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GtfAdapter

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

Example usage

The uri shorthand works for plain or gzipped GTF:

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

genes.gtf infers GtfAdapter 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.gtf',
  assemblyNames: ['hg38'],
}

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

used to load plain-text GTF files (optionally gzipped). Loads the whole file into memory, so prefer the GtfTabixAdapter for large files.

Config slots

These slots go inside the track's adapter: "adapter": { "type": "GtfAdapter", ... }. 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
gtfLocation
fileLocation = { uri: '/path/to/my.gtf', locationType: 'UriLocation' }		path to gtf file, also allows for gzipped gtf
aggregateField
string = 'gene_name'		attribute naming the parent gene that transcripts are aggregated into. transcripts are grouped by gene_id where the file has one (gene names are not unique within a reference), so this is the gene label, and the grouping key only for files with no gene_id