novel promoter swap from gene fusion

[kgaonkar6]

From @jharenza regarding reviewer's comment:

How the authors handle the annotation of fusions if they don't necessarily fall in exon-exon boundaries? For example in MALAT1-GLI1 fusions, the break happens in the middle of the gene body of MALAT1 (a non-coding gene) and the break on the GLI1 can happen some bases upstream on exon 5-6. Would an important fusion like be annotated correctly and not filtered away? How would you classify this fusion since it is not "in-frame" (there is no frame on the MALAT1, since it is non-coding)?  Would it provide some annotation saying that is likely a "promoter-swap" kind of event? I understand most fusions occur in exons borders but I would like to know if this tool is able to handle interesting real biology cases like the one described

Can we add some annotation saying that a fusion is likely to be a "promoter-swap" kind of event?

For this and similar fasta sequence(epitope etc) analysis standard fusion format will also need to extract fusion sequence from caller input