Reverting removing bucketing logic

hms-dbmi · Jan 9, 2024 · a63e6dd · a63e6dd
1 parent bf5e6f5
commit a63e6dd
Showing 1 changed file with 1 addition and 17 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
@@ -62,7 +62,7 @@ public BigInteger getPatientIdsForIntersectionOfVariantSets(Set<Integer> patient
 
             int patientsInScopeSize = patientsInScope.size();
             BigInteger patientsInScopeMask = createMaskForPatientSet(patientsInScope);
-/*            for(int x = 0;
+            for(int x = 0;
                 x < variantBucketPartitions.size() && matchingPatients[0].bitCount() < patientsInScopeSize + 4;
                 x++) {
                 List<List<String>> variantBuckets = variantBucketPartitions.get(x);
@@ -80,22 +80,6 @@ public BigInteger getPatientIdsForIntersectionOfVariantSets(Set<Integer> patient
                         });
                     });
                 });
-            }*/
-
-            for (String variantSpec : variantsInScope) {
-                Optional<VariantMasks> masksForVariant = variantService.getMasks(variantSpec, new VariantBucketHolder<>());
-                if (masksForVariant.isEmpty()) {
-                    log.info(variantSpec + " not found");
-                }
-                masksForVariant.ifPresent(masks -> {
-                    BigInteger heteroMask = masks.heterozygousMask == null ? variantService.emptyBitmask() : masks.heterozygousMask;
-                    BigInteger homoMask = masks.homozygousMask == null ? variantService.emptyBitmask() : masks.homozygousMask;
-                    BigInteger orMasks = heteroMask.or(homoMask);
-                    BigInteger andMasks = orMasks.and(patientsInScopeMask);
-                    synchronized(matchingPatients) {
-                        matchingPatients[0] = matchingPatients[0].or(andMasks);
-                    }
-                });
             }
             return matchingPatients[0];
         }else {