Better clarify the terms used throughout the PDF report

[armish]

Some replacement/addition suggestions that I think will help better clarify some of the fields/terms in the report for a first-time user and/or for an average bfx-savvy researcher:

• COMMAND LINE ARGUMENTS
  • Include Vaxrank version that is used to generate the report
• For each variant:
  • Reads supporting ... allele -> DNA reads
  • Reads supporting ... (maybe add what percent this corresponds to?)
  • Top score -> Top vaccine score
• For each predicted effect:
  • Highlight "Effect description" value using the same colors that you use to highlight the mutant aa within the table header right below
• For each vaccine peptides for variant X:
  • Length -> Length of the peptide window for searching vaccines
  • Expression score -> add units? FPKM/TPM (optionally: percentile)
  • Mutant amino acids -> Mutant amino acids within the window
  • Mutation distance from edge -> Mutation distance from edge(s)
  • Manufacturability -> if possible, add range for each metric?
• For each Predicted mutant epitopes
  • Table headers:
  • Sequence -> Peptide sequence
  • IC50 -> IC50 (predicted binding affinity of the mutant peptide)
  • Normalized binding score -> Normalized binding score (\frac{IC50{tumor}}{IC50{normal}})
  • Maybe move the "Allele" column closer to the "Sequence" one to emphasize that those metrics belong to that particular pair and "Allele" is not a result