Quick pass of FindBugs 'should be static inner class' fixes.

public/java/src/org/broadinstitute/sting/gatk/walkers/ClipReads.java

@@ -574,7 +574,7 @@ public class ClipReads extends ReadWalker<ClipReads.ReadClipperWithData, ClipRea
         }
     }
 
-    public class ReadClipperWithData extends ReadClipper {
+    public static class ReadClipperWithData extends ReadClipper {
         private ClippingData data;
 
         public ReadClipperWithData(GATKSAMRecord read, List<SeqToClip> clipSeqs) {

public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java

@@ -103,7 +103,7 @@ public class HaplotypeScore extends InfoFieldAnnotation implements StandardAnnot
         return map;
     }
 
-    private class HaplotypeComparator implements Comparator<Haplotype> {
+    private static class HaplotypeComparator implements Comparator<Haplotype> {
 
         public int compare(Haplotype a, Haplotype b) {
             if (a.getQualitySum() < b.getQualitySum())

public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java

@@ -208,7 +208,7 @@ public class SNPGenotypeLikelihoodsCalculationModel extends GenotypeLikelihoodsC
         return new ReadBackedPileupImpl( pileup.getLocation(), BAQedElements );
     }
 
-    public class BAQedPileupElement extends PileupElement {
+    public static class BAQedPileupElement extends PileupElement {
         public BAQedPileupElement( final PileupElement PE ) {
             super(PE.getRead(), PE.getOffset(), PE.isDeletion(), PE.isBeforeDeletedBase(), PE.isAfterDeletedBase(), PE.isBeforeInsertion(), PE.isAfterInsertion(), PE.isNextToSoftClip());
         }

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

@@ -124,7 +124,7 @@ public class ConstrainedMateFixingManager {
         return first;
     }
 
-    private class SAMRecordHashObject {
+    private static class SAMRecordHashObject {
         public SAMRecord record;
         public boolean wasModified;
 

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

@@ -332,7 +332,7 @@ public class RealignerTargetCreator extends RodWalker<RealignerTargetCreator.Eve
 
     private enum EVENT_TYPE { POINT_EVENT, INDEL_EVENT, BOTH }
 
-    class EventPair {
+    static class EventPair {
         public Event left, right;
         public TreeSet<GenomeLoc> intervals = new TreeSet<GenomeLoc>();
 

public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java

@@ -329,7 +329,7 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
 
 
     /* Private class used to store the intermediate variants in the integer random selection process */
-    private class RandomVariantStructure {
+    private static class RandomVariantStructure {
         private VariantContext vc;
 
         RandomVariantStructure(VariantContext vcP) {

public/java/src/org/broadinstitute/sting/utils/clipping/ClippingOp.java

@@ -538,7 +538,7 @@ public class ClippingOp {
         return 0;
     }
 
-    private class CigarShift {
+    private static class CigarShift {
         private Cigar cigar;
         private int shiftFromStart;
         private int shiftFromEnd;