diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/PrintCoverageWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/PrintCoverageWalker.java
index 5fdf93270..315cb0506 100644
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/PrintCoverageWalker.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/PrintCoverageWalker.java
@@ -12,7 +12,7 @@ import org.broadinstitute.sting.gatk.refdata.rodDbSNP;
 import org.broadinstitute.sting.gatk.walkers.By;
 import org.broadinstitute.sting.gatk.walkers.DataSource;
 import org.broadinstitute.sting.gatk.walkers.LocusWalker;
-import org.broadinstitute.sting.playground.indels.SWPairwiseAlignment;
+import org.broadinstitute.sting.utils.SWPairwiseAlignment;
 import org.broadinstitute.sting.playground.utils.GenotypeLikelihoods;
 import org.broadinstitute.sting.utils.Pair;
 import org.broadinstitute.sting.utils.cmdLine.Argument;
@@ -93,4 +93,4 @@ public class PrintCoverageWalker extends LocusWalker<Integer, Integer> {
     }
 
 
-}
\ No newline at end of file
+}
diff --git a/java/src/org/broadinstitute/sting/playground/indels/IndelInspectorMain.java b/java/src/org/broadinstitute/sting/playground/indels/IndelInspectorMain.java
index 9adae4cc6..73ac54b5f 100755
--- a/java/src/org/broadinstitute/sting/playground/indels/IndelInspectorMain.java
+++ b/java/src/org/broadinstitute/sting/playground/indels/IndelInspectorMain.java
@@ -14,8 +14,7 @@ import net.sf.picard.reference.ReferenceSequenceFileWalker;
 import net.sf.picard.reference.ReferenceSequence;
 
 import net.sf.samtools.*;
-import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.GenomeLocParser;
+import org.broadinstitute.sting.utils.*;
 
 public class IndelInspectorMain extends CommandLineProgram {
 
diff --git a/java/src/org/broadinstitute/sting/playground/indels/PileBuilder.java b/java/src/org/broadinstitute/sting/playground/indels/PileBuilder.java
index c8c3d479b..c8647628b 100755
--- a/java/src/org/broadinstitute/sting/playground/indels/PileBuilder.java
+++ b/java/src/org/broadinstitute/sting/playground/indels/PileBuilder.java
@@ -5,7 +5,7 @@ import net.sf.samtools.*;
 import java.util.*;
 import java.io.File;
 
-import org.broadinstitute.sting.utils.PrimitivePair;
+import org.broadinstitute.sting.utils.*;
 import org.broadinstitute.sting.playground.utils.CountedObject;
 import org.broadinstitute.sting.playground.utils.CountedObjectComparatorAdapter;
 
@@ -167,7 +167,7 @@ public class PileBuilder implements RecordPileReceiver {
                            r.getCigar(), r.getAlignmentStart() - startOnRef );
                }
                totalMismatches += AlignmentUtils.numMismatches(r,referenceSequence);
-               AlignmentUtils.collectAndCountIndels(r,all_indels);
+               //AlignmentUtils.collectAndCountIndels(r,all_indels);
            }
 
            if ( mVerbosityLevel >= ALIGNMENTS ) {
@@ -249,7 +249,7 @@ public class PileBuilder implements RecordPileReceiver {
                     rtest.setReadString(r.getReadString());
                     rtest.setReadUmappedFlag(r.getReadUnmappedFlag());
                     rtest.setCigar(cig);
-                    AlignmentUtils.collectAndCountIndels(rtest,new_indels);
+                    //AlignmentUtils.collectAndCountIndels(rtest,new_indels);
                     new_mismatches += AlignmentUtils.numMismatches(rtest,referenceSequence);
                 }
  //           pileAligns.colorprint(true);