Major changes
- Added a model for epitopes
- Optionally, output a table with all annotated epitopes obtained from a set of input neoantigens (option --with-all-neoepitopes)
- Additional command line tool neofox-epitope that accepts epitopes as input. The epitopes may be associated with a particular HLA allele or alternatively paired with each of the HLA alleles defined in a given patient
- MHC-II weak binder threshold changed from 10 to 5
- Output JSON file with reference resources metadata with the aim of documenting the reference data versions
Minor changes
- Neoantigen model is simplified by removing the Mutation entity
- Annotations are renamed with the aim of making them more self explanatory
- Always output tabular and JSON data as opposed to choosing output format
- Input parameters --candidate-file and --json-file are simplified into --input-file. The format of the input is inferred from the file - extension, being valid extensions *.txt and *.tsv for tabular format; and *.json for JSON format.
- Recognition potential is now also annotated when mutation not in anchor positions
- Dask cluster is now closed in a cleaner way
- Some of the binaries are now optionally read from the PATH
- All temporary files from MHC prediction are removed now, this caused troubles for large datasets
- Now all relevant peptides of length 8-14 are considerd while MHC-I prediction (previously: 8-11)