Fix aggregate inclusion binding threshold and add new --aggregate-inclusion-count-limit parameter

[susannasiebert]

This PR fixes an issue we recently discovered where using the --allele-specific-binding-thresholds parameter would not use the --aggregate-inclusion-binding-threshold but instead fall back on selecting entries to be included based on the --binding-threshold as the cutoff. With this PR, the --aggregate-inclusion-binding-threshold will now also be respected/used, even if the --allele-specific-binding-thresholds is set.

However after fixing this bug we discovered that it leads to a large number of peptide candidates being included with the default cutoff of 5000 (particularly for frameshift variants), exceeding GitHub file size limits for the pVACview demo data (specifically, the metrics file) and slowness when loading the data in pVACview.

To solve this, this PR also adds a new parameter --aggregate-inclusion-count-limit (default: 15) which, for variants exceeding 15 peptides passing the --aggregate-inclusion-binding-threshold, will limit the included entries to those of the 15 best peptides (as defined by our algorithm for selecting the best peptide per variant).

By limiting the number of peptides included for each variant, there are less outliers with a large number of candidates. This previously resulted in us limiting the number of candidates displayed in the pVACview anchor heatmap. With this update, this limitation has been removed and all included peptides candidates are now shown in the anchor heatmap.

[susannasiebert]

TODO:

• Update all example data
• Update documentation to document new parameter and new column
• Update pVACview screenshots used in documentation and tutorial showing aggregated report