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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.

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' },
    },
  },
}

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

reads a set of per-chromosome VCF files, keyed by refName, instead of a single combined VCF (useful for large call sets split by chromosome)

Config slots

These slots go inside the track's adapter: "adapter": { "type": "SplitVcfTabixAdapter", ... }. This adapter 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. An index the map names says which kind it is by 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 = 5_000_000		The same 5 Mb VcfTabixAdapter declares, for the same reason: this adapter implements getRegionByteSize, so its reads are byte-gated, and without a limit of its own 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 lists no samples of its own (a MAF track discovering its species from the file) takes the table's rows as its samples
densityAdapter
maybeFrozen		optional quantitative sub-adapter (e.g. a BigWigAdapter over a features-per-bin bigWig) drawn as a density band where the region is too large to fetch features; leave it unset to disable