Fix Uploaded_variation

[ainefairbrother]

This PR aims to fix #1930.

Previously, Uploaded_variation was displaying a minimised start position instead of the original input.

Example input:

##fileformat=VCFv4.2
##source=test
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
chr2	47806652	.	G	GTAAC	.	PASS	.
chr2	47806652	.	GTAAC	G	.	PASS	.
chr2	47806652	.	G	A	.	PASS	.
chr2	47806652	.	GT	G	.	PASS	.
chr2	47806652	.	G	GTAAC,A	.	PASS	.

VEP command:

./vep \
-i in.vcf \
-o out.tsv \
--offline \
--dir_cache tabixconverted \
--cache_version 115 \
--format vcf \
--cache \
--fasta Homo_sapiens.GRCh38.dna.toplevel.fa.gz \
--refseq \
--pick \
--hgvs \
--symbol \
--canonical \
--tab \
--assembly GRCh38 \
--force_overwrite \
--no_escape \
--show_ref_allele \
--uploaded_allele

Output before fix:

#Uploaded_variation
chr2_47806653_G/GTAAC
chr2_47806653_GTAAC/G
chr2_47806652_G/A
chr2_47806653_GT/G
chr2_47806652_G/GTAAC/A

Output after fix:

chr2_47806652_G/GTAAC
chr2_47806652_GTAAC/G
chr2_47806652_G/A
chr2_47806652_GT/G
chr2_47806652_G/GTAAC/A

For multi-allelic inputs, this simply reverts to legacy behaviour, as this output seems acceptable, but also multi-allelic/Uploaded_allele handling is a known bug, and out of scope for this PR.

[likhitha-surapaneni]

Thanks @ainefairbrother ,

Testing examples:
VCF input:
chr3 46358466 . AA AAG . PASS ., UPLOADED_ALLELE=AA/AAG. Should Uploaded_variation be chr3_46358466_AA/AAG or chr3_46358467_A/AG

VEP input:
For 3 46358468 46358467 -/G 1, UPLOADED_ALLELE=-/G. Should Uploaded_variation be 3_46358468_-/G or 3_46358467_A/AG