Is there a way to get these metrics on a whole genome scale?

I might do a hack where I create a bed & interval files covering the entire genome.

• HS_Penalty_20X - "hybrid selection penalty" incurred to get 80% of target bases to 20X.
  
• HS_LIBRARY_SIZE - estimated number of unique molecules in the selected part of the library.
  

I'm guessing for HS_LIBRARY_SIZE this is # of reads left post duplicates removed for whole genome sequencing?

But for HS_PENALTY_20X should I just calculate this manually? Using the formula in the documentation:

• PF_ALIGNED_BASES / ($REFERENCE_SIZE * 20) = HS_PENALTY_20X.

That doesn't seem like it will work... :-p