Fix NPE in logging

hms-dbmi · Mar 22, 2024 · 1f16776 · 1f16776
1 parent da5a4b1
commit 1f16776
Show file tree

Hide file tree

Showing 2 changed files with 4 additions and 1 deletion.
diff --git a/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/etl/genotype/GenomicDatasetMerger.java b/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/etl/genotype/GenomicDatasetMerger.java
@@ -60,9 +60,11 @@ private void validate() {
 
     public VariantStore mergeVariantStore(Map<String, FileBackedJsonIndexStorage<Integer, ConcurrentHashMap<String, VariableVariantMasks>>> mergedChromosomeMasks) {
         mergedVariantStore.setVariantMaskStorage(mergedChromosomeMasks);
-        mergedVariantStore.setPatientIds(mergePatientIds());
         return mergedVariantStore;
     }
+    public void mergePatients() {
+        mergedVariantStore.setPatientIds(mergePatientIds());
+    }
 
     /**
      * Since both sets of variant indexes reference a different variant spec list, we need to re-index

diff --git a/...main/java/edu/harvard/hms/dbmi/avillach/hpds/etl/genotype/GenomicDatasetMergerRunner.java b/...main/java/edu/harvard/hms/dbmi/avillach/hpds/etl/genotype/GenomicDatasetMergerRunner.java
@@ -46,6 +46,7 @@ public static void main(String[] args) throws IOException, ClassNotFoundExceptio
         Map<String, FileBackedByteIndexedInfoStore> infoStores2 = loadInfoStores(genomicDirectory2);
 
         GenomicDatasetMerger genomicDatasetMerger = new GenomicDatasetMerger(VariantStore.readInstance(genomicDirectory1),VariantStore.readInstance(genomicDirectory2), infoStores1, infoStores2, outputDirectory);
+        genomicDatasetMerger.mergePatients();
 
         Map<String, FileBackedJsonIndexStorage<Integer, ConcurrentHashMap<String, VariableVariantMasks>>> mergedChromosomeMasks = genomicDatasetMerger.mergeChromosomeMasks();
         VariantStore mergedVariantStore = genomicDatasetMerger.mergeVariantStore(mergedChromosomeMasks);