From 6dc7d872ece8610b0f08a90bc12452984aa26c52 Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Thu, 25 Oct 2012 10:06:13 -0400
Subject: [PATCH] Fix GenotypeAndValidate to handle SNPs and indels as reported
 on the forum.  Recent changes to the UnifiedArgumentCollection made this stop
 working.  Adding in JIRA to create integration tests for this tool.

---
 .../sting/gatk/walkers/validation/GenotypeAndValidate.java   | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/GenotypeAndValidate.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/GenotypeAndValidate.java
index 832c0ede3..79b6e17f6 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/GenotypeAndValidate.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/GenotypeAndValidate.java
@@ -333,8 +333,9 @@ public class GenotypeAndValidate extends RodWalker<GenotypeAndValidate.CountedDa
         snpEngine = new UnifiedGenotyperEngine(getToolkit(), uac);
 
         // Adding the INDEL calling arguments for UG
-        uac.GLmodel = GenotypeLikelihoodsCalculationModel.Model.INDEL;
-        indelEngine = new UnifiedGenotyperEngine(getToolkit(), uac);
+        UnifiedArgumentCollection uac_indel = new UnifiedArgumentCollection(uac);
+        uac_indel.GLmodel = GenotypeLikelihoodsCalculationModel.Model.INDEL;
+        indelEngine = new UnifiedGenotyperEngine(getToolkit(), uac_indel);
 
         // make sure we have callConf set to the threshold set by the UAC so we can use it later.
         callConf = uac.STANDARD_CONFIDENCE_FOR_CALLING;