Added a copy() method for ReadBackedPileups

necessary to create new alignment contexts with hard-copies of the pileup.

public/java/src/org/broadinstitute/sting/utils/pileup/AbstractReadBackedPileup.java

@@ -1054,6 +1054,11 @@ public abstract class AbstractReadBackedPileup<RBP extends AbstractReadBackedPil
     public FragmentCollection<PileupElement> toFragments() {
         return FragmentUtils.create(this);
     }
+
+    @Override
+    public ReadBackedPileup copy() {
+        return new ReadBackedPileupImpl(loc, (PileupElementTracker<PileupElement>) pileupElementTracker.copy());
+    }
 }
 
 

public/java/src/org/broadinstitute/sting/utils/pileup/PileupElementTracker.java

@@ -34,11 +34,20 @@ import java.util.*;
  */
 abstract class PileupElementTracker<PE extends PileupElement> implements Iterable<PE> {
     public abstract int size();
+    public abstract PileupElementTracker<PE> copy();
 }
 
 class UnifiedPileupElementTracker<PE extends PileupElement> extends PileupElementTracker<PE> {
     private final List<PE> pileup;
 
+    @Override
+    public UnifiedPileupElementTracker<PE> copy() {
+        UnifiedPileupElementTracker<PE> result = new UnifiedPileupElementTracker<PE>();
+        for(PE element : pileup)
+            result.add(element);
+        return result;
+    }
+
     public UnifiedPileupElementTracker() { pileup = new LinkedList<PE>(); }
     public UnifiedPileupElementTracker(List<PE> pileup) { this.pileup = pileup; }
 
@@ -65,6 +74,14 @@ class PerSamplePileupElementTracker<PE extends PileupElement> extends PileupElem
         pileup = new HashMap<String,PileupElementTracker<PE>>();
     }
 
+    public PerSamplePileupElementTracker<PE> copy() {
+        PerSamplePileupElementTracker<PE> result = new PerSamplePileupElementTracker<PE>();
+        for (Map.Entry<String, PileupElementTracker<PE>> entry : pileup.entrySet())
+            result.addElements(entry.getKey(), entry.getValue());
+
+        return result;
+    }
+
     /**
      * Gets a list of all the samples stored in this pileup.
      * @return List of samples in this pileup.

public/java/src/org/broadinstitute/sting/utils/pileup/ReadBackedPileup.java

@@ -283,4 +283,12 @@ public interface ReadBackedPileup extends Iterable<PileupElement>, HasGenomeLoca
      * @return
      */
     public FragmentCollection<PileupElement> toFragments();
+
+    /**
+     * Creates a full copy (not shallow) of the ReadBacked Pileup
+     *
+     * @return
+     */
+    public ReadBackedPileup copy();
+
 }