Skip to main content

BigBedAdapter

Note: this document is automatically generated from configuration objects in our source code. See Config guide for more info

Also note: this document represents the config API for the current released version of jbrowse. If you are not using the current version, please cross reference the markdown files in our repo of the checked out git tag

Source code

GitHub page

Docs​

BigBedAdapter - Pre-processor / simplified config​

preprocessor to allow minimal config:

{
  "type": "BigBedAdapter",
  "uri": "yourfile.bigBed"
}

BigBedAdapter - Slots​

slot: bigBedLocation​

bigBedLocation: {
      type: 'fileLocation',
      defaultValue: {
        uri: '/path/to/my.bb',
        locationType: 'UriLocation',
      },
    }

slot: scoreColumn​

scoreColumn: {
      type: 'string',
      description: 'The column to use as a "score" attribute',
      defaultValue: '',
    }

slot: aggregateField​

aggregateField: {
      type: 'string',
      description: 'An attribute to aggregate features with',
      defaultValue: 'geneName2',
    }

slot: disableGeneHeuristic​

disableGeneHeuristic: {
      type: 'boolean',
      description:
        '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)',
      defaultValue: false,
    }