Pvacseq

This release adds handling for DNPs and MNPs missense mutations.

This version adds a new option `--additonal-report-columns` to the `pvacseq run` command which can be use to append additional columns of data to the report. Right now the only value supported for this option is sample_name which appends a column with the sample name to the final report.

We updated the logic that determines whether or not a corresponding wildtype epitope for a mutant epitope is included in the report. Previously, we would only include the corresponding wildtype epitope if the number of **consecutive** matching amino acids between mutant and wildtype epitope was larger then half of the total number of amino acids in the epitope. We now use the **total** number of matching amino acids between the mutant epitope and the corespondig wildtype epitope across the whole length of the epitope to make that determination. The total number of matching amino acids needs to be larger than half of the length of the epitope. Otherwise the corresponding wildtype epitope is reported as “NA”.

With this release any execution of `pvacseq run` will create a log file of the inputs used. This log file is then used when executing another run with the same output directory. This ensures that you can only write to the same output directory if identical parameters are used.

This is a hotfix release. It fixes an error introduced in a previous version that would occur when using a local installation of the IEDB tools and is related to some filtering we do on the output from the IEDB tools. More information can be found on GitHub issue 278.

This version improves the sorting of the final report file. The file will now be sorted by “Gene Name” and “Mutation” and within these categories by the MT score - either “Median MT Score” or “Best MT score” depending on the top-score-metric used.

This release implements a 60 second wait between each request to the IEDB RESTful API in order to decrease the load on their servers. We recommend the usage of the standalone IEDB tools for long-running processes with many variants, prediction algorithm, epitope lengths, or alleles.

There also have been various bugfixes in this release.

This version updates the IEDB RESTful API URL to the new target announced in IEDB Analysis Resource v2.15.1.

This release introduces a change in how invalid alleles are handeled. Previously, the pipeline would throw a fatal error. The pipeline will now proceed but invalid alleles will be skipped.

This version also has improved error handling around calling standalone IEDB installations.

This release fixes a couple of bugs related to the processing of frameshift variants.

This release fixes a couple of minor bugs. Firstly, the pipeline will now skip variants that result in the loss of a start codon. Secondly, this release fixes a bug that would result in an error when the input VCF doesn’t contain any sample genotype information. VCFs with no samples will now be fully processed through the pipeline.