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);
}
