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BigMafAdapter

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

Reads a UCSC bigMaf file, a BigBed that holds a MAF multiple alignment block in each record.

Example usage

samples names the rows in the order they are drawn, and has to match the species keys in the file — a bigMaf has the alignment but no 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',
    uri: 'https://example.com/multiz.bb',
    samples: ['hg38', 'panTro6', 'rheMac10', 'mm39'],
  },
}

Config slots

Adapter slots go inside the track's adapter: "adapter": { "type": "BigMafAdapter", ... }. It also accepts the shorthand keys uri, baseUri, nhUri 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
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.
samples
frozen = []		string[] or {id:string,label:string,color?:string,assemblyName?:string,assemblyConfigLocation?:UriLocation}[]; assemblyName makes rows for that sample navigable to the genome named by assemblyName, and assemblyConfigLocation gives the location to load that assembly from when the session lacks it
nhLocation
maybeFileLocation		newick tree naming and ordering the species rows; its leaf names are the sample ids, and any samples entries supply label/color overrides matched by id
summaryAdapter
maybeFrozen		optional swappable sub-adapter (typically a BigBedAdapter over UCSC bigMafSummary.bb, which is published alongside the bigMaf) used for cheap zoom-out rendering; leave it unset to disable
samplesTsvLocation
maybeFileLocation		optional tab-separated table of per-sample metadata. It needs a header row, and its first column is the sample name exactly as the adapter spells it: a VCF sample, a MultiWiggle subtrack's name, a MAF species id. Every other column (population, tissue, ...) becomes an attribute of that sample, which the multi-row displays group, sort, color and tooltip rows by; a MAF adapter reads the label, color and assemblyName columns onto its species rows, over its samples entries. The table also narrows the adapter's samples to the ones it lists, and a table naming none of them is an error. An adapter that names no samples (a MAF track discovering its species from the file) takes the table's rows as its samples
framesAdapter
maybeFrozen		optional sub-adapter (typically a BigBedAdapter over a UCSC multizwayFrames.bb) supplying each species' CDS reading frames for the frames strip, the codon view and the codon conservation band; leave it unset to disable

Retired keys

An older config may still write these. Each loads without an error, and jbrowse validate reports it as stale.

KeyOn load
annotationAdaptermoved into a current slot