diff --git a/public/java/src/org/broadinstitute/sting/gatk/contexts/ReferenceContext.java b/public/java/src/org/broadinstitute/sting/gatk/contexts/ReferenceContext.java
index 1290319e2..af330bba9 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/contexts/ReferenceContext.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/contexts/ReferenceContext.java
@@ -177,7 +177,7 @@ public class ReferenceContext {
      * @return The base at the given locus from the reference.
      */
     public byte getBase() {
-        return getBases()[(int)(locus.getStart() - window.getStart())];
+        return getBases()[(locus.getStart() - window.getStart())];
     }
 
     /**
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/LeftAlignIndels.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/LeftAlignIndels.java
index b08def44f..6b9bd04d2 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/LeftAlignIndels.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/LeftAlignIndels.java
@@ -82,7 +82,7 @@ public class LeftAlignIndels extends ReadWalker<Integer, Integer> {
 
     public Integer map(ReferenceContext ref, GATKSAMRecord read, ReadMetaDataTracker metaDataTracker) {
         // we can not deal with screwy records
-        if ( read.getCigar().numCigarElements() == 0 ) {
+        if ( read.getReadUnmappedFlag() || read.getCigar().numCigarElements() == 0 ) {
             emit(read);
             return 0;
         }