Compute dynamic read depth limits

This builds on #189 

Here were use the `windowFoldLoci` to sum up aggregate statistics on the read (average depth, average insert size)  Later I want to change these to be more complete distributions (so we can computer std dev, percentiles).  

There is a new command line option `-approx-depth-limits` which estimates the max and min read depths using the sample statistics.
I'm not sure what the comment above is related to?  Using the specific normal samples average read depth?  Or the fact that num reads will be different depending on different number of partitions?  

Average read depth won't change due to more paritions, but something like average insert size may (i.e. more partitions => more duplicates => more emphasis on the insert sizes of the duplicated reads could possibly bias (or even just change by 1 or 2 which may change results) Is that what you were referring to?