Version 4.1

Version 4.1.0

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

  • This release adds support for two new prediction algorithms: BigMHC and DeepImmuno (#1063). BigMHC includes predictions for elution (BigMHC_EL) and immunogenicity (BigMHC_IM). DeepImmuno is a prediction algorithms for immunogenicty.

  • This release includes several updates to pVACview (#1012):

    • The tab containing the anchor heatmaps for each well-binding peptide of a variant has been moved to the “Transcript and Peptide Set Data” panel.

    • The anchor heatmap tab now also contains a table of all the per-length and per-allele anchor weights for each position in a peptide.

    • The pVACtools version is now displayed at the bottom of the sidebar.

    • A new panel has been added to show the tiering parameters currently applied.

    • Where there are multiple transcript sets for a variant, the one containing the best peptide is now selected by default.

  • This release adds a new command pvactools download_wdls (#1055). This command can be used to download WDL workflow files for pVACseq and pVACfuse.

Version 4.1.1

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

  • The previous version updated how the all_epitopes.tsv file was parsed when creating the aggregated report and NA values are now parsed as native pandas nan. However, this update was not handled correctly for the Mutation Position column, leading to errors with NA values in that column. This release fixes this error. (#1079)

  • The previous version would write the DeepImmuno output file in the same location for multiple prediction calls. This would lead to errors when running in multi-threaded mode. This releases updates the code to write DeepImmuno outputs to unique file locations. (#1078)

  • This release updates how the list of combinatorial class II alleles is created in order to return it as a sorted list, creating a consistent order when writing the input.yml log file. (#1077)

  • This release updates the GitHub commit for the pVACview demo data in order to pull the latest version of this data, including DeepImmuno and BigMHC prediction data. (#1073)

  • This release fixes an issue where the pVACvector visualization images were saved in a low resolution format resulting in blurry images. (#1071)

  • This release fixes an issue where the method to determine the matched wildtype result didn’t return where appropriate, causing the mutation position to not be set correctly. (#1082)

  • This release fixes some typos. (#1072)