From a0196c9f5bc5f79ddd83570692c6f60b22fd8445 Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Wed, 8 Aug 2012 14:34:16 -0400
Subject: [PATCH] Quick pass of FindBugs 'method invokes inefficient Number
 constructor' fixes.

---
 .../sting/gatk/refdata/VariantContextAdaptors.java              | 1 -
 .../sting/gatk/walkers/indels/SomaticIndelDetector.java         | 2 +-
 .../org/broadinstitute/sting/utils/SequenceDictionaryUtils.java | 2 +-
 .../broadinstitute/sting/utils/recalibration/QualQuantizer.java | 2 +-
 4 files changed, 3 insertions(+), 4 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java b/public/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java
index 1b75a2c70..2b46414a8 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java
+++ b/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);
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SomaticIndelDetector.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SomaticIndelDetector.java
index 84a65b9b2..ba16fd709 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SomaticIndelDetector.java
+++ b/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;
     }
 
 
diff --git a/public/java/src/org/broadinstitute/sting/utils/SequenceDictionaryUtils.java b/public/java/src/org/broadinstitute/sting/utils/SequenceDictionaryUtils.java
index d7a390692..9e10fd670 100755
--- a/public/java/src/org/broadinstitute/sting/utils/SequenceDictionaryUtils.java
+++ b/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());
         }
     }
 
diff --git a/public/java/src/org/broadinstitute/sting/utils/recalibration/QualQuantizer.java b/public/java/src/org/broadinstitute/sting/utils/recalibration/QualQuantizer.java
index 62edd5fac..a5a3104a0 100644
--- a/public/java/src/org/broadinstitute/sting/utils/recalibration/QualQuantizer.java
+++ b/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);
         }
 
         /**