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@susannasiebert susannasiebert released this 23 Jan 16:06
· 586 commits to master since this release
v4.0.7
96c255a

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

  • The multithreading capabilities in pVACtools are not available for Mac OSX. Attempting to use the -t parameter would result in the forked processes crashing but the run would still complete successfully leading to results with incomplete data. This release will result in an error when multithreading is used under Mac OSX.
  • We’ve observed issues with IEDB’s API sometimes returning incorrect or incomplete data. This results in downstream errors. This release updates the prediction calling to log such occurrences and to retry the API when they are observed.
  • MHCflurry sometimes returns no binding affinity percentile data. This resulted in errors when parsing such prediction data. This release fixes our parsing logic to handle this case.
  • TSL parsing of the input VCF in pVACseq used to be limited to human data only. This release adds support for TSL parsing in mouse data.
  • When running with the –noncanonical flag, the exons.csv file will contain exon postions for all possible transcript combinations. However, the transcripts weren’t being taken into account when parsing this file to determine the fusion positions. This release fixes this issue by looking up the positions for the specific transcripts of the record currently being parsed.
  • When using BLASTp for the reference proteome match step, we applied the word-size parameter in order to only return perfect matches. However, for short sequences, word-size must be less than half the query length, or reliable hits can be missed. This release updates how the word-size parameter is calculated in order to meet this criteria.
  • This release addresses in error in pVACview that would occur in the Transcripts in Set window when there are no peptides passing the aggregate inclusion binding threshold.
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