Update threshold caller to output proper alternates

`ADAMVariant` requires that `referenceAllele != alternateAllele`

The proper way to encode a Ref/Ref variant is using the Ref/Ref in the genotype alleles for any alternate.
This changes:
 - NoCall variants to have an arbitrary alternate "<ALT>"
 - Ref/Ref variants to have an abritrary alternate "<ALT>"
 - Het calls to have exactly one variant allele and one reference allele
 - Makes a catch-all for cases where there are more than 2 alleles that pass the filter or there are multiple reference alleles for different references

Fixes #198
cool, I don't have a sense how bad/weird that is. would you like to be rudely notified if that ever happens? I feel like it is maybe a thing we should know about; it is a symptom of corner-cutting in our data representation, could be good to know if/when that happens so we know whether it's important to correct