Fixing bug when annotating MELT with missing AD (#95).

Closes: #95
Related-Issue: #95
Projected-Results-Impact: none

CHANGES.md

@@ -1,5 +1,9 @@
 # Changelog
 
+## v0.32 (work in progress)
+
+- Fixing bug when annotating MELT with missing AD (#95).
+
 ## v0.31
 
 - Interpret `FORMAT/SQ` as Float (#93).

pom.xml

@@ -4,7 +4,7 @@
 	<groupId>com.github.bihealth</groupId>
 	<artifactId>VarfishAnnotator</artifactId>
 	<packaging>pom</packaging>
-	<version>0.31</version>
+	<version>0.32-SNAPSHOT</version>
 
 	<name>${project.groupId}:${project.artifactId}</name>
 	<description>Variant annotation for Varfish</description>

varfish-annotator-cli/pom.xml

@@ -11,7 +11,7 @@
   <parent>
     <groupId>com.github.bihealth</groupId>
     <artifactId>VarfishAnnotator</artifactId>
-    <version>0.31</version>
+    <version>0.32-SNAPSHOT</version>
   </parent>
 
   <properties>

varfish-annotator-core/pom.xml

@@ -11,7 +11,7 @@
 	<parent>
 		<groupId>com.github.bihealth</groupId>
 		<artifactId>VarfishAnnotator</artifactId>
-		<version>0.31</version>
+		<version>0.32-SNAPSHOT</version>
 	</parent>
 
 	<properties>

varfish-annotator-core/src/main/java/com/github/bihealth/varfish_annotator/annotate_svs/CallerSupportMelt.java

@@ -52,7 +52,8 @@ protected void buildSampleGenotypeImpl(
       SampleGenotypeBuilder builder, VariantContext ctx, int alleleNo, String sample) {
     final Genotype genotype = ctx.getGenotype(sample);
     final int dp = genotype.getDP();
-    final int ad = genotype.getAD().length > 0 ? genotype.getAD()[0] : 0;
+    final int ad =
+        (genotype.getAD() != null && genotype.getAD().length > 0) ? genotype.getAD()[0] : 0;
     builder.setPairedEndCoverage(dp);
     builder.setPairedEndVariantSupport(ad);
     builder.setSplitReadCoverage(0);

varfish-annotator-core/src/main/java/com/github/bihealth/varfish_annotator/annotate_svs/GenotypeRecord.java

@@ -7,6 +7,7 @@
 import com.google.common.collect.ComparisonChain;
 import com.google.common.collect.ImmutableList;
 import com.google.common.collect.ImmutableMap;
+import java.math.BigDecimal;
 import java.util.*;
 import java.util.ArrayList;
 import java.util.Collection;
@@ -292,14 +293,21 @@ private static Map<String, Object> jsonObjectToMap(JSONObject jsonObject) {
     final Map<String, Object> result = new TreeMap<>();
     for (String key : jsonObject.keySet()) {
       final Object value = jsonObject.get(key);
-      if (value instanceof Integer || value instanceof Double || value instanceof String) {
+      if (value instanceof Integer
+          || value instanceof Double
+          || value instanceof Float
+          || value instanceof String) {
         result.put(key, value);
+      } else if (value instanceof BigDecimal) {
+        final BigDecimal bdValue = (BigDecimal) value;
+        result.put(key, bdValue.doubleValue());
       } else if (value instanceof JSONObject) {
         result.put(key, jsonObjectToMap((JSONObject) value));
       } else if (value instanceof JSONArray) {
         result.put(key, ((JSONArray) value).toList());
       } else {
-        throw new RuntimeException("Cannot handle JSON object: " + value);
+        throw new RuntimeException(
+            "Cannot handle JSON object: " + value + " of type " + value.getClass());
       }
     }
     return result;