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.
Maybe consider calling renaming this to something like "automatic-depth-limits" or "compute-depth-limits"? It's a nit, but the main point here for the user seems to be that it will automatically compute the limits using a heuristic. May also want to note that the other depth limit arguments are ignored in this case (if that's right)