GCContentTrack

Auto-generated from the config schema in the source — see the config guide for concepts. Provided by the gccontent plugin. View source.

Example usage#

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

GC skew over a small, overlapping sliding window for a smoother signal (windowDelta under windowSize overlaps the windows):

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

GC content, or GC skew, of the assembly's sequence, computed as the view moves by a GCContentAdapter and drawn by the wiggle display. The adapter holds the window, the step and the mode; the track menu's GC parameters and GC skew write them there. The reference sequence track's menu has "Add GC content track", which makes one.

Related links#

• Display: LinearWiggleDisplay (state model)
• Adapter: GCContentAdapter
• Base config: BaseTrack
• Config guide: Supported file types
• Config guide: Tracks
• Developer guide: Custom track and display types

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.

types.array(
  types.union(
    ...pluginManager
      .getDisplayElements()
      .map(d =>
        d.configSchema === linearWiggleDisplayConfigSchema
          ? gcWiggleConfigSchema
          : d.configSchema,
      ),
  ),
)

Retired keys#

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