Fix NPE in logging

hms-dbmi · Mar 22, 2024 · da5a4b1 · da5a4b1
1 parent 60b16ba
commit da5a4b1
Showing 1 changed file with 2 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
@@ -283,7 +283,8 @@ public FileBackedJsonIndexStorage<Integer, ConcurrentHashMap<String, VariableVar
             ConcurrentHashMap<String, VariableVariantMasks> maskMap = merged.get(key);
             maskMap.keySet().stream().sorted().limit(5).forEach(variantSpec -> {
                 VariableVariantMasks variableVariantMasks = maskMap.get(variantSpec);
-                Set<Integer> patientsWithVariant = VariableVariantMasks.patientMaskToPatientIdSet(variableVariantMasks.heterozygousMask.union(variableVariantMasks.homozygousMask), Arrays.asList(mergedVariantStore.getPatientIds()));
+                VariantMask union = Optional.ofNullable(variableVariantMasks.heterozygousMask).orElse(VariantMask.emptyInstance()).union(Optional.ofNullable(variableVariantMasks.homozygousMask).orElse(VariantMask.emptyInstance()));
+                Set<Integer> patientsWithVariant = VariableVariantMasks.patientMaskToPatientIdSet(union, Arrays.asList(mergedVariantStore.getPatientIds()));
                 log.info("Patients with variant [" + variantSpec + "]: " + Joiner.on(",").join(patientsWithVariant));
             });