ReadConnections

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

The alignments display's readConnections setting: the band of connections between mates and split segments, drawn as arcs or as the read cloud, which plots each pair at its insert size. The connectors drawn over the pileup's own rows are pileup.connectors. Both paint a connection its insert size and orientation class, in the colors the reads' encoding.color declares for that field, and the display's filter picks the connections both draw, by its connection and breakpoint fields.

Example usage#

{
  type: 'LinearAlignmentsDisplay',
  readConnections: { show: true, mark: 'rule' },
}

{
  type: 'LinearAlignmentsDisplay',
  readConnections: { show: true, ordinaryPairs: { show: false } },
  filter: [{ field: 'connection.interchrom', equal: true }],
}

{
  type: 'LinearAlignmentsDisplay',
  readConnections: { show: false },
  pileup: { connectors: { show: false } },
}

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.