Fix vaf calculations

For per-library vaf: Instead of dividing by the total depth (across all libraries) we need to
divide by the depth in just that one library.

For total vaf: Instead of summing up per-library vaf we need to
calculate the coverage and depth directly.
I could (and probably should) along with a number of other functions in this module.  Furthermore, I would store the libraries as a hash on the BamReadcount entry instead of as a list so that this lookup would be faster.  I'm not sure it should be in this PR though.