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.