adapt calcObservedMutations for seq containing ambiguous character

[Julian Zhou]

currently under progress.

also involves adaptation of helper function binMutationsByRegion, and any function that calls calcObservedMutations (as its output format will change)

[Jason Vander Heiden]

See the C++ implementations in alakazam for counting mismatches considering ambiguous characters. See alakazam::seqDist.

It can handle DNA or amino acids (or whatever) by just passing it a different substitution matrix: See getDNAMatrix(), getAAMatrix()

You might be able to just wrap this code (which is oodles faster).

[Julian Zhou]

Will keep in mind in future. For now, built on existing code.

[Julian Zhou]

Pushed in commit a234379