GCContentTrack

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

Example usage#

A standalone GCContentTrack (use this instead of the ReferenceSequenceTrack display when you want GC as its own track). The sequence comes from the assembly named in assemblyNames, so the adapter needs nothing but its type:

{
  type: 'GCContentTrack',
  trackId: 'gc',
  name: 'GC content',
  assemblyNames: ['hg38'],
  adapter: { type: 'GCContentAdapter' },
}

GC-skew mode with a small, overlapping sliding window for a smoother signal (windowDelta smaller than windowSize means windows overlap). The displayDefaults object shorthand applies settings to whichever display uses them — equivalent to writing a full displays: [{ type, displayId, ... }] array. See configuring displays:

{
  type: 'GCContentTrack',
  trackId: 'gc',
  name: 'GC skew',
  assemblyNames: ['hg38'],
  adapter: { type: 'GCContentAdapter' },
  displayDefaults: { gcMode: 'skew', windowSize: 50, windowDelta: 10 },
}

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

used for having a gc content track outside of the "reference sequence display"

Related links#

• Display: LinearGCContentTrackDisplay (state model)
• Base config: BaseTrack
• Guide: Custom track and display types
• Guide: Tracks

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.

pluginManager.pluggableConfigSchemaType(
  'text search adapter',
)