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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:

{
  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 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
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.
nhLocation
fileLocation = { uri: '/path/to/my.nh', locationType: 'UriLocation' }		newick tree
summaryAdapter
frozen = null		The zoom-out tier. 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. Point it at a BedTabixAdapter over the summary BED maf2bed --summary writes, or at a BigBedAdapter over a UCSC bigMafSummary.bb covering the same alignment.
annotationAdapter
frozen = null		The CDS reading frames, in the same shape and read by the same code as the other three MAF adapters' — the display looks the slot up by path off the parent track (['adapter', 'annotationAdapter']) and is otherwise format-blind. This adapter was the one of the four that never declared it, so the read simply returned undefined and every consumer of it — the CDS strip, the codon row coloring, the codon conservation band, and the menu rows that gate on the slot's presence — was silently unavailable on a .maf.gz track, with nothing on screen saying why.