Create fusion transcript objects to map exons covering the breakpoints

[Caralyn Reisle]

In addition to creating the fusion chromosome, we will also need to create a fusion transcript for mapping of the exons that are part of the actual fusion transcript. This will be the more straighforward use of the FusionTranscript.build as it will take in the PreTranscript

[Abbey Reisle]

1. create fusion transcipt

• load annotations, reference and use annotate events and FusionTranscript build

2. create fusion chromosone

• create 2 "PreChromosone" (PreTranscript) objects that contain the information for all the genes on the chromosone instead of exonsranscript class a list of genes that have the necessary behaviour from the exon class
  -for this we'll need to provide the PreT

3. output files

• generate gtf file
• generate fa file