diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/InbreedingCoeffUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/InbreedingCoeffUnitTest.java
index 888d761af..d76a5351d 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/InbreedingCoeffUnitTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/annotator/InbreedingCoeffUnitTest.java
@@ -59,6 +59,7 @@ import org.testng.annotations.Test;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.List;
+import java.util.Set;
 
 /**
  * Created with IntelliJ IDEA.
@@ -102,7 +103,10 @@ public class InbreedingCoeffUnitTest {
     private VariantContext makeVC(String source, List<Allele> alleles, Genotype... genotypes) {
         int start = 10;
         int stop = start; // alleles.contains(ATC) ? start + 3 : start;
-        return new VariantContextBuilder(source, "1", start, stop, alleles).genotypes(Arrays.asList(genotypes)).filters(null).make();
+        return new VariantContextBuilder(source, "1", start, stop, alleles)
+                .genotypes(Arrays.asList(genotypes))
+                .filters((String)null)
+                .make();
     }
 
     @Test
diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/PosteriorLikelihoodsUtilsUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/PosteriorLikelihoodsUtilsUnitTest.java
index e24623998..d6213ccde 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/PosteriorLikelihoodsUtilsUnitTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/PosteriorLikelihoodsUtilsUnitTest.java
@@ -134,7 +134,7 @@ public class PosteriorLikelihoodsUtilsUnitTest extends BaseTest {
     private VariantContext makeVC(String source, List<Allele> alleles, Genotype... genotypes) {
         int start = 10;
         int stop = start; // alleles.contains(ATC) ? start + 3 : start;
-        return new VariantContextBuilder(source, "1", start, stop, alleles).genotypes(Arrays.asList(genotypes)).filters(null).make();
+        return new VariantContextBuilder(source, "1", start, stop, alleles).genotypes(Arrays.asList(genotypes)).filters((String)null).make();
     }
 
     @Test
diff --git a/public/gatk-root/pom.xml b/public/gatk-root/pom.xml
index 206f655b1..f24468fb2 100644
--- a/public/gatk-root/pom.xml
+++ b/public/gatk-root/pom.xml
@@ -64,7 +64,7 @@
             <dependency>
                 <groupId>com.google.code.cofoja</groupId>
                 <artifactId>cofoja</artifactId>
-                <version>1.0-r139</version>
+                <version>1.2-20140817</version>
             </dependency>
             <dependency>
                 <groupId>com.github.samtools</groupId>
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/AnnotationInterfaceManager.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/AnnotationInterfaceManager.java
index 37b570c87..56c4087c3 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/AnnotationInterfaceManager.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/AnnotationInterfaceManager.java
@@ -133,7 +133,7 @@ public class AnnotationInterfaceManager {
 
         // note that technically an annotation can work on both the INFO and FORMAT fields
         for ( Class c : classes )
-            annotations.add(pluginManager.createByType(c));
+            annotations.add((T)pluginManager.createByType(c));
 
         return annotations;
     }
diff --git a/public/repo/com/google/code/cofoja/cofoja/1.0-r139/cofoja-1.0-r139.jar b/public/repo/com/google/code/cofoja/cofoja/1.0-r139/cofoja-1.0-r139.jar
deleted file mode 100644
index 2cbdd380d..000000000
Binary files a/public/repo/com/google/code/cofoja/cofoja/1.0-r139/cofoja-1.0-r139.jar and /dev/null differ
diff --git a/public/repo/com/google/code/cofoja/cofoja/1.0-r139/cofoja-1.0-r139.pom b/public/repo/com/google/code/cofoja/cofoja/1.0-r139/cofoja-1.0-r139.pom
deleted file mode 100644
index 5a6fb69b9..000000000
--- a/public/repo/com/google/code/cofoja/cofoja/1.0-r139/cofoja-1.0-r139.pom
+++ /dev/null
@@ -1,9 +0,0 @@
-<project xmlns="http://maven.apache.org/POM/4.0.0"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
-  <modelVersion>4.0.0</modelVersion>
-  <groupId>com.google.code.cofoja</groupId>
-  <artifactId>cofoja</artifactId>
-  <name>cofoja</name>
-  <version>1.0-r139</version>
-</project>
diff --git a/public/repo/com/google/code/cofoja/cofoja/1.2-20140817/cofoja-1.2-20140817.jar b/public/repo/com/google/code/cofoja/cofoja/1.2-20140817/cofoja-1.2-20140817.jar
new file mode 100644
index 000000000..2b105c88c
Binary files /dev/null and b/public/repo/com/google/code/cofoja/cofoja/1.2-20140817/cofoja-1.2-20140817.jar differ
diff --git a/public/repo/com/google/code/cofoja/cofoja/1.2-20140817/cofoja-1.2-20140817.pom b/public/repo/com/google/code/cofoja/cofoja/1.2-20140817/cofoja-1.2-20140817.pom
new file mode 100644
index 000000000..92fbea553
--- /dev/null
+++ b/public/repo/com/google/code/cofoja/cofoja/1.2-20140817/cofoja-1.2-20140817.pom
@@ -0,0 +1,89 @@
+<project xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd" xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
+  <modelVersion>4.0.0</modelVersion>
+
+  <groupId>com.google.java.contract</groupId>
+  <artifactId>cofoja</artifactId>
+  <version>1.2-20140817</version>
+  <name>Contracts for Java</name>
+  <description>Contracts for Java is a contract programming framework for Java.</description>
+  <url>http://code.google.com/p/cofoja</url>
+
+  <issueManagement>
+    <system>code.google.com</system>
+    <url>http://code.google.com/p/cofoja/issues</url>
+  </issueManagement>
+
+  <inceptionYear>2010</inceptionYear>
+
+  <licenses>
+    <license>
+      <name>GNU Lesser General Public License, version 2.1 or later</name>
+      <url>http://www.gnu.org/licenses/lgpl-2.1.html</url>
+      <distribution>repo</distribution>
+    </license>
+  </licenses>
+
+  <scm>
+    <connection>scm:svn:http://cofoja.googlecode.com/svn/trunk/</connection>
+    <developerConnection>scm:svn:https://cofoja.googlecode.com/svn/trunk/</developerConnection>
+    <url>http://code.google.com/p/cofoja/source/browse</url>
+  </scm>
+
+  <properties>
+    <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
+  </properties>
+
+    <developers>
+        <developer>
+            <id>andreasleitner</id>
+            <name>Andreas Leitner</name>
+            <email>andreasleitner@google.com</email>
+            <organization>Google</organization>
+            <organizationUrl>http://www.google.com</organizationUrl>
+            <roles>
+                <role>Developer</role>
+            </roles>
+        </developer>
+        <developer>
+            <id>davidmorgan</id>
+            <name>David Morgan</name>
+            <email>davidmorgan@google.com</email>
+            <organization>Google</organization>
+            <organizationUrl>http://www.google.com</organizationUrl>
+            <roles>
+                <role>Developer</role>
+            </roles>
+        </developer>
+        <developer>
+            <id>lenh</id>
+            <name>Nhat Minh Lê</name>
+            <email>nhat.minh.le@huoc.org</email>
+            <roles>
+                <role>Developer</role>
+            </roles>
+        </developer>
+    </developers>
+
+    <dependencies>
+        <dependency>
+            <groupId>org.ow2.asm</groupId>
+            <artifactId>asm-all</artifactId>
+            <version>5.0.4</version>
+            <scope>compile</scope>
+        </dependency>
+        <dependency>
+            <groupId>junit</groupId>
+            <artifactId>junit</artifactId>
+            <version>4.8.2</version>
+            <scope>test</scope>
+        </dependency>
+        <dependency>
+            <groupId>com.sun</groupId>
+            <artifactId>tools</artifactId>
+            <version>1.5.0</version>
+            <scope>system</scope>
+            <systemPath>${toolsjar}</systemPath>                                                                                 
+        </dependency>
+    </dependencies>
+
+</project>