Skip to main content

RefNameAliasAdapter

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​

can read "chromAliases" type files from UCSC or any tab separated file of refName aliases

RefNameAliasAdapter - Slots​

slot: location​

location: {
      type: 'fileLocation',
      defaultValue: {
        uri: '/path/to/my/aliases.txt',
        locationType: 'UriLocation',
      },
    }

slot: refNameColumn​

by default, the "ref names that match the fasta" are assumed to be in the first column (0), change this variable if needed

refNameColumn: {
      type: 'number',
      defaultValue: 0,
    }