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BigMafAdapter

Auto-generated config schema for the current JBrowse release — see the config guide for concepts. Provided by the maf plugin. View source.

Example usage

samples names the rows in the order they are drawn, and has to match the species keys in the file — a bigMaf carries the alignment but not a display order, so an omitted or misspelled name shows as a missing row rather than an error:

{
  type: 'MafTrack',
  trackId: 'my_track',
  name: 'My track',
  assemblyNames: ['hg38'],
  adapter: {
    type: 'BigMafAdapter',
    bigBedLocation: { uri: 'https://example.com/multiz.bb' },
    samples: ['hg38', 'panTro6', 'rheMac10', 'mm39'],
  },
}

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

used to configure BigMaf adapter

Config slots

These slots go inside the track's adapter: "adapter": { "type": "BigMafAdapter", ... }. This adapter has no uri shorthand — give it the location slots below. 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
samples
frozen = []		string[] or {id:string,label:string,color?:string,assemblyName?:string,assemblyConfigLocation?:UriLocation}[]; assemblyName makes rows for that sample navigable to its own genome, and assemblyConfigLocation says where to load that assembly from when the session lacks it
bigBedLocation
fileLocation = { uri: '/path/to/my.bb', locationType: 'UriLocation' }		location of the bigMaf file — a BigBed whose extra field holds the MAF alignment block, as built by UCSC's mafToBigMaf followed by bedToBigBed -type=bed3+1 -as=bigMaf.as -tab.
nhLocation
fileLocation = { uri: '/path/to/my.nh', locationType: 'UriLocation' }		newick tree
summaryAdapter
frozen = null		optional swappable sub-adapter (e.g. a BigBedAdapter over UCSC bigMafSummary.bb) used for cheap zoom-out rendering; null disables it
annotationAdapter
frozen = null		optional sub-adapter (typically a BigBedAdapter over a UCSC multizwayFrames.bb) supplying per-species CDS reading frames for the gene-structure overlay and codon view; null disables it