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MafTabixAdapter

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

Example usage

{
  type: 'MafTrack',
  trackId: 'my_track',
  name: 'My track',
  assemblyNames: ['hg38'],
  adapter: {
    type: 'MafTabixAdapter',
    bedGzLocation: { uri: 'https://example.com/multiz.bed.gz' },
    index: { location: { uri: 'https://example.com/multiz.bed.gz.tbi' } },
    nhLocation: { uri: 'https://example.com/multiz.nh' },
  },
}

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

Multiple alignment format converted to a bgzipped, tabix-indexed BED. The nhLocation newick tree orders and labels the species rows; refAssemblyName names the MAF's reference species when it differs from the assembly name.

Config slots

These slots go inside the track's adapter: "adapter": { "type": "MafTabixAdapter", ... }. It also accepts the shorthand keys uri, baseUri, csi, 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
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
bedGzLocation
fileLocation = { uri: '/path/to/my.bed.gz', locationType: 'UriLocation' }		location of the bgzip-compressed BED that maf2bed writes from a MAF: one line per alignment block, with every species' aligned bases packed into the last column.
refAssemblyName
string = ''		name of the MAF's reference species, spelled as it appears in the file's s lines (the hg38 of hg38.chr1). Set it when that differs from the JBrowse assembly name; left empty, the reference row is looked up by the queried assembly's name and falls back to the block's first species.
nhLocation
fileLocation = { uri: '/path/to/my.nh', locationType: 'UriLocation' }		newick tree
summaryAdapter
frozen = null		The zoom-out tier. A tabix MAF carries every species' bases on one line, so a wide read downloads the whole alignment and the byte gate blocks it; without this slot the track simply has no zoom-out path. Point it at a BedTabixAdapter over the summary BED maf2bed --summary writes (one merged run per species, no sequence), or at a BigBedAdapter over a UCSC bigMafSummary.bb covering the same alignment.
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
index.indexType
stringEnum (TBI, CSI) = 'TBI'		TBI is the usual tabix output. CSI is required for a reference longer than 512 Mb, which TBI cannot address.
index.location
fileLocation = { uri: '/path/to/my.gz.tbi', locationType: 'UriLocation' }		location of the tabix index. Only needed when it is not named <file>.tbi (or .csi), which is what the uri shorthand assumes.