Quick pass of FindBugs 'method invokes inefficient Number constructor' fixes.

public/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java

@@ -309,7 +309,6 @@ public class VariantContextAdaptors {
             int index = hapmap.getStart() - ref.getWindow().getStart();
             if ( index < 0 )
                 return null; // we weren't given enough reference context to create the VariantContext
-            Byte refBaseForIndel = new Byte(ref.getBases()[index]);
 
             HashSet<Allele> alleles = new HashSet<Allele>();
             Allele refSNPAllele = Allele.create(ref.getBase(), true);

public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SomaticIndelDetector.java

@@ -1304,7 +1304,7 @@ public class SomaticIndelDetector extends ReadWalker<Integer,Integer> {
 
     @Override
     public Integer reduceInit() {
-        return new Integer(0);
+        return 0;
     }
 
 

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

@@ -329,7 +329,7 @@ public class SequenceDictionaryUtils {
      */
     private static class CompareSequenceRecordsByIndex implements Comparator<SAMSequenceRecord> {
         public int compare(SAMSequenceRecord x, SAMSequenceRecord y) {
-            return new Integer(x.getSequenceIndex()).compareTo(y.getSequenceIndex());
+            return Integer.valueOf(x.getSequenceIndex()).compareTo(y.getSequenceIndex());
         }
     }
 

public/java/src/org/broadinstitute/sting/utils/recalibration/QualQuantizer.java

@@ -223,7 +223,7 @@ public class QualQuantizer {
 
         @Override
         public int compareTo(final QualInterval qualInterval) {
-            return new Integer(this.qStart).compareTo(qualInterval.qStart);
+            return Integer.valueOf(this.qStart).compareTo(qualInterval.qStart);
         }
 
         /**