Skip to main content

LGVSyntenyPileup

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

The LGVSyntenyDisplay's pileup setting: the Pileup object with collapsed defaulting to on, so an all-vs-all track faceted by mate assembly draws each mate genome as one band, repeat depth shown as darker shading rather than as extra rows. The alignments display defaults it off, where a section is a read category and the stack is the information.

Example usage

{ type: 'LGVSyntenyDisplay', pileup: { collapsed: false } }

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
collapsed
boolean = true		draw each facet section as a single row rather than a stack
Inherited from Pileup7 slots
show
boolean = true		draw the pileup band
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