# HtsgetBamAdapter

Auto-generated config schema for the current JBrowse release — see the
[config guide](https://jbrowse.org/jb2-staging/docs/config_guide) for concepts. Provided by the `alignments`
plugin.
[View source](https://github.com/GMOD/jbrowse-components/blob/main/plugins/alignments/src/HtsgetBamAdapter/configSchema.ts).

## Example usage

```js
{
  type: 'AlignmentsTrack',
  trackId: 'my_track',
  name: 'My track',
  assemblyNames: ['hg38'],
  adapter: {
    type: 'HtsgetBamAdapter',
    htsgetBase: 'https://htsget.example.com/reads',
    htsgetTrackId: 'NA12878',
  },
}
```

_See the **Config slots** section below for all available configuration fields._

Used to fetch data from Htsget endpoints in BAM format, using the gmod/bam
library

## Related links

- **Track:** [AlignmentsTrack](../alignmentstrack)
- **Display:** [LinearAlignmentsDisplay](../linearalignmentsdisplay)

## Config slots

These slots go inside the track's `adapter`:
`"adapter": { "type": "HtsgetBamAdapter", ... }`. This adapter has no `uri`
[shorthand](https://jbrowse.org/jb2-staging/docs/config_guides/file_types#the-uri-shorthand) — give it the
location slots below. Slot types (`fileLocation`, `frozen`, ...) are explained
in the [config slot types reference](https://jbrowse.org/jb2-staging/docs/config_guides/slot_types). Slots a
base configuration contributes are listed here too, so this table is the whole
surface.

<!-- prettier-ignore -->
| Slot | Description |
| --- | --- |
| <span id="slot-htsgetbase">**htsgetBase**</span><br>[`fileLocation`](https://jbrowse.org/jb2-staging/docs/config_guides/slot_types#filelocation) = <code>{ uri: '', locationType: 'UriLocation' }</code> | The endpoint tickets are requested from. `htsgetTrackId` is appended to it, so a trailing slash produces a doubled one in the request path. |
| <span id="slot-htsgettrackid">**htsgetTrackId**</span><br>[`string`](https://jbrowse.org/jb2-staging/docs/config_guides/slot_types#string) = <code>''</code> | the trackId, which is appended to the base URL |