private static string GetPositionAnnotation(IPosition position, IAnnotationResources resources, string[] sampleNames, bool preloadRequired)
{
if (preloadRequired)
{
resources.SingleVariantPreLoad(position);
}
IAnnotatedPosition annotatedPosition = resources.Annotator.Annotate(position);
string json = annotatedPosition?.GetJsonString();
if (json == null)
{
throw new UserErrorException("No variant is provided for annotation");
}
var outputJsonStream = new MemoryStream();
using (var jsonWriter = new JsonWriter(outputJsonStream, null, resources, Date.CurrentTimeStamp, sampleNames, true))
{
WriteAnnotatedPosition(annotatedPosition, jsonWriter, json);
jsonWriter.WriteGenes(resources.Annotator.GetGeneAnnotations());
}
outputJsonStream.Position = 0;
return(Encoding.UTF8.GetString(outputJsonStream.ToArray()));
}
private static void CheckGenomeAssembly(IAnnotationResources annotationResources, VcfReader vcfReader)
{
if (vcfReader.InferredGenomeAssembly != GenomeAssembly.Unknown && vcfReader.InferredGenomeAssembly != annotationResources.Annotator.Assembly)
{
throw new UserErrorException($"A mismatch between genome assemblies was found. The input VCF uses {vcfReader.InferredGenomeAssembly} whereas annotation was configured for {annotationResources.Annotator.Assembly}.");
}
}
private static void SetMitochondrialAnnotationBehavior(IAnnotationResources annotationResources, IVcfReader vcfReader)
{
if (vcfReader.IsRcrsMitochondrion && annotationResources.Annotator.Assembly == GenomeAssembly.GRCh37 ||
annotationResources.Annotator.Assembly == GenomeAssembly.GRCh38 ||
annotationResources.ForceMitochondrialAnnotation)
{
annotationResources.Annotator.EnableMitochondrialAnnotation();
}
}
private static VcfReader GetVcfReader(Stream headerStream, Stream vcfStream, IAnnotationResources annotationResources,
IVcfFilter vcfFilter, IMitoHeteroplasmyProvider mitoHeteroplasmyProvider)
{
var vcfReader = FileUtilities.GetStreamReader(vcfStream);
StreamReader headerReader;
if (headerStream == null)
{
headerReader = vcfReader;
}
else
{
headerReader = FileUtilities.GetStreamReader(headerStream);
vcfStream.Position = Tabix.VirtualPosition.From(annotationResources.InputStartVirtualPosition).BlockOffset;
}
return(VcfReader.Create(headerReader, vcfReader, annotationResources.SequenceProvider,
annotationResources.RefMinorProvider, annotationResources.Recomposer, vcfFilter, annotationResources.VidCreator, mitoHeteroplasmyProvider));
}
public JsonWriter(Stream jsonStream, Stream indexStream, IAnnotationResources annotationResources, string creationTime, string[] sampleNames, bool leaveOpen) : this(jsonStream, indexStream, annotationResources.AnnotatorVersionTag, creationTime, annotationResources.VepDataVersion, annotationResources.DataSourceVersions, annotationResources.SequenceProvider.Assembly.ToString(), sampleNames, leaveOpen)
{
}
