4.0.2

This is a bugfix release. It fixes the following problem(s):

• Arriba annotated fusion sequences may contain characters that aren’t supported. This update skips such sequences.
• The --aggregate-report-evaluation parameter in the standalone pvacseq generate_protein_fasta command was previously set up with nargs in order to allow specifying multiple values. However, this conflicts with required positional parameters. The parameter definiton was updated so that multiple values are now specified as a comma-separated list.
• pVACfuse would previously fail in an odd way when none of the fusions in the input were processable. This update now exits pVACfuse more gracefully in this case.
• The reference proteome similarity step would previously fail when an epitope’s full peptide sequence wasn’t found in the input fasta. It now skips such epitopes and marks the Reference Match column as Not Run.
• There was a mismatch in how proximal variants were incorporated into the n-mer fasta files vs the “master” fasta file which had the potential of epitopes not being present in the “master” fasta file. This update brings both file creation steps in sync.