Made it properly general with output files.
Fixed some bad matrix operations.
Added window stat stuff.
Clean up
Refactored interval into base depth object.

Windows will now be  comprised of intervals somewhat and can become larger than interval (target regions)
Refactored depth to be a numpy array from the start
Small break....
Fixed cnv_caller
Windows now larger that exons.

Windows currently grow to the left. Need to implement backing up and
also moving to the left and coming forward.
Added merged windows and cleaned up all the parsing.

Removed window size and also removed various other flags.
Added a dependency of pybedtools to merge intervals and get target
region counts.
Fixed some of the stats issues.

Still need to make the stats stuff a little cleaner.