Don't Count X for AA Diversity Chart

[emmahodcroft]

With the update to allow recovery of ambiguous sites for Fasta-input in augur, there's now the possibility for many AA sites be 'X' at the tips. At the moment, these are counted as 'mutations' for the diversity chart:

Before the change:

But these should probably be disregarded from 'entropy' and 'count', as 'N' is in nucleotide data. I introduced a similar check as is already present for nucleotides in 'counts'. However, I decided that we may be interested in gaps ('-') in AA alignments (as this is a little more stringent than gaps in nucleotides, since they must be in-frame), so I allowed this to be counted both in 'entropy' and 'counts'. We can change this in future if it doesn't seem to actually be informative.

After the change:

[jameshadfield]

Thanks @emmahodcroft this seems very sensible. I'll try and take a look at this over the next ~4 days, but if you don't hear from me feel free to merge 👍