hammerlab/guacamole — pull request #203 by arahuja (2014-10-31 20:03:07+00:00)
Title: 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 ""
- Ref/Ref variants to have an abritrary alternate ""
- 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