JPFinnigan

It might be useful to also implement this logic in varcode/topiary. Presumably, one would want downstream tools to be aware of the presence and relative strandedness of secondary germline/somatic variants...

Apologies if you have already implemented MaSuRCA, but this utility and PEAR seemingly performs a similar function, but MaSuRCA can also be utilized for the "super-read" assembly workflow in StringTie....