Skip to main content

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

The alignments displays' modifications setting configures the modifications and bisulfite fields of AlignmentsBaseColor. The by-type view paints each MM/ML call its type's color above threshold; unmodified: 'calls' paints the unmodified side blue as well, and unmodified: 'all' 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
unmodified
stringEnum (hidden, calls, all) = 'hidden'		unmodified sites painted blue: 'hidden' none, 'calls' the calls more likely unmodified, under modifications and bisulfite alike, and 'all' every cytosine in the context as well, the ones the basecaller left implicit included; 'all' is the methylation view
cytosineContext
stringEnum = 'CG'		cytosine context 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