Version 5.1

Version 5.1.0

This is a minor feature release. It adds the following features:

  • This update allows pVACvector to remove peptides in order to find a partial solution if a full solution cannot be found. The number of peptides permitted to be removed can be controlled by the --allow-n-peptide-exclusion parameter. by @susannasiebert in https://github.com/griffithlab/pVACtools/pull/1168

  • This update adds functionalities to pVACvector to prevent the core neoantigen candidate from getting clipped. by @susannasiebert in https://github.com/griffithlab/pVACtools/pull/1174

  • When only elution algorithms are chosen and no binding affinity algorithms, the pipelines will now output a warning message that no aggregated report can be created. by @ldhtnp in https://github.com/griffithlab/pVACtools/pull/1165

  • When creating the aggregated report, the Best Peptide for some variants may not match the aggregate inclusion criteria and no detail information would be available for this peptide when investigating the variant. This update ensures that the Best Peptide is always included in the metrics file and counted toward the Num Included Peptides count. by @susannasiebert in https://github.com/griffithlab/pVACtools/pull/1177

  • The evaluation buttons in pVACview will now be colored green for Accept, red for Reject, and orange for Review to visually differentiate the different statuses. by @susannasiebert in https://github.com/griffithlab/pVACtools/pull/1173

It also fixes the following problem(s):

  • This release removes two parameters from pVACvector: --aggregate-inclusion-binding-threshold and --aggregate-inclusion-count-limit which are not applicable to this pipeline. by @susannasiebert in https://github.com/griffithlab/pVACtools/pull/1180

  • This release fixes various pVACview bugs. Specifically, it fixes a bug that would result in pVACview crashing when a variant with a Num Included Peptides of 0 was selected. It also fixes a bug where re-tiering the candidates before selecting evaluations would result in evaluations being associated with incorrect variants. Additionally, it fixes several deprecation warnings and typos. by @susannasiebert in https://github.com/griffithlab/pVACtools/pull/1173