diff --git a/java/src/org/broadinstitute/sting/secondarybase/AnnotateSecondaryBase.java b/java/src/org/broadinstitute/sting/secondarybase/AnnotateSecondaryBase.java
index ba7494074..c3117ec44 100755
--- a/java/src/org/broadinstitute/sting/secondarybase/AnnotateSecondaryBase.java
+++ b/java/src/org/broadinstitute/sting/secondarybase/AnnotateSecondaryBase.java
@@ -47,13 +47,6 @@ public class AnnotateSecondaryBase extends CommandLineProgram {
     protected int execute() {
         BasecallingTrainingSet trainingSet = new BasecallingTrainingSet(BUSTARD_DIR, LANE, CYCLE_BEGIN, CYCLE_END, TRAINING_LIMIT);
 
-        /*
-        // This doesn't work right now...
-        // Find alignments with zero mismatches and store them until we've picked up TRAINING_LIMIT alignments
-        System.out.println("Loading training set from the first " + TRAINING_LIMIT + " perfect reads in the aligned data...");
-        trainingSet.loadPreAlignedTrainingSet(SAM_IN, REFERENCE);
-        */
-
         // Iterate through raw Firecrest data and store the first N reads up to TRAINING_LIMIT
         System.out.println("Loading training set from the first " + TRAINING_LIMIT + " reads in the raw data...");
         trainingSet.loadFirstNUnambiguousReadsTrainingSet();
@@ -68,41 +61,21 @@ public class AnnotateSecondaryBase extends CommandLineProgram {
         SAMFileHeader sfh = new SAMFileHeader();
         SAMFileWriter sfw = new SAMFileWriterFactory().makeSAMOrBAMWriter(sfh, false, SAM_OUT);
 
+        BasecallingStats bstats = new BasecallingStats();
         IlluminaParser iparser = new IlluminaParser(BUSTARD_DIR, LANE, CYCLE_BEGIN, CYCLE_END);
+        
         RawRead rr;
-
-        int basesConsistent = 0, basesTotal = 0, readsTotal = 0;
-
-        while (readsTotal < CALLING_LIMIT && (rr = iparser.next()) != null) {
+        while (bstats.getReadsTotal() < CALLING_LIMIT && (rr = iparser.next()) != null) {
             FourProbRead fpr = model.call(rr);
 
-            SAMRecord sr = constructSAMRecord(rr, fpr, sfh, RUN_BARCODE);
-            sfw.addAlignment(sr);
-
-            for (int cycle = 0; cycle < fpr.size(); cycle++) {
-                int rawBaseIndex = BaseUtils.simpleBaseToBaseIndex((char) rr.getSequence()[cycle]);
-                int fpBaseIndex = fpr.get(cycle).indexAtRank(0);
-
-                if (rawBaseIndex >= 0 && fpBaseIndex >= 0) {
-                    basesTotal++;
-
-                    if (rawBaseIndex == fpBaseIndex) {
-                        basesConsistent++;
-                    }
-                }
-            }
-
-            if (basesTotal % 10000 == 0 && basesTotal > 0) {
-                System.out.printf("%% bases consistent: %d/%d (%4.4f)\r", basesConsistent, basesTotal, ((double) basesConsistent)/((double) basesTotal));
-            }
-
-            readsTotal++;
+            sfw.addAlignment(constructSAMRecord(rr, fpr, sfh, RUN_BARCODE));
+            bstats.update(rr, fpr, 10000);
         }
 
         iparser.close();
         sfw.close();
 
-        System.out.printf("%% bases consistent: %d/%d (%4.4f)\n", basesConsistent, basesTotal, ((double) basesConsistent)/((double) basesTotal));
+        System.out.printf("%% bases consistent: %d/%d (%4.4f)\n", bstats.getBasesConsistent(), bstats.getBasesTotal(), bstats.getPercentConsistent());
         System.out.println("Done.");
 
         return 0;
diff --git a/java/src/org/broadinstitute/sting/secondarybase/BasecallingStats.java b/java/src/org/broadinstitute/sting/secondarybase/BasecallingStats.java
new file mode 100755
index 000000000..8a2dfabd4
--- /dev/null
+++ b/java/src/org/broadinstitute/sting/secondarybase/BasecallingStats.java
@@ -0,0 +1,83 @@
+package org.broadinstitute.sting.secondarybase;
+
+import org.broadinstitute.sting.utils.BaseUtils;
+
+/**
+ * BasecallingStats is a utility class to aggregate and emit basecalling
+ * stats (total bases seen and consistency between basecalling methods).
+ *
+ * @author Kiran Garimella
+ */
+public class BasecallingStats {
+    private int basesConsistent = 0;
+    private int basesTotal = 0;
+    private int readsTotal = 0;
+
+    /**
+     * Constructor that does nothing.
+     */
+    public BasecallingStats() {}
+
+    /**
+     * Return the number of bases called identically by two different methods.
+     *
+     * @return the number of consistent bases.
+     */
+    public int getBasesConsistent() {
+        return basesConsistent;
+    }
+
+    /**
+     * Return the total number of bases seen.
+     *
+     * @return the total number of bases seen.
+     */
+    public int getBasesTotal() {
+        return basesTotal;
+    }
+
+    /**
+     * Return the total number of reads seen.
+     *
+     * @return the total number of reads seen.
+     */
+    public int getReadsTotal() {
+        return readsTotal;
+    }
+
+    /**
+     * Return the percent of bases called consistently by two different methods.
+     *
+     * @return the percent of bases called consistently
+     */
+    public double getPercentConsistent() {
+        return ((double) getBasesConsistent())/((double) getReadsTotal());
+    }
+
+    /**
+     * Updates the number of bases seen, the number of reads seen, and the number of consistent bases.
+     *
+     * @param rr   the raw Illumina read
+     * @param fpr  the FourProb read
+     */
+    public void update(RawRead rr, FourProbRead fpr, int updateInterval) {
+        for (int cycle = 0; cycle < fpr.size(); cycle++) {
+            int rawBaseIndex = BaseUtils.simpleBaseToBaseIndex((char) rr.getSequence()[cycle]);
+            int fpBaseIndex = fpr.get(cycle).indexAtRank(0);
+
+            if (rawBaseIndex >= 0 && fpBaseIndex >= 0) {
+                basesTotal++;
+
+                if (rawBaseIndex == fpBaseIndex) {
+                    basesConsistent++;
+                }
+            }
+        }
+
+        if (basesTotal % updateInterval == 0 && basesTotal > 0) {
+            System.out.printf("%% bases consistent: %d/%d (%4.4f)\r", basesConsistent, basesTotal, ((double) basesConsistent)/((double) basesTotal));
+        }
+
+        readsTotal++;
+    }
+}