public void SplitReadInSample()
{
var annotatedVariant = DataUtilities.GetVariant(DataUtilities.EmptyCachePrefix, null,
"chr7 127717248 MantaINV:267944:0:1:2:0:0 T <INV> . PASS END=140789466;SVTYPE=INV;SVLEN=13072218;INV5 PR:SR 78,0:65,0 157,42:252,63");
Assert.NotNull(annotatedVariant);
var sample1 = JsonUtilities.GetSampleJson(annotatedVariant, 0);
Assert.Equal("{\"splitReadCounts\":[65,0],\"pairedEndReadCounts\":[78,0]}", sample1);
var sample2 = JsonUtilities.GetSampleJson(annotatedVariant, 1);
Assert.Equal("{\"splitReadCounts\":[252,63],\"pairedEndReadCounts\":[157,42]}", sample2);
}
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);
}
