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PairwiseIndexedPAFAdapter

Auto-generated config schema for the current JBrowse release — 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',
  },
}

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

a tabix-indexed PAF (PIF) for large synteny datasets. The uri shorthand auto-resolves the .tbi index (pass csi: true for a .csi index).

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.

SlotDescription
pifGzLocation
fileLocation = 
{ uri: '/path/to/data/file.pif.gz', locationType: 'UriLocation' }
location of pairwise tabix indexed PAF (pif)
coarseBpPerPxThreshold
number = 10000		bpPerPx threshold at which a view on "Level of detail: automatic" switches from the per-row CIGAR tier (lowercase t/q prefix) to the coarse no-CIGAR tier (uppercase T/Q prefix), when make-pif was run with a coarse tier. No coarse tier present in the file = always uses the fine tier. Should be at least make-pif's --coarse gap: below it, coarse ribbons are drawn straight across indels wide enough to see.
advanced
assemblyNames
stringArray = []		Array of assembly names to use for this file. The query assembly name is the first value in the array, target assembly name is the second
targetAssembly
string = ''		Alternative to assemblyNames: the target assembly name
queryAssembly
string = ''		Alternative to assemblyNames: the query assembly name
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.