internal static IAnnotatedVariant GetVariant(string cachePath, ISupplementaryAnnotationReader saReader, string vcfLine, IConservationScoreReader csReader) { var annotationSource = ResourceUtilities.GetAnnotationSource(cachePath, saReader, csReader); return(GetVariant(annotationSource, vcfLine)); }
/// <summary> /// creates a new annotation source with data from the micro-cache file /// </summary> internal static IAnnotationSource GetAnnotationSource(string cachePath, ISupplementaryAnnotationReader saReader, IConservationScoreReader conservationScoreReader = null, ISupplementaryAnnotationProvider customAnnotationProvider = null, ISupplementaryAnnotationProvider customIntervalProvider = null) { var streams = GetAnnotationSourceStreams(cachePath); var renamer = ChromosomeRenamer.GetChromosomeRenamer(GetReadStream($"{cachePath}.bases")); var saProvider = new MockSupplementaryAnnotationProvider(saReader, renamer); PerformanceMetrics.DisableOutput = true; return(new NirvanaAnnotationSource(streams, saProvider, conservationScoreReader, customAnnotationProvider, customIntervalProvider, null)); }