GCContentAdapter

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

Computes GC content (or GC skew) from an assembly's sequence at render time, so there is no data file to prepare: the sequence comes from the assembly the track is displayed against. Each score is the op over a window of bases, one every step; the GCContentTrack menu's GC parameters write all three.

Only A, C, G and T count. N and the ambiguity codes are left out of both the fraction and its denominator, so a window holding no A, C, G or T, such as an assembly gap, has no score, nor does a skew window holding no G or C.

Example usage#

{
  type: 'GCContentTrack',
  trackId: 'my_track',
  name: 'My track',
  assemblyNames: ['hg38'],
  adapter: {
    type: 'GCContentAdapter',
  },
}

GC skew in fixed 10 kb windows every 1 kb:

{
  type: 'GCContentTrack',
  trackId: 'my_track',
  name: 'My track',
  assemblyNames: ['hg38'],
  adapter: {
    type: 'GCContentAdapter',
    op: 'skew',
    window: 10000,
    step: 1000,
  },
}

Related links#

• Track: GCContentTrack
• Display: LinearWiggleDisplay
• User guide: GC content track
• Config guide: Supported file types

Config slots#

Adapter slots go inside the track's adapter: "adapter": { "type": "GCContentAdapter", ... }. GCContentAdapter has no uri shorthand — give it the location slots below. 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.

Retired keys#

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