rRNA missing from snps.tab + impact of annotation on variants?

[SJohnsonMayo]

This might be a duplicate of #111 but I don't think that it was fixed -- I'm not seeing any rRNA variants in my snps.tab I've tried using the original .gbk (NZ_CP071982), and I've tried reannotating it with Prokka (this also seems to change the number of variants in the VCFs quite a bit?). The rRNA features are present in /reference/ref/ref.gff, but don't seem to be making it through to the final output. If anyone's run into this issue and had any luck figuring it out, I'd be grateful for any guidance!

Thanks!