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BgzipTaffyAdapter

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

Example usage

The uri shorthand auto-resolves the sibling .tai index:

{
  type: 'MafTrack',
  trackId: 'my_track',
  name: 'My track',
  assemblyNames: ['hg38'],
  adapter: {
    type: 'BgzipTaffyAdapter',
    uri: 'https://example.com/aln.taf.gz',
  },
}

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

used to configure BgzipTaffy adapter

Config slots

These slots go inside the track's adapter: "adapter": { "type": "BgzipTaffyAdapter", ... }. 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
samples
frozen = []		string[] or {id:string,label:string,color?:string,assemblyName?:string}[]; assemblyName makes rows for that sample navigable to its own genome
tafGzLocation
fileLocation = { uri: '/path/to/my.taf.gz', locationType: 'UriLocation' }		bgzip taffy file
taiLocation
fileLocation = { uri: '/path/to/my.taf.gz.tai', locationType: 'UriLocation' }		taffy index
nhLocation
fileLocation = { uri: '/path/to/my.nh', locationType: 'UriLocation' }		newick tree
summaryAdapter
frozen = null		The zoom-out tier, on the same terms as BgzipMafAdapter's: the .tai makes a read cost the span on screen rather than the blocks it lands in, but cost is span × depth and a deep alignment runs out of the second factor. Measured against HPRC's published v2.0 TAF index, 464 haplotypes cost about 2 compressed bytes per bp, flat from 100 kb up — a ninth of the same alignment's MAF, and still 354 MB for chr6 whole. TAF moves the ceiling out by about 10x; it does not remove it. Point this at a BedTabixAdapter over a maf2bed --summary BED, or at a BigBedAdapter over a UCSC bigMafSummary.bb.
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