Simplify some function names

[Jason Vander Heiden]

I think we can simplify some of the function names. For example:

calcDBClonalConsensus
calcDBExpectedMutations
calcDBObservedMutations

Also, these lines of code in the BASELINe vignette are bleeding into the margin.

[Jason Vander Heiden]

calcDBClonalConsensus renamed to collapseByClone and vignette issues fixed. We won't bother renaming the mutation counters.