ref genome requirement

[cnobles]

There is no flag or requirement to initialize run without specified Genome supplied in processing parameters.

If "hg18" is specified, then Rpackage "BSgenome.Hsapiens.UCSC.hg18" should be required to start run. Likewise, other reference genomes should be able to be used.

[esherm]

This was originally intended as a feature in that intSiteCaller would process as far as it could and at least give some sort of output before crashing. You could easily check for the reference genome by calling get_reference_genome (which lives in programFlow.R) from the original call to processMetadata() rather than waiting for postTrimReads()

Duplicate of esherm#27