From ce617b2dfc8a24a71c4afaea01b4d885bdbd62a7 Mon Sep 17 00:00:00 2001
From: Guillermo del Angel <delangel@broadinstitute.org>
Date: Sun, 25 Mar 2012 10:20:21 -0400
Subject: [PATCH] Bug fix to previous UnifiedGenotyperEngine refactoring,
 removed debug code

---
 build.xml                                                     | 4 ++--
 .../sting/gatk/walkers/genotyper/UnifiedGenotyper.java        | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/build.xml b/build.xml
index 9715071cd..8e9de2272 100644
--- a/build.xml
+++ b/build.xml
@@ -955,8 +955,8 @@
                 <jvmarg value="-Dpipeline.run=${pipeline.run}" />
                 <jvmarg value="-Djava.io.tmpdir=${java.io.tmpdir}" />
                 <jvmarg line="${cofoja.jvm.args}"/>
-                 <jvmarg value="-Xdebug"/>  
-                 <jvmarg value="-Xrunjdwp:transport=dt_socket,server=y,suspend=y,address=5678"/>  
+                <!-- <jvmarg value="-Xdebug"/> --> 
+                <!-- <jvmarg value="-Xrunjdwp:transport=dt_socket,server=y,suspend=y,address=5678"/> -->  
 
                 <classfileset dir="${java.public.test.classes}" includes="**/@{testtype}.class"/>
                 <classfileset dir="${java.private.test.classes}" erroronmissingdir="false">
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
index 820d58837..9a6b3b1dd 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
@@ -221,7 +221,7 @@ public class UnifiedGenotyper extends LocusWalker<VariantCallContext, UnifiedGen
             verboseWriter.println("AFINFO\tLOC\tREF\tALT\tMAF\tF\tAFprior\tAFposterior\tNormalizedPosterior");
 
         annotationEngine = new VariantAnnotatorEngine(Arrays.asList(annotationClassesToUse), annotationsToUse, annotationsToExclude, this, getToolkit());
-        UG_engine = new UnifiedGenotyperEngine(getToolkit(), UAC, logger, verboseWriter, annotationEngine, samples, samples.size());
+        UG_engine = new UnifiedGenotyperEngine(getToolkit(), UAC, logger, verboseWriter, annotationEngine, samples, 2*samples.size());
 
         // initialize the header
         Set<VCFHeaderLine> headerInfo = getHeaderInfo();