VCFAnnotator updates to skip REF alleles and emit correct INFO field definitions #299
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…REF allele is included
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Dec 14, 2023
jsstevenson
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Dec 14, 2023
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Implemented changes for #295 and #296.
The VCFAnnotator tool now accepts an additional parameter that controls whether VRS computation is performed for REF alleles in addition to ALT alleles. For large scale VRS computation on VCF input, this will allow users to reduce compute time and costs if REF allele VRS IDs are not required.
The VRS INFO field definitions in the output VCF have also been modified to have the correct value for the
Numberattribute: eitherRorAdepending on whether REF alleles are included. This change also required passing the VRS INFO field values to the VCF output writer as arrays, rather than strings.