diff --git a/java/src/org/broadinstitute/sting/utils/sam/AlignmentUtils.java b/java/src/org/broadinstitute/sting/utils/sam/AlignmentUtils.java
index 99a5bbb55..29d946410 100644
--- a/java/src/org/broadinstitute/sting/utils/sam/AlignmentUtils.java
+++ b/java/src/org/broadinstitute/sting/utils/sam/AlignmentUtils.java
@@ -70,7 +70,7 @@ public class AlignmentUtils {
      * on the read of length <code>nReadBases</code> starting at (0-based) position <code>readIndex</code>.
      * @param r Aligned read to count mismatches for
      * @param refSeq Chunk of reference sequence that subsumes the alignment
-     * @param refIndex Zero-based position on <code>refSeq</code> where the alighnment for the whole read starts
+     * @param refIndex Zero-based position on <code>refSeq</code> where the alignment for the whole read starts
      * @param readIndex Zero-based position on the read, the mismatches will be counted only from this position on
      * @param nReadBases Length of continuous stretch on the read, along which mismatches will be counted 
      * @return
@@ -491,7 +491,7 @@ public class AlignmentUtils {
                 if(!atDeletion) {
                     alignmentPos += elementLength;
                 } else {
-                    if( pos + elementLength >= pileupOffset ) {
+                    if( pos + elementLength - 1 >= pileupOffset ) {
                         return alignmentPos + (pileupOffset - pos);
                     } else {
                         pos += elementLength;
@@ -500,7 +500,7 @@ public class AlignmentUtils {
                 }
                 break;
             case M:
-                if( pos + elementLength >= pileupOffset ) {
+                if( pos + elementLength - 1 >= pileupOffset ) {
                     return alignmentPos + (pileupOffset - pos);
                 } else {
                     pos += elementLength;
@@ -602,7 +602,7 @@ public class AlignmentUtils {
         if ( r.getReadUnmappedFlag() ) return true;
 
         // our life would be so much easier if all sam files followed the specs. In reality,
-        // sam files (including those generated by maq or bwa) miss headers alltogether. When
+        // sam files (including those generated by maq or bwa) miss headers altogether. When
         // reading such a SAM file, reference name is set, but since there is no sequence dictionary,
         // null is always returned for referenceIndex. Let's be paranoid here, and make sure that
         // we do not call the read "unmapped" when it has only reference name set with ref. index missing
@@ -624,7 +624,7 @@ public class AlignmentUtils {
         if ( r.getMateUnmappedFlag() ) return true;
 
         // our life would be so much easier if all sam files followed the specs. In reality,
-        // sam files (including those generated by maq or bwa) miss headers alltogether. When
+        // sam files (including those generated by maq or bwa) miss headers altogether. When
         // reading such a SAM file, reference name is set, but since there is no sequence dictionary,
         // null is always returned for referenceIndex. Let's be paranoid here, and make sure that
         // we do not call the read "unmapped" when it has only reference name set with ref. index missing