diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/HapmapPoolAllelicInfoWalker.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/HapmapPoolAllelicInfoWalker.java
index 98e188fac..1ad28eaee 100755
--- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/HapmapPoolAllelicInfoWalker.java
+++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/HapmapPoolAllelicInfoWalker.java
@@ -68,11 +68,11 @@ public class HapmapPoolAllelicInfoWalker extends LocusWalker<String, PrintWriter
         long pos = loc.getStart();
         char refBase = Character.toUpperCase(ref.getBase());
         List<Pair<Genotype, Genotype>> chips = getChips(sampleNames, tracker);
-        Pair<Genotype,Pair<Integer,Integer>> alleleFreqInfo = ctt.getPooledAlleleFrequency(chips,refBase);
+        Pair<Integer,Pair<Integer,Integer>> alleleFreqInfo = ctt.getPooledAlleleFrequency(chips,refBase);
         char alternate;
-        if ( alleleFreqInfo.getFirst() != null && alleleFreqInfo.getFirst().isVariant(refBase)) {
+        if ( alleleFreqInfo.first == ConcordanceTruthTable.VARIANT ) {
             //System.out.println(refBase + " " + alleleFreqInfo.getFirst().getBases());
-            alternate = getAlternateBase(alleleFreqInfo.getFirst(),refBase);
+            alternate = getAlternateBase(chips,refBase);
 
         } else {
             return null; // early return
@@ -96,8 +96,8 @@ public class HapmapPoolAllelicInfoWalker extends LocusWalker<String, PrintWriter
 
         // sanity check
         if ( refBase == alternate ) {
-            if ( alleleFreqInfo.getFirst().isVariant(refBase) ) {
-                logger.warn("Called as a variant! Ref: "+ refBase +"Chip data: " + alleleFreqInfo.getFirst().getBases());
+            if ( alleleFreqInfo.first == ConcordanceTruthTable.VARIANT ) {
+                ;//logger.warn("Called as a variant! Ref: "+ refBase +"Chip data: " + alleleFreqInfo.getFirst().getBases());
             }
         }
 
@@ -105,12 +105,16 @@ public class HapmapPoolAllelicInfoWalker extends LocusWalker<String, PrintWriter
 
     }
 
-    public char getAlternateBase(Genotype g, char ref) {
-        char[] bases = g.getBases().toCharArray();
-        if ( Character.toUpperCase(bases[0]) != ref )
-            return bases[0];
-        else
-            return bases[1];
+    public char getAlternateBase(List<Pair<Genotype, Genotype>> chips, char ref) {
+        for ( Pair<Genotype, Genotype> chip : chips ) {
+            Genotype g = chip.first;
+            char[] bases = g.getBases().toCharArray();
+            if ( Character.toUpperCase(bases[0]) != ref )
+                return bases[0];
+            if ( Character.toUpperCase(bases[1]) != ref )
+                return bases[1];
+        }
+        return ref;
     }
 
     public PrintWriter reduce(String s, PrintWriter p) {
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/ConcordanceTruthTable.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/ConcordanceTruthTable.java
index cd75f2659..efa300559 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/ConcordanceTruthTable.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/ConcordanceTruthTable.java
@@ -18,18 +18,18 @@ import java.util.*;
  * the Broad Institute nor MIT can be responsible for its use, misuse, or functionality.
  */
 public class ConcordanceTruthTable {
-    private static final int TRUE_POSITIVE = 0;
-    private static final int TRUE_NEGATIVE = 1;
-    private static final int FALSE_POSITIVE = 2;
-    private static final int FALSE_NEGATIVE = 3;
-    private static final int VARIANT = 1;
+    public static final int TRUE_POSITIVE = 0;
+    public static final int TRUE_NEGATIVE = 1;
+    public static final int FALSE_POSITIVE = 2;
+    public static final int FALSE_NEGATIVE = 3;
+    public static final int VARIANT = 1;
     private static final String[] POOL_HEADERS = {"TP","TN","FP","FN"};
 
-    private static final int REF = 0;
-    private static final int VAR_HET = 1;
-    private static final int VAR_HOM = 2;
-    private static final int UNKNOWN = 3;
-    private static final int NO_CALL = 3;   // synonym
+    public static final int REF = 0;
+    public static final int VAR_HET = 1;
+    public static final int VAR_HOM = 2;
+    public static final int UNKNOWN = 3;
+    public static final int NO_CALL = 3;   // synonym
     private static final String[] TRUTH_NAMES = {"IS_REF", "IS_VAR_HET", "IS_VAR_HOM", "UNKNOWN"};
     private static final String[] CALL_NAMES = {"CALLED_REF", "CALLED_VAR_HET", "CALLED_VAR_HOM", "NO_CALL"};