Optimization: track alleles in the PerReadAlleleLikelihoodMap with a HashSet

-- The previous version of PerReadAlleleLikelihoodMap only stored the alleles in an ArrayList, and used ArrayList.contains() to determine if an allele was already present in the map.  This is very slow with many alleles.  Now keeps both the ArrayList (for get() performance) and a Set of alleles for contains().

public/java/src/org/broadinstitute/sting/utils/genotyper/PerReadAlleleLikelihoodMap.java

@@ -42,13 +42,13 @@ import java.util.*;
  *   For each read, this holds underlying alleles represented by an aligned read, and corresponding relative likelihood.
  */
 public class PerReadAlleleLikelihoodMap {
-    protected final List<Allele> alleles;
-    protected final Map<GATKSAMRecord, Map<Allele, Double>> likelihoodReadMap;
+    /** A set of all of the allele, so we can efficiently determine if an allele is already present */
+    private final Set<Allele> allelesSet = new HashSet<>();
+    /** A list of the unique allele, as an ArrayList so we can call get(i) efficiently */
+    protected final List<Allele> alleles = new ArrayList<>();
+    protected final Map<GATKSAMRecord, Map<Allele, Double>> likelihoodReadMap = new LinkedHashMap<>();
 
-    public PerReadAlleleLikelihoodMap() {
-        likelihoodReadMap = new LinkedHashMap<GATKSAMRecord,Map<Allele,Double>>();
-        alleles = new ArrayList<Allele>();
-    }
+    public PerReadAlleleLikelihoodMap() { }
 
     /**
      * Add a new entry into the Read -> ( Allele -> Likelihood ) map of maps.
@@ -61,18 +61,20 @@ public class PerReadAlleleLikelihoodMap {
         if ( a == null ) throw new IllegalArgumentException("Cannot add a null allele to the allele likelihood map");
         if ( likelihood == null ) throw new IllegalArgumentException("Likelihood cannot be null");
         if ( likelihood > 0.0 ) throw new IllegalArgumentException("Likelihood must be negative (L = log(p))");
+
         Map<Allele,Double> likelihoodMap = likelihoodReadMap.get(read);
         if (likelihoodMap == null){
             // LinkedHashMap will ensure iterating through alleles will be in consistent order
-            likelihoodMap = new LinkedHashMap<Allele, Double>();
+            likelihoodMap = new LinkedHashMap<>();
         }
         likelihoodReadMap.put(read,likelihoodMap);
 
         likelihoodMap.put(a,likelihood);
 
-        if (!alleles.contains(a))
+        if (!allelesSet.contains(a)) {
+            allelesSet.add(a);
             alleles.add(a);
-
+        }
     }
 
     public ReadBackedPileup createPerAlleleDownsampledBasePileup(final ReadBackedPileup pileup, final double downsamplingFraction) {
@@ -165,6 +167,7 @@ public class PerReadAlleleLikelihoodMap {
     }
 
     public void clear() {
+        allelesSet.clear();
         alleles.clear();
         likelihoodReadMap.clear();
     }