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

Source file


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: [],
'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: '',
'A human readable display name for the assembly e.g. "Homo sapiens (hg38)" while the assembly name may just be "hg38"',