When we use FILTER field from a VCF file in --custom argument, the delimiter for FILTER, which is ;, is replaced by , (see). The reason is ; have specific meaning in certain file type - for example, in VCF where this FILTER is going to put under INFO,; is used as delimiter to split up different fields in it.
But we also replace any , with & if found within any specific value under CSQ INFO field (see). That is because in CSQ field , is used as delimiter to separate different records.
And thus a ; can become a & in VCF CSQ field. Which causes the confusion mentioned in the issue above.
To avoid error replace ; with %3B which we are already doing for VCF file (see).
Cons:
Other output format (tab, vep text) will now have %3B instead of , as delimiter.
To avoid that, according to @nuno-agostinho's suggestion utilized convert_arrayref function to keep the ; and let the OutputFactory method handle the delimiter substitution. Default VEP format needed to replace ; by %3B too.
ENSVAR-6276 https://github.com/Ensembl/ensembl-vep/issues/1646
When we use
FILTERfield from a VCF file in--customargument, the delimiter for FILTER, which is;, is replaced by,(see). The reason is;have specific meaning in certain file type - for example, in VCF where thisFILTERis going to put underINFO,;is used as delimiter to split up different fields in it.But we also replace any
,with&if found within any specific value underCSQINFO field (see). That is because inCSQfield,is used as delimiter to separate different records.And thus a
;can become a&in VCF CSQ field. Which causes the confusion mentioned in the issue above.To avoid error replace
;with%3Bwhich we are already doing for VCF file (see).Cons: Other output format (tab, vep text) will now have
%3Binstead of,as delimiter. To avoid that, according to @nuno-agostinho's suggestion utilized convert_arrayref function to keep the;and let the OutputFactory method handle the delimiter substitution. Default VEP format needed to replace;by%3Btoo.