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());
}
