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BgzipMafAdapter

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; nhUri names the Newick tree:

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

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

A bgzip-compressed MAF with a Taffy .tai index — the form whole-genome multiple alignments are actually distributed in. HPRC release 2 publishes hprc-v2.1-mc-grch38.full.maf.gz (53 GB, 464 haplotypes) with a sibling .tai, and Cactus/taffy write the pair for any HAL export. The index gives random access, so a locus is a small ranged read rather than a download: a 10 kb query against HPRC's own index resolves to about 924 KB.

Use BgzipTaffyAdapter for TAF (taffy's own, more compact format), MafTabixAdapter for a maf2bed BED, and BigMafAdapter for bigMaf.

Config slots

These slots go inside the track's adapter: "adapter": { "type": "BgzipMafAdapter", ... }. 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
mafGzLocation
fileLocation = { uri: '/path/to/my.maf.gz', locationType: 'UriLocation' }		bgzip-compressed MAF file
taiLocation
fileLocation = { uri: '/path/to/my.maf.gz.tai', locationType: 'UriLocation' }		The Taffy index. The same .tai format BgzipTaffyAdapter reads — it describes bgzf virtual offsets against reference coordinates and does not care which text format sits inside — so taffy index produces it for a MAF as readily as for a TAF.
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
nhLocation
fileLocation = { uri: '/path/to/my.nh', locationType: 'UriLocation' }		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
frozen = null		optional swappable sub-adapter (a BedTabixAdapter over a maf2bed --summary BED, or a BigBedAdapter over UCSC bigMafSummary.bb) used for cheap zoom-out rendering; null disables it. The .tai makes a read cost the span on screen rather than the blocks it lands in, which is why this slot was left off at first — but span is only half of it. Cost is span × depth, and measured against HPRC's own v2.1 index the constant is about 19 compressed bytes per bp at 464 haplotypes, flat from 100 kb up: 1 Mb is a 19 MB read and chr1 whole is 4.4 GB. So a deep alignment still runs out, just linearly instead of by block
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. The display looks this slot up by path off the parent track and is otherwise format-blind, so every MAF adapter takes it the same way