diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ErrorModel.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ErrorModel.java
index 8e4ca9595..26ff4db24 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ErrorModel.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ErrorModel.java
@@ -262,18 +262,19 @@ public class ErrorModel  {
     }
 
     public String toString() {
-        String result = "(";
+        StringBuilder result = new StringBuilder("(");
         boolean skipComma = true;
         for (double v : probabilityVector.getProbabilityVector()) {
             if (skipComma) {
                 skipComma = false;
             }
             else {
-                result += ",";
+                result.append(",");
             }
-            result += String.format("%.4f", v);
+            result.append(String.format("%.4f", v));
         }
-        return result + ")";
+        result.append(")");
+        return result.toString();
     }
     
     public static int getTotalReferenceDepth(HashMap<String, ErrorModel>  perLaneErrorModels) {
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInput.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInput.java
index fdc333676..d11747766 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInput.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInput.java
@@ -351,7 +351,6 @@ public class ProduceBeagleInput extends RodWalker<Integer, Integer> {
     }
 
     public static class CachingFormatter {
-        private int maxCacheSize = 0;
         private String format;
         private LRUCache<Double, String> cache;
 
@@ -379,7 +378,6 @@ public class ProduceBeagleInput extends RodWalker<Integer, Integer> {
         }
 
         public CachingFormatter(String format, int maxCacheSize) {
-            this.maxCacheSize = maxCacheSize;
             this.format = format;
             this.cache = new LRUCache<Double, String>(maxCacheSize);
         }
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PreciseNonNegativeDouble.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PreciseNonNegativeDouble.java
index b68739b48..d3f4f6266 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PreciseNonNegativeDouble.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PreciseNonNegativeDouble.java
@@ -86,7 +86,7 @@ class PreciseNonNegativeDouble implements Comparable<PreciseNonNegativeDouble> {
         if (Math.abs(logValDiff) <= EQUALS_THRESH)
             return 0; // this.equals(other)
 
-        return new Double(Math.signum(logValDiff)).intValue();
+        return (int)Math.signum(logValDiff);
     }
 
     public boolean equals(PreciseNonNegativeDouble other) {
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasing.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasing.java
index f49e8f8c0..d8ae6b28b 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasing.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasing.java
@@ -870,7 +870,7 @@ public class ReadBackedPhasing extends RodWalker<PhasingStatsAndOutput, PhasingS
 
             int useOnLeft, useOnRight;
             if (numOnLeft <= numOnRight) {
-                int halfToUse = new Double(Math.floor(numToUse / 2.0)).intValue(); // skimp on the left [floor], and be generous with the right side
+                int halfToUse = numToUse / 2; // skimp on the left [floor], and be generous with the right side
                 useOnLeft = Math.min(halfToUse, numOnLeft);
                 useOnRight = Math.min(numToUse - useOnLeft, numOnRight);
             }
diff --git a/public/java/src/org/broadinstitute/sting/utils/SWPairwiseAlignment.java b/public/java/src/org/broadinstitute/sting/utils/SWPairwiseAlignment.java
index bc1158a4d..500598765 100755
--- a/public/java/src/org/broadinstitute/sting/utils/SWPairwiseAlignment.java
+++ b/public/java/src/org/broadinstitute/sting/utils/SWPairwiseAlignment.java
@@ -377,59 +377,6 @@ public class SWPairwiseAlignment {
         return w_open+(k-1)*w_extend; // gap
     }
 
-    private void print(int[][] s) {
-        for ( int i = 0 ; i < s.length ; i++) {
-            for ( int j = 0; j < s[i].length ; j++ ) {
-                System.out.printf(" %4d",s[i][j]);
-            }
-            System.out.println();
-        }
-    }
-
-    private void print(double[][] s) {
-        for ( int i = 0 ; i < s.length ; i++) {
-            for ( int j = 0; j < s[i].length ; j++ ) {
-                System.out.printf(" %4g",s[i][j]);
-            }
-            System.out.println();
-        }
-    }
-
-    private void print(int[][] s, String a, String b) {
-
-        System.out.print("        ");
-        for ( int j = 1 ; j < s[0].length ; j++) System.out.printf(" %4c",b.charAt(j-1)) ;
-        System.out.println();
-
-        for ( int i = 0 ; i < s.length ; i++) {
-            if ( i > 0 ) System.out.print(a.charAt(i-1));
-            else System.out.print(' ');
-            System.out.print("  ");
-            for ( int j = 0; j < s[i].length ; j++ ) {
-                System.out.printf(" %4d",s[i][j]);
-            }
-            System.out.println();
-        }
-    }
-
-
-    private void print(double[][] s, String a, String b) {
-
-        System.out.print("");
-        for ( int j = 1 ; j < s[0].length ; j++) System.out.printf(" %4c",b.charAt(j-1)) ;
-        System.out.println();
-
-        for ( int i = 0 ; i < s.length ; i++) {
-            if ( i > 0 ) System.out.print(a.charAt(i-1));
-            else System.out.print(' ');
-            System.out.print("  ");
-            for ( int j = 0; j < s[i].length ; j++ ) {
-                System.out.printf(" %2.1f",s[i][j]);
-            }
-            System.out.println();
-        }
-    }
-
     private void print(double[] s, byte[] a, byte[] b) {
            int n = a.length+1;
            int m = b.length+1;