Implement #467, bigwigCompare and bamCompare can return the mean of two files. Also, fix some bigwigCompare documentation.

Fix #464, make --sortRegions descend, rather than no, the default selected option if advanced options are shown for consistency with the program defaults.

Fixed plotCorrelation -l with --outFileCorMatrix

line 165 caused an error when you used the "-l" parameter to label the samples. 
TypeError: list indices must be integers, not list

Therefore, I changed the line so that it now works!

use numpy masked arrays for median to properly handle NaNs (see #457)

replaced numpy mean, median, sum etc by nympy masked arrays (numpy.ma) that properly handle missing data

Fingerprint summation