ALS-6330: Implement createMaskForPatientSet for patient merging genom…

…ic processor
hms-dbmi · Jun 11, 2024 · 9d17741 · 9d17741
1 parent dd89834
commit 9d17741
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Showing 2 changed files with 6 additions and 2 deletions.
diff --git a/...c/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/GenomicProcessorParentImpl.java b/...c/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/GenomicProcessorParentImpl.java
@@ -64,7 +64,7 @@ public VariantMask createMaskForPatientSet(Set<Integer> patientSubset) {
         VariantMask result = nodes.parallelStream()
                 .map(node -> node.createMaskForPatientSet(patientSubset))
                 .reduce(VariantMask::union)
-                .orElse(VariantMask.emptyInstance());
+                .orElseGet(VariantMask::emptyInstance);
         return result;
     }
 

diff --git a/...u/harvard/hms/dbmi/avillach/hpds/processing/GenomicProcessorPatientMergingParentImpl.java b/...u/harvard/hms/dbmi/avillach/hpds/processing/GenomicProcessorPatientMergingParentImpl.java
@@ -90,7 +90,11 @@ public Set<Integer> patientMaskToPatientIdSet(VariantMask patientMask) {
 
     @Override
     public VariantMask createMaskForPatientSet(Set<Integer> patientSubset) {
-        throw new RuntimeException("Not implemented");
+        return nodes.stream()
+                .map(node -> new SizedVariantMask(node.createMaskForPatientSet(patientSubset), node.getPatientIds().size()))
+                .reduce(this::appendMask)
+                .map(SizedVariantMask::getVariantMask)
+                .orElseGet(VariantMask::emptyInstance);
     }
 
     @Override