convert v1 variants

[pnrobinson]

@ielis @julesjacobsen -- this is a v1 to v2 converted that assumes that the v1 phenopacket variant is causal for the disease and that the v1 phenopacket has exactly one disease. I am not sure how to convert SPDI variants but probably via VRS objects.

[ielis]

Hi @pnrobinson, I went through the V1->V2 code and I think it's almost ready to go. As you know, it is fairly straightforward to convert almost everything except for genes, variants, and part of Biosample in the v1 phenopackets.

There are 3 outstanding issues:

• [ ] can you check V1ToV2ConverterImpl#toV2Interpretation if it is doing what it should? The method maps each v1 Variant into GenomicInterpretation and creates one Interpretation for a given v1 Disease.
• [x] we need to work on conversion of SPDI to v2 VariationDescriptor
• [ ] there is no Variant field in v2 Biosample. Do we omit the Variants from v1 Biosample? This will likely do little if any damage, right?

Other than this, I think we can wrap this up.

[ielis]

SPDI allele is now turned into a VRS Expression using the VariationDescriptorBuilder.spdi() method.