diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeLikelihoods.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeLikelihoods.java
index ea961d0c2..8322e18b1 100644
--- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeLikelihoods.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeLikelihoods.java
@@ -3,6 +3,7 @@ package org.broadinstitute.sting.gatk.walkers.genotyper;
 import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.utils.*;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
+import org.broadinstitute.sting.utils.pileup.PileupElement;
 import org.broadinstitute.sting.utils.genotype.DiploidGenotype;
 
 import static java.lang.Math.log10;
@@ -277,20 +278,18 @@ public class GenotypeLikelihoods implements Cloneable {
     public int add(ReadBackedPileup pileup, boolean ignoreBadBases) {
         int n = 0;
 
-        for (int i = 0; i < pileup.getReads().size(); i++) {
-            int offset = pileup.getOffsets().get(i);
+        for ( PileupElement p : pileup ) {
+            byte base = p.getBase();
             // ignore deletions
-            if ( offset == -1 )
+            if ( base == PileupElement.DELETION_BASE )
                 continue;
 
-            SAMRecord read = pileup.getReads().get(i);
-            char base = (char)read.getReadBases()[offset];
-            byte qual = read.getBaseQualities()[offset];
-            if ( ! ignoreBadBases || ! badBase(base) ) {
-                n += add(base, qual, read, offset);
+            byte qual = p.getQual();
+            if ( ! ignoreBadBases || ! badBase((char)base) ) {
+                n += add((char)base, qual, p.getRead(), p.getOffset());
             }
         }
-
+        
         return n;
     }
 
diff --git a/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFGenotypeCall.java b/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFGenotypeCall.java
index 4fc900cd5..eeec0bdd2 100755
--- a/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFGenotypeCall.java
+++ b/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFGenotypeCall.java
@@ -250,7 +250,7 @@ public class VCFGenotypeCall extends AlleleConstrainedGenotype implements ReadBa
      * @return the number of reads we're backed by
      */
     public int getReadCount() {
-       return (mCoverage > 0 ? mCoverage : (mPileup != null ? mPileup.getReads().size() : 0));
+       return (mCoverage > 0 ? mCoverage : (mPileup != null ? mPileup.size() : 0));
     }
 
     /**