Fix bug where the incorrect neoantigen fasta entry was used for ref proteome search #1153
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In the current implementation, the algorithm might use an incorrect neoantigen fasta entry when picking the longer peptide sequence for a neoantigen candidate in cases where multiple variant entries/alts are located at the same position. The fix is to carry the unique variant Index from the all_epitopes file in the the aggregate file since the Index corresponds to the fasta headers.
Closes #1150