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SyntenyIndels

Auto-generated from the config schema in the source — see the config guide for concepts. Built into JBrowse core. View source.

The linear synteny and dotplot views' indels part: the insertions and deletions inside each alignment, read from its CIGAR. show: false draws each alignment as one block or one straight segment; an opacity of 0 leaves each indel a gap.

Example usage

{ type: 'LinearSyntenyView', indels: { show: false } }
{ type: 'LinearSyntenyView', indels: { encoding: { opacity: 0 } } }

Config slots

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.

SlotDescription
show
boolean = true		draw the indels inside each alignment; off draws each alignment as one block
encoding
SyntenyIndelsEncoding sub-schema		The part's channels: encoding.opacity.
encoding.opacity
ConfigurationSchema(
  'SyntenyIndelsOpacity',
  {
    value: {
      type: 'maybeNumber',
      description:
        "0 leaves each indel a gap; unset, or any other value, paints it in its operation's color",
    },
  },
  { shorthand: 'value', writes: 'whole', closed: true },
)
0 leaves each indel a gap; unset, or any other value, paints it in its operation's color.
value
maybeNumber		0 leaves each indel a gap; unset, or any other value, paints it in its operation's color