PileupBasesUnmodified

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 bases.unmodified layer: the unmodified side of the modifications and bisulfite fields, in blue. Under modifications it is the methylation view: every cytosine in the context, those a read's 5mC calls left implicit included, is painted 5mC, 5hmC or unmethylated, with no probability floor. Other modification types draw as they do without it.

Example usage#

{
  type: 'LinearAlignmentsDisplay',
  pileup: {
    bases: {
      show: true,
      encoding: { color: 'modifications' },
      unmodified: { show: true },
    },
  },
}

Config slots#

A setting written to it names members one by one: a member left out stays as it is, and null resets one. 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.