AlignmentsTrack

Auto-generated config schema for the current JBrowse release — see the config guide for concepts. Provided by the alignments plugin. View source.

Example usage#

A BAM track — swap the adapter to CramAdapter with a uri to a .cram for CRAM:

{
  type: 'AlignmentsTrack',
  trackId: 'ngs-reads',
  name: 'NGS reads',
  assemblyNames: ['hg38'],
  adapter: {
    type: 'BamAdapter',
    uri: 'https://example.com/sample.bam',
  },
}

sample.bam infers BamAdapter and AlignmentsTrack 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.

{
  trackId: 'ngs-reads',
  uri: 'https://example.com/sample.bam',
  assemblyNames: ['hg38'],
}

The same track with appearance settings in place. Rather than writing out the full displays array, you can list them in a displayDefaults object — JBrowse works out which display they belong to and applies them for you (here, the LinearAlignmentsDisplay), so you don't have to know display names:

{
  type: 'AlignmentsTrack',
  trackId: 'ngs-reads',
  name: 'NGS reads',
  assemblyNames: ['hg38'],
  adapter: {
    type: 'BamAdapter',
    uri: 'https://example.com/sample.bam',
  },
  displayDefaults: { colorBy: { type: 'pairOrientation' }, height: 250 },
}

See the Config slots section below for all available configuration fields.

has very little config; most config and state logic is on the display

Related links#

• Display: LinearAlignmentsDisplay (state model)
• Adapter: BamAdapter
• Adapter: CramAdapter
• Adapter: HtsgetBamAdapter
• Adapter: SamAdapter
• Base config: BaseTrack
• Guide: Custom track and display types
• Guide: Supported file types
• Guide: Tracks

Config slots#

These slots are top-level fields of the track config, alongside trackId and name. 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.

pluginManager.pluggableConfigSchemaType(
  'text search adapter',
)