diff --git a/playground/java/src/org/broadinstitute/sting/gatk/walkers/AlleleFrequencyMetricsWalker.java b/playground/java/src/org/broadinstitute/sting/gatk/walkers/AlleleFrequencyMetricsWalker.java
new file mode 100755
index 000000000..9439b4d99
--- /dev/null
+++ b/playground/java/src/org/broadinstitute/sting/gatk/walkers/AlleleFrequencyMetricsWalker.java
@@ -0,0 +1,89 @@
+package org.broadinstitute.sting.gatk.walkers;
+
+import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
+import org.broadinstitute.sting.gatk.refdata.rodDbSNP;
+import org.broadinstitute.sting.gatk.walkers.AlleleFrequencyWalker;
+import org.broadinstitute.sting.gatk.walkers.BasicLociWalker;
+import org.broadinstitute.sting.gatk.LocusContext;
+import org.broadinstitute.sting.utils.AlleleFrequencyEstimate;
+
+import java.util.List;
+
+/**
+ * Created by IntelliJ IDEA.
+ * User: andrewk
+ * Date: Mar 18, 2009
+ * Time: 5:28:58 PM
+ * To change this template use File | Settings | File Templates.
+ */
+
+public class AlleleFrequencyMetricsWalker extends BasicLociWalker<Integer, Integer> {
+
+    long dbsnp_tp=0;
+    long dbsnp_fp=0;
+    long num_snps=0;
+    long num_loci=0;
+    double LOD_cutoff = 5;
+
+    //public void calculateMetrics(List<ReferenceOrderedDatum> rodData, AlleleFrequencyWalker.AlleleFrequencyEstimate alleleFreq) {
+    public Integer map(List<ReferenceOrderedDatum> rodData, char ref, LocusContext context) {
+
+        //AlleleFrequencyWalker = AlleleFrequencyWalker();
+        AlleleFrequencyEstimate alleleFreq = new AlleleFrequencyWalker().map(rodData, ref, context);
+
+
+        boolean is_dbSNP_SNP = false;
+
+        for ( ReferenceOrderedDatum datum : rodData ) {
+            if ( datum != null && datum instanceof rodDbSNP) {
+                rodDbSNP dbsnp = (rodDbSNP)datum;
+                if (dbsnp.isSNP()) is_dbSNP_SNP = true;
+            }
+        }
+
+        if (alleleFreq.getQstar() > 0.0 && alleleFreq.getLogOddsVarRef() >= LOD_cutoff) { // we confidently called it a SNP!
+            if (is_dbSNP_SNP) {
+                dbsnp_tp += 1;
+            }else{
+                dbsnp_fp += 1;
+            }
+        }
+
+        if (alleleFreq.getQstar() > 0.0 && alleleFreq.getLogOddsVarRef() >= LOD_cutoff) {
+            //System.out.println(alleleFreq.getLogOddsVarRef());
+            num_snps++;
+        }
+        num_loci++;
+
+        return 1;
+    }
+
+    public void printMetrics() {
+        System.out.println("\nAllele Frequency Metrics:\n");
+        System.out.printf("Precision of LOD >= %.0f SNPs w.r.t dbSNP: %.2f\n", LOD_cutoff, (float)dbsnp_tp / (dbsnp_fp + dbsnp_tp) * 100);
+        System.out.printf("\\--TP: %d\n", dbsnp_tp);
+        System.out.printf("\\--FP: %d\n", dbsnp_fp);
+        System.out.println();
+        System.out.printf("SNPs (LOD > %.0f): %d\n", LOD_cutoff, num_snps);
+        System.out.printf("Total loci: %d\n", num_loci);
+        System.out.printf("SNPs / loci: 1/%.0f\n", (float)num_loci/num_snps);
+        System.out.println();
+        
+    }
+
+
+    public void onTraversalDone() {
+        printMetrics();
+    }
+
+
+    public Integer reduceInit() { return 0; }
+
+    public Integer reduce(Integer alleleFreq, Integer sum) {
+
+        //System.out.printf("%s %.2f\n", alleleFreq.asString(), alleleFreq.logOddsVarRef);
+        return 0;//value + sum;
+    }
+
+    
+}
diff --git a/playground/java/src/org/broadinstitute/sting/gatk/walkers/AlleleFrequencyWalker.java b/playground/java/src/org/broadinstitute/sting/gatk/walkers/AlleleFrequencyWalker.java
index 6767adf47..b9d382094 100755
--- a/playground/java/src/org/broadinstitute/sting/gatk/walkers/AlleleFrequencyWalker.java
+++ b/playground/java/src/org/broadinstitute/sting/gatk/walkers/AlleleFrequencyWalker.java
@@ -1,16 +1,16 @@
 package org.broadinstitute.sting.gatk.walkers;
-
 //import org.broadinstitute.sting.gatk.iterators.LocusIterator;
 import org.broadinstitute.sting.gatk.LocusContext;
+import org.broadinstitute.sting.utils.AlleleFrequencyEstimate;
 import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
 import org.broadinstitute.sting.gatk.refdata.rodDbSNP;
-import org.broadinstitute.sting.utils.AlleleFrequencyMetrics;
+import org.broadinstitute.sting.utils.AlleleFrequencyEstimate;
 import net.sf.samtools.SAMRecord;
 
 import java.util.List;
 import java.util.Arrays;
 
-public class AlleleFrequencyWalker extends BasicLociWalker<AlleleFrequencyWalker.AlleleFrequencyEstimate, Integer> {
+public class AlleleFrequencyWalker extends BasicLociWalker<AlleleFrequencyEstimate, Integer> {
 
     public AlleleFrequencyEstimate map(List<ReferenceOrderedDatum> rodData, char ref, LocusContext context) {
 
@@ -50,6 +50,7 @@ public class AlleleFrequencyWalker extends BasicLociWalker<AlleleFrequencyWalker
         for (byte b : bases)
             base_counts[nuc2num[b]]++;
 
+        
         // Find alternate allele - 2nd most frequent non-ref allele
         // (maybe we should check for ties and eval both or check most common including quality scores)
         int altnum = -1; // start with first base numerical identity (0,1,2,3)
@@ -77,14 +78,11 @@ public class AlleleFrequencyWalker extends BasicLociWalker<AlleleFrequencyWalker
                     //System.out.printf("  DBSNP %s on %s => %s%n", dbsnp.toSimpleString(), dbsnp.strand, Utils.join("/", dbsnp.getAllelesFWD()));
                     System.out.printf("ROD: %s ",dbsnp.toMediumString());
                 }
-
             }
         }
         if (debug >= 1) System.out.format(" %s\n", base_string);
         if (debug >= 2) System.out.println();
 
-        alleleMetrics.calculateMetrics(rodData, alleleFreq);
-
         return alleleFreq;
     }
 
@@ -181,40 +179,6 @@ public class AlleleFrequencyWalker extends BasicLociWalker<AlleleFrequencyWalker
         }
     }
 
-    public class AlleleFrequencyEstimate {
-        //AlleleFrequencyEstimate();
-        char ref;
-        char alt;
-        int N;
-        double qhat;
-        double qstar;
-        double logOddsVarRef;
-
-        public double getQstar() {return qstar;}
-        public double getLogOddsVarRef() {return logOddsVarRef;}
-
-
-        public AlleleFrequencyEstimate (char ref, char alt, int N, double qhat, double qstar, double logOddsVarRef) {
-            this.ref = ref;
-            this.alt = alt;
-            this.N = N;
-            this.qhat = qhat;
-            this.qstar = qstar;
-            this.logOddsVarRef = logOddsVarRef;
-        }
-
-        public String asString () {
-            // Print out the called bases
-            // Notes: switched from qhat to qstar because qhat doesn't work at n=1 (1 observed base) where having a single non-ref
-            //        base has you calculate qstar = 0.0 and qhat = 0.49 and that leads to a genotype predicition of AG according
-            //        to qhat, but AA according to qstar.  This needs to be further investigated to see whether we really want
-            //        to use qstar, but make N (number of chormosomes) switch to n (number of reads at locus) for n=1
-            long numNonrefBases = Math.round(qstar * N);
-            long numRefBases = N - numNonrefBases;
-            return repeat(ref, numRefBases) + repeat(alt, numNonrefBases);
-        }
-    }
-
     static double logOdds(double prob1, double prob2)  {
         return Math.log10(prob1 / (1-prob1)) - Math.log10(prob2 / (1-prob2));
     }
@@ -327,15 +291,8 @@ public class AlleleFrequencyWalker extends BasicLociWalker<AlleleFrequencyWalker
         p_G_N_2[0] = 0.999;
         p_G_N_2[1] = 1e-3;
         p_G_N_2[2] = 1e-5;
-
-        alleleMetrics = new AlleleFrequencyMetrics();
     }
 
-    AlleleFrequencyMetrics alleleMetrics;
-    
-    public void onTraversalDone() {
-        alleleMetrics.printMetrics();
-    }
 
 
     void print_base_qual_matrix(double [][]quals, int numReads) {
diff --git a/playground/java/src/org/broadinstitute/sting/utils/AlleleFrequencyEstimate.java b/playground/java/src/org/broadinstitute/sting/utils/AlleleFrequencyEstimate.java
new file mode 100755
index 000000000..bd010e1d2
--- /dev/null
+++ b/playground/java/src/org/broadinstitute/sting/utils/AlleleFrequencyEstimate.java
@@ -0,0 +1,42 @@
+package org.broadinstitute.sting.utils;
+
+import org.broadinstitute.sting.gatk.walkers.AlleleFrequencyWalker;
+
+public class AlleleFrequencyEstimate {
+    //AlleleFrequencyEstimate();
+    char ref;
+    char alt;
+    int N;
+    double qhat;
+    double qstar;
+    double logOddsVarRef;
+
+    public double getQstar() {
+        return qstar;
+    }
+
+    public double getLogOddsVarRef() {
+        return logOddsVarRef;
+    }
+
+
+    public AlleleFrequencyEstimate(char ref, char alt, int N, double qhat, double qstar, double logOddsVarRef) {
+        this.ref = ref;
+        this.alt = alt;
+        this.N = N;
+        this.qhat = qhat;
+        this.qstar = qstar;
+        this.logOddsVarRef = logOddsVarRef;
+    }
+
+    public String asString() {
+        // Print out the called bases
+        // Notes: switched from qhat to qstar because qhat doesn't work at n=1 (1 observed base) where having a single non-ref
+        //        base has you calculate qstar = 0.0 and qhat = 0.49 and that leads to a genotype predicition of AG according
+        //        to qhat, but AA according to qstar.  This needs to be further investigated to see whether we really want
+        //        to use qstar, but make N (number of chormosomes) switch to n (number of reads at locus) for n=1
+        long numNonrefBases = Math.round(qstar * N);
+        long numRefBases = N - numNonrefBases;
+        return AlleleFrequencyWalker.repeat(ref, numRefBases) + AlleleFrequencyWalker.repeat(alt, numNonrefBases);
+    }
+}
\ No newline at end of file
diff --git a/playground/java/src/org/broadinstitute/sting/utils/AlleleFrequencyMetrics.java b/playground/java/src/org/broadinstitute/sting/utils/AlleleFrequencyMetrics.java
deleted file mode 100755
index 07c1a8ced..000000000
--- a/playground/java/src/org/broadinstitute/sting/utils/AlleleFrequencyMetrics.java
+++ /dev/null
@@ -1,65 +0,0 @@
-package org.broadinstitute.sting.utils;
-
-import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
-import org.broadinstitute.sting.gatk.refdata.rodDbSNP;
-import org.broadinstitute.sting.gatk.walkers.AlleleFrequencyWalker;
-
-import java.util.List;
-
-/**
- * Created by IntelliJ IDEA.
- * User: andrewk
- * Date: Mar 18, 2009
- * Time: 5:28:58 PM
- * To change this template use File | Settings | File Templates.
- */
-
-
-public class AlleleFrequencyMetrics {
-
-    long dbsnp_tp=0;
-    long dbsnp_fp=0;
-    long num_snps=0;
-    long num_loci=0;
-
-    public void calculateMetrics(List<ReferenceOrderedDatum> rodData, AlleleFrequencyWalker.AlleleFrequencyEstimate alleleFreq) {
-
-        boolean is_dbSNP_SNP = false;
-
-        for ( ReferenceOrderedDatum datum : rodData ) {
-            if ( datum != null && datum instanceof rodDbSNP) {
-                rodDbSNP dbsnp = (rodDbSNP)datum;
-                if (dbsnp.isSNP()) is_dbSNP_SNP = true;
-            }
-        }
-
-        if (alleleFreq.getQstar() > 0.0 && alleleFreq.getLogOddsVarRef() >= 5.0) { // we confidently called it a SNP!
-            if (is_dbSNP_SNP) {
-                dbsnp_tp += 1;
-            }else{
-                dbsnp_fp += 1;
-            }
-        }
-
-        if (alleleFreq.getQstar() > 0.0) num_snps++;
-        num_loci++;
-
-    }
-
-    public void printMetrics() {
-        System.out.println("\nAllele Frequency Metrics:\n");
-        System.out.printf("Precision of LOD >= 5 SNPs w.r.t dbSNP: %.2f\n", (float)dbsnp_tp / (dbsnp_fp + dbsnp_tp) * 100);
-        System.out.printf("\\--TP: %d\n", dbsnp_tp);
-        System.out.printf("\\--FP: %d\n", dbsnp_fp);
-        System.out.println();
-        System.out.printf("SNPs (LOD > 0): %d\n", num_snps);
-        System.out.printf("Total loci: %d\n", num_loci);
-        System.out.printf("SNPs / loci: 1/%.0f\n", (float)num_loci/num_snps);
-        System.out.println();
-        
-
-
-
-    }
-    
-}