Update leafcutter_cluster_regtools.py

[boxiangliu]

Changed line 392: refine_cluster() -> if (count/float(totN) >= cutoff and count >= readcutoff): to if (count/float(totN) >= cutoff and totN >= readcutoff):

[TimD1]

Seconding this issue, @davidaknowles .

As is, leafcutter filters each junction if the per-junction read count is less than --minclureads instead of filtering each cluster if the total number of reads supporting all junctions in a cluster are less than --minclureads.

Based on the command-line help info, this is not the intended behavior.

-m MINCLUREADS, --minclureads=MINCLUREADS
                        minimum reads in a cluster (default 30 reads)