From ecde77a814798c3c8b826adeb69e101d9f48ba11 Mon Sep 17 00:00:00 2001
From: bbimber <bbimber@gmail.com>
Date: Thu, 8 Feb 2024 06:40:13 -0800
Subject: [PATCH] Add hook to force VCF sorting after merge in special cases

---
 .../sequenceanalysis/pipeline/VariantProcessingJob.java      | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/VariantProcessingJob.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/VariantProcessingJob.java
index bce9d08f0..1c34d1e14 100644
--- 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();
     }