Merge pull request #666 from awab-ahmed/fix-spanning-deletion-error-a…

…nd-conseqTypes fix spanning deletion annotation
opencb · Sep 21, 2023 · 85fbba4 · 85fbba4
2 parents c9af263 + a3149be
commit 85fbba4
Show file tree

Hide file tree

Showing 4 changed files with 32 additions and 3 deletions.
diff --git a/...rc/main/java/org/opencb/cellbase/core/variant/annotation/VariantAnnotationCalculator.java b/...rc/main/java/org/opencb/cellbase/core/variant/annotation/VariantAnnotationCalculator.java
@@ -1071,7 +1071,12 @@ private ProteinVariantAnnotation getProteinAnnotation(ConsequenceType consequenc
     }
 
     private ConsequenceTypeCalculator getConsequenceTypeCalculator(Variant variant) throws UnsupportedURLVariantFormat {
-        switch (VariantAnnotationUtils.getVariantType(variant)) {
+        VariantType variantType = VariantAnnotationUtils.getVariantType(variant);
+        if (variantType == null) {
+            logger.error("There is no ConsequenceTypeCalculator for variant %s because it doesn't have a valid type", variant);
+            throw new UnsupportedURLVariantFormat("Invalid variant type");
+        }
+        switch (variantType) {
             case SNV:
                 return new ConsequenceTypeSNVCalculator();
             case INSERTION:
@@ -1097,7 +1102,7 @@ private ConsequenceTypeCalculator getConsequenceTypeCalculator(Variant variant)
             default:
                 logger.error("There is no ConsequenceTypeCalculator for variant %s of type %s",
                         variant,
-                        VariantAnnotationUtils.getVariantType(variant)
+                        variantType
                 );
                 throw new UnsupportedURLVariantFormat();
         }

diff --git a/...ore/src/main/java/org/opencb/cellbase/core/variant/annotation/VariantAnnotationUtils.java b/...ore/src/main/java/org/opencb/cellbase/core/variant/annotation/VariantAnnotationUtils.java
@@ -658,6 +658,9 @@ protected static StringBuilder appendChromosome(String chromosome, StringBuilder
     }
 
     public static VariantType getVariantType(Variant variant) throws UnsupportedURLVariantFormat {
+        if (variant.isSpanningDeletion()) {
+            return null;
+        }
         if (variant.getType() == null) {
             variant.setType(Variant.inferType(variant.getReference(), variant.getAlternate()));
         }

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
@@ -38,6 +38,7 @@
 import java.nio.file.Path;
 import java.nio.file.Paths;
 import java.util.*;
+import java.util.concurrent.ExecutionException;
 import java.util.stream.Collectors;
 
 import static org.junit.Assert.*;
@@ -2537,6 +2538,26 @@ public void testLongMNVConsequenceTypesFailsForAboveThresholdLength() throws Exc
         variantAnnotationCalculator.getAllConsequenceTypesByVariant(aboveThresholdVariant, queryOptions);
     }
 
+    @Test
+    public void testSpanningDeletionAnnotation() throws ExecutionException, InterruptedException {
+        Variant variant = new Variant("10:133754330:GCCC:*");
+        QueryOptions queryOptions = new QueryOptions("useCache", false);
+        queryOptions.put("include", "consequenceType,hgvs");
+        queryOptions.put("normalize", true);
+        queryOptions.put("skipDecompose", false);
+        QueryResult<VariantAnnotation> cellBaseDataResult = variantAnnotationCalculator
+                .getAnnotationByVariant(variant, queryOptions);
+        assertTrue(cellBaseDataResult.getResult().get(0).getConsequenceTypes().isEmpty());
+        assertTrue(cellBaseDataResult.getResult().get(0).getHgvs().isEmpty());
+    }
+
+    @Test(expected = UnsupportedURLVariantFormat.class)
+    public void testSpanningDeletionConsequenceTypeThrowsException() {
+        Variant variant = new Variant("10:133754330:GCCC:*");
+        QueryOptions queryOptions = new QueryOptions("useCache", false);
+        variantAnnotationCalculator.getAllConsequenceTypesByVariant(variant, queryOptions);
+    }
+
     public String getSequenceOntologyTerms(String transcriptID, List<ConsequenceType> consequenceTypeList){
         for (ConsequenceType consequenceType : consequenceTypeList) {
             if (consequenceType.getEnsemblTranscriptId().equals(transcriptID)){

diff --git a/pom.xml b/pom.xml
@@ -25,7 +25,7 @@
         <cellbase.version>4.12.6</cellbase.version>
         <compileSource>1.8</compileSource>
         <java-common-libs.version>3.7.5</java-common-libs.version>
-        <biodata.version>1.5.6</biodata.version>
+        <biodata.version>1.5.7</biodata.version>
         <bionetdb.version>0.1.0</bionetdb.version>
         <jackson.version>2.10.5</jackson.version>
         <protobuf.version>3.1.0</protobuf.version>