Handle null variant masks

hms-dbmi · Mar 16, 2024 · 3cd01c3 · 3cd01c3
1 parent 165d380
commit 3cd01c3
Showing 1 changed file with 11 additions and 5 deletions.
diff --git a/...rc/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/PatientVariantJoinHandler.java b/...rc/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/PatientVariantJoinHandler.java
@@ -81,12 +81,18 @@ public VariantMask getPatientIdsForIntersectionOfVariantSets(Set<Integer> patien
                     variantBucket.forEach(variantSpec -> {
                         Optional<VariableVariantMasks> variantMask = variantService.getMasks(variantSpec, bucketCache);
                         variantMask.ifPresentOrElse(masks -> {
-                            VariantMask heteroMask = masks.heterozygousMask;
-                            VariantMask homoMask = masks.homozygousMask;
-                            VariantMask orMasks = heteroMask.union(homoMask);
+                            VariantMask heterozygousMask = masks.heterozygousMask;
+                            VariantMask homozygousMask = masks.homozygousMask;
                             //log.info("Patients with variant " + variantSpec + ": " + (orMasks.bitCount() - 4));
-                            synchronized(matchingPatients) {
-                                matchingPatients[0] = matchingPatients[0].union(orMasks);
+                            if (heterozygousMask != null) {
+                                synchronized(matchingPatients) {
+                                    matchingPatients[0] = matchingPatients[0].union(heterozygousMask);
+                                }
+                            }
+                            if (homozygousMask != null) {
+                                synchronized(matchingPatients) {
+                                    matchingPatients[0] = matchingPatients[0].union(homozygousMask);
+                                }
                             }
                         }, () -> missingVariants.add(variantSpec));
                     });