Add hook to force VCF sorting after merge in special cases

BimberLab · Feb 8, 2024 · ecde77a · ecde77a
1 parent a397296
commit ecde77a
Showing 1 changed file with 5 additions and 0 deletions.
diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/VariantProcessingJob.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/VariantProcessingJob.java
@@ -124,6 +124,11 @@ public boolean scatterMethodRequiresSort()
             return false;
         }
 
+        if (getParameterJson().optBoolean("scatterGather.forceVcfSort", false))
+        {
+            return true;
+        }
+
         return !doAllowSplitContigs();
     }