Fix mistaken string == equality comparison in GencodeFunctotation.java

[jamesemery]

It was noticed while doing #8351 that the GencodeFunctotation.equals() method has the following line in it

if (geneTranscriptType != that.geneTranscriptType) return false; 

Unfortunately the geneTranscriptType is stored as a Sting and thus this should NOT be expected to succeed in almost any case. As it stands fixing this innocuous oversight seems to break several of the combinatorial funcotator tests and an integration test. Somebody should fix this behavior (easy) and validate that the test changes are within tolerable levels (hard).