Skip to main content

Pileup

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

The alignments display's pileup setting: the band of stacked reads, its read height and layout cap, and the parts drawn on each read.

Example usage

{
  type: 'LinearAlignmentsDisplay',
  pileup: { readHeight: 3, showSoftClipping: true },
}

Config slots

A setting written to it names members one by one: a member left out stays as it is, and null resets one. 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
show
boolean = true		draw the pileup band
readHeight
number = 7		The one compactness setting: the spacing between reads follows from it (featureSpacingForHeight), and the Normal, Compact and Super-compact presets (7, 3, 1) and the fit-mode squeeze all write or read it.
maxLayoutHeight
number = 6000		the tallest the pileup's layout grows in pixels; reads past it are not stacked, and coverage still counts them. Not the display's growMaxHeight, which caps how tall the track grows
advanced
showMismatches
boolean = true		draw how reads differ from the reference: per-base mismatches, insertion markers and deletion bars. The line joining a spliced read across its introns draws either way, since it shows the exon blocks are one read (PILEUP_MARKS)
showSoftClipping
boolean = false		draw the soft-clipped ends of each read
showOutline
maybeBoolean		Unset, the outline follows the unit: drawn under unit: 'chain'.
advanced
showConnectors
boolean = false		draw a connector over the pileup from each read to its mate or split segment: a straight line for a normal pair within one displayed region, a curve otherwise. Under unit: 'chain' a link between displayed regions curves either way. The arc and read-cloud band is readConnections
fadeLowBaseQuality
boolean = false		fade each mismatch base by its Phred base quality: opaque from 50 up, fading linearly below
fadeLowFrequency
boolean = true		fade each sub-pixel mismatch, insertion, deletion and clip mark by the share of reads at its position that have it: a mark every read has stays opaque, and one under the depth-dependent noise threshold drops to the sub-pixel floor and, past one base per pixel, takes no clicks. Off draws them all at full opacity. The coverage band is not faded (see runCoveragePipeline)
advanced