Investigate VCFOutputRenderer to see if it can be made to behave more like MafOutputRenderer

[jonn-smith]

Feature request

Tool(s) or class(es) involved

Funcotator, MafOutputRenderer, VcfOutputRenderer

Description

For VCFs, we render each funcotation separately, then concatenate strings. This approach has the drawback of being less flexible in terms of ordering the fields (and setting up aliases), but that has not mattered yet. Regardless, it means that all string operations (e.g. excluding fields and sanitizing values) must be in the same method (in this case renderSanitizedFuncotationForVcf) and that method must work on a funcotation.

For MAFs, we flatten out the funcotations and put the fields into a giant map. Then we do the changes to field names and values on that map. But by the time I want to exclude fields and sanitize, the map is already made, so we do not render individual funcotations. Therefore no need for a renderSantiziedFuncotationForMaf.

We should investigate how easy it would be to generalize an output renderer to use the map convention like in MafOutputRenderer so we can bubble up that functionality. Since there are only 2 output types now, it might be best to do it before we get more of them.