Downstream changes for get_end fix in VCF parser

[nakib103]

Depends on Ensembl/ensembl-io#171

Skipping variant:

We were skipping SV deletion type variant if start >= end. The case start = end can be a valid case, for example, when SVLEN=1.
Fixed that check to see if start > end or if there is no SVLEN or END information.

Unit test fix:

AnnotationSource_File_VCF.t

The type is exact and the custom line is as follows -

21	25585735	del2	TG	T	67	SEGDUP;RF

So it deletes the G at 25585736 position. Correct way to represent it in SVLEN is with POS=25585736, REF=T (always use the base before polymorphism happens) and SVELN=1 (the difference between ref and alt sequence).

Parser_VCF.t

The BND are case affected by the ensembl-io change because it does not have any SVLEN and END. The end here we will be now end=start. Before it was getting end=start+ref length-1. END position are not exactly clear for BND but the former ones seems more clear.