Handle invalid pVACfuse characters by trimming sequence #1130
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susannasiebert
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Previously, sequences with invalid characters would be skipped, which might lead to downstream errors if an invalid character was located in the flanking sequence because shorter epitope lengths/flanking lengths would include such sequences and longer epitope lengths would exclude such sequences. The fasta with the longest flanking length for the run is being used as the fasta for the calculate reference proteome similarity and netchop step in order to retrieve a longer sequence around the fusion position. In the previous implementation, the sequences for such variants would be missing from this fasta, leading to errors.
Closes #1125