Number of Reads and length are not written with gencode annotation

The RPKM is printed in the output, but "length" and "reads" is not. I think this is because the

outputGFForiginalLines(...)

method is used and it seems to only append the RPKM.

I added a test in

FluxCapacitorReadsOutputTest

(commented for now) to verify this.

micha, can you take a look, at least if I am right?