diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReadsWalker.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReadsWalker.java
index 095149bae..1b11cbd4e 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReadsWalker.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReadsWalker.java
@@ -663,7 +663,7 @@ public class ReduceReadsWalker extends ReadWalker<LinkedList<GATKSAMRecord>, Red
      * @return Returns true if the read is the original read that went through map().
      */
     private boolean isOriginalRead(LinkedList<GATKSAMRecord> list, GATKSAMRecord read) {
-        return isWholeGenome() || (list.getFirst().equals(read) && ReadUtils.getReadAndIntervalOverlapType(read, intervalList.first()) == ReadUtils.ReadAndIntervalOverlap.OVERLAP_CONTAINED);
+        return isWholeGenome() || list.getFirst().equals(read);
     }
 
     /**
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffObjectsWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffObjectsWalker.java
index 1dc28b0e7..2b7a5612b 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffObjectsWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffObjectsWalker.java
@@ -25,6 +25,7 @@
 package org.broadinstitute.sting.gatk.walkers.diffengine;
 
 import org.broadinstitute.sting.commandline.Argument;
+import org.broadinstitute.sting.commandline.Input;
 import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
@@ -144,7 +145,7 @@ public class DiffObjectsWalker extends RodWalker<Integer, Integer> {
      * files to do the comparison.  Conceptually master is the original file contained the expected
      * results, but this doesn't currently have an impact on the calculations, but might in the future.
      */
-    @Argument(fullName="master", shortName="m", doc="Master file: expected results", required=true)
+    @Input(fullName="master", shortName="m", doc="Master file: expected results", required=true)
     File masterFile;
 
     /**
@@ -152,7 +153,7 @@ public class DiffObjectsWalker extends RodWalker<Integer, Integer> {
      * files to do the comparison.  Conceptually test is the derived file from master, but this
      * doesn't currently have an impact on the calculations, but might in the future.
      */
-    @Argument(fullName="test", shortName="t", doc="Test file: new results to compare to the master file", required=true)
+    @Input(fullName="test", shortName="t", doc="Test file: new results to compare to the master file", required=true)
     File testFile;
 
     /**