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GtfTabixAdapter

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

Reads bgzip-compressed, tabix-indexed GTF files.

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: 'GtfTabixAdapter',
    uri: 'https://example.com/genes.gtf.gz',
  },
}

JBrowse infers GtfTabixAdapter and FeatureTrack from genes.gtf.gz, 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.gz',
  assemblyNames: ['hg38'],
}

Config slots

Adapter slots go inside the track's adapter: "adapter": { "type": "GtfTabixAdapter", ... }. 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
gtfGzLocation
fileLocation = { uri: '/path/to/my.gtf.gz', locationType: 'UriLocation' }		location of the bgzip-compressed GTF, sorted by position. Must be bgzip rather than plain gzip, which tabix cannot index.
index
TabixIndex		The tabix index location and its kind. The uri shorthand derives both, so a config using it states neither.
dontRedispatch
stringArray = [ 'chromosome', 'region', 'contig', 'supercontig', 'scaffold' ]		the GtfTabixAdapter 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 annotation 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
aggregateField
string = 'gene_name'		attribute naming the parent gene that the adapter aggregates transcripts into. The adapter groups transcripts 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