Version 5.5 =========== Version 5.5.0 ------------- This is a minor feature release. It adds the following features: * Add a new parameter ``--top-score-metric2`` that allows users to set whether to prioritize ic50 or percentile scores when creating the filtered and aggregated reports. by @Jaz2021 in https://github.com/griffithlab/pVACtools/pull/1267 * If an unsupported amino acid is the last/first amino acid in the peptide sequence, clip it so that the sequence can still be included in the run. by @susannasiebert in https://github.com/griffithlab/pVACtools/pull/1266 It also fixes the following pVACsplice bugs: * Remove option for DA and N anchors in pVACsplice. Splice sites with the DA anchor (known donor and acceptor) don't result in any novel epitopes (the splice site peptide sequence predicted by pVACsplice is identical to the WT sequence). For the N anchor, there isn't enough information to construct a splice site peptide sequence with our current approach since both the donor and acceptor are not observed in the reference. by @susannasiebert in https://github.com/griffithlab/pVACtools/pull/1283 * Add a missing import statement and fix an issue in get_mutated_peptide_with_flanking_sequence where, for certain variants, the mutated peptide was not being determined correctly. by @susannasiebert in https://github.com/griffithlab/pVACtools/pull/1282 * Fix an issue in the pVACsplice calculate reference proteome similarity step where, for certain variants, the start position of the peptide to query was not being determined correctly. by @susannasiebert in https://github.com/griffithlab/pVACtools/pull/1278 * Add better handling of pVACsplice frameshifts where the downstream sequence may not have been fully included in the query sequence for the calculate reference proteome similarity step. by @susannasiebert in https://github.com/griffithlab/pVACtools/pull/1285 * Handle cases in pVACsplice where no processable neoepitopes were found so that the run exits gracefully with better stdout messages. by @susannasiebert in https://github.com/griffithlab/pVACtools/pull/1286 * Fix documentation of the input fasta parameter in pvacsplice calculate_reference_proteome_similarity to point to the correct location. by @susannasiebert in https://github.com/griffithlab/pVACtools/pull/1288 Version 5.5.1 ------------- This is a bugfix release. It fixes the following problem(s): * Fix a couple of issues with the new `--top-score-metric2` by @susannasiebert in https://github.com/griffithlab/pVACtools/pull/1291 * When adding the ``--top-score-metric2`` option, the logic for determining the included candidates during aggregate report creation was amended to compare either the IC50 or percentile to the aggregate inclusion binding threshold. This logic should not have been changed and instead only the IC50 should be compared to the aggregate inclusion binding threshold, no matter which ``--top-score-metric2`` was selected. This specific change has been reverted * In order to achieve deterministic results when using the percentile ``--top-score-metric2`` option, a peptides.sort() call was used. This release replaces this with a better way of finding the best peptide by using the IC50 as a secondary sort criteria. Version 5.5.2 ------------- This is a bugfix release. It fixes the following problem(s): * Remove unused --top-score-metric2 parameter from pVACvector. by @ldhtnp in https://github.com/griffithlab/pVACtools/pull/1304 * Speedup processing of AGFusion exon files. by @susannasiebert in https://github.com/griffithlab/pVACtools/pull/1301 * Added biotype parameter to pVACvector when running with an input VCF. by @ldhtnp in https://github.com/griffithlab/pVACtools/pull/1297 Version 5.5.3 ------------- This is a bugfix release. It fixes the following problem(s): * Fix a bug in the reference proteome similarity step that may result in an ``IndexError: string index out of range`` error. by @susannasiebert in https://github.com/griffithlab/pVACtools/pull/1313 * Improve handling of inframe indels in repetitive region to upstream filter out variants that don't result in novel neoantigen candidates and to better find a matched wildtype epitope. by @susannasiebert in https://github.com/griffithlab/pVACtools/pull/1314 Version 5.5.4 ------------- This is a bugfix release. It fixes the following problem(s): * Fix an issue where the output parsing of MHCflurryEL in pVACfuse and pVACsplice where only the smallest epitope length would have results. by @susannasiebert in https://github.com/griffithlab/pVACtools/pull/1320 * Fix per-allele counts in the aggregated report. by @susannasiebert in https://github.com/griffithlab/pVACtools/pull/1316 * Fix a few bugs where standalone commands weren't working with all_epitopes/filtered TSVs. by @susannasiebert in https://github.com/griffithlab/pVACtools/pull/1324 * Update ``--top-score-metric2`` parameter help text for clarity and remove unnecessary usage. by @susannasiebert in https://github.com/griffithlab/pVACtools/pull/1321