AlignmentsBaseColor

Auto-generated config schema for the current JBrowse release — see the config guide for concepts. Provided by the alignments plugin. View source.

Example usage#

{ type: 'LinearAlignmentsDisplay', baseColor: 'modifications' }

{
  type: 'LinearAlignmentsDisplay',
  color: { field: 'tags.HP' },
  baseColor: { field: 'modifications' },
  modifications: { twoColor: true },
}

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

The alignments displays' baseColor setting: the per-base variable painted as a cell per base over the reads, whatever color fills them with. modifications paints the MM/ML calls and bisulfite the conversion state against the reference, both under the display's modifications settings; baseQuality and base paint every aligned base. A string is the field. While a modification field paints, mismatches draw grey, and a read with no color of its own takes a pale strand tint.

Config slots#

These slots go on a display entry: "displays": [{ "type": "AlignmentsBaseColor", ... }], or in the track's displayDefaults when this is its default display. 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.