Pvactools

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.

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.
- An unneeded import statement for the PyVCF package had the potential to cause errors while running the pVACseq pipeline.

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 NetMHCstabpan and/or NetChop.

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

- This fixes an issue introduced in the previous release where VCF entries with no VAF value would result in an error.
- This release adds a new constraint to the vaf cutoff command line arguments to ensure that they are a fraction between 0 and 1.
- This release also fixes an issue where the wrong binding filter class was being used when running pVACfuse with allele-specific binding cutoffs.

This is a bugfix release. It fixes the following problem(s):
- When using the --additional-report-columns parameter in pVACview/pVACfuse, no contents were previously written to the additional columns.
- MHCflurry may return no value for the percentile binding score. This would previously result in an error which has been fixed in this release.
- Variants in a VCF may contain an empty AF field, which was previously not being handled correctly in all cases, resulting in an error.

This release also includes some minor improvements:
- When running the pVACseq pipeline there would be a lot of warning messages about missing position column parameters. These would mostly be noise because the underlying consequence type wasn’t supported by pVACseq to begin with. This release removes these warning messages for mutations with consequences that are not supported by pVACseq.

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

- Newer versions of Ensembl annotations added genes without a HUGO gene name. Variants on those genes cause downstream errors in the aggregate report creation when running the pVACseq pipeline. This release fixes this error.