correct ECNTH calc.

Schaudge · Sep 30, 2024 · 3dcbce1 · 3dcbce1
1 parent fe4e3e9
commit 3dcbce1
Showing 1 changed file with 1 addition and 1 deletion.
diff --git a/...main/java/org/broadinstitute/hellbender/tools/walkers/mutect/SomaticGenotypingEngine.java b/...main/java/org/broadinstitute/hellbender/tools/walkers/mutect/SomaticGenotypingEngine.java
@@ -269,7 +269,7 @@ public CalledHaplotypes callMutations(
         }
         final List<VariantContext> outputCallsWithEventCountAnnotation = outputCalls.stream()
                 .map(vc -> new VariantContextBuilder(vc)
-                        .attribute(GATKVCFConstants.EVENT_COUNT_IN_HAPLOTYPE_KEY, eventCountAnnotations.containsKey(vc) ? eventCountAnnotations.get(vc): 0)
+                        .attribute(GATKVCFConstants.EVENT_COUNT_IN_HAPLOTYPE_KEY, eventCountAnnotations.getOrDefault(vc, Collections.singletonList(0)))
                         .attribute(GATKVCFConstants.EVENT_COUNT_IN_REGION_KEY, potentialSomaticEventsInRegion.size()).make())
                 .collect(Collectors.toList());
         return new CalledHaplotypes(outputCallsWithEventCountAnnotation, calledHaplotypes);