BedpeAdapter

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

Example usage#

{
  type: 'VariantTrack',
  trackId: 'my_track',
  name: 'My track',
  assemblyNames: ['hg38'],
  adapter: {
    type: 'BedpeAdapter',
    uri: 'https://example.com/sv.bedpe',
  },
}

sv.bedpe infers BedpeAdapter and VariantTrack 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: 'my_track',
  uri: 'https://example.com/sv.bedpe',
  assemblyNames: ['hg38'],
}

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

intended for SVs in a single assembly

Related links#

• Track: VariantTrack
• Display: ChordVariantDisplay
• Display: LDDisplay
• Display: LinearMultiSampleVariantDisplay
• Display: LinearMultiSampleVariantMatrixDisplay
• Display: LinearPairedArcDisplay
• Display: LinearVariantDisplay
• Guide: Structural variants (Cancer GIAB)
• Guide: Structural variants from Hi-C
• Guide: Supported file types

Config slots#

These slots go inside the track's adapter: "adapter": { "type": "BedpeAdapter", ... }. It also accepts the shorthand keys uri, baseUri in place of writing a location slot out. 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.