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BaseAssembly

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​

This corresponds to the assemblies section of the config

BaseAssembly - Identifier​

slot: name​

BaseAssembly - Slots​

slot: aliases​

aliases are "reference name aliases" e.g. aliases for hg38 might be "GRCh38"

aliases: {
        type: 'stringArray',
        defaultValue: [],
        description: 'Other possible names for the assembly',
      }

slot: sequence​

sequence refers to a reference sequence track that has an adapter containing, importantly, a sequence adapter such as IndexedFastaAdapter

sequence: pluginManager.getTrackType('ReferenceSequenceTrack')!
        .configSchema

slot: refNameColors​

refNameColors: {
        type: 'stringArray',
        defaultValue: [],
        description:
          'Define custom colors for each reference sequence. Will cycle through this list if there are not enough colors for every sequence.',
      }

slot: refNameAliases.adapter​

refNameAliases help resolve e.g. chr1 and 1 as the same entity the data for refNameAliases are fetched from an adapter, that is commonly a tsv like chromAliases.txt from UCSC or similar

adapter: pluginManager.pluggableConfigSchemaType('adapter')

slot: cytobands.adapter​

cytoband data is fetched from an adapter, and can be displayed by a view type as ideograms

adapter: pluginManager.pluggableConfigSchemaType('adapter')

slot: displayName​

displayName: {
        type: 'string',
        defaultValue: '',
        description:
          'A human readable display name for the assembly e.g. "Homo sapiens (hg38)" while the assembly name may just be "hg38"',
      }