When we create the fasta file for making binding predictions, we only include n-1 flanking amino acids so that each n-length substring of the peptide overlaps the mutation position. However, for inframe insertions that duplicate of a longer region, the insertion position (insertion start) is not where the mutated amino acids start (which is at the end of the duplicated region). Currently, not enough flanking amino acids are included in the fasta file pVACseq creates. This PR extends the end of the MT and WT peptide sequences for inframe insertions by the length of the insertion on top of the specified flanking region. This ensures that the duplicated portion of the WT sequence is always fully included.
When we create the fasta file for making binding predictions, we only include n-1 flanking amino acids so that each n-length substring of the peptide overlaps the mutation position. However, for inframe insertions that duplicate of a longer region, the insertion position (insertion start) is not where the mutated amino acids start (which is at the end of the duplicated region). Currently, not enough flanking amino acids are included in the fasta file pVACseq creates. This PR extends the end of the MT and WT peptide sequences for inframe insertions by the length of the insertion on top of the specified flanking region. This ensures that the duplicated portion of the WT sequence is always fully included.
Closes #1152