diff --git a/build.xml b/build.xml
index ce07138b6..9715071cd 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 0eb35d299..820d58837 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);
+        UG_engine = new UnifiedGenotyperEngine(getToolkit(), UAC, logger, verboseWriter, annotationEngine, samples, samples.size());
 
         // initialize the header
         Set<VCFHeaderLine> headerInfo = getHeaderInfo();
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 1382306c6..6af3bbd1e 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
@@ -115,11 +115,11 @@ public class UnifiedGenotyperEngine {
     // ---------------------------------------------------------------------------------------------------------
     @Requires({"toolkit != null", "UAC != null"})
     public UnifiedGenotyperEngine(GenomeAnalysisEngine toolkit, UnifiedArgumentCollection UAC) {
-        this(toolkit, UAC, Logger.getLogger(UnifiedGenotyperEngine.class), null, null, SampleUtils.getSAMFileSamples(toolkit.getSAMFileHeader()));
+        this(toolkit, UAC, Logger.getLogger(UnifiedGenotyperEngine.class), null, null, SampleUtils.getSAMFileSamples(toolkit.getSAMFileHeader()), 2*(SampleUtils.getSAMFileSamples(toolkit.getSAMFileHeader()).size()));
     }
 
-    @Requires({"toolkit != null", "UAC != null", "logger != null", "samples != null && samples.size() > 0"})
-    public UnifiedGenotyperEngine(GenomeAnalysisEngine toolkit, UnifiedArgumentCollection UAC, Logger logger, PrintStream verboseWriter, VariantAnnotatorEngine engine, Set<String> samples) {
+    @Requires({"toolkit != null", "UAC != null", "logger != null", "samples != null && samples.size() > 0","N>0"})
+    public UnifiedGenotyperEngine(GenomeAnalysisEngine toolkit, UnifiedArgumentCollection UAC, Logger logger, PrintStream verboseWriter, VariantAnnotatorEngine engine, Set<String> samples, int N) {
         this.BAQEnabledOnCMDLine = toolkit.getArguments().BAQMode != BAQ.CalculationMode.OFF;
         genomeLocParser = toolkit.getGenomeLocParser();
         this.samples = new TreeSet<String>(samples);
@@ -130,7 +130,8 @@ public class UnifiedGenotyperEngine {
         this.verboseWriter = verboseWriter;
         this.annotationEngine = engine;
 
-        N = 2 * this.samples.size();
+        this.N = N;
+        
         log10AlleleFrequencyPriorsSNPs = new double[UAC.MAX_ALTERNATE_ALLELES][N+1];
         log10AlleleFrequencyPriorsIndels = new double[UAC.MAX_ALTERNATE_ALLELES][N+1];
         computeAlleleFrequencyPriors(N, log10AlleleFrequencyPriorsSNPs, UAC.heterozygosity);
@@ -703,7 +704,7 @@ public class UnifiedGenotyperEngine {
         for (int i = 0; i < glmClasses.size(); i++) {
             Class<? extends GenotypeLikelihoodsCalculationModel> glmClass = glmClasses.get(i);
             String key = glmClass.getSimpleName().replaceAll("GenotypeLikelihoodsCalculationModel","").toUpperCase();
-            System.out.println("KEY:"+key+"\t" + glmClass.getSimpleName());
+            //System.out.println("KEY:"+key+"\t" + glmClass.getSimpleName());
             try {
                 Object args[] = new Object[]{UAC,logger};
                 Constructor c = glmClass.getDeclaredConstructor(UnifiedArgumentCollection.class, Logger.class);
diff --git a/public/java/src/org/broadinstitute/sting/utils/MathUtils.java b/public/java/src/org/broadinstitute/sting/utils/MathUtils.java
index ad4264d4a..34394ff39 100644
--- a/public/java/src/org/broadinstitute/sting/utils/MathUtils.java
+++ b/public/java/src/org/broadinstitute/sting/utils/MathUtils.java
@@ -1050,7 +1050,7 @@ public class MathUtils {
 
     /**
      * Given two log-probability vectors, compute log of vector product of them:
-     * in Matlab notation, return log(10.*x'*10.^y)
+     * in Matlab notation, return log10(10.*x'*10.^y)
      * @param x vector 1
      * @param y vector 2
      * @return a double representing log (dotProd(10.^x,10.^y)
@@ -1065,7 +1065,7 @@ public class MathUtils {
             tmpVec[k] = x[k]+y[k];
         }
 
-        return sumLog10(tmpVec);
+        return log10sumLog10(tmpVec);
 
 
 
diff --git a/public/java/test/org/broadinstitute/sting/utils/MathUtilsUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/MathUtilsUnitTest.java
index 482f4da80..9e01eb5ae 100755
--- a/public/java/test/org/broadinstitute/sting/utils/MathUtilsUnitTest.java
+++ b/public/java/test/org/broadinstitute/sting/utils/MathUtilsUnitTest.java
@@ -284,6 +284,18 @@ public class MathUtilsUnitTest extends BaseTest {
         Assert.assertTrue(compareDoubleArrays(MathUtils.normalizeFromLog10(new double[] {-1.0, -3.0, -1.0, -2.0}), new double[] {0.1 * 1.0 / 0.211, 0.001 * 1.0 / 0.211, 0.1 * 1.0 / 0.211, 0.01 * 1.0 / 0.211}));
     }
 
+    @Test
+    public void testDotProduct() {
+        Assert.assertEquals(MathUtils.dotProduct(new Double[]{-5.0,-3.0,2.0}, new Double[]{6.0,7.0,8.0}),-35.0);
+        Assert.assertEquals(MathUtils.dotProduct(new Double[]{-5.0}, new Double[]{6.0}),-30.0);
+    }
+
+    @Test
+    public void testLogDotProduct() {
+        Assert.assertEquals(MathUtils.logDotProduct(new double[]{-5.0,-3.0,2.0}, new double[]{6.0,7.0,8.0}),10.0);
+        Assert.assertEquals(MathUtils.logDotProduct(new double[]{-5.0}, new double[]{6.0}),1.0);
+    }
+
     /**
      * Private function used by testNormalizeFromLog10()
      */