# BedTabixAdapter
Auto-generated config schema for the current JBrowse release — see the [config guide](https://jbrowse.org/jb2/docs/config_guide) for concepts. Provided by the `bed` plugin. [View source](https://github.com/GMOD/jbrowse-components/blob/main/plugins/bed/src/BedTabixAdapter/configSchema.ts).
## Example usage
The `uri` shorthand auto-resolves the `.tbi` index; add `csi: true` for a
`.csi` index instead:
```js
{
type: 'FeatureTrack',
trackId: 'my_track',
name: 'My track',
assemblyNames: ['hg38'],
adapter: {
type: 'BedTabixAdapter',
uri: 'https://example.com/features.bed.gz',
},
}
```
`features.bed.gz` infers `BedTabixAdapter` and `FeatureTrack` on its own, and `name` defaults to the file name. In a config declaring one assembly, `assemblyNames` comes from there too — see [the shortest track](https://jbrowse.org/jb2/docs/config_guides/tracks#the-shortest-track).
```js
{
trackId: 'my_track',
uri: 'https://example.com/features.bed.gz',
assemblyNames: ['hg38'],
}
```
_See the **Config slots** section below for all available configuration fields._
## Related links
- **Track:** [FeatureTrack](../featuretrack)
- **Display:** [LinearArcDisplay](../lineararcdisplay)
- **Display:** [LinearBasicDisplay](../linearbasicdisplay)
- **Display:** [LinearMultiRowFeatureDisplay](../linearmultirowfeaturedisplay)
- **Display:** [LinearScoreDisplay](../linearscoredisplay)
- **Extended by:** [GWASAdapter](../gwasadapter)
## Config slots
These slots go inside the track's `adapter`: `"adapter": { "type": "BedTabixAdapter", ... }`. It also accepts the [shorthand](https://jbrowse.org/jb2/docs/config_guides/file_types#the-uri-shorthand) keys `uri`, `baseUri`, `csi` in place of writing a location slot out. 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 |
| --- | --- |
| **bedGzLocation**
[`fileLocation`](https://jbrowse.org/jb2/docs/config_guides/slot_types#filelocation) = { uri: '/path/to/my.bed.gz', locationType: 'UriLocation' } | location of the bgzip-compressed BED, sorted by position. Must be bgzip rather than plain gzip, which tabix cannot index. |
| **columnNames**
`stringArray` = [] | List of column names. A column named like a standard BED column is parsed as that column's type (chromStart numeric, blockSizes a numeric list); any other column is text |
| **scoreColumn**
[`string`](https://jbrowse.org/jb2/docs/config_guides/slot_types#string) = '' | The column to use as a "score" attribute |
| **autoSql**
[`string`](https://jbrowse.org/jb2/docs/config_guides/slot_types#string) = '' | The autoSql definition for the data fields in the file |
| **disableGeneHeuristic**
[`boolean`](https://jbrowse.org/jb2/docs/config_guides/slot_types#boolean) = false | Disable the heuristic that auto-detects BED12 features as gene/transcript structures. Useful for files that have BED12-like structure but are not genes (e.g. tandem duplications) |
| **index.indexType**
[`stringEnum`](https://jbrowse.org/jb2/docs/config_guides/slot_types#stringenum) (TBI, CSI) = 'TBI' | `TBI` is the usual `tabix` output. `CSI` is required for a reference longer than 512 Mb, which TBI cannot address. |
| **index.location**
[`fileLocation`](https://jbrowse.org/jb2/docs/config_guides/slot_types#filelocation) = { uri: '/path/to/my.gz.tbi', locationType: 'UriLocation' } | location of the tabix index. Only needed when it is not named `.tbi`, which is what the `uri` shorthand assumes — a `.csi` beside the file is reached with `csi: true` rather than by spelling this out. |
| **densityAdapter**
[`frozen`](https://jbrowse.org/jb2/docs/config_guides/slot_types#frozen) = null | optional quantitative sub-adapter (e.g. a BigWigAdapter over a features-per-bin bigWig) drawn as a density band where the region is too large to fetch features; null disables it |