Fix Mutation Position column

[susannasiebert]

This PR makes the following updates:

• The Mutation Position column (in the all_epitopes.tsv and filtered.tsv pVACseq reports) and the Pos column (in the aggregated pVACseq report) now reflects the position(s) in the mutant epitope that are different from the matched wildtype epitope. This is different from the previous behaviors, particular for indels, where previously this column was trying to reflect where the mutation occurred. However, this has proven difficult to programmatically determine correctly for cases with proximal variants, in repetitive regions, or where the mutant amino acid(s) are similar the wildtype amino acid(s). For inframe indels, this column might now mark some positions as "mutated" because wildtype amino acids get shifted in relation in this type of variants. These shifted amino acids, although not technically mutated, are now different between mutant and wildtype and marked as such. We do believe that this is the better approach because it allows us to evaluate the absolute differences between the matched wildtype and mutant epitopes.
• These columns are now NA if the wildtype epitope is NA
• For making the anchor position evaluation, epitopes with more than two Mutation Position entries are auto-passed.

Closes #1195 and #1191