/// <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));
}
