public static ExitCodes Annotate(Stream headerStream, Stream inputVcfStream, Stream outputJsonStream, Stream outputJsonIndexStream, AnnotationResources annotationResources, IVcfFilter vcfFilter, bool ignoreEmptyChromosome = false) { var logger = outputJsonStream is BlockGZipStream ? new ConsoleLogger() : (ILogger) new NullLogger(); var metrics = new PerformanceMetrics(logger); using (annotationResources) using (var vcfReader = GetVcfReader(headerStream, inputVcfStream, annotationResources, vcfFilter)) using (var jsonWriter = new JsonWriter(outputJsonStream, outputJsonIndexStream, annotationResources, Date.CurrentTimeStamp, vcfReader.GetSampleNames(), false)) { try { CheckGenomeAssembly(annotationResources, vcfReader); SetMitochondrialAnnotationBehavior(annotationResources, vcfReader); int previousChromIndex = -1; IPosition position; while ((position = vcfReader.GetNextPosition()) != null) { if (ignoreEmptyChromosome && position.Chromosome.IsEmpty()) { continue; } if (previousChromIndex != position.Chromosome.Index) { annotationResources.PreLoad(position.Chromosome); } previousChromIndex = UpdatePerformanceMetrics(previousChromIndex, position.Chromosome, metrics); var annotatedPosition = position.Variants != null?annotationResources.Annotator.Annotate(position) : null; string json = annotatedPosition?.GetJsonString(); if (json != null) { jsonWriter.WriteJsonEntry(annotatedPosition.Position, json); } metrics.Increment(); } jsonWriter.WriteAnnotatedGenes(annotationResources.Annotator.GetGeneAnnotations()); } catch (Exception e) { e.Data[ExitCodeUtilities.VcfLine] = vcfReader.VcfLine; throw; } } metrics.ShowAnnotationTime(); return(ExitCodes.Success); }
public static ExitCodes Annotate(Stream headerStream, Stream inputVcfStream, Stream outputJsonStream, Stream outputJsonIndexStream, AnnotationResources annotationResources, IVcfFilter vcfFilter, bool ignoreEmptyChromosome) { var metrics = annotationResources.Metrics; PerformanceMetrics.ShowAnnotationHeader(); IChromosome currentChromosome = new EmptyChromosome("dummy"); int numVariants = 0; IMitoHeteroplasmyProvider mitoHeteroplasmyProvider = MitoHeteroplasmyReader.GetProvider(); using (var vcfReader = GetVcfReader(headerStream, inputVcfStream, annotationResources, vcfFilter, mitoHeteroplasmyProvider)) using (var jsonWriter = new JsonWriter(outputJsonStream, outputJsonIndexStream, annotationResources, Date.CurrentTimeStamp, vcfReader.GetSampleNames(), false)) { try { CheckGenomeAssembly(annotationResources, vcfReader); SetMitochondrialAnnotationBehavior(annotationResources, vcfReader); IPosition position; while ((position = vcfReader.GetNextPosition()) != null) { IChromosome chromosome = position.Chromosome; if (ignoreEmptyChromosome && chromosome.IsEmpty()) { continue; } if (chromosome.Index != currentChromosome.Index) { if (!currentChromosome.IsEmpty()) { metrics.ShowAnnotationEntry(currentChromosome, numVariants); } numVariants = 0; metrics.Preload.Start(); annotationResources.PreLoad(chromosome); metrics.Preload.Stop(); metrics.Annotation.Start(); currentChromosome = chromosome; } var annotatedPosition = position.Variants != null?annotationResources.Annotator.Annotate(position) : null; string json = annotatedPosition?.GetJsonString(); if (json != null) { jsonWriter.WritePosition(annotatedPosition.Position, json); } numVariants++; } jsonWriter.WriteGenes(annotationResources.Annotator.GetGeneAnnotations()); } catch (Exception e) { e.Data[ExitCodeUtilities.VcfLine] = vcfReader.VcfLine; throw; } } if (!currentChromosome.IsEmpty()) { metrics.ShowAnnotationEntry(currentChromosome, numVariants); } metrics.ShowSummaryTable(); return(ExitCodes.Success); }