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PAFAdapter

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

A PAF has no index, but it needs the query and target assembly names (query first):

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

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

Gotcha

assemblyNames is [query, target], which is the reverse of the order minimap2 and nucmer take their inputs (minimap2 target.fa query.fa). Getting it backwards silently draws every alignment against the wrong assembly rather than erroring. Set the named queryAssembly and targetAssembly fields instead and the ordering can't be misread.

Config slots

These slots go inside the track's adapter: "adapter": { "type": "PAFAdapter", ... }. 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
pafLocation
fileLocation = { uri: '/path/to/file.paf', locationType: 'UriLocation' }		location of the PAF file (minimap2, wfmash, and similar). May be gzipped. There is no index, so the whole alignment is read into memory — convert anything large with jbrowse make-pif and use the PairwiseIndexedPAFAdapter instead.
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