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MashMapAdapter

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: 'MashMapAdapter',
    uri: 'https://example.com/aln.out',
    queryAssembly: 'hg19',
    targetAssembly: 'hg38',
  },
}

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

used to load MashMap .out alignment files (query and target assembly required)

Config slots

These slots go inside the track's adapter: "adapter": { "type": "MashMapAdapter", ... }. 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
outLocation
fileLocation = { uri: '/path/to/mashmap.out', locationType: 'UriLocation' }		location of the MashMap .out file — PAF-like records with MashMap's approximate identity in place of a CIGAR, so the bands it draws are mapping blocks with no base-level alignment inside them.
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