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BgzipFastaAdapter

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 and .gzi indexes:

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

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

Config slots

These slots go inside the track's adapter: "adapter": { "type": "BgzipFastaAdapter", ... }. 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.gz', locationType: 'UriLocation' }		location of the bgzip-compressed FASTA. Must be bgzip rather than plain gzip — samtools faidx cannot index the latter, and only bgzip supports the per-block random access that keeps a base-level view to one range request.
faiLocation
fileLocation = { uri: '/path/to/seq.fa.gz.fai', locationType: 'UriLocation' }		location of the samtools faidx index (.fai). It supplies the reference names and lengths as well as the offsets into the uncompressed sequence, so the assembly cannot load without it.
metadataLocation
fileLocation = 
{ uri: '/path/to/fa.metadata.yaml', locationType: 'UriLocation' }
Optional metadata file
gziLocation
fileLocation = { uri: '/path/to/seq.fa.gz.gzi', locationType: 'UriLocation' }		location of the bgzip block index (.gzi), written beside the .fai by samtools faidx on a bgzipped FASTA. It maps uncompressed offsets to compressed ones, which is what makes a range request possible at all.