diff --git a/public/java/src/org/broadinstitute/sting/utils/locusiterator/ReadStateManager.java b/public/java/src/org/broadinstitute/sting/utils/locusiterator/ReadStateManager.java
index 8fbd302a8..9728bdb1c 100644
--- a/public/java/src/org/broadinstitute/sting/utils/locusiterator/ReadStateManager.java
+++ b/public/java/src/org/broadinstitute/sting/utils/locusiterator/ReadStateManager.java
@@ -28,7 +28,6 @@ package org.broadinstitute.sting.utils.locusiterator;
 import com.google.java.contract.Ensures;
 import com.google.java.contract.Requires;
 import net.sf.picard.util.PeekableIterator;
-import org.apache.log4j.Logger;
 import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 
 import java.util.*;
diff --git a/public/java/src/org/broadinstitute/sting/utils/sam/AlignmentUtils.java b/public/java/src/org/broadinstitute/sting/utils/sam/AlignmentUtils.java
index 2208302fb..e48d1ca4c 100644
--- a/public/java/src/org/broadinstitute/sting/utils/sam/AlignmentUtils.java
+++ b/public/java/src/org/broadinstitute/sting/utils/sam/AlignmentUtils.java
@@ -581,8 +581,11 @@ public final class AlignmentUtils {
      */
     @Ensures({"result != null"})
     public static Cigar consolidateCigar( final Cigar c ) {
-        if( c == null ) { throw new IllegalArgumentException("Cigar cannot be null"); }
-        if( c.isEmpty() ) { return c; }
+        if ( c == null ) { throw new IllegalArgumentException("Cigar cannot be null"); }
+
+        // fast check to determine if there's anything worth doing before we create new Cigar and actually do some work
+        if ( ! needsConsolidation(c) )
+            return c;
 
         final Cigar returnCigar = new Cigar();
         int sumLength = 0;
@@ -601,13 +604,33 @@ public final class AlignmentUtils {
             lastElement = cur;
         }
 
-        if( sumLength > 0 ) {
+        if ( sumLength > 0 ) {
             returnCigar.add(new CigarElement(sumLength, lastElement.getOperator()));
         }
 
         return returnCigar;
     }
 
+    /**
+     * Does the cigar C need to be consolidated?
+     *
+     * @param c a non-null cigar
+     * @return true if so
+     */
+    private static boolean needsConsolidation(final Cigar c) {
+        if ( c.numCigarElements() <= 1 )
+            return false; // fast path for empty or single cigar
+
+        CigarOperator lastOp = null;
+        for( final CigarElement cur : c.getCigarElements() ) {
+            if ( cur.getLength() == 0 || lastOp == cur.getOperator() )
+                return true;
+            lastOp = cur.getOperator();
+        }
+
+        return false;
+    }
+
     /**
      * Takes the alignment of the read sequence <code>readSeq</code> to the reference sequence <code>refSeq</code>
      * starting at 0-based position <code>refIndex</code> on the <code>refSeq</code> and specified by its <code>cigar</code>.