Update logic around VCF sorting in VariantProcessingJob

BimberLab · Feb 9, 2024 · 8258db3 · 8258db3
1 parent ecde77a
commit 8258db3
Showing 1 changed file with 5 additions and 4 deletions.
diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/VariantProcessingJob.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/VariantProcessingJob.java
@@ -119,14 +119,15 @@ private void validateScatterForTask()
 
     public boolean scatterMethodRequiresSort()
     {
-        if (_scatterGatherMethod == null || !_scatterGatherMethod.mayRequireSort())
+        if (getParameterJson().optBoolean("scatterGather.forceVcfSort", false))
         {
-            return false;
+            getLogger().debug("forceVcfSort was set");
+            return true;
         }
 
-        if (getParameterJson().optBoolean("scatterGather.forceVcfSort", false))
+        if (_scatterGatherMethod == null || !_scatterGatherMethod.mayRequireSort())
         {
-            return true;
+            return false;
         }
 
         return !doAllowSplitContigs();