Fix results when enabling --no_stats

[nuno-agostinho]

ENSVAR-4494: related with #1034

When running --no_stats, consequences for --hgvs can be wrongly calculated. This PR adds missing logic required when running --no_stats to return the expected results.

However, this adds extra steps that can make VEP slower with -no_stats -- we need to benchmark how slow adding this can be for a large amount of variants.

Testing

Running with or without --no_stats --hgvs should return the same results when using the following input VCF:

#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT
chr3	42210085	.	C	CGGAGGA,CGGA	359	PASS	.
chr14	24300643	.	A	AGAGGAG,AGAG	694	PASS	.

[serge2016]

Hello! Hope to see update here very much!