Local running

Now options for running by job submission, dry run, or local.

A few fixes to the util boxes. Functions moved to more appropriate places. A script so that the system utility "cat" no longer need be called.

Open reference mapping has been integrated into reference mapping. usearch options leveraged to reduce file writing and reading.

intersect.py was removed from the main pipeline. There is now a check for intersection. Doing the actual intersection has been relegated to a utility script.