diff --git a/public/java/src/org/broadinstitute/sting/utils/clipreads/ClippingOp.java b/public/java/src/org/broadinstitute/sting/utils/clipreads/ClippingOp.java
index 5449906b2..5789b606a 100644
--- a/public/java/src/org/broadinstitute/sting/utils/clipreads/ClippingOp.java
+++ b/public/java/src/org/broadinstitute/sting/utils/clipreads/ClippingOp.java
@@ -4,6 +4,7 @@ import net.sf.samtools.Cigar;
 import net.sf.samtools.CigarElement;
 import net.sf.samtools.CigarOperator;
 import net.sf.samtools.SAMRecord;
+import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.sam.ReadUtils;
 
 import java.util.Vector;
@@ -72,48 +73,45 @@ public class ClippingOp {
                 break;
             case HARDCLIP_BASES:
             case SOFTCLIP_BASES:
-                if ( ! clippedRead.getReadUnmappedFlag() ) {
+                if ( clippedRead.getReadUnmappedFlag() ) {
                     // we can't process unmapped reads
-
-                    //System.out.printf("%d %d %d%n", stop, start, clippedRead.getReadLength());
-                    int myStop = stop;
-                    if ( (stop + 1 - start) == clippedRead.getReadLength() ) {
-                        // BAM representation issue -- we can't SOFTCLIP away all bases in a read, just leave it alone
-                        //Walker.logger.info(String.format("Warning, read %s has all bases clip but this can't be represented with SOFTCLIP_BASES, just leaving it alone", clippedRead.getReadName()));
-                        //break;
-                        myStop--; // just decrement stop
-                    }
-
-                    if ( start > 0 && myStop != clippedRead.getReadLength() - 1 )
-                        throw new RuntimeException(String.format("Cannot apply soft clipping operator to the middle of a read: %s to be clipped at %d-%d",
-                                clippedRead.getReadName(), start, myStop));
-
-                    Cigar oldCigar = clippedRead.getCigar();
-
-                    int scLeft = 0, scRight = clippedRead.getReadLength();
-                    if ( start == 0 )
-                        scLeft = myStop + 1;
-                    else
-                        scRight = start;
-
-                    Cigar newCigar = softClip(oldCigar, scLeft, scRight);
-                    clippedRead.setCigar(newCigar);
-
-                    int newClippedStart = getNewAlignmentStartOffset(newCigar, oldCigar);
-                    int newStart = clippedRead.getAlignmentStart() + newClippedStart;
-                    clippedRead.setAlignmentStart(newStart);
-
-                    if ( algorithm == ClippingRepresentation.HARDCLIP_BASES )
-                        clippedRead = ReadUtils.hardClipSoftClippedBases(clippedRead);
-                    //System.out.printf("%s clipping at %d %d / %d %d => %s and %d%n", oldCigar.toString(), start, stop, scLeft, scRight, newCigar.toString(), newStart);
-                } else if  ( algorithm == ClippingRepresentation.HARDCLIP_BASES ) {
-                    // we can hard clip unmapped reads
-                    if ( clippedRead.getReadNegativeStrandFlag() )
-                        clippedRead = ReadUtils.hardClipBases(clippedRead, 0, start, null);
-                    else
-                        clippedRead = ReadUtils.hardClipBases(clippedRead, start, start + getLength(), null);
+                    throw new UserException("Read Clipper cannot soft/hard clip unmapped reads");
                 }
+
+                //System.out.printf("%d %d %d%n", stop, start, clippedRead.getReadLength());
+                int myStop = stop;
+                if ( (stop + 1 - start) == clippedRead.getReadLength() ) {
+                    // BAM representation issue -- we can't SOFTCLIP away all bases in a read, just leave it alone
+                    //Walker.logger.info(String.format("Warning, read %s has all bases clip but this can't be represented with SOFTCLIP_BASES, just leaving it alone", clippedRead.getReadName()));
+                    //break;
+                    myStop--; // just decrement stop
+                }
+
+                if ( start > 0 && myStop != clippedRead.getReadLength() - 1 )
+                    throw new RuntimeException(String.format("Cannot apply soft clipping operator to the middle of a read: %s to be clipped at %d-%d",
+                            clippedRead.getReadName(), start, myStop));
+
+                Cigar oldCigar = clippedRead.getCigar();
+
+                int scLeft = 0, scRight = clippedRead.getReadLength();
+                if ( start == 0 )
+                    scLeft = myStop + 1;
+                else
+                    scRight = start;
+
+                Cigar newCigar = softClip(oldCigar, scLeft, scRight);
+                clippedRead.setCigar(newCigar);
+
+                int newClippedStart = getNewAlignmentStartOffset(newCigar, oldCigar);
+                int newStart = clippedRead.getAlignmentStart() + newClippedStart;
+                clippedRead.setAlignmentStart(newStart);
+
+                if ( algorithm == ClippingRepresentation.HARDCLIP_BASES )
+                    clippedRead = ReadUtils.hardClipSoftClippedBases(clippedRead);
+                //System.out.printf("%s clipping at %d %d / %d %d => %s and %d%n", oldCigar.toString(), start, stop, scLeft, scRight, newCigar.toString(), newStart);
+
                 break;
+
             default:
                 throw new IllegalStateException("Unexpected Clipping operator type " + algorithm);
         }
diff --git a/public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java b/public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java
index 448fc828f..16a02abdc 100644
--- a/public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java
+++ b/public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java
@@ -618,8 +618,8 @@ public class ReadUtils {
              (read.getUnclippedStart() > interval.getStop()) )
             return ReadAndIntervalOverlap.NO_OVERLAP;
 
-        else if ( (read.getUnclippedStart() > interval.getStart()) &&
-                  (read.getUnclippedEnd() < interval.getStop()) )
+        else if ( (read.getUnclippedStart() >= interval.getStart()) &&
+                  (read.getUnclippedEnd() <= interval.getStop()) )
             return ReadAndIntervalOverlap.CONTAINED;
 
         else if ( (read.getUnclippedStart() < interval.getStart()) &&