JunctionFilter
Auto-generated from the config schema in the source — see the config guide for concepts. Provided by the alignments plugin. View source.
The splice junctions the alignments display draws, its filter.junctions:
a supporting-read floor, and the non-canonical junctions as a category,
only, exclude or unset for unfiltered, as a read category is. Every
part that draws junctions reads it: the sashimi arcs, their read counts and
the tables engine's junctions.
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 |
|---|---|
minReadsnumber = 2 | a junction draws only with at least this many supporting reads; 1 draws every junction |
nonCanonicalmaybeStringEnum (only, exclude) | only, exclude, or unset for unfiltered: junctions whose splice motif is none of GT-AG, GC-AG or AT-AC. The motif is read off the reference, so filtering needs a sequence adapter, and a junction whose motif could not be read counts as canonical |