missing p values in assess_significance.R

[s-juross]

There is a problem inside assess_significance.R. The object normals is empty therefore it seems like the intervals in _CNVs overlap the intervals in _ratio.txt (which seems odd).
If I understand it correctly the object normals contains the unchanged CN regions. I plotted the _ratio values and there were a few green dots so there should be some data for the object normals. I use test data from chromosome 12.
As a consequence, no p-values can be estimated.
My question is: where is the source of the problem - maybe a incorrect _CNV file or a problem with the computation of the .bed files?

CNV_config.txt