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MashMapAdapter

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

Reads MashMap .out alignment files, which need the query and target assembly names.

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',
  },
}

Config slots

Adapter 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