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ReferenceSequenceTrack

Auto-generated config schema for the current JBrowse release — see the config guide for concepts. Provided by the sequence plugin. View source.

Example usage

Usually authored as the sequence member of an assembly rather than a top-level track:

sequence: {
  type: 'ReferenceSequenceTrack',
  trackId: 'hg38-ref',
  adapter: {
    type: 'IndexedFastaAdapter',
    uri: 'https://example.com/hg38.fa',
  },
}

See the Config slots section below for all available configuration fields.

Overview

used to display base level DNA sequence tracks

ReferenceSequenceTrack - Identifier

Every ReferenceSequenceTrack has a unique trackId, a required top-level field that identifies it (not one of the config slots below).

Config slots

These slots are top-level fields of the track config, alongside trackId and name. Slot types (fileLocation, frozen, ...) are explained in the config slot types reference. Slots a base configuration contributes are listed here too, so this table is the whole surface.

SlotDescription
adapter
pluginManager.pluggableConfigSchemaType('adapter')		configuration for track adapter
displays
types.array(pluginManager.pluggableConfigSchemaType('display'))		configuration for the displays e.g. LinearReferenceSequenceDisplay
name
string = ''		optional track name, otherwise uses the "Reference sequence (assemblyName)"
sequenceType
string = 'dna'		either dna or pep
description
string = ''		a description of the track
metadata
frozen = {}		anything to add about this track
formatAbout
FormatAboutConfigSchemaFactory()		jexl callbacks that add, rewrite or hide fields in this track's About dialog. Two slots, listed at FormatAbout.