Fix nullpointer in getTypedListValue

molgenis · Aug 23, 2024 · 8a548c7 · 8a548c7
1 parent 1f348b1
commit 8a548c7
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Showing 2 changed files with 62 additions and 11 deletions.
diff --git a/src/main/java/org/molgenis/vcf/decisiontree/utils/VcfUtils.java b/src/main/java/org/molgenis/vcf/decisiontree/utils/VcfUtils.java
@@ -262,7 +262,8 @@ public static Object getTypedVcfValue(Field field, String stringValue) {
 
 
   public static Object getTypedVcfListValue(Field field, String stringValue) {
-    String[] stringValues = stringValue.split(field.getSeparator().toString());
+    String separator = field.getSeparator() != null ? field.getSeparator().toString() : ",";
+    String[] stringValues = stringValue.split(separator);
     List<Object> values = new ArrayList<>();
     for (String value : stringValues) {
       values.add(getTypedVcfValue(field, value));

diff --git a/src/test/resources/field_metadata.json b/src/test/resources/field_metadata.json
@@ -17,9 +17,17 @@
         "MT"
       ]
     },
-    "ALR": {
-      "label": "Allelic length ranges",
-      "description": "Straglr: Allelic length ranges",
+    "ACR": {
+      "label": "Allelic copy ranges",
+      "description": "Straglr: Allelic copy ranges",
+      "numberType": "PER_GENOTYPE",
+      "numberCount": 2,
+      "separator": "-",
+      "type": "FLOAT"
+    },
+    "AC": {
+      "label": "Allelic copies",
+      "description": "Straglr: Allelic copies",
       "numberType": "PER_GENOTYPE",
       "numberCount": 2,
       "separator": "-",
@@ -159,6 +167,48 @@
           "separator": "&",
           "type": "STRING"
         },
+        "FATHMM_MKL_NC": {
+          "label": "FATHMM-MKL-NC",
+          "description": "Predict the Functional Consequences of Non-Coding Single Nucleotide Variants (SNVs)",
+          "numberType": "NUMBER",
+          "numberCount": 1,
+          "type": "FLOAT"
+        },
+        "GDB_PRO": {
+          "label": "GDB_PRO",
+          "description": "Highest GREEN-DB constraint score for overlapping promotor regions.",
+          "numberType": "NUMBER",
+          "numberCount": 1,
+          "type": "FLOAT"
+        },
+        "GDB_ENH": {
+          "label": "GDB_ENH",
+          "description": "Highest GREEN-DB constraint score for overlapping enhancer regions.",
+          "numberType": "NUMBER",
+          "numberCount": 1,
+          "type": "FLOAT"
+        },
+        "GDB_BIV": {
+          "label": "GDB_BIV",
+          "description": "Highest GREEN-DB constraint score for overlapping bivalent regions.",
+          "numberType": "NUMBER",
+          "numberCount": 1,
+          "type": "FLOAT"
+        },
+        "GDB_SIL": {
+          "label": "GDB_SIL",
+          "description": "Highest GREEN-DB constraint score for overlapping silencer regions.",
+          "numberType": "NUMBER",
+          "numberCount": 1,
+          "type": "FLOAT"
+        },
+        "GDB_INS": {
+          "label": "GDB_INS",
+          "description": "Highest GREEN-DB constraint score for overlapping insulater regions.",
+          "numberType": "NUMBER",
+          "numberCount": 1,
+          "type": "FLOAT"
+        },
         "Feature_type": {
           "label": "Feature Type.",
           "description": "The VEP feature type",
@@ -349,6 +399,13 @@
           "separator": "&",
           "type": "INTEGER"
         },
+        "ReMM": {
+          "label": "ReMM",
+          "description": "The Regulatory Mendelian Mutation (ReMM) score was created for relevance prediction of non-coding variations (SNVs and small InDels) in the human genome (hg19) in terms of Mendelian diseases.",
+          "numberType": "NUMBER",
+          "numberCount": 1,
+          "type": "FLOAT"
+        },
         "SIFT": {
           "label": "SIFT",
           "description": "SIFT score.",
@@ -413,13 +470,6 @@
           "type": "STRING",
           "required": true
         },
-        "VIPL": {
-          "label": "VIP labels",
-          "description": "VIP decision tree labels",
-          "numberType": "NUMBER",
-          "numberCount": 1,
-          "type": "STRING"
-        },
         "VIPP": {
           "label": "VIP path",
           "description": "VIP decision tree path",