Visual improvements to reporting by various scripts

[malachig]

• For get_neoantigen_qc.py and get_FDA_thresholds.py . Avoid really long decimals for human readability. e.g. duplication rates look like this. "12.929599656902 (%)". We currently manually change these to look like "12.9%". Throughout the report, in most places we could use 1-4 decimal points. Looking at an example one can see what look reasonable.

• In these same results, for very long integers, use commas in report. e.g. "283794038" -> "283,794,038"
  For hla_comparison.py. Make sure that whenever there is a pair of HLA alleles for the same gene ... e.g. HLA_A-1, HLA_A-2 where the values are "A02:01 A01:01". Make sure these pairs are always listed alphabetically. This helps to see across the predictions if they are identical or not.

• For generate_reviews_files.py currently fails to run if the .xlsx input file has the extra header row. This line currently says "Exported data". pVACview generates this on export of results.

• For color_peptides51mer.py thresholds are used to decide if a class I peptide is colored red, or a class II peptide bolded, and whether these alleles listed in "RESTRICTING HLA ALLELE" column. We would like to be able to configure those, but they are currently hard coded?

[evelyn-schmidt]

Human readable decimals fixed in PR31! Docker version6!