From c8e17a7adf410aa540f6e51091160f56bd4231e2 Mon Sep 17 00:00:00 2001
From: Guillermo del Angel <delangel@broadinstitute.org>
Date: Tue, 30 Oct 2012 13:57:54 -0400
Subject: [PATCH] totally experimental UG feature, to be removed

---
 .../sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java   | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
index 3c4a97ec1..d9b46ad36 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
@@ -190,6 +190,9 @@ public class UnifiedGenotyperEngine {
                     final VariantContext vc = calculateLikelihoods(tracker, refContext, stratifiedContexts, AlignmentContextUtils.ReadOrientation.COMPLETE, null, true, model, perReadAlleleLikelihoodMap);
                     if ( vc != null )
                         results.add(calculateGenotypes(tracker, refContext, rawContext, stratifiedContexts, vc, model, true, perReadAlleleLikelihoodMap));
+                    else if (UAC.OutputMode == OUTPUT_MODE.EMIT_ALL_SITES)
+                        results.add(generateEmptyContext(tracker, refContext, null, rawContext));
+
                 }
             }        
         }