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BaseLinearAlignmentsDisplay

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

The slots LinearAlignmentsDisplay and LGVSyntenyDisplay share: the coverage, pileup and read connection bands, and the filter, unit, facet, sort and color every band reads. LinearAlignmentsDisplay adds the sashimi band, filter.junctions, baseColor and modifications, which apply only to reads; a synteny block has no introns, basecaller tags or qualities.

Config slots

BaseLinearAlignmentsDisplay is a shared base schema, not a type you name in a config. Set these slots on one of the configs under Extended by above, each of which lists them as inherited and shows the shape in an example. 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
height
number = 250		Starting height in pixels for the bands together; heightMode decides what a pileup deeper than this does
unit
stringEnum (read, chain) = 'read'		The unit one row draws: a read, or a chain of a read, its mate and its split segments (the "View as pairs" menu row)
filter
BaseAlignmentsFilter		Every test the display applies, and every test must hold. The read members (the flag masks, minMapq, readName, tags and the read categories spliced, svSignal, alone and split, each "only", "exclude" or unset) run before every band, so coverage counts only the reads they pass; by default flagExclude drops unmapped, QC-failed and duplicate reads (1540). connections tests the connections the arcs, the read cloud and the connectors over the pileup draw.
facet
SectionFacet		In-track stacked grouping, one labelled section per value: a read dimension (strand, firstOfPairStrand, pairOrientation, pairing, split, spliced, svSignal, mapq, mateRefName, mateAssembly), a tag (tags.HP), or any other field. { field: "tags.HP", domain: ["2", "1"] } stacks the listed values first.
collapseSections
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.
sort
AlignmentsSort		The pileup's row order: a whole-window order (position, length, spliced, split) or a column sort at one base ({ type: "strand", pos, refName }).
color
AlignmentsColor		The read fill: "steelblue" paints every read, { field: "strand" } a read dimension's own vocabulary and { field: "tags.HP" } a SAM tag.
scales
ValueScale		The coverage band's value scale — the one thing on this display drawn against an axis, the pileup has no value and the arcs use arcBandYScale. symlogConstant starts at 1 rather than the wiggle family's 0, which makes symlog exactly log(depth+1): the knee sits at one read, the smallest depth there is. domainQuantile stays at 1, the deepest base in view; the Coverage axis panel's Clip extreme outliers writes 0.99, which stops the axis at twice the 99th percentile of the covered bins' peaks, and misses a collapsed-repeat pile-up once it covers more than 1% of the view.
showLegend
boolean = false		Show the color-scheme legend overlay. Defaults to off
coverage
CoverageBand		The coverage histogram band: show, height (default 45), showInterbaseIndicators and minAlleleFraction, a flat floor on each allele segment's share of its position's depth, distinct from pileup.fadeLowFrequency.
pileup
Pileup		The stacked reads: show, readHeight (default 7), maxLayoutHeight, and the parts drawn on each read.
readConnections
ReadConnections		The connections between mates and split segments: show (default off), mark (arc or cloud), height, placement, lineWidth, color and showOrdinaryPairs; filter.connections filters the connections drawn.
heightMode
stringEnum (fixed, grow, fit) = 'fixed'		Track-sizing strategy — how the track responds when there are more reads than fit (shared vocabulary with the canvas feature display, exposed in the "Track sizing" menu). fixed (the default) keeps pileup.readHeight and scrolls; grow expands the track to show every read at that height; fit squeezes reads so every uncollapsed section fills the display without scrolling
growMaxHeight
number = 800		Ceiling in pixels for the "autogrow track height" sizing mode; a pileup deeper than this grows to the ceiling and scrolls the rest. Does not apply to the fixed or fit modes, and does not limit how much is laid out (see pileup.maxLayoutHeight)
advanced
Inherited from BaseLinearDisplay2 slots
fetchSizeLimit
number = 1000000		maximum data to attempt to download for a given track, used if adapter doesn't specify one
advanced
forceLoad
boolean = false		Declarative equivalent of the "Force load" button on the "too much data" banner: when true the display always renders, however large the region or dense the features. Off by default (the gate guards against huge downloads). Set it on a view no one can interact with — an embedded / notebook view, or a screenshot — where the region is known and you want it drawn without a click.
advanced