Skip to main content

IndexedFastaAdapter

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

Reads an uncompressed FASTA reference sequence through its samtools faidx index, fetching the bases in view as byte ranges.

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',
  },
}

Config slots

Adapter 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
maybeFileLocation		Optional metadata file