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BedpeAdapter

Auto-generated from the config schema in the source. See the config guide for concepts. Provided by the bed plugin. View source.

Reads BEDPE files of paired breakends, such as structural variant calls within a single assembly.

Example usage

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

JBrowse infers BedpeAdapter and VariantTrack from sv.bedpe, 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'],
}

Config slots

Adapter 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.

Slot Description
bedpeLocation
fileLocation = { uri: '/path/to/my.bedpe.gz', locationType: 'UriLocation' }		 can be plaintext or gzipped, not indexed so loaded into memory on startup
columnNames
stringArray = []		 List of column names