1.4.0

This version adds the following features:

• pVACvector now tests spacers iteratively. During the first iteration, the first spacer in the list of --spacers gets tested. In the next iteration, the next spacer in the list gets added to the pool of spacers to tests, and so on. If at any point a valid ordering is found, pVACvector will finish its run and output the result. This might result in a slightly less optimal (but still valid) ordering but improves runtime significantly.
• If, after testing all spacers, no valid ordering if found, pVACvector will clip the beginning and/or ends of problematic peptides by one amino acid. The order finding process is then repeated on the updated list of peptides. This process may be repeated a number of times, depending on the value of the --max-clip-length parameter.
• This version adds a standalone command to create the pVACvector visualizations that can be run by calling pvacvector visualize using a pVACvector result file as the input.
• We removed the --aditional-input-file-list option to pVACseq. Readcount and expression information are now taken directly from the VCF annotations. Instructions on how to add these annotations to your input VCF can be found on the Input File Preparation page.
• We added support for variants to pVACseq that are only annotated as protein_altering_variant without a more specific consequence of missense_variant, inframe_insertion, inframe_deletion, or frameshift_variant.
• We resolved some syntax differences that prevented pVACtools from being run under python 3.6 or python 3.7. pVACtools should now be compatible with all python >=3.5 versions.