Version 3.1
===========

Version 3.1.0
-------------

This release adds the following new features:

- When running the pipelines with the ``--netmhc-stab`` flag enabled, the
  ``NetMHCstab allele`` column now also reports the distance of the
  NetMHCstabpan allele when that allele is not identical to the ``HLA Allele``
  of the original result.
- When running the pipelines with a set of individual class II alleles, the pipeline now
  also auto-generates valid combinations of these alleles so that users no
  longer need to explicitly provide these combinations.

This release also fixes the following problem(s):

- Some class I alleles are not supported by NetMHCstabpan and will lead to an
  error when attempt to make predictions with them. This release will skip
  such alleles for the stability prediction step.
- For very large result sets the filtering steps would stall or be killed
  because the steps would run out of memory. This release fixes this issue.
- This release adds better handling of timeout errors while running

Version 3.1.1
-------------

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

- The ``--exclude-NAs`` flag was not being passed along correctly to the main
  pipeline and didn't have any effect on downstream filtering.
- The aggregate report creation step had some inefficiencies which caused its
  runtime to be much longer than necessary.
  NetMHCstabpan and/or NetChop.
- An unneeded import statement for the PyVCF package had the potential to
  cause errors while running the pVACseq pipeline.

Version 3.1.2
-------------

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

- It fixes an issue with parsing class II IEDB output files when running
  pVACfuse or pVACbind, which resulted in the wrong binding prediction scores
  being associated with certain epitopes.
- It adds missing import statements to pVACvector.

Version 3.1.3
-------------

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

- It fixes an issue with the reference proteome match step where stop lost
  mutations would throw a fatal error.