Transgene

1. Support for fusion peptides from a bedpe fusion predictions file
2. Multithreading support for parsing and filtering snvs
3. Support for filtering of OxoG variant artefacts
4. Support for properly handling X's in the IAR
5. Support for properly handling mutations affecting the same codon
6. Support for properly handling SNPEff messing up the translation by 1 AA

Major refactor to Transgene. Beginning of a new development schema.
1. Implemented RNA-aware mutation selection for only expressed events.
2. Implemented read-backed phasing for chained events.
3. Chained peptides are now the correct length.
4. Added a CI test and all the required materials to run the test.
5. Added logging