Version 4.2
===========

Version 4.2.0
-------------

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

- We added two new modules to pVACview: a :ref:`neofox_module` to visualize
  NeoFox neoantigen annotations and a :ref:`custom_module` to visualize
  neoantigen data in a TSV file, for example output files from VaxRank,
  NeoPredPipe, or antigen.garnish.2.
- We added a :ref:`vignette <pvacseq_vignette>` to our documentation to provide
  an extended tutorial on how evaluate neoantigen candidates using pVACview.

This release also fixes the following bug(s):

- When running pVACfuse with Arriba input data, the 3' transcript was not
  being parsed correctly. This release fixes this issue.

Version 4.2.1
-------------

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

- When running the reference protome similarity step with a reference protome
  peptide fasta file and a species other than human or mouse, the run would be aborted
  with an error that the refseq_protein_prot BLASTp database was incompatible with
  the species. This error should not be emitted in this circumstance since
  BLASTp is not run when using a reference proteome peptide fasta file. This
  release fixes this error and allows users to run the reference proteome
  similarity step on non-human and non-mouse data with a reference proteome peptide fasta.