# SyntenyIndels

Auto-generated from the config schema in the source — see the [config guide](https://jbrowse.org/jb2/docs/config_guide) for concepts. Built into JBrowse core. [View source](https://github.com/GMOD/jbrowse-components/blob/main/packages/synteny-core/src/syntenyIndelsConfigSchema.ts).

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

```js
{ type: 'LinearSyntenyView', indels: { show: false } }
```

```js
{ type: 'LinearSyntenyView', indels: { encoding: { opacity: 0 } } }
```

## Config slots

Slot types (`fileLocation`, `frozen`, ...) are explained in the [config slot types reference](https://jbrowse.org/jb2/docs/config_guides/slot_types). Slots a base configuration contributes are listed here too, so this table is the whole surface.

| Slot | Description |
| --- | --- |
| **show**<br>[`boolean`](https://jbrowse.org/jb2/docs/config_guides/slot_types#boolean) = <code>true</code> | draw the indels inside each alignment; off draws each alignment as one block |
| **encoding**<br>[SyntenyIndelsEncoding sub-schema](#slot-encodingopacity) | The part's channels: `encoding.opacity`. |
| **encoding.opacity**<br><code>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 }, )</code> | `0` leaves each indel a gap; unset, or any other value, paints it in its operation's color. |
| **value**<br>[`maybeNumber`](https://jbrowse.org/jb2/docs/config_guides/slot_types#the-maybe-types) | 0 leaves each indel a gap; unset, or any other value, paints it in its operation's color |