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BaseAssembly

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

Source file​

packages/core/assemblyManager/assemblyConfigSchema.ts

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"',
      }