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PileupMismatchesOpacity

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

The pileup's mismatches.encoding.opacity: unset, every mismatched base draws opaque; baseQuality fades each one by its Phred base quality through a linear scale, by default from transparent at 0 to opaque from 50 up. A string is the field. A base whose read carries no qualities draws opaque.

Example usage

{
  type: 'LinearAlignmentsDisplay',
  pileup: { mismatches: { encoding: { opacity: 'baseQuality' } } },
}
{
  type: 'LinearAlignmentsDisplay',
  pileup: {
    mismatches: {
      encoding: {
        opacity: {
          field: 'baseQuality',
          scale: { domain: [0, 30], range: [0.2, 1] },
        },
      },
    },
  },
}

Config slots

A setting written to it replaces it whole, since its members are alternatives: a member left out returns to its default. 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
field
maybeStringEnum (baseQuality)		baseQuality fades each mismatched base by its Phred quality; unset draws them opaque
scale
PileupMismatchesOpacityScale sub-schema		How a base quality maps to an opacity.
scale.domain
stringArray = ['0', '50']		the Phred qualities that take the first and the last opacity in range
scale.range
stringArray = ['0', '1']		the opacities, 0 to 1, at the two ends of the domain
scale.clamp
boolean = true		a quality past the domain takes the nearer end of the range; off, the line runs on until the base is fully opaque or gone