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AlignmentsModifications

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

Example usage

{
  type: 'LinearAlignmentsDisplay',
  baseColor: 'modifications',
  modifications: { fillUnmarked: true, cytosineContext: 'CHG' },
}
{
  type: 'LinearAlignmentsDisplay',
  baseColor: 'modifications',
  modifications: { shownModifications: ['a'], threshold: 50 },
}

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

The alignments displays' modifications setting: what the modifications and bisulfite fields of AlignmentsBaseColor draw. The by-type view paints each MM/ML call its type's color above threshold; twoColor paints the unmodified side blue as well, and fillUnmarked paints every cytosine in cytosineContext whether the basecaller listed it or not, which is the methylation view.

Config slots

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
threshold
number = 10		hide a call whose probability is under this percent in the by-type view; the two-color view cuts at 50 and the methylation fill paints every cytosine
twoColor
boolean = false		paint the unmodified side blue as well as the modified side its color, under modifications and bisulfite alike
fillUnmarked
boolean = false		paint every cytosine in the context as methylated or unmethylated, the ones the basecaller left implicit included; the methylation view
cytosineContext
stringEnum = 'CG'		which cytosines the methylation fill and bisulfite paint: CG, CHG, CHH or all
shownModifications
stringArray = []		the modification type codes drawn (m, h, a, ...); empty draws every type the reads carry