Fixing merge conflict

public/java/src/org/broadinstitute/sting/gatk/iterators/LocusIteratorByState.java

@@ -318,6 +318,7 @@ public class LocusIteratorByState extends LocusIterator {
                         continue;
 
                     if (op == CigarOperator.D) {
+                        // TODO -- LIBS is totally busted for deletions so that reads with Ds right before Is in their CIGAR are broken; must fix
                         if (readInfo.includeReadsWithDeletionAtLoci()) {            // only add deletions to the pileup if we are authorized to do so
                             pile.add(new PileupElement(read, readOffset, true, isBeforeDeletion, isAfterDeletion, isBeforeInsertion, isAfterInsertion, isNextToSoftClip, null, nextOp == CigarOperator.D ? nextElementLength : -1));
                             size++;

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

@@ -97,7 +97,6 @@ public class DepthPerAlleleBySample extends GenotypeAnnotation implements Standa
             if (!vc.getAlleles().contains(a))
                 continue; // sanity check - shouldn't be needed
             alleleCounts.put(a,alleleCounts.get(a)+1);
-
         }
         final int[] counts = new int[alleleCounts.size()];
         counts[0] = alleleCounts.get(vc.getReference());