ConnectionFilter
Auto-generated from the config schema in the source — see the config guide for concepts. Provided by the alignments plugin. View source.
The connections between mates and split segments the alignments display
draws, its filter.connections: two connection categories, each only,
exclude or unset for unfiltered, as a read category is, and the reads an
inter-chromosomal breakpoint must gather. Every part that draws connections
reads it: the arcs, the read cloud, the connectors over the pileup
(pileup.showConnectors) and the tables engine's arcs. Which pairs are
ordinary is each mark's own test, so readConnections.showOrdinaryPairs
sits with the band.
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.
| Slot | Description |
|---|---|
interchrommaybeStringEnum (only, exclude) | only, exclude, or unset for unfiltered: connections to a mate or split segment on another chromosome, an arc or a connector where both chromosomes are displayed and a tick at each breakpoint otherwise |
offscreenMatesmaybeStringEnum (only, exclude) | only, exclude, or unset for unfiltered: connections to a mate or split segment elsewhere on the same chromosome and outside the loaded window, drawn as vertical lines. A connector joins two laid-out reads, so it is never one |
minInterchromReadsnumber = 2 | an inter-chromosomal connection draws only with at least this many reads clustered at its breakpoint, counted over one fragment length on both sides; 1 draws every one, and a split read is exempt |