I've been seeing cases where due to some library construction artifact a read has random-ish bases attached to its start/end. These can get aligned (1/2 bases, with the rest soft-clipped) to the next junction and cause that junction to have much more support than it should.

To remove this evidence from the junction, I was looking to implement an additional check that doesn't allow reads to support a junction if they anchor too lightly on the flanks of the junction. I'm aware of the -a argument, but that only controls whether the junction is valid. Once. a junction is valid, reads will be added to it regardless of their individual flanking status.

If this will be implemented as optional (non-default) behavior, would you consider accepting it into the codebase?

Thanks!