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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, the mark each read draws as, the layout cap, and the parts drawn on each read.

Example usage

{
  type: 'LinearAlignmentsDisplay',
  pileup: { mark: { height: 3 }, softClips: { show: true } },
}

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
show
boolean = true		draw the pileup band
collapsed
boolean = false		Only consulted while facet is in effect. When set, each section draws as one row instead of a stack, and tint shading shows overlap depth instead of row count: the compact reading for a track with many sections (an all-vs-all synteny track's mate genomes). A section expanded from its label chip opts back out and draws a true stack. On the pileup rather than facet, which a share link writing facet: 'HP' replaces whole. The Show menu's "Collapse groups to one row" writes it.
mark
PileupMark		The bar each read draws as: height.
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
mismatches
PileupMismatches		How reads differ from the reference: show, and encoding.opacity, the fade by base quality.
softClips
PileupSoftClips		The soft-clipped ends of each read: show.
connectors
PileupConnectors		Lines over the pileup joining each read to its mate or split segment: show.
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
advanced