Version 5.5

Version 5.5.0

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

It also fixes the following pVACsplice bugs:

  • Remove option for DA and N anchors in pVACsplice. Splice sites with the DA anchor (known donor and acceptor) don’t result in any novel epitopes (the splice site peptide sequence predicted by pVACsplice is identical to the WT sequence). For the N anchor, there isn’t enough information to construct a splice site peptide sequence with our current approach since both the donor and acceptor are not observed in the reference. by @susannasiebert in https://github.com/griffithlab/pVACtools/pull/1283

  • Add a missing import statement and fix an issue in get_mutated_peptide_with_flanking_sequence where, for certain variants, the mutated peptide was not being determined correctly. by @susannasiebert in https://github.com/griffithlab/pVACtools/pull/1282

  • Fix an issue in the pVACsplice calculate reference proteome similarity step where, for certain variants, the start position of the peptide to query was not being determined correctly. by @susannasiebert in https://github.com/griffithlab/pVACtools/pull/1278

  • Add better handling of pVACsplice frameshifts where the downstream sequence may not have been fully included in the query sequence for the calculate reference proteome similarity step. by @susannasiebert in https://github.com/griffithlab/pVACtools/pull/1285

  • Handle cases in pVACsplice where no processable neoepitopes were found so that the run exits gracefully with better stdout messages. by @susannasiebert in https://github.com/griffithlab/pVACtools/pull/1286

  • Fix documentation of the input fasta parameter in pvacsplice calculate_reference_proteome_similarity to point to the correct location. by @susannasiebert in https://github.com/griffithlab/pVACtools/pull/1288

Version 5.5.1

This is a bugfix release. It fixes the following problem(s):

  • Fix a couple of issues with the new –top-score-metric2 by @susannasiebert in https://github.com/griffithlab/pVACtools/pull/1291

    • When adding the --top-score-metric2 option, the logic for determining the included candidates during aggregate report creation was amended to compare either the IC50 or percentile to the aggregate inclusion binding threshold. This logic should not have been changed and instead only the IC50 should be compared to the aggregate inclusion binding threshold, no matter which --top-score-metric2 was selected. This specific change has been reverted

    • In order to achieve deterministic results when using the percentile --top-score-metric2 option, a peptides.sort() call was used. This release replaces this with a better way of finding the best peptide by using the IC50 as a secondary sort criteria.

Version 5.5.2

This is a bugfix release. It fixes the following problem(s):

Version 5.5.3

This is a bugfix release. It fixes the following problem(s):

Version 5.5.4

This is a bugfix release. It fixes the following problem(s):