uri: '/path/to/fa.metadata.yaml', locationType: 'UriLocation' }
Optional metadata file