Add annotation checks to ValidateVariants

[ldgauthier]

Ideally for GnarlyGenotyper inputs and outputs, check to make sure required Gnarly annotations are present, AS annotation lengths are correct, necessary VQSR annotations are present.

[ldgauthier]

After Jonathan's recent modifications I'm a little confused about what should happen if a reference isn't provided -- should it ever error or just warn? @jamesemery I ended up changing the expected behavior of one of the tests, but I'm happy to change it back if we can define the correct behavior.

[gatk-bot]

Travis reported job failures from build 28077 Failures in the following jobs:

Test Type	JDK	Job ID	Logs
variantcalling	openjdk8	28077.4	logs