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SplitVcfTabixAdapter

Auto-generated from the config schema in the source — see the config guide for concepts. Provided by the variants plugin. View source.

Reads a set of tabix-indexed VCF files, one per chromosome and keyed by refName, for a large call set split by chromosome.

Example usage

{
  type: 'VariantTrack',
  trackId: 'my_track',
  name: 'My track',
  assemblyNames: ['hg38'],
  adapter: {
    type: 'SplitVcfTabixAdapter',
    vcfGzLocationMap: {
      chr1: { uri: 'chr1.vcf.gz' },
      chr2: { uri: 'chr2.vcf.gz' },
    },
    indexLocationMap: {
      chr1: { uri: 'chr1.vcf.gz.tbi' },
      chr2: { uri: 'chr2.vcf.gz.tbi' },
    },
  },
}

Config slots

Adapter slots go inside the track's adapter: "adapter": { "type": "SplitVcfTabixAdapter", ... }. SplitVcfTabixAdapter has no uri shorthand — give it the location slots below. 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
vcfGzLocationMap
frozen = {}		object like {chr1:{uri:'url to file'}}
indexLocationMap
frozen = {}		object like {chr1:{uri:'url to index'}}
indexType
stringEnum (TBI, CSI) = 'TBI'		index flavor for the entries this adapter derives, i.e. the ones indexLocationMap does not name. The adapter reads the kind of an index in the map from its .csi/.tbi extension, so one map can mix the two. CSI is required for a reference longer than 512 Mb, which TBI cannot address.
fetchSizeLimit
number = 5000000		The same 5 Mb VcfTabixAdapter declares, for the same reason: this adapter implements getRegionByteSize, so its reads are byte-gated, and without a limit on the adapter the gate falls back to the display config's conservative 1 Mb (resolveByteLimit prefers the adapter's). That gated a split VCF five times tighter than the single-file VCF beside it, on a block-granular tabix estimate that already over-quotes small regions.
advanced
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 names no samples (a MAF track discovering its species from the file) takes the table's rows as its samples