From d6fba66240112d86a48f27e8af76d5cd28a79aca Mon Sep 17 00:00:00 2001
From: Awab Ahmed <awab.ahmed@genomicsengland.co.uk>
Date: Wed, 20 Sep 2023 13:12:25 +0100
Subject: [PATCH] fix spanning deletion annotation

---
 .../VariantAnnotationCalculator.java          |  9 ++++++--
 .../annotation/VariantAnnotationUtils.java    |  3 +++
 .../impl/VariantAnnotationCalculatorTest.java | 21 +++++++++++++++++++
 pom.xml                                       |  2 +-
 4 files changed, 32 insertions(+), 3 deletions(-)

diff --git a/cellbase-core/src/main/java/org/opencb/cellbase/core/variant/annotation/VariantAnnotationCalculator.java b/cellbase-core/src/main/java/org/opencb/cellbase/core/variant/annotation/VariantAnnotationCalculator.java
index a0df55d77..356b11a90 100644
--- a/cellbase-core/src/main/java/org/opencb/cellbase/core/variant/annotation/VariantAnnotationCalculator.java
+++ b/cellbase-core/src/main/java/org/opencb/cellbase/core/variant/annotation/VariantAnnotationCalculator.java
@@ -1078,7 +1078,12 @@ 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:
@@ -1104,7 +1109,7 @@ 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/cellbase-core/src/main/java/org/opencb/cellbase/core/variant/annotation/VariantAnnotationUtils.java b/cellbase-core/src/main/java/org/opencb/cellbase/core/variant/annotation/VariantAnnotationUtils.java
index 7be2151fd..383d122ba 100644
--- a/cellbase-core/src/main/java/org/opencb/cellbase/core/variant/annotation/VariantAnnotationUtils.java
+++ b/cellbase-core/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
index d434dce98..c712d4c4e 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
@@ -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.*;
@@ -2437,6 +2438,26 @@ 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
index 85adc8ada..77a905767 100644
--- a/pom.xml
+++ b/pom.xml
@@ -25,7 +25,7 @@
         <cellbase.version>4.12.5</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>