feature request: partialSjdbScore #1137
Description
STAR currently prioritizes annotated junctions (alignment bonus = 2) over non-annotated junctions (no bonus). I would like to request an intermediate partialSjdbScore, such that novel junctions where one side of the junction is annotated are prioritized over novel junctions where neither side is annotated.
A technicality: it is possible to have a junction where both sides are annotated (as half-junctions) but the full junction is not (as a pair). I suppose we should prioritize this over a junction with only one side annotated, but behind a fully annotated junction, which would mean needing to bump the full sjdbScore to at least 3 if we wanted to be able to cover this case.
For more background see https://groups.google.com/g/rna-star/c/p6CPlPzfbbA. (By the way, I have noticed one or two cases where this happens even in the absence of a genomic variant, i.e. a half-annotated junction should be aligned to but STAR chooses a nearby spelling instead even in the absence of a genomic variant.) Thank you!