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BedpeAdapter

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​

intended for SVs in a single assembly

BedpeAdapter - Pre-processor / simplified config​

preprocessor to allow minimal config:

{
  "type": "BedpeAdapter",
  "uri": "yourfile.bedpe.gz"
}

BedpeAdapter - Slots​

slot: bedpeLocation​

bedpeLocation: {
      type: 'fileLocation',
      description:
        'can be plaintext or gzipped, not indexed so loaded into memory on startup',
      defaultValue: {
        uri: '/path/to/my.bedpe.gz',
        locationType: 'UriLocation',
      },
    }

slot: columnNames​

columnNames: {
      type: 'stringArray',
      description: 'List of column names',
      defaultValue: [],
    }