diff --git a/public/java/src/org/broadinstitute/sting/utils/SimpleTimer.java b/public/java/src/org/broadinstitute/sting/utils/SimpleTimer.java
index 342087b41..6d228640f 100644
--- a/public/java/src/org/broadinstitute/sting/utils/SimpleTimer.java
+++ b/public/java/src/org/broadinstitute/sting/utils/SimpleTimer.java
@@ -58,7 +58,7 @@ public class SimpleTimer {
      */
     @Requires("running == false")
     @Ensures({"result != null", "elapsed == 0l"})
-    public SimpleTimer start() {
+    public synchronized SimpleTimer start() {
         elapsed = 0l;
         restart();
         return this;
@@ -73,7 +73,7 @@ public class SimpleTimer {
      */
     @Requires("running == false")
     @Ensures("result != null")
-    public SimpleTimer restart() {
+    public synchronized SimpleTimer restart() {
         running = true;
         startTime = currentTime();
         return this;
@@ -101,7 +101,7 @@ public class SimpleTimer {
      */
     @Requires("running == true")
     @Ensures({"result != null", "elapsed >= old(elapsed)", "running == false"})
-    public SimpleTimer stop() {
+    public synchronized SimpleTimer stop() {
         running = false;
         elapsed += currentTime() - startTime;
         return this;
@@ -116,11 +116,10 @@ public class SimpleTimer {
     @Ensures({
             "result >= (elapsed/1000.0)",
             "result >= 0"})
-    public double getElapsedTime() {
+    public synchronized double getElapsedTime() {
         return (running ? (currentTime() - startTime + elapsed) : elapsed) / 1000.0;
     }
 
-
     public void printElapsedTime(PrintStream out) {
         out.printf("SimpleTimer %s: %.2f%n", name, getElapsedTime());
     }
diff --git a/public/java/src/org/broadinstitute/sting/utils/sam/AlignmentUtils.java b/public/java/src/org/broadinstitute/sting/utils/sam/AlignmentUtils.java
index 344eccb83..b8e892101 100644
--- a/public/java/src/org/broadinstitute/sting/utils/sam/AlignmentUtils.java
+++ b/public/java/src/org/broadinstitute/sting/utils/sam/AlignmentUtils.java
@@ -353,7 +353,7 @@ public class AlignmentUtils {
                 break;
             case D:
             case N:
-                refPos++;
+                refPos += elementLength;
                 break;
             case M:
                 for ( int jjj = 0; jjj < elementLength; jjj++ ) {