PairwiseIndexedPAFAdapter

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

Example usage#

{
  type: 'SyntenyTrack',
  trackId: 'my_track',
  name: 'My track',
  assemblyNames: ['hg19', 'hg38'],
  adapter: {
    type: 'PairwiseIndexedPAFAdapter',
    uri: 'https://example.com/aln.pif.gz',
    queryAssembly: 'hg19',
    targetAssembly: 'hg38',
  },
}

Reads a tabix-indexed PAF (PIF) file, fetching only the alignments in view, for large synteny datasets. The uri shorthand auto-resolves the .tbi index (pass csi: true for a .csi index).

Related links#

• Track: SyntenyTrack
• Display: ChordSyntenyDisplay
• Display: DotplotDisplay
• Display: LGVSyntenyDisplay
• Display: LinearMarkDisplay
• Display: LinearSyntenyDisplay
• Display: MultiWaySyntenyDisplay
• Config guide: Supported file types
• Config guide: Synteny track
• Developer guide: PIF (Pairwise Indexed Format)

Config slots#

These slots go inside the track's adapter: "adapter": { "type": "PairwiseIndexedPAFAdapter", ... }. 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.

{ uri: '/path/to/data/file.pif.gz', locationType: 'UriLocation' }