Skip to main content

UnindexedFastaAdapter

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

Example usage

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

Reads a plain (non-bgzipped) FASTA file with no index. The adapter holds the whole sequence in memory, so use IndexedFastaAdapter for large genomes.

Config slots

These slots go inside the track's adapter: "adapter": { "type": "UnindexedFastaAdapter", ... }. 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
rewriteRefNames
string = ''		jexl expression rewriting each sequence name as the FASTA is parsed, e.g. jexl:split(refName, ' ')[0] to keep only the first word of a description line. Left empty, names are used as written; an expression returning nothing falls back to the original name.
callback args: refName
fastaLocation
fileLocation = { uri: '/path/to/seq.fa', locationType: 'UriLocation' }		location of the plain FASTA. With no index there are no byte offsets to seek to, so the whole file is downloaded and parsed on first use and held in memory.
metadataLocation
maybeFileLocation		Optional metadata file