MarkLocus

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

Example usage#

A BEDPE-like file whose second end sits in its own columns:

{
  mark: 'link',
  encoding: { x2: { chrom: 'chrom2', pos: 'start2' } },
}

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

A mark's far end as a position that may lie on another sequence: pos, the feature field holding its coordinate, and chrom, the field holding its refName, as a paired record states its mate. Writing a field name directly on the encoding lands in pos, on the feature's own sequence. Left unwritten behind a mate step, it is the other end the step found.

Config slots#

These slots go on a display entry: "displays": [{ "type": "MarkLocus", ... }], 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.