diff --git a/build.xml b/build.xml
index 2a23f74c1..986d89213 100644
--- a/build.xml
+++ b/build.xml
@@ -28,6 +28,7 @@
 
     <property name="build.dir" value="build" />
     <property name="dist.dir" value="dist" />
+    <property name="lib.dir" value="lib" />
     <property name="external.dir" value="external" />
     <property name="public.dir" value="public" />
     <property name="private.dir" value="private" />
@@ -44,11 +45,11 @@
     <property name="queue-extensions.source.dir" value="${build.dir}/queue-extensions/src" />
     
     <!-- Contracts for Java -->
-    <!-- uncomment out to enable building contracts -->
-    <property name="use.contracts" value="true" /> 
+    <!-- To disable, run with -Duse.contracts=false -->
+    <property name="use.contracts" value="true" />
     <property name="java.contracts" value="${build.dir}/java/contracts" />
-    <property name="cofojaDir" value="settings/repository/com.google/"/>
-    <property name="cofoja.jar" value="${cofojaDir}/cofoja-1.0-20110609.jar"/>
+    <property name="contracts.version" value="1.0-20110609" />
+    <property name="cofoja.jar" value="${lib.dir}/cofoja-${contracts.version}.jar"/>
     
     <!-- where to find the tribble distro -->
     <property name="tribble.dir" value="tribble" />
@@ -69,7 +70,7 @@
 
     <property environment="env"/>
 
-    <property name="drmaa.jar" value="${env.SGE_ROOT}/lib/drmaa.jar" />
+    <property name="drmaa.jar" value="${env.SGE_ROOT}/${lib.dir}/drmaa.jar" />
 
     <patternset id="java.source.pattern">
         <include name="${java.public.source.dir}/**/*.java" />
@@ -103,7 +104,7 @@
     </patternset>
     
     <path id="external.dependencies">
-      <fileset dir="lib">
+      <fileset dir="${lib.dir}">
         <patternset refid="dependency.mask" />
       </fileset>
     </path>
@@ -128,14 +129,14 @@
         <!-- ivy properties -->
         <property name="ivy.install.version" value="2.2.0"/>
         <property name="ivy.home" value="${user.home}/.ant"/>
-        <property name="ivy.jar.dir" value="${ivy.home}/lib"/>
+        <property name="ivy.jar.dir" value="${ivy.home}/${lib.dir}"/>
         <property name="ivy.jar.file" value="ivy-${ivy.install.version}.jar"/>
         <property name="ivy.settings.dir" value="settings"/>
         <property file="${ivy.settings.dir}/ivysettings.properties"/>
   
-      <mkdir dir="lib"/>
+      <mkdir dir="${lib.dir}"/>
       <mkdir dir="${ivy.jar.dir}"/>
-      <copy file="${cofoja.jar}" toFile="lib/cofoja.jar"/>
+
       <get src="http://repo1.maven.org/maven2/org/apache/ivy/ivy/${ivy.install.version}/${ivy.jar.file}"
            dest="${ivy.jar.dir}/${ivy.jar.file}"
            usetimestamp="true"/>
@@ -147,7 +148,7 @@
     </target>
 
     <target name="init.gridengine" depends="init" if="include.gridengine">
-        <copy todir="lib" file="${drmaa.jar}"/>
+        <copy todir="${lib.dir}" file="${drmaa.jar}"/>
     </target>
 
     <target name="resolve" depends="init.resolve,init,init.gridengine"
@@ -229,6 +230,10 @@
         <equals arg1="${gatk.target}" arg2="private" casesensitive="false" />
       </condition>
 
+      <condition property="include.contracts">
+        <equals arg1="${use.contracts}" arg2="true" />
+      </condition>
+
       <!-- Create the build directory structure used by compile -->
       <mkdir dir="${build.dir}"/>
       <mkdir dir="${java.classes}"/>
@@ -252,7 +257,7 @@
     <target name="init.scala.compile" depends="resolve"
             description="Initializes the scala ant tasks from scala-compiler.jar">
         <path id="scala.classpath">
-            <fileset dir="lib">
+            <fileset dir="${lib.dir}">
                 <include name="scala-compiler-*.jar"/>
                 <include name="scala-library-*.jar"/>
             </fileset>
@@ -287,7 +292,7 @@
             depends="gatk.compile.public.source,gatk.compile.private.source,gatk.compile.external.source" 
             description="compile the GATK source" />
 
-   <target name="gatk.contracts.public" depends="gatk.compile.source">
+   <target name="gatk.contracts.public" depends="gatk.compile.source" if="include.contracts">
         <javac fork="true" memoryMaximumSize="512m" srcdir="${java.public.source.dir}" destdir="${java.contracts}" debug="true" debuglevel="lines,vars,source" tempdir="${java.io.tmpdir}" >
             <classpath>
                 <path refid="external.dependencies" />
@@ -299,7 +304,16 @@
         </javac>   
    </target>
 
-   <target name="gatk.contracts.private" depends="gatk.compile.source" if="include.private">
+    <target name="check.contracts.private" depends="gatk.contracts.public">
+        <condition property="include.contracts.private">
+          <and>
+            <isset property="include.contracts" />
+            <isset property="include.private" />
+          </and>
+        </condition>
+    </target>
+
+   <target name="gatk.contracts.private" depends="check.contracts.private" if="include.contracts.private">
         <javac fork="true" memoryMaximumSize="512m" srcdir="${java.private.source.dir}" destdir="${java.contracts}" debug="true" debuglevel="lines,vars,source" tempdir="${java.io.tmpdir}" >
             <classpath>
                 <path refid="external.dependencies" />
@@ -312,7 +326,7 @@
    </target>
 
     <target name="gatk.contracts" depends="gatk.contracts.public,gatk.contracts.private" 
-            description="create GATK contracts" if="use.contracts" />
+            description="create GATK contracts" if="include.contracts" />
     
     <target name="gatk.compile" depends="tribble,init,resolve,gatk.compile.source,gatk.contracts" />
 
@@ -452,7 +466,7 @@
     <target name="init.jar" depends="sting.compile,extracthelp">
         <mkdir dir="${dist.dir}"/>
         <copy todir="${dist.dir}">
-            <fileset dir="lib" includes="*.jar"/>
+            <fileset dir="${lib.dir}" includes="*.jar"/>
         </copy>
     </target>
 
@@ -663,7 +677,7 @@
                 <path refid="external.dependencies" />
                 <pathelement location="${java.classes}"/>
                 <pathelement location="${java.contracts}"/>
-                <pathelement location="lib/testng-5.14.1.jar"/>
+                <pathelement location="${lib.dir}/testng-5.14.1.jar"/>
             </classpath>
             <compilerarg value="-proc:none"/>
 <!-- 
@@ -687,7 +701,7 @@
                 <path refid="scala.dependencies"/>
                 <pathelement location="${scala.test.classes}"/>
                 <pathelement location="${java.test.classes}"/>
-                <pathelement location="lib/testng-5.14.1.jar"/>
+                <pathelement location="${lib.dir}/testng-5.14.1.jar"/>
             </classpath>
         </scalac>
     </target>
@@ -727,9 +741,13 @@
                 <equals arg1="${pipeline.run}" arg2="$${pipeline.run}" />
             </condition>
 
+            <condition property="cofoja.jvm.args" value="-javaagent:${cofoja.jar} -Dcom.google.java.contract.log.contract=false" else="">
+                <isset property="include.contracts" />
+            </condition>
+
             <mkdir dir="${report}/@{testtype}"/>
             <echo message="Sting: Running @{testtype} test cases!"/>
-            <taskdef resource="testngtasks" classpath="lib/testng-5.14.1.jar"/>
+            <taskdef resource="testngtasks" classpath="${lib.dir}/testng-5.14.1.jar"/>
             <testng outputDir="${report}/@{testtype}"
                     haltOnFailure="false" failureProperty="test.failure"
                     verbose="2"
@@ -740,9 +758,7 @@
                 <jvmarg value="-Djava.awt.headless=true" />
                 <jvmarg value="-Dpipeline.run=${pipeline.run}" />
                 <jvmarg value="-Djava.io.tmpdir=${java.io.tmpdir}" />
-                <!-- needs to be if -->
-                <!--jvmarg value="-javaagent:lib/cofoja.jar"/-->
-                <!--jvmarg value="-Dcom.google.java.contract.log.contract=false"/-->
+                <jvmarg line="${cofoja.jvm.args}"/>
 <!--                 <jvmarg value="-Xdebug"/> -->
 <!--                 <jvmarg value="-Xrunjdwp:transport=dt_socket,server=y,suspend=y,address=5005"/> -->
                 <classpath>
@@ -820,7 +836,7 @@
 
     <!-- copy the compiled library -->
     <target name="tribble.compile.copy" description="Copies the compiled tribble library" depends="tribble.compile" if="tribble.compile.exists">
-        <copy todir="lib">
+        <copy todir="${lib.dir}">
             <fileset dir="${tribble.dir}/dist" includes="*.jar"/>
         </copy>
     </target>
@@ -828,7 +844,7 @@
     <!-- copy the precompiled library -->
     <target name="tribble.library.copy" description="Copies the precompiled tribble library" depends="tribble.init" unless="tribble.compile.exists">
         <echo message="Copying the Tribble Library..."/>
-        <copy todir="lib">
+        <copy todir="${lib.dir}">
             <fileset dir="settings/repository/org.broad" includes="tribble*.jar"/>
         </copy>
     </target>
@@ -921,8 +937,8 @@
       <pathconvert property="required.picard.jars" pathsep=":">
         <fileset dir="${basedir}">
 	     <include name="staging" />
-	     <include name="lib/picard-*.*.*.jar" />
-	     <include name="lib/sam-*.jar" />
+	     <include name="${lib.dir}/picard-*.*.*.jar" />
+	     <include name="${lib.dir}/sam-*.jar" />
 	   </fileset>
       </pathconvert>
       <echo message="required.picard.jars=${required.picard.jars}" />
@@ -944,7 +960,7 @@
     <!-- Find bug tasks                                                                   -->
     <!-- ******************************************************************************** -->
     <path id="findbugs.classpath">
-      <fileset dir="lib" erroronmissingdir="true" includes="*.jar"/>
+      <fileset dir="${lib.dir}" erroronmissingdir="true" includes="*.jar"/>
     </path>
     <target         name="findbugs" depends="dist">
         <antcall    target  ="resolve">
@@ -969,7 +985,7 @@
     <target name="clean" description="clean up" depends="tribble.clean,clean.javadoc">
         <delete dir="out"/>
         <delete dir="${build.dir}"/>
-        <delete dir="lib"/>
+        <delete dir="${lib.dir}"/>
         <delete dir="staging"/>
         <delete dir="${dist.dir}"/>
         <delete dir="pipelinetests"/>
diff --git a/ivy.xml b/ivy.xml
index c2a6c4ccd..ce724bc3c 100644
--- a/ivy.xml
+++ b/ivy.xml
@@ -60,6 +60,10 @@
     <dependency org="net.sourceforge.findbugs" name="jsr305" rev="1.3.2" conf="test"/>
     <dependency org="com.google.code.caliper" name="caliper" rev="1.0-SNAPSHOT" conf="test" />
 
+    <!-- Contracts for Java and dependencies -->
+    <dependency org="com.google.code.cofoja" name="cofoja" rev="1.0-20110609" />
+    <dependency org="asm" name="asm-all" rev="3.3.1" />
+
     <!-- POI, for reading pipeline files -->
     <dependency org="org.apache.poi" name="poi" rev="3.8-beta3" />
     <dependency org="org.apache.poi" name="poi-ooxml" rev="3.8-beta3" />
diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java
index cd0f52c68..01344a117 100755
--- a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java
+++ b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java
@@ -225,7 +225,7 @@ public abstract class AbstractVCFCodec implements FeatureCodec, NameAwareCodec,
             loc = pos + alleles.get(0).length() - 1;
         } else if ( !isSingleNucleotideEvent(alleles) ) {
             ArrayList<Allele> newAlleles = new ArrayList<Allele>();
-            loc = clipAlleles(pos, ref, alleles, newAlleles);
+            loc = clipAlleles(pos, ref, alleles, newAlleles, lineNo);
             alleles = newAlleles;
         }
 
@@ -504,7 +504,7 @@ public abstract class AbstractVCFCodec implements FeatureCodec, NameAwareCodec,
      * @param clippedAlleles output list of clipped alleles
      * @return a list of alleles, clipped to the reference
      */
-    protected static long clipAlleles(long position, String ref, List<Allele> unclippedAlleles, List<Allele> clippedAlleles) {
+    protected static long clipAlleles(long position, String ref, List<Allele> unclippedAlleles, List<Allele> clippedAlleles, int lineNo) {
 
         // Note that the computation of forward clipping here is meant only to see whether there is a common
         // base to all alleles, and to correctly compute reverse clipping,
@@ -522,6 +522,8 @@ public abstract class AbstractVCFCodec implements FeatureCodec, NameAwareCodec,
                 }
                 if (a.length() - reverseClipped <= forwardClipping || a.length() - forwardClipping == 0)
                     clipping = false;
+                else if (ref.length() == reverseClipped)
+                    generateException("bad alleles encountered", lineNo);
                 else if (a.getBases()[a.length()-reverseClipped-1] != ref.getBytes()[ref.length()-reverseClipped-1])
                     clipping = false;
             }
diff --git a/settings/ivysettings.xml b/settings/ivysettings.xml
index 1e47fa847..b77414df9 100644
--- a/settings/ivysettings.xml
+++ b/settings/ivysettings.xml
@@ -25,5 +25,6 @@
     <module organisation="javax.activation" resolver="java.net" />
     <module organisation="net.java.dev.jna" resolver="maven2-repository.dev.java.net" />
     <module organisation="com.google.code.caliper" resolver="projects" />
+    <module organisation="com.google.code.cofoja" resolver="projects" />
   </modules>
 </ivysettings>
diff --git a/settings/repository/com.google/cofoja-1.0-20110609.jar b/settings/repository/com.google.code.cofoja/cofoja-1.0-20110609.jar
similarity index 100%
rename from settings/repository/com.google/cofoja-1.0-20110609.jar
rename to settings/repository/com.google.code.cofoja/cofoja-1.0-20110609.jar
diff --git a/settings/repository/com.google.code.cofoja/cofoja-1.0-20110609.xml b/settings/repository/com.google.code.cofoja/cofoja-1.0-20110609.xml
new file mode 100644
index 000000000..38d4e88f1
--- /dev/null
+++ b/settings/repository/com.google.code.cofoja/cofoja-1.0-20110609.xml
@@ -0,0 +1,3 @@
+<ivy-module version="1.0">
+    <info organisation="com.google.code.cofoja" module="cofoja" revision="1.0-20110609" status="integration" publication="20110609114800" />
+</ivy-module>