public void NextToGene() { var annotatedVariant = DataUtilities.GetVariant(Resources.CacheGRCh37("ENST00000546909_chr14_Ensembl84"), "14 19443847 14_19462000 G <CNV> . PASS SVTYPE=CNV;END=19462000;CN=0;CNscore=13.41;LOH=0;ensembl_gene_id=ENSG00000257990,ENSG00000257558"); Assert.NotNull(annotatedVariant); AssertUtilities.CheckJsonDoesNotContain("\"overlappingGenes\":[\"RP11-536C10.15\"]", annotatedVariant); AssertUtilities.CheckJsonDoesNotContain("ENST00000546909", annotatedVariant); }
public void InsertionReciprocalOverlap() { var annotatedVariant = DataUtilities.GetVariant(DataUtilities.EmptyCachePrefix, Resources.MiniSuppAnnot("chr1_756265_756269.nsa"), "1 756267 . T <INS> . PASS SVTYPE=INS;END=756267"); Assert.NotNull(annotatedVariant); AssertUtilities.CheckJsonDoesNotContain("\"reciprocalOverlap\":NaN", annotatedVariant); AssertUtilities.CheckJsonContains("esv1032937", annotatedVariant); AssertUtilities.CheckJsonDoesNotContain("\"reciprocalOverlap\"", annotatedVariant); }
public void LossOfHeterozygosityTest() { var annotatedVariant = DataUtilities.GetVariant(DataUtilities.EmptyCachePrefix, null, "1 11131485 Canvas:REF:1:11131486:16833263 N <CNV> 61 PASS SVTYPE=LOH;END=16833263 RC:BC:CN:MCC . 84:9227:2:2"); Assert.NotNull(annotatedVariant); AssertUtilities.CheckJsonDoesNotContain("\"variantType\":\"loss_of_heterozygosity\"", annotatedVariant); AssertUtilities.CheckJsonContains("\"variantType\":\"copy_number_variation\"", annotatedVariant); AssertUtilities.CheckJsonDoesNotContain("\"altAllele\":\"LOH\"", annotatedVariant); AssertUtilities.CheckSampleCount(2, annotatedVariant); var sample = JsonUtilities.GetSampleJson(annotatedVariant, 1); Assert.Contains("lossOfHeterozygosity", sample); }