Issue 18: Implement genotype IDs to support variants with multiple alleles

[apriltuesday]

Closes #18
Better expected output diff here

Note that in this implementation, ref/ref genotypes have no consequence or gene annotated; these will be annotated in other genotypes associated with the same variant though. For example:

RSID	Genotype ID	Gene	Consequence	Annotation text
rs3766246	21_36070377_G_A,A	ENSG00000159228	SO_0001583	"AA genotype has increased risk..."
rs3766246	21_36070377_G_A,A	ENSG00000185917	SO_0001627	"AA genotype has increased risk..."
rs3766246	21_36070377_G_A,G	ENSG00000159228	SO_0001583	"AG genotype has increased risk..."
rs3766246	21_36070377_G_A,G	ENSG00000185917	SO_0001627	"AG genotype has increased risk..."
rs3766246	21_36070377_G_G,G	.	.	"GG genotype has decreased risk..."

We might need a follow-up issue to modify this behaviour.

I've also added counts for multi-allelic variants as requested by OT, will post the numbers once I run the entire dataset but here's what the report looks like for the test set:

Total clinical annotations: 10
	With RS: 9 (90.00%)
		1. Exploded by allele: 30 (3.3x)
		2. Exploded by drug: 66 (2.2x)
		3. Exploded by phenotype: 78 (1.2x)
Total evidence strings: 80
	With CHEBI: 62 (77.50%)
	With EFO phenotype: 30 (37.50%)
	With functional consequence: 39 (48.75%)
	With VEP gene: 39 (48.75%)
Gene comparisons per annotation
	With PGKB genes: 8 (80.00%)
	With VEP genes: 6 (60.00%)
	PGKB genes != VEP genes: 8 (80.00%)
Total RS: 9
	With parsed alleles: 7 (77.78%)
		With >2 alleles: 1 (14.29%)

[tcezard]

Looks good.

[M-casado]

Note that in this implementation, ref/ref genotypes have no consequence or gene annotated

Couldn't we use the reference_genome term from SO. I assume getting the context gene would be fairly easy as well.

[apriltuesday]

Couldn't we use the reference_genome term from SO. I assume getting the context gene would be fairly easy as well.

I was going to ask OT what they prefer but yes, we could get the gene & return a SO term (another possibility is no_sequence_alteration)

[M-casado]

LGTM, just a few small comments