Downstream changes for get_end fix in VCF parser #1773
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Depends on Ensembl/ensembl-io#171
Skipping variant:
We were skipping SV deletion type variant if
start >= end
. The casestart = 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 -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 gettingend=start+ref length-1
. END position are not exactly clear for BND but the former ones seems more clear.