Version 5.4 =========== Version 5.4.0 ------------- This is a minor feature release. It adds the following features: * Add functionality to add gene of interest identification. by @susannasiebert in https://github.com/griffithlab/pVACtools/pull/1229 A new option ``--genes-of-interest-file`` has been added. This option allows users to specify a file path containing genes name that are of particular importance to their research. Neoantigens resulting from variants on one of these genes will be marked in the all_epitopes.tsv and filtered.tsv files in a new ``Gene of Interest`` column (``True``/``False``). If this option is not specified, `a default list of common cancer genes `_ is used. Version 5.4.1 ------------- This is a bugfix release. It fixes the following problem(s): * Ensure that the files in the supporting_files directory, including the default genes of interest list, are included in the distribution Otherwise the Mark Genes Of Interest step would fail with a file-not-found error. Version 5.4.2 ------------- This is a bugfix release. It fixes the following problem(s): * Handle cases where the peptide sequence for a variant is missing from the fasta during reference proteome similarity matching. Instead of throwing in error, skip such entries and mark Ref Prot column as "Not Run". by @susannasiebert in https://github.com/griffithlab/pVACtools/pull/1253 * Write a log message for the above cases. by @susannasiebert in https://github.com/griffithlab/pVACtools/pull/1259 * Fix bug in processing inframe deletions during aggregation causing the variant type to not be set correctly. by @susannasiebert in https://github.com/griffithlab/pVACtools/pull/1255 * Respect ``--anchor-types`` parameter in pVACsplice. Previously, even when specifying this parameter it would be ignored and a hard-coded list of anchors would be used. by @susannasiebert in https://github.com/griffithlab/pVACtools/pull/1258 * Update description of the ``--starfusion-file`` parameter to reflect that it can be used with Arriba data. by @susannasiebert in https://github.com/griffithlab/pVACtools/pull/1263 Version 5.4.3 ------------- This is a bugfix release. It fixes the following problem(s): * Fixed IC50/%ile WT sorting to use numerical sorting instead of string sorting. by @ldhtnp in https://github.com/griffithlab/pVACtools/pull/1265 * Bugfixes for the pvacsplice generate_protein_fasta command to handle sequences shorter than the flanking sequence length and sequences with unsupported amino acids. by @susannasiebert in https://github.com/griffithlab/pVACtools/pull/1268