find-aa-mutations not working, post-merge with Rohan's branch

[lincoln-harris]

exiting gracefully, but not actually finding variants. I tested on remade artificial vcfs as well as real vcfs, same behavior seen for both. returns empty matrix with only the cell names. merged with rvanheusen/aa-mutations. have also checked out raw versions of rvanheusen/aa-mutations and rvanheusen/mutation-counts-cleanup, and same behavior is observed

[lincoln-harris]

interestingly count-mutations works perfectly, but I assume this is because it does not depend on ProteinVariantPredictor class, while find-aa-mutations does

[lincoln-harris]

RESOLVED: works when I use gencode's references (.gtf, .fa)