diff --git a/public/java/src/org/broadinstitute/sting/utils/activeregion/ActiveRegion.java b/public/java/src/org/broadinstitute/sting/utils/activeregion/ActiveRegion.java
index 764be2ac7..4fcc6a879 100644
--- a/public/java/src/org/broadinstitute/sting/utils/activeregion/ActiveRegion.java
+++ b/public/java/src/org/broadinstitute/sting/utils/activeregion/ActiveRegion.java
@@ -58,9 +58,9 @@ public class ActiveRegion implements HasGenomeLocation, Comparable<ActiveRegion>
     }
 
     public byte[] getActiveRegionReference( final IndexedFastaSequenceFile referenceReader, final int padding ) {
-        return referenceReader.getSubsequenceAt( activeRegionLoc.getContig(),
-                Math.max(1, activeRegionLoc.getStart() - padding),
-                Math.min(referenceReader.getSequenceDictionary().getSequence(activeRegionLoc.getContig()).getSequenceLength(), activeRegionLoc.getStop() + padding) ).getBases();
+        return referenceReader.getSubsequenceAt( extendedLoc.getContig(),
+                Math.max(1, extendedLoc.getStart() - padding),
+                Math.min(referenceReader.getSequenceDictionary().getSequence(extendedLoc.getContig()).getSequenceLength(), extendedLoc.getStop() + padding) ).getBases();
     }
 
     public byte[] getFullReference( final IndexedFastaSequenceFile referenceReader ) {
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 71e08ef23..4e2fd1446 100755
--- a/public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java
+++ b/public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java
@@ -447,7 +447,7 @@ public class ReadUtils {
 
             if (goalReached) {
                 // Is this base's reference position within this cigar element? Or did we use it all?
-                boolean endsWithinCigar = shift <= cigarElement.getLength();
+                boolean endsWithinCigar = shift < cigarElement.getLength();
 
                 // If it isn't, we need to check the next one. There should *ALWAYS* be a next one
                 // since we checked if the goal coordinate is within the read length, so this is just a sanity check.