public void OverlappingTranscripts() { var annotationSource = ResourceUtilities.GetAnnotationSource(Resources.CacheGRCh37("chr1_89500_911300_Ensembl84_pos"), null) as NirvanaAnnotationSource; annotationSource?.EnableReportAllSvOverlappingTranscripts(); var annotatedVariant = DataUtilities.GetVariant(annotationSource, "chr1\t900000\t.\tG\t<DEL>\t.\tPASS\tEND=911300;SVTYPE=DEL"); Assert.NotNull(annotatedVariant); var overlappingTranscriptIds = JsonUtilities.GetOverlappingTranscriptIds(annotatedVariant.AnnotatedAlternateAlleles.First()); var expectedTranscripts = new List <string> { "ENST00000338591", "ENST00000379410", "ENST00000379409", "ENST00000379407", "ENST00000480267", "ENST00000491024", "ENST00000433179", "ENST00000341290", "ENST00000479361" }; Assert.True(expectedTranscripts.OrderBy(t => t).SequenceEqual(overlappingTranscriptIds.OrderBy(t => t))); Assert.Contains("{\"transcript\":\"ENST00000338591\",\"hgnc\":\"KLHL17\",\"isCanonical\":true,\"partialOverlap\":true}", annotatedVariant.ToString()); Assert.Contains("{\"transcript\":\"ENST00000379409\",\"hgnc\":\"PLEKHN1\"}", annotatedVariant.ToString()); }