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MafTabixAdapter

Auto-generated from the config schema in the source — 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' },
  },
}

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
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.
index
TabixIndex		The tabix index location and its kind. The uri shorthand derives both, so a config using it states neither.
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
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 (a BedTabixAdapter over a maf2bed --summary BED, or a BigBedAdapter over UCSC bigMafSummary.bb) used for cheap zoom-out rendering; leave it unset to disable. 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
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 lists no samples of its own (a MAF track discovering its species from the file) takes the table's rows as its samples
annotationAdapter
maybeFrozen		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; leave it unset to disable. 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