Пример #1
0
        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);
        }
Пример #2
0
        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);
        }
Пример #3
0
        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);
        }