Audit GenomeLocParser overloads for validation arguments.

[jamesemery]

In the work on #7295 it became clear that there are a lot of overlapping overloads of the createGenomeLoc() method that has already caused some confusion since some overloads will skip the reference validation step. Somebody should audit all of the uses of GenomeLocParser and evaluate where validation is and isn't appropriate (possibly if you want an unvalidated genomeLoc use a SimpleInterval?) and wire them accordingly.

[jamesemery]

As it turns out some of the createGenomeLoc() instances are being used by the GermlineCNVPipeline tests (evidently in ValidateVariants) and will fail if genome validation is enabled. This should be investigated.