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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 tier (uppercase T/Q prefix), whose CIGAR is folded to its large indels. The file has the last word: one with no coarse tier (make-pif --no-coarse) serves the fine tier at every zoom, and a threshold below the --coarse bound its #pif header states is raised to that bound, since below it the coarse tier is served at zooms where the indels it folded away are 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.