Version 3.1¶
Version 3.1.0¶
This release adds the following new features:
When running the pipelines with the
--netmhc-stab
flag enabled, theNetMHCstab allele
column now also reports the distance of the NetMHCstabpan allele when that allele is not identical to theHLA 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.