public void BasicCustomIntervalOutput()
{
var customIntervalProvider = new MockCustomIntervalProvider(ResourceUtilities.GetReadStream(Resources.CustomIntervals("chr1_IcslIntervals_69090_69091.nci")), _renamer);
var annotationSource = ResourceUtilities.GetAnnotationSource(DataUtilities.EmptyCachePrefix, null, null, customIntervalProvider);
var annotatedVariant = DataUtilities.GetVariant(annotationSource,
"chr1 69092 . T C . LowGQX;HighDPFRatio END=10244;BLOCKAVG_min30p3a GT:GQX:DP:DPF .:.:0:1");
Assert.NotNull(annotatedVariant);
const string expectedJson = "{\"altAllele\":\"C\",\"refAllele\":\"T\",\"begin\":69092,\"chromosome\":\"chr1\",\"end\":69092,\"variantType\":\"SNV\",\"vid\":\"1:69092:C\",\"IcslIntervals\":[{\"Start\":69091,\"End\":70008,\"gene\":\"OR4F5\",\"assesment\":\"Some_evidence_of_constraint\",\"score\":0.0,\"exacScore\":3.60208899915}]}";
var observedJson = JsonUtilities.GetFirstAlleleJson(annotatedVariant);
Assert.Equal(expectedJson, observedJson);
}
public void AddVariantToJsonOutputTests()
{
var customIntervals = new List <ICustomInterval>
{
new VariantAnnotation.DataStructures.CustomInterval("chr1", 118165685, 118165692, "Test", null, null)
};
var customIntervalProvider = new MockCustomIntervalProvider(customIntervals, _renamer);
var annotationSource = ResourceUtilities.GetAnnotationSource(Resources.CacheGRCh37("ENST00000006101_chr17_Ensembl84"), null, null, customIntervalProvider);
var annotatedVariant = DataUtilities.GetVariant(annotationSource,
"chr1 118165691 rs1630312 C T 156.00 PASS . GT:GQ:GQX:DP:DPF:AD 0/1:169:155:27:0:13,14");
var observedResult = annotatedVariant.ToString();
Assert.Contains("Start", observedResult);
Assert.Contains("Test", observedResult);
Assert.DoesNotContain("customIntervals", observedResult);
}
