Skip to main content

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, encoding and legend every band reads. LinearAlignmentsDisplay adds the sashimi band, the junction filter fields and pileup.bases, 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/link supplementary alignments" menu row)
filter
FieldPredicate		The alignments drawn, a list of FieldPredicate entries every one of which must hold. The flags, mapq and tags decide which reads count, so coverage, the sashimi junctions and the insert-size colors count only the reads they pass: flags.UNMAP and the other samtools flag names, mapq (MAPQ 255, none reported, passes a floor), and tags.HP and any other tag. name and the read categories pick which of those reads the pileup, the arcs, the consensus and an export draw, and leave coverage whole: spliced per alignment, and svSignal, alone and split over a read, its mate and its split segments together, each taking equal: true or false. A facet on a category gives its own coverage. junction.reads, junction.canonical (a split junction reads no motif and counts as canonical, so equal: false hides it), junction.class (splice for an N gap, or a split read's deletion, duplication or inversion) and junction.source (gap or split) test the sashimi junctions, and connection.interchrom, connection.offscreen and breakpoint.reads the connections the arcs, the read cloud and the connectors draw.

A written list merges with the defaults by field: unmapped, QC-failed and duplicate reads out (flags.UNMAP, flags.QCFAIL and flags.DUP equal: false), and junction.reads and breakpoint.reads at least 2. An entry replaces its own field's defaults, and an entry naming a field with no test, such as { field: "flags.DUP" }, only removes them.
facet
SectionFacet		In-track stacked grouping, one labelled section per value: a read dimension (strand, firstOfPairStrand, pairOrientation, pairing, split, spliced, svKind, mapq, mateRefName, mateAssembly), a tag (tags.HP), or any other field. { field: "tags.HP", sort: ["2", "1"] } stacks the listed values first.
sort
AlignmentsSort		The pileup's row order by one field: a whole-window order (position, length, spliced, split, svSignal) or a column sort at one base ({ field: "strand", pos, refName }).
encoding
AlignmentsEncoding		The channels the reads paint through: encoding.color, the read fill.
legend
HiddenLegend		The display's key: show, off by default.
coverage
CoverageBand		The coverage histogram band: show, height (default 45), encoding.y, its depth axis, and the interbase and alleles layers, each with a show and a filter; alleles.filter floors each allele segment's share of its position's depth, distinct from pileup.fadeLowFrequency. The read cloud's insert-size axis is a fixed log scale no setting reaches.
pileup
Pileup		The stacked reads: show, mark.height (default 7), maxLayoutHeight, and the parts drawn on each read.
readConnections
ReadConnections		The connections between mates and split segments: show (default off), mark (link, the arcs, or rule, the read cloud), height, placement, encoding (color and strokeWidth) and ordinaryPairs; the connection and breakpoint filter fields filter the connections drawn.
tooltip
ReadTooltip		The read hover's first line, a ReadTooltip object: the field it reads off each read. A bare string is the field.
heightMode
stringEnum (fixed, grow, fit) = 'fixed'		Track-sizing strategy — how the track responds when there are more reads than fit (the menu sets fit from "Read height → Fit to track height" and grow from "Advanced → Track height → Grow the track"). fixed (the default) keeps pileup.mark.height 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 "Grow the track" 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		bytes a region may fetch before the display asks first; an adapter that sets its own limit overrides this
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