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, each mismatched base fades by its Phred base quality through a linear scale, by default from 0.1 at Q5 to opaque from Q20 up. A number is a constant opacity for every mismatch, written to value: 1 draws them all opaque. A string is the field. A base whose read carries no qualities draws opaque.

Example usage#

{
  type: 'LinearAlignmentsDisplay',
  pileup: { mismatches: { encoding: { opacity: 1 } } },
}

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

Config slots#

A setting written to it replaces it whole: 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.