AlignmentsBaseColor

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

The pileup.bases.encoding.color channel: the per-base variable painted as a cell per base over the reads, whatever encoding.color fills them with. modifications paints the MM/ML calls and bisulfite the conversion state against the reference, both through pileup.bases.filter and unmodified; baseQuality and base paint every aligned base. A string is the field. While a modification field paints, mismatches draw grey, and a read that no encoding.color paints takes a pale strand tint.

Example usage#

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

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.