Create main mutate function

[Caralyn Reisle]

The main mutate function needs to

• remap the genes on the new mutant chr using the _mutate functions
• return the mutant chromosome set (should remove the original chromosomes that became part of the fusion chromsome. Only need the mutant copies)
• build the regulat fusion transcript object.
• use the fusion transcript object to create a new mutant 'gene' object to add to the annotations ( the coordinates given for the fusion transcript will need to be shifted since they are relative to the gene start and not the fusion chromosome)