/// <summary> /// returns the desired JSON variant /// </summary> internal static IAnnotatedVariant GetVariant(IAnnotationSource annotationSource, string vcfLine) { var variant = VcfUtilities.GetVcfVariant(vcfLine); UnifiedJson.NeedsVariantComma = false; return(annotationSource?.Annotate(variant)); }
private static void WriteOmim(IAnnotationSource annotator, UnifiedJsonWriter unifiedJsonWriter) { var omimAnnotations = new List <string>(); annotator.AddGeneLevelAnnotation(omimAnnotations); var annotionOutput = UnifiedJson.GetGeneAnnotation(omimAnnotations, "omim"); unifiedJsonWriter.Write(annotionOutput); }
private static UnifiedJsonWriter GetJsonWriter(StreamWriter streamWriter, string jsonCreationTime, IAnnotationSource annotator, LiteVcfReader reader) { return(new UnifiedJsonWriter(streamWriter, jsonCreationTime, annotator.GetDataVersion(), annotator.GetDataSourceVersions(), annotator.GetGenomeAssembly(), reader.SampleNames)); }