diff --git a/java/src/org/broadinstitute/sting/utils/classloader/JVMUtils.java b/java/src/org/broadinstitute/sting/utils/classloader/JVMUtils.java
index 4b2873108..404bd80b6 100755
--- a/java/src/org/broadinstitute/sting/utils/classloader/JVMUtils.java
+++ b/java/src/org/broadinstitute/sting/utils/classloader/JVMUtils.java
@@ -80,6 +80,16 @@ public class JVMUtils {
                !Modifier.isInterface(clazz.getModifiers());
     }
 
+    /**
+     * Is the specified class anonymous?  The plugin manager (for one) generally requires that
+     * plugin classes be named so that they can easily be specified from the command line.
+     * @param clazz The class on which to perform the anonymous check.
+     * @return True if the class is anonymous; false otherwise.
+     */
+    public static boolean isAnonymous(Class clazz) {
+        return clazz.isAnonymousClass();
+    }
+
     /**
      * Retrieve all fields available in this object, regardless of where they are declared or
      * whether they're accessible.
diff --git a/java/src/org/broadinstitute/sting/utils/classloader/PluginManager.java b/java/src/org/broadinstitute/sting/utils/classloader/PluginManager.java
index 25c1c76a2..b9f5a2421 100644
--- a/java/src/org/broadinstitute/sting/utils/classloader/PluginManager.java
+++ b/java/src/org/broadinstitute/sting/utils/classloader/PluginManager.java
@@ -133,6 +133,10 @@ public class PluginManager<PluginType> {
         // Load all classes types filtering them by concrete.
         Set<Class<? extends PluginType>> allTypes = reflections.getSubTypesOf(pluginType);
         for( Class<? extends PluginType> type: allTypes ) {
+            // The plugin manager does not support anonymous classes; to be a plugin, a class must have a name.
+            if(JVMUtils.isAnonymous(type))
+                continue;
+
             if( JVMUtils.isConcrete(type) )
                 plugins.add(type);
             else
diff --git a/settings/repository/edu.mit.broad/picard-private-parts-1816.jar b/settings/repository/edu.mit.broad/picard-private-parts-1859.jar
similarity index 84%
rename from settings/repository/edu.mit.broad/picard-private-parts-1816.jar
rename to settings/repository/edu.mit.broad/picard-private-parts-1859.jar
index 33238a46f..f738f1462 100644
Binary files a/settings/repository/edu.mit.broad/picard-private-parts-1816.jar and b/settings/repository/edu.mit.broad/picard-private-parts-1859.jar differ
diff --git a/settings/repository/edu.mit.broad/picard-private-parts-1816.xml b/settings/repository/edu.mit.broad/picard-private-parts-1859.xml
similarity index 58%
rename from settings/repository/edu.mit.broad/picard-private-parts-1816.xml
rename to settings/repository/edu.mit.broad/picard-private-parts-1859.xml
index a2dad75a1..6c35ccd1c 100644
--- a/settings/repository/edu.mit.broad/picard-private-parts-1816.xml
+++ b/settings/repository/edu.mit.broad/picard-private-parts-1859.xml
@@ -1,3 +1,3 @@
 <ivy-module version="1.0">
-    <info organisation="edu.mit.broad" module="picard-private-parts" revision="1816" status="integration" publication="20110102175300" />
+    <info organisation="edu.mit.broad" module="picard-private-parts" revision="1859" status="integration" publication="20110427114200" />
 </ivy-module>
diff --git a/settings/repository/net.sf/picard-1.42.773.xml b/settings/repository/net.sf/picard-1.42.773.xml
deleted file mode 100644
index 3ccf0dd2f..000000000
--- a/settings/repository/net.sf/picard-1.42.773.xml
+++ /dev/null
@@ -1,3 +0,0 @@
-<ivy-module version="1.0">
-    <info organisation="net.sf" module="picard" revision="1.42.773" status="release" />
-</ivy-module>
diff --git a/settings/repository/net.sf/picard-1.42.773.jar b/settings/repository/net.sf/picard-1.44.794.jar
similarity index 67%
rename from settings/repository/net.sf/picard-1.42.773.jar
rename to settings/repository/net.sf/picard-1.44.794.jar
index 4280f2cfb..f095ec053 100644
Binary files a/settings/repository/net.sf/picard-1.42.773.jar and b/settings/repository/net.sf/picard-1.44.794.jar differ
diff --git a/settings/repository/net.sf/picard-1.44.794.xml b/settings/repository/net.sf/picard-1.44.794.xml
new file mode 100644
index 000000000..3f7a3483c
--- /dev/null
+++ b/settings/repository/net.sf/picard-1.44.794.xml
@@ -0,0 +1,3 @@
+<ivy-module version="1.0">
+    <info organisation="net.sf" module="picard" revision="1.44.794" status="release" />
+</ivy-module>
diff --git a/settings/repository/net.sf/sam-1.42.773.xml b/settings/repository/net.sf/sam-1.42.773.xml
deleted file mode 100644
index 53d6d3eab..000000000
--- a/settings/repository/net.sf/sam-1.42.773.xml
+++ /dev/null
@@ -1,3 +0,0 @@
-<ivy-module version="1.0">
-    <info organisation="net.sf" module="sam" revision="1.42.773" status="release" />
-</ivy-module>
diff --git a/settings/repository/net.sf/sam-1.42.773.jar b/settings/repository/net.sf/sam-1.44.794.jar
similarity index 90%
rename from settings/repository/net.sf/sam-1.42.773.jar
rename to settings/repository/net.sf/sam-1.44.794.jar
index 75f280d17..3e4bc5f88 100644
Binary files a/settings/repository/net.sf/sam-1.42.773.jar and b/settings/repository/net.sf/sam-1.44.794.jar differ
diff --git a/settings/repository/net.sf/sam-1.44.794.xml b/settings/repository/net.sf/sam-1.44.794.xml
new file mode 100644
index 000000000..b29fb49d4
--- /dev/null
+++ b/settings/repository/net.sf/sam-1.44.794.xml
@@ -0,0 +1,3 @@
+<ivy-module version="1.0">
+    <info organisation="net.sf" module="sam" revision="1.44.794" status="release" />
+</ivy-module>