diff --git a/java/src/org/broadinstitute/sting/gatk/filters/MalformedReadFilter.java b/java/src/org/broadinstitute/sting/gatk/filters/MalformedReadFilter.java
index ca6387d8d..d56b8b780 100644
--- a/java/src/org/broadinstitute/sting/gatk/filters/MalformedReadFilter.java
+++ b/java/src/org/broadinstitute/sting/gatk/filters/MalformedReadFilter.java
@@ -72,8 +72,8 @@ public class MalformedReadFilter implements SamRecordHeaderFilter {
      * @return true if read end is valid, false otherwise.
      */
     private static boolean checkInvalidAlignmentEnd( SAMRecord read ) {
-        // Alignment ends prior to its beginning
-        if( !read.getReadUnmappedFlag() && read.getAlignmentEnd() != -1 && read.getAlignmentEnd() < read.getAlignmentStart() )
+        // Alignment aligns to negative number of bases in the reference.
+        if( !read.getReadUnmappedFlag() && read.getAlignmentEnd() != -1 && (read.getAlignmentEnd()-read.getAlignmentStart()+1)<0 )
             return false;
         return true;
     }
@@ -105,7 +105,7 @@ public class MalformedReadFilter implements SamRecordHeaderFilter {
         if( !read.getReadUnmappedFlag() &&
             read.getAlignmentStart() != -1 &&
             read.getAlignmentStart() != SAMRecord.NO_ALIGNMENT_START &&
-            read.getAlignmentBlocks().size() == 0 )
+            read.getAlignmentBlocks().size() < 0 )
             return false;
         return true;
     }
diff --git a/java/src/org/broadinstitute/sting/gatk/traversals/TraverseReads.java b/java/src/org/broadinstitute/sting/gatk/traversals/TraverseReads.java
index 31a85cc28..4cb5b4949 100755
--- a/java/src/org/broadinstitute/sting/gatk/traversals/TraverseReads.java
+++ b/java/src/org/broadinstitute/sting/gatk/traversals/TraverseReads.java
@@ -92,7 +92,6 @@ public class TraverseReads<M,T> extends TraversalEngine<M,T,ReadWalker<M,T>,Read
             // update the number of reads we've seen
             ReadMetrics readMetrics = dataProvider.getShard().getReadMetrics();
             readMetrics.incrementNumIterations();
-            readMetrics.incrementNumReadsSeen();
 
             // if the read is mapped, create a metadata tracker
             ReadMetaDataTracker tracker = (read.getReferenceIndex() >= 0) ? rodView.getReferenceOrderedDataForRead(read) : null;