Neoepiscope

* Predicts neopeptides from A-to-I edits in REDIportal database with `--rna-edits`

Updates translation algorithm for increased accuracy
- Compatible with annotated stop codon readthrough (retains X as unknown amino acid)
- Compatible with selenocysteine transcripts (retains X and flags as possible selenocysteine)
- Supports annotated start codons of noncanonical sequence

Updates GRCh38 annotations to GENCODE v35

- Eliminates python 2 compatibility
- Updates binding affinity predictions for MHCflurry v2 compatibility

- Adds functionality for reporting mutation-level expression
- Adds functionality for reporting/filtering on transcript-level expression
- Adds functionality for the mm10 genome build
- Adds functionality for `NetMHCpan` v4.1 and `NetMHCIIpan` v4.0
- Fixes bug in `mhcnuggets` binding predictions

* Updates MHC allele processing for binding predictions
* Changes warning to note in `neoepiscope swap`
* Updates run instructions in README

* Adds support for mouse genome build mm9
* Fixes bug in running with user-supplied genome builds