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BedAdapter

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​

BedAdapter - Pre-processor / simplified config​

preprocessor to allow minimal config:

{
  "type": "BedAdapter",
  "uri": "yourfile.bed"
}

BedAdapter - Slots​

slot: bedLocation​

bedLocation: {
      type: 'fileLocation',
      description: 'path to bed file, also allows gzipped bed',
      defaultValue: {
        uri: '/path/to/my.bed.gz',
        locationType: 'UriLocation',
      },
    }

slot: columnNames​

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

slot: scoreColumn​

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

slot: autoSql​

autoSql: {
      type: 'string',
      description: 'The autoSql definition for the data fields in the file',
      defaultValue: '',
    }

slot: colRef​

colRef: {
      type: 'number',
      description: 'The column to use as a "refName" attribute',
      defaultValue: 0,
    }

slot: colStart​

colStart: {
      type: 'number',
      description: 'The column to use as a "start" attribute',
      defaultValue: 1,
    }

slot: colEnd​

colEnd: {
      type: 'number',
      description: 'The column to use as a "end" attribute',
      defaultValue: 2,
    }