1.5.10

This is a hotfix release. It fixes the following issues:

• A stray character at the end of one file was causing a syntax error in Python 3.8. The character has been removed. pVACtools should now be 3.8 compatible although some dependencies might not be compatible yet.

1.5.9

This is a hotfix release. It fixes the following issues:

• Some variant consequences supported by pVACseq would not actually result in a amino acid change (e.g., inframe_insertion&incomplete_terminal_codon_variant). These types of variants were not being filtered out correctly and would cause an error when trying to create the peptide fasta sequences. This issue has been fixed and these variants are now being filtered out upstream.
• Running pVACseq on a non-human VCF would cause an error in the top score filter since the transcript identifiers would not match the expected format. This has been fixed and the top score filter now supports non-human transcripts.
• There was an error in setting up the standalone pvacfuse generate_protein_fasta command which would result in an error when trying to run this command. This has now been fixed.

1.5.8

This is a hotfix release. It fixes the following issues:

• The pvacseq run, pvacfuse run, and pvacbind run commands would previously error out when running with both MHC class I and MHC class II algorithms but one or the other would not produce an all_eptiopes.tsv file. This version fixes this bug.
• MHCflurry version 1.6.0 and higher changed the output file headers. This would cause errors when trying to parse these output files. pVACtools now supports both the old and the new headers.
• AGFusion updated their output file naming convention in newer versions and is now outputting .exons.csv files instead of .exons.txt files. pVACfuse is now able to process either version.

1.5.7

This is a hotfix release. It fixes the following issues:

• The pvacbind run command would previously allow fasta input files with duplicated headers. However, it would silently skip subsequent entries with duplicated headers even if the fasta sequence was novel. With this release pVACbind will now error out if a duplicate fasta header is encounterd.

1.5.6

This is a hotfix release. It fixes the following issues:

• The pvacbind run command would previously error out if one of the input sequences would contain a X stop codon. This update will remove the X amino acid and the downstream sequence before further processing the remaining protein sequence.
• A bug in the pvacfuse top_score_filter code would previsouly result in an error when trying to run this command. This has now been fixed.

1.5.5

This is a hotfix release. It fixes the following issues:

• The pvacfuse run command would previously output a misleading warning message if an AGFusion input directory didn’t contain any processable fusion entries. This warning message has been fixed.
• Between VEP versions, the Downstream protein sequence prediction for some frameshift mutations was changed to now include a leading wildtype amino acid. This potential difference in VEP-predicted Downstream protein sequences was not accounted for and would result in frameshift mutation protein prediction that would duplicate this leading wildtype amino acid. This version updates our prediction pipeline to remove this duplicated amino acid and output a fatal error if the Downstream protein sequence does not contain the leading wildtype amino acid.

1.5.4

This is a hotfix release. It fixes the following issues:

• The pvacseq generate_protein_fasta command would previously error out when running with a selected peptide_sequence_length that would reduce in peptides < 7 amino acids long. This error would occur when calculating manufacturability metrics. This release now only calculates these metrics for peptides >=7 amino acids long.
• We updated the calculation for the flanking sequence length when generating peptide sequences to result in peptides that are closer in length to the requested peptide_sequence_length.
• This release fixes an edge case where a frameshift mutation impacted the first amino acid of a transcript. This case would previously throw a fatal error but will now be processed as expected.

1.5.3

This is a hotfix release. It fixes the following issues:

• pVACbind would previously throw an error if a peptide sequence in the input fasta was shorter than one of the chosen epitope lengths. This issue has been fixed by first parsing the input fasta and creating individual fasta files for each epitope length that enforce a minimum length of the peptide sequences matching the respective epitope length.
• Previous versions of pVACtools resolved an issue where IEDB would output a warning line if one of the epitope sequences only contained A, C, G, or T amino acids, since those sequences could also be nuclotide sequences. However, this issue was only fixed in pVACseq, not pVACbind, or pVACvector. This release fixes this issue for all tools.
• The wrappers for NetChop or NetMHCstabpan split the set of input epitopes into chunks of 100 before processing. Due to a bug in the file splitting logic, one epitope for each chunk over 100 would be errenously dropped. This effectively would result in less epitopes being returned in the filtered report than if running the pipelines without NetChop or NetMHCstabpan.

1.5.2

This is a hotfix release. It fixes the following issues:

• AGFusion exon files may be comma-delimited. Previously, the file parser assumed the files were tab-delimited. This release now allows AGFusion inputs that are comma- or tab-delimited

1.5.1

This is a hotfix release. It fixes the following issues:

• There was a syntax error in tools/pvacseq/generate_condensed_ranked_report.py that would result in an error when running the pvacseq generate-condensed-ranked-report commands.
• We were previously not correctly catching cases where the intermediate fasta for making binding prediction was empty. This would result in errors downstream.