Merge branch 'master' of ssh://ni.broadinstitute.org/humgen/gsa-scr1/chartl/dev/unstable

public/java/src/org/broadinstitute/sting/utils/MathUtils.java

@@ -1613,4 +1613,36 @@ public class MathUtils {
 
     }
 
+    /**
+     * Creates an integer out of a bitset
+     *
+     * @param bitSet the bitset
+     * @return an integer with the bitset representation
+     */
+    public static int intFrom(final BitSet bitSet) {
+        int integer = 0;
+        for (int bitIndex = bitSet.nextSetBit(0); bitIndex >= 0; bitIndex = bitSet.nextSetBit(bitIndex+1))
+            integer |= 1 << bitIndex;
+
+        return integer;
+    }
+
+    /**
+     * Creates a BitSet representation of a given integer
+     *
+     * @param integer the number to turn into a bitset
+     * @return a bitset representation of the integer
+     */
+    public static BitSet bitSetFrom(int integer) {
+        BitSet bitSet = new BitSet((int) Math.ceil(Math.sqrt(integer)));
+        int bitIndex = 0;
+        while (integer > 0) {
+            if (integer%2 > 0)
+                bitSet.set(bitIndex);
+            bitIndex++;
+            integer /= 2;
+        }
+        return bitSet;
+    }
+
 }

public/java/test/org/broadinstitute/sting/utils/MathUtilsUnitTest.java

@@ -205,6 +205,16 @@ public class MathUtilsUnitTest extends BaseTest {
         }
     }
 
+    @Test(enabled = true)
+    public void testIntAndBitSetConversion() {
+        Assert.assertEquals(428,    MathUtils.intFrom(MathUtils.bitSetFrom(428)));
+        Assert.assertEquals(239847, MathUtils.intFrom(MathUtils.bitSetFrom(239847)));
+        Assert.assertEquals(12726,  MathUtils.intFrom(MathUtils.bitSetFrom(12726)));
+        Assert.assertEquals(0,      MathUtils.intFrom(MathUtils.bitSetFrom(0)));
+        Assert.assertEquals(1,      MathUtils.intFrom(MathUtils.bitSetFrom(1)));
+        Assert.assertEquals(65536,  MathUtils.intFrom(MathUtils.bitSetFrom(65536)));
+    }
+
     private boolean hasUniqueElements(Object[] x) {
         for (int i = 0; i < x.length; i++)
             for (int j = i + 1; j < x.length; j++)
@@ -220,10 +230,10 @@ public class MathUtilsUnitTest extends BaseTest {
         return set.isEmpty();
     }
 
-
     private void p (Object []x) {
         for (Object v: x)
             System.out.print((Integer) v + " ");
         System.out.println();
     }
+
 }