Merge in candidate gene handling, and exomiser 2 score handling.

Code to process VCF files automatically now needs to be upgraded to Exomiser 2, and cache clearing still needs to be automatically triggered by a patient listener.
Good catch, Sergiu. This class isn't used anymore. I originally just used
it in place of a Variant object, but that complicated things and ended up
being more headache than it was worth so I refactored it out. I've removed
this class and committed these changes.

Thanks,
Orion

In
similarity-data-impl/src/main/java/org/phenotips/data/similarity/internal/CandidateGene.java:

> + * Software Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA
> + * 02110-1301 USA, or see the FSF site: http://www.fsf.org.
> + */
> +package org.phenotips.data.similarity.internal;
> +
> +import org.phenotips.data.similarity.Variant;
> +
> +import net.sf.json.JSONObject;
> +
> +/**
> + * A variant representation of a candidate gene.
> + *
> + * @version $Id$
> + * @since
> + */
> +public class CandidateGene implements Variant

This class doesn't seem to be used anywhere.

Also, why doesn't it store a gene name or any type of gene identifier?

—
Reply to this email directly or view it on GitHub
<https://github.com/phenotips/patient-network/pull/33/files#r15914850>.