nypermutated crosstab

I have added a hypermutation crosstab around line 182. This shows
counts of all metadata types split on hypermutation status.
I have also added a line that modifies the metadata2 variable (lines
59-61). It adds the hypermutated clasification variable on to the
metadata2 variables. I have also assigned NA values in metadata2 to
"[Not Available]". This is so that when I run the MDSPlot function it
can plot and colour according to metadata2 variables which previously
would have containd NA values.