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ReferenceSequenceTrack

Auto-generated from the config schema in the source — 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',
  },
}

Overview

Holds an assembly's reference sequence, which LinearReferenceSequenceDisplay draws base by base.

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
adapter config		configuration for track adapter
displays
list of display configs		configuration for the displays e.g. LinearReferenceSequenceDisplay
name
string = ''		optional track name, otherwise uses the "Reference sequence (assemblyName)"
sequenceType
stringEnum (dna, pep) = 'dna'		pep for a protein sequence, which draws one row of residues with no reverse or translation rows
description
string = ''		a description of the track
metadata
frozen = {}		anything to add about this track
formatAbout
FormatAbout		jexl callbacks that add, rewrite or hide fields in this track's About dialog.

Retired keys

An older config may still write these. Each loads without an error, and jbrowse validate reports it as stale.

KeyOn load
rpcDriverNameignored
renderingignored