diff --git a/java/src/org/broadinstitute/sting/secondarybase/FourProb.java b/java/src/org/broadinstitute/sting/secondarybase/FourProb.java
deleted file mode 100755
index d15a6abdc..000000000
--- a/java/src/org/broadinstitute/sting/secondarybase/FourProb.java
+++ /dev/null
@@ -1,100 +0,0 @@
-package org.broadinstitute.sting.secondarybase;
-
-import org.broadinstitute.sting.utils.Utils;
-import org.broadinstitute.sting.utils.QualityUtils;
-
-/**
- * FourProb represents four base hypotheses, their probabilities, and their ranking among one another.
- *
- * @author Kiran Garimella
- */
-public class FourProb {
-    private double[] baseProbs;
-    private int[] baseIndices;
-
-    /**
-     * Constructor for FourProb.
-     *
-     * @param baseLikes  the unsorted base hypothesis probabilities (in ACGT order).
-     */
-    public FourProb(double[][] baseLikes) {
-        double[] baseProbs = new double[4];
-        for (int baseCurIndex = 0; baseCurIndex < 4; baseCurIndex++) {
-            for (int basePrevIndex = 0; basePrevIndex < baseLikes.length; basePrevIndex++) {
-                baseProbs[baseCurIndex] += baseLikes[basePrevIndex][baseCurIndex];
-            }
-        }
-
-        int[] baseIndices = {0, 1, 2, 3};
-        
-        Integer[] perm = Utils.SortPermutation(baseProbs);
-        double[] ascendingBaseProbs = Utils.PermuteArray(baseProbs, perm);
-        int[] ascendingBaseIndices = Utils.PermuteArray(baseIndices, perm);
-
-        this.baseProbs = new double[4];
-        this.baseIndices = new int[4];
-
-        for (int i = 0; i < 4; i++) {
-            this.baseProbs[i] = ascendingBaseProbs[3 - i];
-            this.baseIndices[i] = ascendingBaseIndices[3 - i];
-        }
-    }
-
-    /**
-     * Returns the index of the base at the specified rank.
-     *
-     * @param rank (0 = best, 3 = worst) the rank of the base whose index should be returned
-     * @return the index (0, 1, 2, 3).
-     */
-    public int indexAtRank(int rank) { return baseIndices[rank]; }
-
-    /**
-     * Returns the base label of the base at the specified rank.
-     * @param rank (0 = best, 3 = worst) the rank of the base whose index should be returned
-     * @return the base label (A, C, G, T).
-     */
-    public char baseAtRank(int rank) { return baseIndexToBase(indexAtRank(rank)); }
-
-    /**
-     * Returns the probability of the base at the specified rank.
-     * @param rank (0 = best, 3 = worst) the rank of the base whose index should be returned
-     * @return the probability of the base (0.0-1.0)
-     */
-    public double probAtRank(int rank) { return baseProbs[rank]; }
-
-    /**
-     * Returns the quality score of the base at the specified rank.
-     * @param rank (0 = best, 3 = worst) the rank of the base whose index should be returned
-     * @return the quality score of the base (0-40)
-     */
-    public byte qualAtRank(int rank) { return QualityUtils.probToQual(probAtRank(rank)); }
-
-    /**
-     * A utility method to convert a base index into a base label.
-     * @param baseIndex the index of the base (0, 1, 2, 3).
-     * @return A, C, G, T, or '.' if the base index can't be understood.
-     */
-    private char baseIndexToBase(int baseIndex) {
-        switch (baseIndex) {
-            case 0: return 'A';
-            case 1: return 'C';
-            case 2: return 'G';
-            case 3: return 'T';
-            default: return '.';
-        }
-    }
-
-    /**
-     * Prettily formats the FourProb info.
-     * 
-     * @return a prettily formatted Sting containing the base and quality score in rank order.
-     */
-    public String toString() {
-        return (
-                "[" + baseAtRank(0) + ":" + qualAtRank(0) + " "
-                    + baseAtRank(1) + ":" + qualAtRank(1) + " "
-                    + baseAtRank(2) + ":" + qualAtRank(2) + " "
-                    + baseAtRank(3) + ":" + qualAtRank(3) + "]"
-               );
-    }
-}