Initial commit of the random forest classifier.

protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/variantrecalibration/Tranche.java

@@ -124,7 +124,8 @@ public class Tranche {
         final ByteArrayOutputStream bytes = new ByteArrayOutputStream();
         final PrintStream stream = new PrintStream(bytes);
 
-        Collections.sort( tranches, new TrancheTruthSensitivityComparator() );
+        if( tranches.size() > 1 )
+            Collections.sort( tranches, new TrancheTruthSensitivityComparator() );
 
         stream.println("# Variant quality score tranches file");
         stream.println("# Version number " + CURRENT_VERSION);

public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/MathUtils.java

@@ -1531,6 +1531,15 @@ public class MathUtils {
         return sliceListByIndices(sampleIndicesWithoutReplacement(list.size(),N),list);
     }
 
+    /**
+    * Draw N random elements from list with replacement
+    * @param list - the list from which to draw randomly
+    * @param N - the number of elements to draw
+    */
+    public static <T> List<T> randomSample(final List<T> list, final int N) {
+        return sliceListByIndices(sampleIndicesWithReplacement(list.size(),N),list);
+    }
+
     /**
      * Return the likelihood of observing the counts of categories having sampled a population
      * whose categorial frequencies are distributed according to a Dirichlet distribution