diff --git a/cellbase-lib/src/test/java/org/opencb/cellbase/lib/impl/VariantAnnotationCalculatorTest.java b/cellbase-lib/src/test/java/org/opencb/cellbase/lib/impl/VariantAnnotationCalculatorTest.java index ab506fd43b..ea649a3fca 100644 --- a/cellbase-lib/src/test/java/org/opencb/cellbase/lib/impl/VariantAnnotationCalculatorTest.java +++ b/cellbase-lib/src/test/java/org/opencb/cellbase/lib/impl/VariantAnnotationCalculatorTest.java @@ -1965,6 +1965,27 @@ private void initGrch38() throws Exception { variantAnnotationCalculator = new VariantAnnotationCalculator("hsapiens", "GRCh37", dbAdaptorFactory); } + @Test + public void testMissingClinVar() throws Exception { + + Variant variant1 = new Variant("19:11216263:A:AGATTGTAAAGATAAGAGCGAT"); + //Variant variant1 = new Variant("19:11216245:C:CCGACTGCAAGGACAAATCTGA"); + + QueryOptions queryOptions = new QueryOptions("useCache", false); + queryOptions.put("include", "hgvs"); + queryOptions.put("normalize", true); + queryOptions.put("skipDecompose", false); + queryOptions.put("checkAminoAcidChange", true); + queryOptions.put("imprecise", true); + queryOptions.put("phased", false); + + QueryResult queryResult = variantAnnotationCalculator.getAnnotationByVariant(variant1, queryOptions); + + List hgvs = queryResult.getResult().get(0).getHgvs(); + assertEquals(14, hgvs.size()); + + } + @Test public void testClinicalVariantsGrch38() throws Exception {