CalculateGenotypePosteriors allows input VCFs from different references

[ldgauthier]

#2410 added the --sequenceDictionary argument, but how do we make this argument required for certain tools? The GTEx project uses CalculateGenotypePosteriors (yay!) and accidentally mixed and matched some VCFs with understandably unexpected results.

[droazen]

@ldgauthier The easiest way to do this right now is to call getMasterSequenceDictionary() from the tool's onTraversalStart() method, and throw if it returns null.

[droazen]

I'll also mention that as part of #4341 we plan to give tools more control over the arguments inherited from GATKTool, including selectively disabling and redefining engine arguments, so once a mechanism is in place for that CalculateGenotypePosteriors could make --sequence-dictionary required. Currently this ability only exists for a few GATKTool arguments, and the tool has to override methods like requiresReads() to make use of it. Until the ability to do this is generalized, recommend the stopgap solution with the check in onTraversalStart() + a note in the tool's docs.