Skip to main content

Gff3TabixAdapter

Auto-generated config schema for the current JBrowse release — see the config guide for concepts. Provided by the gff3 plugin. View source.

Example usage

The uri shorthand auto-resolves the .tbi index; add csi: true for a .csi index instead:

{
  type: 'FeatureTrack',
  trackId: 'my_track',
  name: 'My track',
  assemblyNames: ['hg38'],
  adapter: {
    type: 'Gff3TabixAdapter',
    uri: 'https://example.com/genes.gff3.gz',
  },
}

genes.gff3.gz infers Gff3TabixAdapter and FeatureTrack on its own, and name defaults to the file name. In a config declaring one assembly, assemblyNames comes from there too — see the shortest track.

{
  trackId: 'my_track',
  uri: 'https://example.com/genes.gff3.gz',
  assemblyNames: ['hg38'],
}

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

used to load bgzip-compressed, tabix-indexed GFF3 files

Config slots

These slots go inside the track's adapter: "adapter": { "type": "Gff3TabixAdapter", ... }. It also accepts the shorthand keys uri, baseUri, csi 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
gffGzLocation
fileLocation = { uri: '/path/to/my.gff.gz', locationType: 'UriLocation' }		location of the bgzip-compressed GFF3, sorted by position. Must be bgzip rather than plain gzip, which tabix cannot index.
dontRedispatch
stringArray = [ 'chromosome', 'region', 'contig', 'supercontig', 'scaffold' ]		the Gff3TabixAdapter has to "redispatch" if it fetches a region and features it finds inside that region extend outside the region we requested. you can disable this for certain feature types to avoid fetching e.g. the entire chromosome

the defaults are the whole-sequence records the common GFF3 sources emit: region (NCBI), supercontig/scaffold (Ensembl, for non-chromosomal sequences), plus chromosome and contig. They span an entire reference and have no children, so letting one expand the fetch would pull a whole chromosome to gain nothing
index.indexType
stringEnum (TBI, CSI) = 'TBI'		TBI is the usual tabix output. CSI is required for a reference longer than 512 Mb, which TBI cannot address.
index.location
fileLocation = { uri: '/path/to/my.gz.tbi', locationType: 'UriLocation' }		location of the tabix index. Only needed when it is not named <file>.tbi (or .csi), which is what the uri shorthand assumes.