public void GetMatchingAnnotations_NoOverlap_ReturnNull()
{
var variant = new RepeatExpansion(ChromosomeUtilities.Chr1, 220, 230, null, null, null, 9, 7);
var sa = _matcher.GetMatchingAnnotations(variant);
Assert.Null(sa);
}
public void Annotate_RepeatExpansion_no_refRepeatCount()
{
var variant = new RepeatExpansion(ChromosomeUtilities.Chr3, Start, End + 1, "A", "<STR3>", null, 10, null);
var annotatedPosition = GetAnnotatedPosition(variant);
_provider.Annotate(annotatedPosition);
var firstVariant = annotatedPosition.AnnotatedVariants[0];
Assert.NotNull(firstVariant);
}
public void Annotate_RepeatExpansion_NotExactMatch_NullPhenotypes()
{
var variant = new RepeatExpansion(ChromosomeUtilities.Chr3, Start, End + 1, "A", "<STR3>", null, 10, 5);
var annotatedPosition = GetAnnotatedPosition(variant);
_provider.Annotate(annotatedPosition);
var firstVariant = annotatedPosition.AnnotatedVariants[0];
Assert.Null(firstVariant.RepeatExpansionPhenotypes);
}
public void GetMatchingAnnotations_Overlap_ReturnEntry()
{
var variant = new RepeatExpansion(ChromosomeUtilities.Chr1, 100, 200, null, null, null, 9, 7);
var sa = _matcher.GetMatchingAnnotations(variant);
var sb = new StringBuilder();
sa.SerializeJson(sb);
string observedResult = sb.ToString();
Assert.Contains("{\"phenotype\":\"A\"", observedResult);
}
public void Annotate_RepeatExpansion_ExactMatch_OnePhenotype()
{
var variant = new RepeatExpansion(ChromosomeUtilities.Chr3, Start, End, "A", "<STR3>", null, 10, 5);
var annotatedPosition = GetAnnotatedPosition(variant);
_provider.Annotate(annotatedPosition);
var firstVariant = annotatedPosition.AnnotatedVariants[0];
Assert.NotNull(firstVariant.RepeatExpansionPhenotypes);
var sb = StringBuilderCache.Acquire();
var jsonObject = new JsonObject(sb);
jsonObject.AddObjectValue(firstVariant.RepeatExpansionPhenotypes.JsonKey,
firstVariant.RepeatExpansionPhenotypes);
const string expectedJson = "\"repeatExpansionPhenotypes\":[{\"phenotype\":\"Spinocerebellar ataxia 7\",\"omimId\":164500,\"classifications\":[\"Normal\"],\"percentile\":6.33}]";
string observedJson = sb.ToString();
Assert.Equal(expectedJson, observedJson);
}