Fix end position for SV insertion types

[nakib103]

#1432

Currently for SV insertions, the end is calculated like so -

$end = $start + SVLEN - 1
or, 
$end = $END // from INFO field

But it is probably more appropriate to say -

$end = $start -1

Because that is the anchoring bases in reference sequence the sequence is inserted. The current implementation adding the SVLEN/END implied a wider length of reference sequence getting affected which is actually not the case.

PS: it will change the consequence, for example the test variant - 1 146985757 . G <INS> . . SVTYPE=INS;SVLEN=17243
previously,

#Uploaded_variation	Location	Allele	Gene	Feature	Feature_type	Consequence	cDNA_position	CDS_position	Protein_position	Amino_acids	Codons	Existing_variation	Extra
1_146985758_<INS>	1:146985758-147003000	insertion	ENSG00000234225	ENST00000425109	Transcript	non_coding_transcript_exon_variant,intron_variant	230-?	-	-	-	-	-	IMPACT=MODIFIER;STRAND=-1;OverlapBP=1070;OverlapPC=63.39
1_146985758_<INS>	1:146985758-147003000	insertion	ENSG00000234225	ENST00000455718	Transcript	non_coding_transcript_exon_variant,intron_variant	185-?	-	-	-	-	-	IMPACT=MODIFIER;STRAND=-1;OverlapBP=719;OverlapPC=79.62
1_146985758_<INS>	1:146985758-147003000	insertion	ENSG00000268043	ENST00000617931	Transcript	coding_sequence_variant,3_prime_UTR_variant,intron_variant	-	-	-	-	-	-	IMPACT=MODIFIER;STRAND=1;OverlapBP=10445;OverlapPC=18.18
1_146985758_<INS>	1:146985758-147003000	insertion	ENSG00000268043	ENST00000698835	Transcript	coding_sequence_variant,3_prime_UTR_variant,intron_variant	-	-	-	-	-	-	IMPACT=MODIFIER;STRAND=1;OverlapBP=10441;OverlapPC=18.04
1_146985758_<INS>	1:146985758-147003000	insertion	ENSG00000268043	ENST00000698937	Transcript	coding_sequence_variant,3_prime_UTR_variant,intron_variant	-	-	-	-	-	-	IMPACT=MODIFIER;STRAND=1;OverlapBP=10441;OverlapPC=18.13

With this fix -

#Uploaded_variation	Location	Allele	Gene	Feature	Feature_type	Consequence	cDNA_position	CDS_position	Protein_position	Amino_acids	Codons	Existing_variation	Extra
1_146985758_insertion	1:146985757-146985758	insertion	ENSG00000268043	ENST00000617931	Transcript	intergenic_variant	-	-	-	-	-	-	IMPACT=MODIFIER;STRAND=1
1_146985758_insertion	1:146985757-146985758	insertion	ENSG00000268043	ENST00000698835	Transcript	intergenic_variant	-	-	-	-	-	-	IMPACT=MODIFIER;STRAND=1
1_146985758_insertion	1:146985757-146985758	insertion	ENSG00000268043	ENST00000698937	Transcript	intergenic_variant	-	-	-	-	-	-	IMPACT=MODIFIER;STRAND=1