Add support for screening of end modifications to long peptides to accommodate manufacture/solubility issues

Conceptually similar in some ways to what happens in pVACvector. In working with peptide manufacturers, there is sometimes a case where the manufacturer wishes to add a few (e.g. 1-3) amino acids to the N- or C-terminus of the proposed long peptide.

It might be desirable to have a tool that would help facilitate the process of screening these altered peptides to see if any predicted strong binding peptides arise that include the altered (non-self and non-tumor) peptides.

Example of what input might look like:

Proposed-long-peptide       N-terminal-additions       C-terminal-additions 
RKNEQFEQEAVAVDSNLRVREKK     RKN                        KK

When pVACbind is run for each given peptide length selected we want to predict binding for those peptides that contain at least one altered amino acid at the end (RKN or KK in this case).

Start by comparing the proposed workflow with pVACvector and the existing pVACbind inputs and peptide-length handling. Define how N-terminal and C-terminal additions are represented, then ensure predictions include only peptides containing at least one altered terminal amino acid. The example input provides the expected three-column shape and screening goal.