diff --git a/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/data/KmerUtil.java b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/data/KmerUtil.java
index 86b9117..866d6c5 100644
--- a/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/data/KmerUtil.java
+++ b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/data/KmerUtil.java
@@ -1,5 +1,5 @@
 /*
- * Copyright 2009-2012 by The Regents of the University of California
+ * Copyright 2009-2013 by The Regents of the University of California
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
  * you may obtain a copy of the License from
diff --git a/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/data/Marshal.java b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/data/Marshal.java
index ecbf1ec..e80d7da 100644
--- a/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/data/Marshal.java
+++ b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/data/Marshal.java
@@ -1,3 +1,17 @@
+/*
+ * Copyright 2009-2013 by The Regents of the University of California
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * you may obtain a copy of the License from
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
 package edu.uci.ics.genomix.data;
 
 public class Marshal {
diff --git a/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/GeneCode.java b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/GeneCode.java
index d9f5c48..416ab49 100644
--- a/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/GeneCode.java
+++ b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/GeneCode.java
@@ -1,5 +1,5 @@
 /*
- * Copyright 2009-2012 by The Regents of the University of California
+ * Copyright 2009-2013 by The Regents of the University of California
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
  * you may obtain a copy of the License from
diff --git a/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/KmerBytesWritable.java b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/KmerBytesWritable.java
index 736dc56..1e0c23e 100644
--- a/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/KmerBytesWritable.java
+++ b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/KmerBytesWritable.java
@@ -1,5 +1,5 @@
 /*
- * Copyright 2009-2012 by The Regents of the University of California
+ * Copyright 2009-2013 by The Regents of the University of California
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
  * you may obtain a copy of the License from
diff --git a/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/KmerBytesWritableFactory.java b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/KmerBytesWritableFactory.java
index 9d458d2..d2e3a94 100644
--- a/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/KmerBytesWritableFactory.java
+++ b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/KmerBytesWritableFactory.java
@@ -1,5 +1,5 @@
 /*
- * Copyright 2009-2012 by The Regents of the University of California
+ * Copyright 2009-2013 by The Regents of the University of California
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
  * you may obtain a copy of the License from
diff --git a/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/NodeWritable.java b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/NodeWritable.java
index 65931a2..df3b79c 100644
--- a/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/NodeWritable.java
+++ b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/NodeWritable.java
@@ -1,3 +1,18 @@
+/*
+ * Copyright 2009-2013 by The Regents of the University of California
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * you may obtain a copy of the License from
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
 package edu.uci.ics.genomix.type;
 
 import java.io.DataInput;
diff --git a/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/PositionListWritable.java b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/PositionListWritable.java
index 34fb0f6..1b1b392 100644
--- a/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/PositionListWritable.java
+++ b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/PositionListWritable.java
@@ -1,3 +1,18 @@
+/*
+ * Copyright 2009-2013 by The Regents of the University of California
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * you may obtain a copy of the License from
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
 package edu.uci.ics.genomix.type;
 
 import java.io.DataInput;
@@ -94,7 +109,6 @@
 
             @Override
             public void remove() {
-                // TODO Auto-generated method stub
             }
         };
         return it;
diff --git a/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/PositionWritable.java b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/PositionWritable.java
index 10821b0..c391c89 100644
--- a/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/PositionWritable.java
+++ b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/PositionWritable.java
@@ -1,3 +1,18 @@
+/*
+ * Copyright 2009-2013 by The Regents of the University of California
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * you may obtain a copy of the License from
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
 package edu.uci.ics.genomix.type;
 
 import java.io.DataInput;
diff --git a/genomix/genomix-hyracks/pom.xml b/genomix/genomix-hyracks/pom.xml
index 8377df6..69d5839 100644
--- a/genomix/genomix-hyracks/pom.xml
+++ b/genomix/genomix-hyracks/pom.xml
@@ -38,15 +38,15 @@
 									<mainClass>edu.uci.ics.genomix.hyracks.driver.Driver</mainClass>
 									<name>genomix</name>
 								</program>
-                                <program>
-                                     <mainClass>edu.uci.ics.hyracks.control.cc.CCDriver</mainClass>
-                                     <name>genomixcc</name>
-                                </program>
-                                <program>
-                                     <mainClass>edu.uci.ics.hyracks.control.nc.NCDriver</mainClass>
-                                     <name>genomixnc</name>
-                                </program>
-                            </programs>
+								<program>
+									<mainClass>edu.uci.ics.hyracks.control.cc.CCDriver</mainClass>
+									<name>genomixcc</name>
+								</program>
+								<program>
+									<mainClass>edu.uci.ics.hyracks.control.nc.NCDriver</mainClass>
+									<name>genomixnc</name>
+								</program>
+							</programs>
 							<repositoryLayout>flat</repositoryLayout>
 							<repositoryName>lib</repositoryName>
 						</configuration>
@@ -261,6 +261,6 @@
 			<type>jar</type>
 			<scope>compile</scope>
 		</dependency>
-		
+
 	</dependencies>
 </project>
diff --git a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/data/accessors/ByteSerializerDeserializer.java b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/data/accessors/ByteSerializerDeserializer.java
index 3826f9b..257d5a3 100644
--- a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/data/accessors/ByteSerializerDeserializer.java
+++ b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/data/accessors/ByteSerializerDeserializer.java
@@ -1,5 +1,5 @@
 /*
- * Copyright 2009-2012 by The Regents of the University of California
+ * Copyright 2009-2013 by The Regents of the University of California
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
  * you may obtain a copy of the License from
@@ -57,4 +57,4 @@
         bytes[offset] = val;
     }
 
-}
\ No newline at end of file
+}
diff --git a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/data/accessors/KmerBinaryHashFunctionFamily.java b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/data/accessors/KmerBinaryHashFunctionFamily.java
index a4cfd3b..130d5ab 100644
--- a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/data/accessors/KmerBinaryHashFunctionFamily.java
+++ b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/data/accessors/KmerBinaryHashFunctionFamily.java
@@ -1,44 +1,44 @@
-/*
- * Copyright 2009-2012 by The Regents of the University of California
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * you may obtain a copy of the License from
- *
- *     http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package edu.uci.ics.genomix.hyracks.data.accessors;
-
-import edu.uci.ics.genomix.hyracks.data.primitive.KmerPointable;
-import edu.uci.ics.hyracks.api.dataflow.value.IBinaryHashFunction;
-import edu.uci.ics.hyracks.api.dataflow.value.IBinaryHashFunctionFamily;
-
-public class KmerBinaryHashFunctionFamily implements IBinaryHashFunctionFamily {
-    private static final long serialVersionUID = 1L;
-
-    @Override
-    public IBinaryHashFunction createBinaryHashFunction(final int seed) {
-
-        return new IBinaryHashFunction() {
-            private KmerPointable p = new KmerPointable();
-
-            @Override
-            public int hash(byte[] bytes, int offset, int length) {
-                if (length + offset >= bytes.length)
-                    throw new IllegalStateException("out of bound");
-                p.set(bytes, offset, length);
-                int hash = p.hash() * (seed + 1);
-                if (hash < 0) {
-                    hash = -(hash + 1);
-                }
-                return hash;
-            }
-        };
-    }
-}
\ No newline at end of file
+/*
+ * Copyright 2009-2013 by The Regents of the University of California
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * you may obtain a copy of the License from
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package edu.uci.ics.genomix.hyracks.data.accessors;
+
+import edu.uci.ics.genomix.hyracks.data.primitive.KmerPointable;
+import edu.uci.ics.hyracks.api.dataflow.value.IBinaryHashFunction;
+import edu.uci.ics.hyracks.api.dataflow.value.IBinaryHashFunctionFamily;
+
+public class KmerBinaryHashFunctionFamily implements IBinaryHashFunctionFamily {
+    private static final long serialVersionUID = 1L;
+
+    @Override
+    public IBinaryHashFunction createBinaryHashFunction(final int seed) {
+
+        return new IBinaryHashFunction() {
+            private KmerPointable p = new KmerPointable();
+
+            @Override
+            public int hash(byte[] bytes, int offset, int length) {
+                if (length + offset >= bytes.length)
+                    throw new IllegalStateException("out of bound");
+                p.set(bytes, offset, length);
+                int hash = p.hash() * (seed + 1);
+                if (hash < 0) {
+                    hash = -(hash + 1);
+                }
+                return hash;
+            }
+        };
+    }
+}
diff --git a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/data/accessors/KmerHashPartitioncomputerFactory.java b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/data/accessors/KmerHashPartitioncomputerFactory.java
index eb0d6bb..f8d4f84 100644
--- a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/data/accessors/KmerHashPartitioncomputerFactory.java
+++ b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/data/accessors/KmerHashPartitioncomputerFactory.java
@@ -1,56 +1,56 @@
-/*
- * Copyright 2009-2012 by The Regents of the University of California
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * you may obtain a copy of the License from
- *
- *     http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package edu.uci.ics.genomix.hyracks.data.accessors;
-
-import java.nio.ByteBuffer;
-
-import edu.uci.ics.hyracks.api.comm.IFrameTupleAccessor;
-import edu.uci.ics.hyracks.api.dataflow.value.ITuplePartitionComputer;
-import edu.uci.ics.hyracks.api.dataflow.value.ITuplePartitionComputerFactory;
-
-public class KmerHashPartitioncomputerFactory implements ITuplePartitionComputerFactory {
-
-    private static final long serialVersionUID = 1L;
-
-    public static int hashBytes(byte[] bytes, int offset, int length) {
-        int hash = 1;
-        for (int i = offset; i < offset + length; i++)
-            hash = (31 * hash) + (int) bytes[i];
-        return hash;
-    }
-
-    @Override
-    public ITuplePartitionComputer createPartitioner() {
-        return new ITuplePartitionComputer() {
-            @Override
-            public int partition(IFrameTupleAccessor accessor, int tIndex, int nParts) {
-                int startOffset = accessor.getTupleStartOffset(tIndex);
-                int fieldOffset = accessor.getFieldStartOffset(tIndex, 0);
-                int slotLength = accessor.getFieldSlotsLength();
-                int fieldLength = accessor.getFieldLength(tIndex, 0);
-
-                ByteBuffer buf = accessor.getBuffer();
-
-                int hash = hashBytes(buf.array(), startOffset + fieldOffset + slotLength, fieldLength);
-                if (hash < 0) {
-                    hash = -(hash + 1);
-                }
-
-                return hash % nParts;
-            }
-        };
-    }
-}
+/*
+ * Copyright 2009-2013 by The Regents of the University of California
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * you may obtain a copy of the License from
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package edu.uci.ics.genomix.hyracks.data.accessors;
+
+import java.nio.ByteBuffer;
+
+import edu.uci.ics.hyracks.api.comm.IFrameTupleAccessor;
+import edu.uci.ics.hyracks.api.dataflow.value.ITuplePartitionComputer;
+import edu.uci.ics.hyracks.api.dataflow.value.ITuplePartitionComputerFactory;
+
+public class KmerHashPartitioncomputerFactory implements ITuplePartitionComputerFactory {
+
+    private static final long serialVersionUID = 1L;
+
+    public static int hashBytes(byte[] bytes, int offset, int length) {
+        int hash = 1;
+        for (int i = offset; i < offset + length; i++)
+            hash = (31 * hash) + (int) bytes[i];
+        return hash;
+    }
+
+    @Override
+    public ITuplePartitionComputer createPartitioner() {
+        return new ITuplePartitionComputer() {
+            @Override
+            public int partition(IFrameTupleAccessor accessor, int tIndex, int nParts) {
+                int startOffset = accessor.getTupleStartOffset(tIndex);
+                int fieldOffset = accessor.getFieldStartOffset(tIndex, 0);
+                int slotLength = accessor.getFieldSlotsLength();
+                int fieldLength = accessor.getFieldLength(tIndex, 0);
+
+                ByteBuffer buf = accessor.getBuffer();
+
+                int hash = hashBytes(buf.array(), startOffset + fieldOffset + slotLength, fieldLength);
+                if (hash < 0) {
+                    hash = -(hash + 1);
+                }
+
+                return hash % nParts;
+            }
+        };
+    }
+}
diff --git a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/data/accessors/KmerNormarlizedComputerFactory.java b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/data/accessors/KmerNormarlizedComputerFactory.java
index 44b0e10..7dd3b14 100644
--- a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/data/accessors/KmerNormarlizedComputerFactory.java
+++ b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/data/accessors/KmerNormarlizedComputerFactory.java
@@ -1,37 +1,37 @@
-/*
- * Copyright 2009-2012 by The Regents of the University of California
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * you may obtain a copy of the License from
- *
- *     http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package edu.uci.ics.genomix.hyracks.data.accessors;
-
-import edu.uci.ics.genomix.hyracks.data.primitive.KmerPointable;
-import edu.uci.ics.hyracks.api.dataflow.value.INormalizedKeyComputer;
-import edu.uci.ics.hyracks.api.dataflow.value.INormalizedKeyComputerFactory;
-
-public class KmerNormarlizedComputerFactory implements INormalizedKeyComputerFactory {
-    private static final long serialVersionUID = 1L;
-
-    @Override
-    public INormalizedKeyComputer createNormalizedKeyComputer() {
-        return new INormalizedKeyComputer() {
-            /**
-             * read one int from Kmer, make sure this int is consistent whith Kmer compartor
-             */
-            @Override
-            public int normalize(byte[] bytes, int start, int length) {
-                return KmerPointable.getIntReverse(bytes, start, length);
-            }
-        };
-    }
-}
\ No newline at end of file
+/*
+ * Copyright 2009-2013 by The Regents of the University of California
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * you may obtain a copy of the License from
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package edu.uci.ics.genomix.hyracks.data.accessors;
+
+import edu.uci.ics.genomix.hyracks.data.primitive.KmerPointable;
+import edu.uci.ics.hyracks.api.dataflow.value.INormalizedKeyComputer;
+import edu.uci.ics.hyracks.api.dataflow.value.INormalizedKeyComputerFactory;
+
+public class KmerNormarlizedComputerFactory implements INormalizedKeyComputerFactory {
+    private static final long serialVersionUID = 1L;
+
+    @Override
+    public INormalizedKeyComputer createNormalizedKeyComputer() {
+        return new INormalizedKeyComputer() {
+            /**
+             * read one int from Kmer, make sure this int is consistent whith Kmer compartor
+             */
+            @Override
+            public int normalize(byte[] bytes, int start, int length) {
+                return KmerPointable.getIntReverse(bytes, start, length);
+            }
+        };
+    }
+}
diff --git a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/data/accessors/ReadIDNormarlizedComputeFactory.java b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/data/accessors/ReadIDNormarlizedComputeFactory.java
deleted file mode 100644
index 1f3efbf..0000000
--- a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/data/accessors/ReadIDNormarlizedComputeFactory.java
+++ /dev/null
@@ -1,26 +0,0 @@
-package edu.uci.ics.genomix.hyracks.data.accessors;
-
-import edu.uci.ics.genomix.data.Marshal;
-import edu.uci.ics.hyracks.api.dataflow.value.INormalizedKeyComputer;
-import edu.uci.ics.hyracks.api.dataflow.value.INormalizedKeyComputerFactory;
-
-public class ReadIDNormarlizedComputeFactory implements INormalizedKeyComputerFactory{
-
-    /**
-     * 
-     */
-    private static final long serialVersionUID = 1L;
-
-    @Override
-    public INormalizedKeyComputer createNormalizedKeyComputer() {
-        return new INormalizedKeyComputer(){
-
-            @Override
-            public int normalize(byte[] bytes, int start, int length) {
-                return Marshal.getInt(bytes, start);
-            }
-            
-        };
-    }
-
-}
diff --git a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/data/accessors/ReadIDPartitionComputerFactory.java b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/data/accessors/ReadIDPartitionComputerFactory.java
index 7229364..6773a73 100644
--- a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/data/accessors/ReadIDPartitionComputerFactory.java
+++ b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/data/accessors/ReadIDPartitionComputerFactory.java
@@ -1,3 +1,18 @@
+/*
+ * Copyright 2009-2013 by The Regents of the University of California
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * you may obtain a copy of the License from
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
 package edu.uci.ics.genomix.hyracks.data.accessors;
 
 import java.nio.ByteBuffer;
@@ -16,7 +31,6 @@
 
     @Override
     public ITuplePartitionComputer createPartitioner() {
-        // TODO Auto-generated method stub
         return new ITuplePartitionComputer() {
             @Override
             public int partition(IFrameTupleAccessor accessor, int tIndex, int nParts) {
diff --git a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/data/primitive/KmerPointable.java b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/data/primitive/KmerPointable.java
index 4ceda78..0457de9 100644
--- a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/data/primitive/KmerPointable.java
+++ b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/data/primitive/KmerPointable.java
@@ -1,145 +1,145 @@
-/*
- * Copyright 2009-2012 by The Regents of the University of California
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * you may obtain a copy of the License from
- *
- *     http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package edu.uci.ics.genomix.hyracks.data.primitive;
-
-import edu.uci.ics.genomix.hyracks.data.accessors.KmerHashPartitioncomputerFactory;
-import edu.uci.ics.hyracks.api.dataflow.value.ITypeTraits;
-import edu.uci.ics.hyracks.data.std.api.AbstractPointable;
-import edu.uci.ics.hyracks.data.std.api.IComparable;
-import edu.uci.ics.hyracks.data.std.api.IHashable;
-import edu.uci.ics.hyracks.data.std.api.INumeric;
-import edu.uci.ics.hyracks.data.std.api.IPointable;
-import edu.uci.ics.hyracks.data.std.api.IPointableFactory;
-
-public final class KmerPointable extends AbstractPointable implements IHashable, IComparable, INumeric {
-    public static final ITypeTraits TYPE_TRAITS = new ITypeTraits() {
-        private static final long serialVersionUID = 1L;
-
-        @Override
-        public boolean isFixedLength() {
-            return false;
-        }
-
-        @Override
-        public int getFixedLength() {
-            return -1;
-        }
-    };
-
-    public static final IPointableFactory FACTORY = new IPointableFactory() {
-        private static final long serialVersionUID = 1L;
-
-        @Override
-        public IPointable createPointable() {
-            return new KmerPointable();
-        }
-
-        @Override
-        public ITypeTraits getTypeTraits() {
-            return TYPE_TRAITS;
-        }
-    };
-
-    public static short getShortReverse(byte[] bytes, int offset, int length) {
-        if (length < 2) {
-            return (short) (bytes[offset] & 0xff);
-        }
-        return (short) (((bytes[offset + length - 1] & 0xff) << 8) + (bytes[offset + length - 2] & 0xff));
-    }
-
-    public static int getIntReverse(byte[] bytes, int offset, int length) {
-        int shortValue = getShortReverse(bytes, offset, length) & 0xffff;
-
-        if (length < 3) {
-            return shortValue;
-        }
-        if (length == 3) {
-            return (((bytes[offset + 2] & 0xff) << 16) + ((bytes[offset + 1] & 0xff) << 8) + ((bytes[offset] & 0xff)));
-        }
-        return ((bytes[offset + length - 1] & 0xff) << 24) + ((bytes[offset + length - 2] & 0xff) << 16)
-                + ((bytes[offset + length - 3] & 0xff) << 8) + ((bytes[offset + length - 4] & 0xff) << 0);
-    }
-
-    public static long getLongReverse(byte[] bytes, int offset, int length) {
-        if (length < 8) {
-            return ((long) getIntReverse(bytes, offset, length)) & 0x0ffffffffL;
-        }
-        return (((long) (bytes[offset + length - 1] & 0xff)) << 56)
-                + (((long) (bytes[offset + length - 2] & 0xff)) << 48)
-                + (((long) (bytes[offset + length - 3] & 0xff)) << 40)
-                + (((long) (bytes[offset + length - 4] & 0xff)) << 32)
-                + (((long) (bytes[offset + length - 5] & 0xff)) << 24)
-                + (((long) (bytes[offset + length - 6] & 0xff)) << 16)
-                + (((long) (bytes[offset + length - 7] & 0xff)) << 8) + (((long) (bytes[offset + length - 8] & 0xff)));
-    }
-
-    @Override
-    public int compareTo(IPointable pointer) {
-        return compareTo(pointer.getByteArray(), pointer.getStartOffset(), pointer.getLength());
-    }
-
-    @Override
-    public int compareTo(byte[] bytes, int offset, int length) {
-
-        if (this.length != length) {
-            return this.length - length;
-        }
-        for (int i = length - 1; i >= 0; i--) {
-            int cmp = (this.bytes[this.start + i] & 0xff) - (bytes[offset + i] & 0xff);
-            if (cmp != 0) {
-                return cmp;
-            }
-        }
-
-        return 0;
-    }
-
-    @Override
-    public int hash() {
-        int hash = KmerHashPartitioncomputerFactory.hashBytes(bytes, start, length);
-        return hash;
-    }
-
-    @Override
-    public byte byteValue() {
-        return bytes[start + length - 1];
-    }
-
-    @Override
-    public short shortValue() {
-        return getShortReverse(bytes, start, length);
-    }
-
-    @Override
-    public int intValue() {
-        return getIntReverse(bytes, start, length);
-    }
-
-    @Override
-    public long longValue() {
-        return getLongReverse(bytes, start, length);
-    }
-
-    @Override
-    public float floatValue() {
-        return Float.intBitsToFloat(intValue());
-    }
-
-    @Override
-    public double doubleValue() {
-        return Double.longBitsToDouble(longValue());
-    }
-}
+/*
+ * Copyright 2009-2013 by The Regents of the University of California
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * you may obtain a copy of the License from
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package edu.uci.ics.genomix.hyracks.data.primitive;
+
+import edu.uci.ics.genomix.hyracks.data.accessors.KmerHashPartitioncomputerFactory;
+import edu.uci.ics.hyracks.api.dataflow.value.ITypeTraits;
+import edu.uci.ics.hyracks.data.std.api.AbstractPointable;
+import edu.uci.ics.hyracks.data.std.api.IComparable;
+import edu.uci.ics.hyracks.data.std.api.IHashable;
+import edu.uci.ics.hyracks.data.std.api.INumeric;
+import edu.uci.ics.hyracks.data.std.api.IPointable;
+import edu.uci.ics.hyracks.data.std.api.IPointableFactory;
+
+public final class KmerPointable extends AbstractPointable implements IHashable, IComparable, INumeric {
+    public static final ITypeTraits TYPE_TRAITS = new ITypeTraits() {
+        private static final long serialVersionUID = 1L;
+
+        @Override
+        public boolean isFixedLength() {
+            return false;
+        }
+
+        @Override
+        public int getFixedLength() {
+            return -1;
+        }
+    };
+
+    public static final IPointableFactory FACTORY = new IPointableFactory() {
+        private static final long serialVersionUID = 1L;
+
+        @Override
+        public IPointable createPointable() {
+            return new KmerPointable();
+        }
+
+        @Override
+        public ITypeTraits getTypeTraits() {
+            return TYPE_TRAITS;
+        }
+    };
+
+    public static short getShortReverse(byte[] bytes, int offset, int length) {
+        if (length < 2) {
+            return (short) (bytes[offset] & 0xff);
+        }
+        return (short) (((bytes[offset + length - 1] & 0xff) << 8) + (bytes[offset + length - 2] & 0xff));
+    }
+
+    public static int getIntReverse(byte[] bytes, int offset, int length) {
+        int shortValue = getShortReverse(bytes, offset, length) & 0xffff;
+
+        if (length < 3) {
+            return shortValue;
+        }
+        if (length == 3) {
+            return (((bytes[offset + 2] & 0xff) << 16) + ((bytes[offset + 1] & 0xff) << 8) + ((bytes[offset] & 0xff)));
+        }
+        return ((bytes[offset + length - 1] & 0xff) << 24) + ((bytes[offset + length - 2] & 0xff) << 16)
+                + ((bytes[offset + length - 3] & 0xff) << 8) + ((bytes[offset + length - 4] & 0xff) << 0);
+    }
+
+    public static long getLongReverse(byte[] bytes, int offset, int length) {
+        if (length < 8) {
+            return ((long) getIntReverse(bytes, offset, length)) & 0x0ffffffffL;
+        }
+        return (((long) (bytes[offset + length - 1] & 0xff)) << 56)
+                + (((long) (bytes[offset + length - 2] & 0xff)) << 48)
+                + (((long) (bytes[offset + length - 3] & 0xff)) << 40)
+                + (((long) (bytes[offset + length - 4] & 0xff)) << 32)
+                + (((long) (bytes[offset + length - 5] & 0xff)) << 24)
+                + (((long) (bytes[offset + length - 6] & 0xff)) << 16)
+                + (((long) (bytes[offset + length - 7] & 0xff)) << 8) + (((long) (bytes[offset + length - 8] & 0xff)));
+    }
+
+    @Override
+    public int compareTo(IPointable pointer) {
+        return compareTo(pointer.getByteArray(), pointer.getStartOffset(), pointer.getLength());
+    }
+
+    @Override
+    public int compareTo(byte[] bytes, int offset, int length) {
+
+        if (this.length != length) {
+            return this.length - length;
+        }
+        for (int i = length - 1; i >= 0; i--) {
+            int cmp = (this.bytes[this.start + i] & 0xff) - (bytes[offset + i] & 0xff);
+            if (cmp != 0) {
+                return cmp;
+            }
+        }
+
+        return 0;
+    }
+
+    @Override
+    public int hash() {
+        int hash = KmerHashPartitioncomputerFactory.hashBytes(bytes, start, length);
+        return hash;
+    }
+
+    @Override
+    public byte byteValue() {
+        return bytes[start + length - 1];
+    }
+
+    @Override
+    public short shortValue() {
+        return getShortReverse(bytes, start, length);
+    }
+
+    @Override
+    public int intValue() {
+        return getIntReverse(bytes, start, length);
+    }
+
+    @Override
+    public long longValue() {
+        return getLongReverse(bytes, start, length);
+    }
+
+    @Override
+    public float floatValue() {
+        return Float.intBitsToFloat(intValue());
+    }
+
+    @Override
+    public double doubleValue() {
+        return Double.longBitsToDouble(longValue());
+    }
+}
diff --git a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/data/primitive/NodeReference.java b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/data/primitive/NodeReference.java
index f98c684..7c1431b 100644
--- a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/data/primitive/NodeReference.java
+++ b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/data/primitive/NodeReference.java
@@ -1,3 +1,18 @@
+/*
+ * Copyright 2009-2013 by The Regents of the University of California
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * you may obtain a copy of the License from
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
 package edu.uci.ics.genomix.hyracks.data.primitive;
 
 import edu.uci.ics.genomix.type.NodeWritable;
@@ -7,13 +22,10 @@
     /**
 	 * 
 	 */
-	private static final long serialVersionUID = 1L;
+    private static final long serialVersionUID = 1L;
 
-	public NodeReference(int kmerSize) {
+    public NodeReference(int kmerSize) {
         super(kmerSize);
-        // TODO Auto-generated constructor stub
     }
 
-
- 
 }
diff --git a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/data/primitive/PositionListReference.java b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/data/primitive/PositionListReference.java
index 49dd263..8885c0f 100644
--- a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/data/primitive/PositionListReference.java
+++ b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/data/primitive/PositionListReference.java
@@ -1,17 +1,32 @@
+/*
+ * Copyright 2009-2013 by The Regents of the University of California
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * you may obtain a copy of the License from
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
 package edu.uci.ics.genomix.hyracks.data.primitive;
 
 import edu.uci.ics.genomix.type.PositionListWritable;
 import edu.uci.ics.hyracks.data.std.api.IValueReference;
 
-public class PositionListReference extends PositionListWritable implements  IValueReference {
+public class PositionListReference extends PositionListWritable implements IValueReference {
 
-	public PositionListReference(int countByDataLength, byte[] byteArray, int startOffset) {
-	    super(countByDataLength, byteArray, startOffset);
+    public PositionListReference(int countByDataLength, byte[] byteArray, int startOffset) {
+        super(countByDataLength, byteArray, startOffset);
     }
 
     /**
 	 * 
 	 */
-	private static final long serialVersionUID = 1L;
+    private static final long serialVersionUID = 1L;
 
 }
diff --git a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/data/primitive/PositionReference.java b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/data/primitive/PositionReference.java
index 1e22529..610f01a 100644
--- a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/data/primitive/PositionReference.java
+++ b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/data/primitive/PositionReference.java
@@ -1,3 +1,18 @@
+/*
+ * Copyright 2009-2013 by The Regents of the University of California
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * you may obtain a copy of the License from
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
 package edu.uci.ics.genomix.hyracks.data.primitive;
 
 import edu.uci.ics.genomix.type.PositionWritable;
@@ -5,9 +20,9 @@
 
 public class PositionReference extends PositionWritable implements IValueReference {
 
-	/**
+    /**
 	 * 
 	 */
-	private static final long serialVersionUID = 1L;
+    private static final long serialVersionUID = 1L;
 
 }
diff --git a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/data/primitive/ReadIDPointable.java b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/data/primitive/ReadIDPointable.java
deleted file mode 100644
index b1e08c4..0000000
--- a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/data/primitive/ReadIDPointable.java
+++ /dev/null
@@ -1,118 +0,0 @@
-package edu.uci.ics.genomix.hyracks.data.primitive;
-
-import edu.uci.ics.genomix.data.Marshal;
-import edu.uci.ics.hyracks.api.dataflow.value.ITypeTraits;
-import edu.uci.ics.hyracks.data.std.api.AbstractPointable;
-import edu.uci.ics.hyracks.data.std.api.IComparable;
-import edu.uci.ics.hyracks.data.std.api.IHashable;
-import edu.uci.ics.hyracks.data.std.api.INumeric;
-import edu.uci.ics.hyracks.data.std.api.IPointable;
-import edu.uci.ics.hyracks.data.std.api.IPointableFactory;
-import edu.uci.ics.hyracks.data.std.primitive.IntegerPointable;
-
-public class ReadIDPointable  extends AbstractPointable implements IHashable, IComparable, INumeric {
-    public static final ITypeTraits TYPE_TRAITS = new ITypeTraits() {
-        private static final long serialVersionUID = 1L;
-
-        @Override
-        public boolean isFixedLength() {
-            return false;
-        }
-
-        @Override
-        public int getFixedLength() {
-            return -1;
-        }
-    };
-
-    public static final IPointableFactory FACTORY = new IPointableFactory() {
-        private static final long serialVersionUID = 1L;
-
-        @Override
-        public IPointable createPointable() {
-            return new IntegerPointable();
-        }
-
-        @Override
-        public ITypeTraits getTypeTraits() {
-            return TYPE_TRAITS;
-        }
-    };
-
-    public static int getInteger(byte[] bytes, int start) {
-        return Marshal.getInt(bytes, start);
-    }
-
-    public static void setInteger(byte[] bytes, int start, int value) {
-        Marshal.putInt(value, bytes, start);
-    }
-
-    public int getInteger() {
-        return getInteger(bytes, start);
-    }
-
-    public void setInteger(int value) {
-        setInteger(bytes, start, value);
-    }
-
-    public int preIncrement() {
-        int v = getInteger();
-        ++v;
-        setInteger(v);
-        return v;
-    }
-
-    public int postIncrement() {
-        int v = getInteger();
-        int ov = v++;
-        setInteger(v);
-        return ov;
-    }
-
-    @Override
-    public int compareTo(IPointable pointer) {
-        return compareTo(pointer.getByteArray(), pointer.getStartOffset(), pointer.getLength());
-    }
-
-    @Override
-    public int compareTo(byte[] bytes, int start, int length) {
-        int v = getInteger();
-        int ov = getInteger(bytes, start);
-        return v < ov ? -1 : (v > ov ? 1 : 0);
-    }
-
-    @Override
-    public int hash() {
-        return getInteger();
-    }
-
-    @Override
-    public byte byteValue() {
-        return (byte) getInteger();
-    }
-
-    @Override
-    public short shortValue() {
-        return (short) getInteger();
-    }
-
-    @Override
-    public int intValue() {
-        return getInteger();
-    }
-
-    @Override
-    public long longValue() {
-        return getInteger();
-    }
-
-    @Override
-    public float floatValue() {
-        return getInteger();
-    }
-
-    @Override
-    public double doubleValue() {
-        return getInteger();
-    }
-}
diff --git a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/dataflow/ConnectorPolicyAssignmentPolicy.java b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/dataflow/ConnectorPolicyAssignmentPolicy.java
index fe44f51..61f16b2 100644
--- a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/dataflow/ConnectorPolicyAssignmentPolicy.java
+++ b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/dataflow/ConnectorPolicyAssignmentPolicy.java
@@ -1,42 +1,42 @@
-/*
- * Copyright 2009-2012 by The Regents of the University of California
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * you may obtain a copy of the License from
- *
- *     http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package edu.uci.ics.genomix.hyracks.dataflow;
-
-import edu.uci.ics.hyracks.api.dataflow.IConnectorDescriptor;
-import edu.uci.ics.hyracks.api.dataflow.connectors.IConnectorPolicy;
-import edu.uci.ics.hyracks.api.dataflow.connectors.IConnectorPolicyAssignmentPolicy;
-import edu.uci.ics.hyracks.api.dataflow.connectors.PipeliningConnectorPolicy;
-import edu.uci.ics.hyracks.api.dataflow.connectors.SendSideMaterializedPipeliningConnectorPolicy;
-import edu.uci.ics.hyracks.dataflow.std.connectors.MToNPartitioningMergingConnectorDescriptor;
-
-/**
- * used by precluster groupby
- */
-public class ConnectorPolicyAssignmentPolicy implements IConnectorPolicyAssignmentPolicy {
-    private static final long serialVersionUID = 1L;
-    private IConnectorPolicy senderSideMaterializePolicy = new SendSideMaterializedPipeliningConnectorPolicy();
-    private IConnectorPolicy pipeliningPolicy = new PipeliningConnectorPolicy();
-
-    @Override
-    public IConnectorPolicy getConnectorPolicyAssignment(IConnectorDescriptor c, int nProducers, int nConsumers,
-            int[] fanouts) {
-        if (c instanceof MToNPartitioningMergingConnectorDescriptor) {
-            return senderSideMaterializePolicy;
-        } else {
-            return pipeliningPolicy;
-        }
-    }
-}
+/*
+ * Copyright 2009-2013 by The Regents of the University of California
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * you may obtain a copy of the License from
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package edu.uci.ics.genomix.hyracks.dataflow;
+
+import edu.uci.ics.hyracks.api.dataflow.IConnectorDescriptor;
+import edu.uci.ics.hyracks.api.dataflow.connectors.IConnectorPolicy;
+import edu.uci.ics.hyracks.api.dataflow.connectors.IConnectorPolicyAssignmentPolicy;
+import edu.uci.ics.hyracks.api.dataflow.connectors.PipeliningConnectorPolicy;
+import edu.uci.ics.hyracks.api.dataflow.connectors.SendSideMaterializedPipeliningConnectorPolicy;
+import edu.uci.ics.hyracks.dataflow.std.connectors.MToNPartitioningMergingConnectorDescriptor;
+
+/**
+ * used by precluster groupby
+ */
+public class ConnectorPolicyAssignmentPolicy implements IConnectorPolicyAssignmentPolicy {
+    private static final long serialVersionUID = 1L;
+    private IConnectorPolicy senderSideMaterializePolicy = new SendSideMaterializedPipeliningConnectorPolicy();
+    private IConnectorPolicy pipeliningPolicy = new PipeliningConnectorPolicy();
+
+    @Override
+    public IConnectorPolicy getConnectorPolicyAssignment(IConnectorDescriptor c, int nProducers, int nConsumers,
+            int[] fanouts) {
+        if (c instanceof MToNPartitioningMergingConnectorDescriptor) {
+            return senderSideMaterializePolicy;
+        } else {
+            return pipeliningPolicy;
+        }
+    }
+}
diff --git a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/dataflow/MapKmerPositionToReadOperator.java b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/dataflow/MapKmerPositionToReadOperator.java
index 8609519..e7f8bee 100644
--- a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/dataflow/MapKmerPositionToReadOperator.java
+++ b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/dataflow/MapKmerPositionToReadOperator.java
@@ -1,3 +1,18 @@
+/*
+ * Copyright 2009-2013 by The Regents of the University of California
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * you may obtain a copy of the License from
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
 package edu.uci.ics.genomix.hyracks.dataflow;
 
 import java.io.DataOutput;
@@ -140,7 +155,7 @@
                 builder2.reset();
                 builder2.addField(pos.getByteArray(), pos.getStartOffset(), PositionReference.INTBYTES);
                 builder2.addField(pos.getByteArray(), pos.getStartOffset() + PositionReference.INTBYTES, 1);
-                
+
                 if (posList2 == null) {
                     builder2.addFieldEndOffset();
                 } else {
diff --git a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/dataflow/MapReadToNodeOperator.java b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/dataflow/MapReadToNodeOperator.java
index 98d21af..cf9d566 100644
--- a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/dataflow/MapReadToNodeOperator.java
+++ b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/dataflow/MapReadToNodeOperator.java
@@ -1,3 +1,18 @@
+/*
+ * Copyright 2009-2013 by The Regents of the University of California
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * you may obtain a copy of the License from
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
 package edu.uci.ics.genomix.hyracks.dataflow;
 
 import java.io.IOException;
diff --git a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/dataflow/ReadsKeyValueParserFactory.java b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/dataflow/ReadsKeyValueParserFactory.java
index 3667d43..8c69201 100644
--- a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/dataflow/ReadsKeyValueParserFactory.java
+++ b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/dataflow/ReadsKeyValueParserFactory.java
@@ -1,5 +1,5 @@
 /*
- * Copyright 2009-2012 by The Regents of the University of California
+ * Copyright 2009-2013 by The Regents of the University of California
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
  * you may obtain a copy of the License from
@@ -69,7 +69,7 @@
 
             private KmerBytesWritable kmer = new KmerBytesWritable(kmerSize);
             private PositionReference pos = new PositionReference();
-            
+
             @Override
             public void parse(LongWritable key, Text value, IFrameWriter writer) throws HyracksDataException {
                 String[] geneLine = value.toString().split("\\t"); // Read the Real Gene Line
@@ -158,4 +158,4 @@
         };
     }
 
-}
\ No newline at end of file
+}
diff --git a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/dataflow/aggregators/AggregateKmerAggregateFactory.java b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/dataflow/aggregators/AggregateKmerAggregateFactory.java
index 6ee7946..52aeb7a 100644
--- a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/dataflow/aggregators/AggregateKmerAggregateFactory.java
+++ b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/dataflow/aggregators/AggregateKmerAggregateFactory.java
@@ -1,3 +1,18 @@
+/*
+ * Copyright 2009-2013 by The Regents of the University of California
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * you may obtain a copy of the License from
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
 package edu.uci.ics.genomix.hyracks.dataflow.aggregators;
 
 import java.io.DataOutput;
@@ -41,7 +56,6 @@
 
             @Override
             public void close() {
-                // TODO Auto-generated method stub
 
             }
 
diff --git a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/dataflow/aggregators/AggregateReadIDAggregateFactory.java b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/dataflow/aggregators/AggregateReadIDAggregateFactory.java
index d0fc24b..92b85b3 100644
--- a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/dataflow/aggregators/AggregateReadIDAggregateFactory.java
+++ b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/dataflow/aggregators/AggregateReadIDAggregateFactory.java
@@ -1,3 +1,18 @@
+/*
+ * Copyright 2009-2013 by The Regents of the University of California
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * you may obtain a copy of the License from
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
 package edu.uci.ics.genomix.hyracks.dataflow.aggregators;
 
 import java.io.DataOutput;
@@ -96,7 +111,6 @@
 
             @Override
             public void reset() {
-                // TODO Auto-generated method stub
 
             }
 
@@ -140,7 +154,6 @@
 
             @Override
             public void close() {
-                // TODO Auto-generated method stub
 
             }
 
diff --git a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/dataflow/aggregators/MergeKmerAggregateFactory.java b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/dataflow/aggregators/MergeKmerAggregateFactory.java
index eab197e..ce178c6 100644
--- a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/dataflow/aggregators/MergeKmerAggregateFactory.java
+++ b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/dataflow/aggregators/MergeKmerAggregateFactory.java
@@ -1,117 +1,116 @@
-/*
- * Copyright 2009-2012 by The Regents of the University of California
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * you may obtain a copy of the License from
- *
- *     http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package edu.uci.ics.genomix.hyracks.dataflow.aggregators;
-
-import java.io.DataOutput;
-import java.io.IOException;
-
-import org.apache.commons.logging.Log;
-import org.apache.commons.logging.LogFactory;
-
-import edu.uci.ics.genomix.hyracks.data.primitive.PositionReference;
-import edu.uci.ics.hyracks.api.comm.IFrameTupleAccessor;
-import edu.uci.ics.hyracks.api.context.IHyracksTaskContext;
-import edu.uci.ics.hyracks.api.dataflow.value.RecordDescriptor;
-import edu.uci.ics.hyracks.api.exceptions.HyracksDataException;
-import edu.uci.ics.hyracks.data.std.util.ArrayBackedValueStorage;
-import edu.uci.ics.hyracks.dataflow.common.comm.io.ArrayTupleBuilder;
-import edu.uci.ics.hyracks.dataflow.std.group.AggregateState;
-import edu.uci.ics.hyracks.dataflow.std.group.IAggregatorDescriptor;
-import edu.uci.ics.hyracks.dataflow.std.group.IAggregatorDescriptorFactory;
-
-public class MergeKmerAggregateFactory implements IAggregatorDescriptorFactory {
-    private static final long serialVersionUID = 1L;
-    private static final Log LOG = LogFactory.getLog(MergeKmerAggregateFactory.class);
-    @Override
-    public IAggregatorDescriptor createAggregator(IHyracksTaskContext ctx, RecordDescriptor inRecordDescriptor,
-            RecordDescriptor outRecordDescriptor, int[] keyFields, int[] keyFieldsInPartialResults)
-            throws HyracksDataException {
-        final int frameSize = ctx.getFrameSize();
-        return new IAggregatorDescriptor() {
-
-            private PositionReference position = new PositionReference();
-
-            @Override
-            public AggregateState createAggregateStates() {
-                return new AggregateState(new ArrayBackedValueStorage());
-            }
-
-            @Override
-            public void init(ArrayTupleBuilder tupleBuilder, IFrameTupleAccessor accessor, int tIndex,
-                    AggregateState state) throws HyracksDataException {
-                ArrayBackedValueStorage inputVal = (ArrayBackedValueStorage) state.state;
-                inputVal.reset();
-                int leadOffset = accessor.getTupleStartOffset(tIndex) + accessor.getFieldSlotsLength();
-                for (int offset = accessor.getFieldStartOffset(tIndex, 1); offset < accessor.getFieldEndOffset(tIndex,
-                        1); offset += PositionReference.LENGTH) {
-                    position.setNewReference(accessor.getBuffer().array(), leadOffset + offset);
-                    inputVal.append(position);
-                }
-                //make a fake feild to cheat caller
-                tupleBuilder.addFieldEndOffset();
-            }
-
-            @Override
-            public void reset() {
-                // TODO Auto-generated method stub
-
-            }
-
-            @Override
-            public void aggregate(IFrameTupleAccessor accessor, int tIndex, IFrameTupleAccessor stateAccessor,
-                    int stateTupleIndex, AggregateState state) throws HyracksDataException {
-                ArrayBackedValueStorage inputVal = (ArrayBackedValueStorage) state.state;
-                int leadOffset = accessor.getTupleStartOffset(tIndex) + accessor.getFieldSlotsLength();
-                for (int offset = accessor.getFieldStartOffset(tIndex, 1); offset < accessor.getFieldEndOffset(tIndex,
-                        1); offset += PositionReference.LENGTH) {
-                    position.setNewReference(accessor.getBuffer().array(), leadOffset + offset);
-                    inputVal.append(position);
-                }
-            }
-
-            @Override
-            public void outputPartialResult(ArrayTupleBuilder tupleBuilder, IFrameTupleAccessor accessor, int tIndex,
-                    AggregateState state) throws HyracksDataException {
-                throw new IllegalStateException("partial result method should not be called");
-            }
-
-            @Override
-            public void outputFinalResult(ArrayTupleBuilder tupleBuilder, IFrameTupleAccessor accessor, int tIndex,
-                    AggregateState state) throws HyracksDataException {
-                DataOutput fieldOutput = tupleBuilder.getDataOutput();
-                ArrayBackedValueStorage inputVal = (ArrayBackedValueStorage) state.state;
-                try {
-                    if (inputVal.getLength() > frameSize/2){
-                        LOG.warn("MergeKmer: output data size is too big: " + inputVal.getLength());
-                    }
-                    fieldOutput.write(inputVal.getByteArray(), inputVal.getStartOffset(), inputVal.getLength());
-                    tupleBuilder.addFieldEndOffset();
-
-                } catch (IOException e) {
-                    throw new HyracksDataException("I/O exception when writing aggregation to the output buffer.");
-                }
-            }
-
-            @Override
-            public void close() {
-                // TODO Auto-generated method stub
-
-            }
-
-        };
-
-    }
-}
+/*
+ * Copyright 2009-2013 by The Regents of the University of California
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * you may obtain a copy of the License from
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package edu.uci.ics.genomix.hyracks.dataflow.aggregators;
+
+import java.io.DataOutput;
+import java.io.IOException;
+
+import org.apache.commons.logging.Log;
+import org.apache.commons.logging.LogFactory;
+
+import edu.uci.ics.genomix.hyracks.data.primitive.PositionReference;
+import edu.uci.ics.hyracks.api.comm.IFrameTupleAccessor;
+import edu.uci.ics.hyracks.api.context.IHyracksTaskContext;
+import edu.uci.ics.hyracks.api.dataflow.value.RecordDescriptor;
+import edu.uci.ics.hyracks.api.exceptions.HyracksDataException;
+import edu.uci.ics.hyracks.data.std.util.ArrayBackedValueStorage;
+import edu.uci.ics.hyracks.dataflow.common.comm.io.ArrayTupleBuilder;
+import edu.uci.ics.hyracks.dataflow.std.group.AggregateState;
+import edu.uci.ics.hyracks.dataflow.std.group.IAggregatorDescriptor;
+import edu.uci.ics.hyracks.dataflow.std.group.IAggregatorDescriptorFactory;
+
+public class MergeKmerAggregateFactory implements IAggregatorDescriptorFactory {
+    private static final long serialVersionUID = 1L;
+    private static final Log LOG = LogFactory.getLog(MergeKmerAggregateFactory.class);
+
+    @Override
+    public IAggregatorDescriptor createAggregator(IHyracksTaskContext ctx, RecordDescriptor inRecordDescriptor,
+            RecordDescriptor outRecordDescriptor, int[] keyFields, int[] keyFieldsInPartialResults)
+            throws HyracksDataException {
+        final int frameSize = ctx.getFrameSize();
+        return new IAggregatorDescriptor() {
+
+            private PositionReference position = new PositionReference();
+
+            @Override
+            public AggregateState createAggregateStates() {
+                return new AggregateState(new ArrayBackedValueStorage());
+            }
+
+            @Override
+            public void init(ArrayTupleBuilder tupleBuilder, IFrameTupleAccessor accessor, int tIndex,
+                    AggregateState state) throws HyracksDataException {
+                ArrayBackedValueStorage inputVal = (ArrayBackedValueStorage) state.state;
+                inputVal.reset();
+                int leadOffset = accessor.getTupleStartOffset(tIndex) + accessor.getFieldSlotsLength();
+                for (int offset = accessor.getFieldStartOffset(tIndex, 1); offset < accessor.getFieldEndOffset(tIndex,
+                        1); offset += PositionReference.LENGTH) {
+                    position.setNewReference(accessor.getBuffer().array(), leadOffset + offset);
+                    inputVal.append(position);
+                }
+                //make a fake feild to cheat caller
+                tupleBuilder.addFieldEndOffset();
+            }
+
+            @Override
+            public void reset() {
+
+            }
+
+            @Override
+            public void aggregate(IFrameTupleAccessor accessor, int tIndex, IFrameTupleAccessor stateAccessor,
+                    int stateTupleIndex, AggregateState state) throws HyracksDataException {
+                ArrayBackedValueStorage inputVal = (ArrayBackedValueStorage) state.state;
+                int leadOffset = accessor.getTupleStartOffset(tIndex) + accessor.getFieldSlotsLength();
+                for (int offset = accessor.getFieldStartOffset(tIndex, 1); offset < accessor.getFieldEndOffset(tIndex,
+                        1); offset += PositionReference.LENGTH) {
+                    position.setNewReference(accessor.getBuffer().array(), leadOffset + offset);
+                    inputVal.append(position);
+                }
+            }
+
+            @Override
+            public void outputPartialResult(ArrayTupleBuilder tupleBuilder, IFrameTupleAccessor accessor, int tIndex,
+                    AggregateState state) throws HyracksDataException {
+                throw new IllegalStateException("partial result method should not be called");
+            }
+
+            @Override
+            public void outputFinalResult(ArrayTupleBuilder tupleBuilder, IFrameTupleAccessor accessor, int tIndex,
+                    AggregateState state) throws HyracksDataException {
+                DataOutput fieldOutput = tupleBuilder.getDataOutput();
+                ArrayBackedValueStorage inputVal = (ArrayBackedValueStorage) state.state;
+                try {
+                    if (inputVal.getLength() > frameSize / 2) {
+                        LOG.warn("MergeKmer: output data size is too big: " + inputVal.getLength());
+                    }
+                    fieldOutput.write(inputVal.getByteArray(), inputVal.getStartOffset(), inputVal.getLength());
+                    tupleBuilder.addFieldEndOffset();
+
+                } catch (IOException e) {
+                    throw new HyracksDataException("I/O exception when writing aggregation to the output buffer.");
+                }
+            }
+
+            @Override
+            public void close() {
+
+            }
+
+        };
+
+    }
+}
diff --git a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/dataflow/aggregators/MergeReadIDAggregateFactory.java b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/dataflow/aggregators/MergeReadIDAggregateFactory.java
index 974dead..73e3093 100644
--- a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/dataflow/aggregators/MergeReadIDAggregateFactory.java
+++ b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/dataflow/aggregators/MergeReadIDAggregateFactory.java
@@ -1,3 +1,18 @@
+/*
+ * Copyright 2009-2013 by The Regents of the University of California
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * you may obtain a copy of the License from
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
 package edu.uci.ics.genomix.hyracks.dataflow.aggregators;
 
 import java.io.DataOutput;
@@ -146,7 +161,6 @@
 
             @Override
             public void reset() {
-                // TODO Auto-generated method stub
 
             }
 
@@ -195,7 +209,7 @@
                         LOG.warn("MergeReadID on read:" + readID + " is of size: " + totalSize + ", current frameSize:"
                                 + frameSize + "\n Recommendate to enlarge the FrameSize");
                     }
-                    if (totalSize > frameSize){
+                    if (totalSize > frameSize) {
                         for (StackTraceElement ste : Thread.currentThread().getStackTrace()) {
                             System.out.println(ste);
                         }
@@ -208,7 +222,6 @@
 
             @Override
             public void close() {
-                // TODO Auto-generated method stub
 
             }
 
diff --git a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/dataflow/io/KMerSequenceWriterFactory.java b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/dataflow/io/KMerSequenceWriterFactory.java
index 0a1ef96..bb8ea16 100644
--- a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/dataflow/io/KMerSequenceWriterFactory.java
+++ b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/dataflow/io/KMerSequenceWriterFactory.java
@@ -1,5 +1,5 @@
 /*
- * Copyright 2009-2012 by The Regents of the University of California
+ * Copyright 2009-2013 by The Regents of the University of California
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
  * you may obtain a copy of the License from
@@ -71,7 +71,7 @@
                     throw new IllegalArgumentException("Not enough kmer bytes");
                 }
                 reEnterKey.setNewReference(tuple.getFieldData(InputKmerField), tuple.getFieldStart(InputKmerField));
-                int countOfPos = tuple.getFieldLength(InputPositionListField)/PositionWritable.LENGTH;
+                int countOfPos = tuple.getFieldLength(InputPositionListField) / PositionWritable.LENGTH;
                 if (tuple.getFieldLength(InputPositionListField) % PositionWritable.LENGTH != 0) {
                     throw new IllegalArgumentException("Invalid count of position byte");
                 }
@@ -96,7 +96,6 @@
 
         @Override
         public void close(DataOutput output) throws HyracksDataException {
-            // TODO Auto-generated method stub
         }
     }
 
diff --git a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/dataflow/io/KMerTextWriterFactory.java b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/dataflow/io/KMerTextWriterFactory.java
index 7ea065d..683fb80 100644
--- a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/dataflow/io/KMerTextWriterFactory.java
+++ b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/dataflow/io/KMerTextWriterFactory.java
@@ -1,5 +1,5 @@
 /*
- * Copyright 2009-2012 by The Regents of the University of California
+ * Copyright 2009-2013 by The Regents of the University of California
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
  * you may obtain a copy of the License from
@@ -12,7 +12,6 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
-
 package edu.uci.ics.genomix.hyracks.dataflow.io;
 
 import java.io.DataOutput;
@@ -33,15 +32,17 @@
 	 * 
 	 */
     private static final long serialVersionUID = 1L;
-    
+
     private final int kmerSize;
+
     public KMerTextWriterFactory(int k) {
-        kmerSize =k;
+        kmerSize = k;
     }
 
     public class TupleWriter implements ITupleWriter {
         private KmerBytesWritable kmer = new KmerBytesWritable(kmerSize);
         private PositionListWritable plist = new PositionListWritable();
+
         @Override
         public void write(DataOutput output, ITupleReference tuple) throws HyracksDataException {
             try {
@@ -69,19 +70,16 @@
 
         @Override
         public void open(DataOutput output) throws HyracksDataException {
-            // TODO Auto-generated method stub
 
         }
 
         @Override
         public void close(DataOutput output) throws HyracksDataException {
-            // TODO Auto-generated method stub
         }
     }
 
     @Override
     public ITupleWriter getTupleWriter(IHyracksTaskContext ctx) throws HyracksDataException {
-        // TODO Auto-generated method stub
         return new TupleWriter();
     }
 
diff --git a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/dataflow/io/NodeSequenceWriterFactory.java b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/dataflow/io/NodeSequenceWriterFactory.java
index 00409ef..affab71 100644
--- a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/dataflow/io/NodeSequenceWriterFactory.java
+++ b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/dataflow/io/NodeSequenceWriterFactory.java
@@ -1,3 +1,17 @@
+/*
+ * Copyright 2009-2013 by The Regents of the University of California
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * you may obtain a copy of the License from
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
 package edu.uci.ics.genomix.hyracks.dataflow.io;
 
 import java.io.DataOutput;
@@ -36,7 +50,7 @@
     public static final int InputFRField = MapReadToNodeOperator.OutputForwardReverseField;
     public static final int InputRFField = MapReadToNodeOperator.OutputReverseForwardField;
     public static final int InputRRField = MapReadToNodeOperator.OutputReverseReverseField;
-    
+
     public static final int InputKmerBytesField = MapReadToNodeOperator.OutputKmerBytesField;
 
     private ConfFactory confFactory;
@@ -60,8 +74,8 @@
         @Override
         public void open(DataOutput output) throws HyracksDataException {
             try {
-                writer = SequenceFile.createWriter(cf.getConf(), (FSDataOutputStream) output, NodeWritable.class, NullWritable.class,
-                        CompressionType.NONE, null);
+                writer = SequenceFile.createWriter(cf.getConf(), (FSDataOutputStream) output, NodeWritable.class,
+                        NullWritable.class, CompressionType.NONE, null);
             } catch (IOException e) {
                 throw new HyracksDataException(e);
             }
@@ -79,7 +93,7 @@
                     tuple.getFieldData(InputRFField), tuple.getFieldStart(InputRFField));
             node.getRRList().setNewReference(tuple.getFieldLength(InputRRField) / PositionWritable.LENGTH,
                     tuple.getFieldData(InputRRField), tuple.getFieldStart(InputRRField));
-            
+
             node.getKmer().setNewReference(
                     Marshal.getInt(tuple.getFieldData(NodeSequenceWriterFactory.InputCountOfKmerField),
                             tuple.getFieldStart(NodeSequenceWriterFactory.InputCountOfKmerField)),
diff --git a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/dataflow/io/NodeTextWriterFactory.java b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/dataflow/io/NodeTextWriterFactory.java
index cec702e..54adf24 100644
--- a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/dataflow/io/NodeTextWriterFactory.java
+++ b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/dataflow/io/NodeTextWriterFactory.java
@@ -1,3 +1,17 @@
+/*
+ * Copyright 2009-2013 by The Regents of the University of California
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * you may obtain a copy of the License from
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
 package edu.uci.ics.genomix.hyracks.dataflow.io;
 
 import java.io.DataOutput;
@@ -31,7 +45,6 @@
 
             @Override
             public void open(DataOutput output) throws HyracksDataException {
-                // TODO Auto-generated method stub
 
             }
 
@@ -71,7 +84,6 @@
 
             @Override
             public void close(DataOutput output) throws HyracksDataException {
-                // TODO Auto-generated method stub
 
             }
 
diff --git a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/driver/Driver.java b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/driver/Driver.java
index 5014a8a..35bd838 100644
--- a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/driver/Driver.java
+++ b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/driver/Driver.java
@@ -1,5 +1,5 @@
 /*
- * Copyright 2009-2012 by The Regents of the University of California
+ * Copyright 2009-2013 by The Regents of the University of California
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
  * you may obtain a copy of the License from
@@ -101,7 +101,7 @@
                     jobGen = new JobGenCreateKmerInfo(job, scheduler, ncMap, numPartitionPerMachine);
                     break;
                 case OUTPUT_MAP_KMER_TO_READ:
-                    jobGen = new JobGenMapKmerToRead(job,scheduler, ncMap, numPartitionPerMachine);
+                    jobGen = new JobGenMapKmerToRead(job, scheduler, ncMap, numPartitionPerMachine);
                     break;
                 case OUTPUT_GROUPBY_READID:
                     jobGen = new JobGenGroupbyReadID(job, scheduler, ncMap, numPartitionPerMachine);
diff --git a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/job/GenomixJobConf.java b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/job/GenomixJobConf.java
index 1f12bb5..d1f47c2 100644
--- a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/job/GenomixJobConf.java
+++ b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/job/GenomixJobConf.java
@@ -1,5 +1,5 @@
 /*
- * Copyright 2009-2012 by The Regents of the University of California
+ * Copyright 2009-2013 by The Regents of the University of California
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
  * you may obtain a copy of the License from
@@ -20,6 +20,7 @@
 import org.apache.hadoop.conf.Configuration;
 import org.apache.hadoop.mapred.JobConf;
 
+@SuppressWarnings("deprecation")
 public class GenomixJobConf extends JobConf {
 
     public static final String JOB_NAME = "genomix";
@@ -50,7 +51,7 @@
 
     public static final int DEFAULT_KMERLEN = 21;
     public static final int DEFAULT_READLEN = 124;
-    public static final int DEFAULT_FRAME_SIZE = 128*1024;
+    public static final int DEFAULT_FRAME_SIZE = 128 * 1024;
     public static final int DEFAULT_FRAME_LIMIT = 4096;
     public static final int DEFAULT_TABLE_SIZE = 10485767;
     public static final long DEFAULT_GROUPBY_HYBRID_INPUTSIZE = 154000000L;
@@ -62,15 +63,14 @@
     public static final boolean DEFAULT_REVERSED = true;
 
     public static final String JOB_PLAN_GRAPHBUILD = "graphbuild";
-    public static final String JOB_PLAN_GRAPHSTAT  = "graphstat";
-    
+    public static final String JOB_PLAN_GRAPHSTAT = "graphstat";
+
     public static final String GROUPBY_TYPE_HYBRID = "hybrid";
     public static final String GROUPBY_TYPE_EXTERNAL = "external";
     public static final String GROUPBY_TYPE_PRECLUSTER = "precluster";
     public static final String OUTPUT_FORMAT_BINARY = "binary";
     public static final String OUTPUT_FORMAT_TEXT = "text";
 
-
     public GenomixJobConf() throws IOException {
         super(new Configuration());
     }
diff --git a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/job/JobGen.java b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/job/JobGen.java
index a9dfc9b..c8cb701 100644
--- a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/job/JobGen.java
+++ b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/job/JobGen.java
@@ -1,5 +1,5 @@
 /*
- * Copyright 2009-2012 by The Regents of the University of California
+ * Copyright 2009-2013 by The Regents of the University of California
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
  * you may obtain a copy of the License from
@@ -18,8 +18,6 @@
 import java.io.Serializable;
 import java.util.UUID;
 
-import org.apache.hadoop.mapred.JobConf;
-
 import edu.uci.ics.hyracks.api.exceptions.HyracksDataException;
 import edu.uci.ics.hyracks.api.exceptions.HyracksException;
 import edu.uci.ics.hyracks.api.job.JobSpecification;
@@ -39,4 +37,4 @@
     }
 
     public abstract JobSpecification generateJob() throws HyracksException;
-}
\ No newline at end of file
+}
diff --git a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/job/JobGenBrujinGraph.java b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/job/JobGenBrujinGraph.java
index 94d619a..02087de 100644
--- a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/job/JobGenBrujinGraph.java
+++ b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/job/JobGenBrujinGraph.java
@@ -1,5 +1,5 @@
 /*
- * Copyright 2009-2012 by The Regents of the University of California
+ * Copyright 2009-2013 by The Regents of the University of California
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
  * you may obtain a copy of the License from
@@ -26,10 +26,8 @@
 
 import edu.uci.ics.genomix.hyracks.data.accessors.KmerHashPartitioncomputerFactory;
 import edu.uci.ics.genomix.hyracks.data.accessors.KmerNormarlizedComputerFactory;
-import edu.uci.ics.genomix.hyracks.data.accessors.ReadIDNormarlizedComputeFactory;
 import edu.uci.ics.genomix.hyracks.data.accessors.ReadIDPartitionComputerFactory;
 import edu.uci.ics.genomix.hyracks.data.primitive.KmerPointable;
-import edu.uci.ics.genomix.hyracks.data.primitive.ReadIDPointable;
 import edu.uci.ics.genomix.hyracks.dataflow.ConnectorPolicyAssignmentPolicy;
 import edu.uci.ics.genomix.hyracks.dataflow.MapKmerPositionToReadOperator;
 import edu.uci.ics.genomix.hyracks.dataflow.MapReadToNodeOperator;
@@ -58,6 +56,7 @@
 import edu.uci.ics.hyracks.data.std.accessors.PointableBinaryComparatorFactory;
 import edu.uci.ics.hyracks.data.std.accessors.PointableBinaryHashFunctionFactory;
 import edu.uci.ics.hyracks.data.std.api.IPointableFactory;
+import edu.uci.ics.hyracks.data.std.primitive.IntegerPointable;
 import edu.uci.ics.hyracks.dataflow.common.data.partition.FieldHashPartitionComputerFactory;
 import edu.uci.ics.hyracks.dataflow.std.base.AbstractOperatorDescriptor;
 import edu.uci.ics.hyracks.dataflow.std.connectors.MToNPartitioningConnectorDescriptor;
@@ -74,6 +73,7 @@
 import edu.uci.ics.hyracks.hdfs.dataflow.HDFSWriteOperatorDescriptor;
 import edu.uci.ics.hyracks.hdfs.scheduler.Scheduler;
 
+@SuppressWarnings("deprecation")
 public class JobGenBrujinGraph extends JobGen {
     /**
      * 
@@ -231,7 +231,7 @@
         int[] keyFields = new int[] { 0 }; // the id of grouped key
         // (ReadID, {(PosInRead,{OtherPositoin..},Kmer) ...}
         ExternalSortOperatorDescriptor sorter = new ExternalSortOperatorDescriptor(jobSpec, frameLimits, keyFields,
-                new IBinaryComparatorFactory[] { PointableBinaryComparatorFactory.of(ReadIDPointable.FACTORY) },
+                new IBinaryComparatorFactory[] { PointableBinaryComparatorFactory.of(IntegerPointable.FACTORY) },
                 MapKmerPositionToReadOperator.readIDOutputRec);
         connectOperators(jobSpec, mapKmerToRead, ncNodeNames, sorter, ncNodeNames, new OneToOneConnectorDescriptor(
                 jobSpec));
@@ -239,9 +239,8 @@
         RecordDescriptor readIDFinalRec = new RecordDescriptor(
                 new ISerializerDeserializer[1 + 2 * MergeReadIDAggregateFactory.getPositionCount(readLength, kmerSize)]);
         Object[] objs = generateAggeragateDescriptorbyType(jobSpec, keyFields, new AggregateReadIDAggregateFactory(),
-                new MergeReadIDAggregateFactory(readLength, kmerSize), new ReadIDPartitionComputerFactory(),
-                new ReadIDNormarlizedComputeFactory(), ReadIDPointable.FACTORY,
-                AggregateReadIDAggregateFactory.readIDAggregateRec, readIDFinalRec);
+                new MergeReadIDAggregateFactory(readLength, kmerSize), new ReadIDPartitionComputerFactory(), null,
+                IntegerPointable.FACTORY, AggregateReadIDAggregateFactory.readIDAggregateRec, readIDFinalRec);
         AbstractOperatorDescriptor readLocalAggregator = (AbstractOperatorDescriptor) objs[0];
         connectOperators(jobSpec, sorter, ncNodeNames, readLocalAggregator, ncNodeNames,
                 new OneToOneConnectorDescriptor(jobSpec));
@@ -367,7 +366,6 @@
         }
         try {
             hadoopJobConfFactory = new ConfFactory(new JobConf(conf));
-            @SuppressWarnings("deprecation")
             InputSplit[] splits = hadoopJobConfFactory.getConf().getInputFormat()
                     .getSplits(hadoopJobConfFactory.getConf(), ncNodeNames.length);
             readSchedule = scheduler.getLocationConstraints(splits);
diff --git a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/job/JobGenCheckReader.java b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/job/JobGenCheckReader.java
index 28e4ff5..a9e6d97 100644
--- a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/job/JobGenCheckReader.java
+++ b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/job/JobGenCheckReader.java
@@ -1,3 +1,17 @@
+/*
+ * Copyright 2009-2013 by The Regents of the University of California
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * you may obtain a copy of the License from
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
 package edu.uci.ics.genomix.hyracks.job;
 
 import java.io.DataOutput;
@@ -31,7 +45,6 @@
     public JobGenCheckReader(GenomixJobConf job, Scheduler scheduler, Map<String, NodeControllerInfo> ncMap,
             int numPartitionPerMachine) throws HyracksDataException {
         super(job, scheduler, ncMap, numPartitionPerMachine);
-        // TODO Auto-generated constructor stub
     }
 
     @Override
@@ -50,56 +63,56 @@
     public AbstractSingleActivityOperatorDescriptor generateRootByWriteKmerReader(JobSpecification jobSpec,
             HDFSReadOperatorDescriptor readOperator) throws HyracksException {
         // Output Kmer
-        HDFSWriteOperatorDescriptor writeKmerOperator = new HDFSWriteOperatorDescriptor(jobSpec, hadoopJobConfFactory.getConf(), new ITupleWriterFactory(){
+        HDFSWriteOperatorDescriptor writeKmerOperator = new HDFSWriteOperatorDescriptor(jobSpec,
+                hadoopJobConfFactory.getConf(), new ITupleWriterFactory() {
 
-            /**
+                    /**
              * 
              */
-            private static final long serialVersionUID = 1L;
-            
-
-            @Override
-            public ITupleWriter getTupleWriter(IHyracksTaskContext ctx) throws HyracksDataException {
-                return new ITupleWriter(){
-
-                    private KmerBytesWritable kmer = new KmerBytesWritable(kmerSize);
-                    private PositionWritable pos = new PositionWritable();
-                    
-                    @Override
-                    public void open(DataOutput output) throws HyracksDataException {
-                        // TODO Auto-generated method stub
-                        
-                    }
+                    private static final long serialVersionUID = 1L;
 
                     @Override
-                    public void write(DataOutput output, ITupleReference tuple) throws HyracksDataException {
-                        try {
-                            if (kmer.getLength() > tuple.getFieldLength(ReadsKeyValueParserFactory.OutputKmerField)) {
-                                throw new IllegalArgumentException("Not enough kmer bytes");
+                    public ITupleWriter getTupleWriter(IHyracksTaskContext ctx) throws HyracksDataException {
+                        return new ITupleWriter() {
+
+                            private KmerBytesWritable kmer = new KmerBytesWritable(kmerSize);
+                            private PositionWritable pos = new PositionWritable();
+
+                            @Override
+                            public void open(DataOutput output) throws HyracksDataException {
                             }
-                            kmer.setNewReference(tuple.getFieldData(ReadsKeyValueParserFactory.OutputKmerField), tuple.getFieldStart(ReadsKeyValueParserFactory.OutputKmerField));
-                            pos.setNewReference(tuple.getFieldData(ReadsKeyValueParserFactory.OutputPosition),
-                                    tuple.getFieldStart(ReadsKeyValueParserFactory.OutputPosition));
 
-                            output.write(kmer.toString().getBytes());
-                            output.writeByte('\t');
-                            output.write(pos.toString().getBytes());
-                            output.writeByte('\n');
-                        } catch (IOException e) {
-                            throw new HyracksDataException(e);
-                        }
+                            @Override
+                            public void write(DataOutput output, ITupleReference tuple) throws HyracksDataException {
+                                try {
+                                    if (kmer.getLength() > tuple
+                                            .getFieldLength(ReadsKeyValueParserFactory.OutputKmerField)) {
+                                        throw new IllegalArgumentException("Not enough kmer bytes");
+                                    }
+                                    kmer.setNewReference(
+                                            tuple.getFieldData(ReadsKeyValueParserFactory.OutputKmerField),
+                                            tuple.getFieldStart(ReadsKeyValueParserFactory.OutputKmerField));
+                                    pos.setNewReference(tuple.getFieldData(ReadsKeyValueParserFactory.OutputPosition),
+                                            tuple.getFieldStart(ReadsKeyValueParserFactory.OutputPosition));
+
+                                    output.write(kmer.toString().getBytes());
+                                    output.writeByte('\t');
+                                    output.write(pos.toString().getBytes());
+                                    output.writeByte('\n');
+                                } catch (IOException e) {
+                                    throw new HyracksDataException(e);
+                                }
+                            }
+
+                            @Override
+                            public void close(DataOutput output) throws HyracksDataException {
+
+                            }
+
+                        };
                     }
 
-                    @Override
-                    public void close(DataOutput output) throws HyracksDataException {
-                        // TODO Auto-generated method stub
-                        
-                    }
-                    
-                };
-            }
-            
-        });
+                });
         connectOperators(jobSpec, readOperator, ncNodeNames, writeKmerOperator, ncNodeNames,
                 new OneToOneConnectorDescriptor(jobSpec));
         jobSpec.addRoot(writeKmerOperator);
diff --git a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/job/JobGenCreateKmerInfo.java b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/job/JobGenCreateKmerInfo.java
index 4ee36a0..5202ba2 100644
--- a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/job/JobGenCreateKmerInfo.java
+++ b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/job/JobGenCreateKmerInfo.java
@@ -1,3 +1,17 @@
+/*
+ * Copyright 2009-2013 by The Regents of the University of California
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * you may obtain a copy of the License from
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
 package edu.uci.ics.genomix.hyracks.job;
 
 import java.util.Map;
@@ -20,7 +34,6 @@
     public JobGenCreateKmerInfo(GenomixJobConf job, Scheduler scheduler, Map<String, NodeControllerInfo> ncMap,
             int numPartitionPerMachine) throws HyracksDataException {
         super(job, scheduler, ncMap, numPartitionPerMachine);
-        // TODO Auto-generated constructor stub
     }
 
     @Override
diff --git a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/job/JobGenGroupbyReadID.java b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/job/JobGenGroupbyReadID.java
index 201be03..5fce20e 100644
--- a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/job/JobGenGroupbyReadID.java
+++ b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/job/JobGenGroupbyReadID.java
@@ -1,3 +1,17 @@
+/*
+ * Copyright 2009-2013 by The Regents of the University of California
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * you may obtain a copy of the License from
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
 package edu.uci.ics.genomix.hyracks.job;
 
 import java.io.DataOutput;
@@ -31,7 +45,6 @@
     public JobGenGroupbyReadID(GenomixJobConf job, Scheduler scheduler, Map<String, NodeControllerInfo> ncMap,
             int numPartitionPerMachine) throws HyracksDataException {
         super(job, scheduler, ncMap, numPartitionPerMachine);
-        // TODO Auto-generated constructor stub
     }
 
     @Override
@@ -71,7 +84,6 @@
 
                     @Override
                     public ITupleWriter getTupleWriter(IHyracksTaskContext ctx) throws HyracksDataException {
-                        // TODO Auto-generated method stub
                         return new ITupleWriter() {
 
                             private KmerBytesWritable kmer = new KmerBytesWritable(kmerSize);
@@ -79,7 +91,6 @@
 
                             @Override
                             public void open(DataOutput output) throws HyracksDataException {
-                                // TODO Auto-generated method stub
 
                             }
 
@@ -131,7 +142,6 @@
 
                             @Override
                             public void close(DataOutput output) throws HyracksDataException {
-                                // TODO Auto-generated method stub
 
                             }
 
diff --git a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/job/JobGenMapKmerToRead.java b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/job/JobGenMapKmerToRead.java
index 2872a2d..6c8feec 100644
--- a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/job/JobGenMapKmerToRead.java
+++ b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/job/JobGenMapKmerToRead.java
@@ -1,3 +1,17 @@
+/*
+ * Copyright 2009-2013 by The Regents of the University of California
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * you may obtain a copy of the License from
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
 package edu.uci.ics.genomix.hyracks.job;
 
 import java.io.DataOutput;
@@ -6,7 +20,6 @@
 
 import edu.uci.ics.genomix.data.Marshal;
 import edu.uci.ics.genomix.hyracks.dataflow.MapKmerPositionToReadOperator;
-import edu.uci.ics.genomix.hyracks.dataflow.ReadsKeyValueParserFactory;
 import edu.uci.ics.genomix.type.KmerBytesWritable;
 import edu.uci.ics.genomix.type.PositionListWritable;
 import edu.uci.ics.hyracks.api.client.NodeControllerInfo;
@@ -33,7 +46,6 @@
     public JobGenMapKmerToRead(GenomixJobConf job, Scheduler scheduler, Map<String, NodeControllerInfo> ncMap,
             int numPartitionPerMachine) throws HyracksDataException {
         super(job, scheduler, ncMap, numPartitionPerMachine);
-        // TODO Auto-generated constructor stub
     }
 
     public AbstractOperatorDescriptor generateRootByWriteMapperFromKmerToReadID(JobSpecification jobSpec,
@@ -56,7 +68,6 @@
 
                             @Override
                             public void open(DataOutput output) throws HyracksDataException {
-                                // TODO Auto-generated method stub
 
                             }
 
@@ -76,7 +87,6 @@
                                             tuple.getFieldData(MapKmerPositionToReadOperator.OutputOtherReadIDListField),
                                             tuple.getFieldStart(MapKmerPositionToReadOperator.OutputOtherReadIDListField));
 
-
                                     String kmerString = "";
                                     if (posInRead > 0) {
                                         if (kmer.getLength() > tuple
@@ -105,7 +115,6 @@
 
                             @Override
                             public void close(DataOutput output) throws HyracksDataException {
-                                // TODO Auto-generated method stub
 
                             }
 
diff --git a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/util/ByteComparatorFactory.java b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/util/ByteComparatorFactory.java
deleted file mode 100644
index b070b56..0000000
--- a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/util/ByteComparatorFactory.java
+++ /dev/null
@@ -1,54 +0,0 @@
-/*
- * Copyright 2009-2012 by The Regents of the University of California
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * you may obtain a copy of the License from
- *
- *     http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package edu.uci.ics.genomix.hyracks.util;
-
-import edu.uci.ics.hyracks.api.dataflow.value.IBinaryComparator;
-import edu.uci.ics.hyracks.api.dataflow.value.IBinaryComparatorFactory;
-import edu.uci.ics.hyracks.api.dataflow.value.IBinaryHashFunction;
-import edu.uci.ics.hyracks.api.dataflow.value.IBinaryHashFunctionFactory;
-
-public class ByteComparatorFactory implements IBinaryComparatorFactory, IBinaryHashFunctionFactory {
-
-    /**
-	 * 
-	 */
-    private static final long serialVersionUID = 1L;
-
-    @Override
-    public IBinaryComparator createBinaryComparator() {
-        return new IBinaryComparator() {
-
-            @Override
-            public int compare(byte[] b1, int s1, int l1, byte[] b2, int s2, int l2) {
-                return b1[s1] - b2[s2];
-            }
-
-        };
-    }
-
-    @Override
-    public IBinaryHashFunction createBinaryHashFunction() {
-        return new IBinaryHashFunction() {
-
-            @Override
-            public int hash(byte[] bytes, int offset, int length) {
-                return bytes[offset];
-            }
-
-        };
-    }
-
-}
diff --git a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/util/StatCountAggregateFactory.java b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/util/StatCountAggregateFactory.java
index f483a9c..26daa96 100644
--- a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/util/StatCountAggregateFactory.java
+++ b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/util/StatCountAggregateFactory.java
@@ -1,5 +1,5 @@
 /*
- * Copyright 2009-2012 by The Regents of the University of California
+ * Copyright 2009-2013 by The Regents of the University of California
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
  * you may obtain a copy of the License from
@@ -12,7 +12,6 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
-
 package edu.uci.ics.genomix.hyracks.util;
 
 import java.io.DataOutput;
@@ -44,7 +43,6 @@
 
         @Override
         public AggregateState createAggregateStates() {
-            // TODO Auto-generated method stub
             return null;
         }
 
@@ -63,7 +61,6 @@
 
         @Override
         public void reset() {
-            // TODO Auto-generated method stub
 
         }
 
@@ -112,7 +109,6 @@
 
         @Override
         public void close() {
-            // TODO Auto-generated method stub
 
         }
 
@@ -122,7 +118,6 @@
     public IAggregatorDescriptor createAggregator(IHyracksTaskContext ctx, RecordDescriptor inRecordDescriptor,
             RecordDescriptor outRecordDescriptor, int[] keyFields, int[] keyFieldsInPartialResults)
             throws HyracksDataException {
-        // TODO Auto-generated method stub
         return new CountAggregator(keyFields);
     }
 
diff --git a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/util/StatSumAggregateFactory.java b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/util/StatSumAggregateFactory.java
deleted file mode 100644
index fb37056..0000000
--- a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/util/StatSumAggregateFactory.java
+++ /dev/null
@@ -1,131 +0,0 @@
-/*
- * Copyright 2009-2012 by The Regents of the University of California
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * you may obtain a copy of the License from
- *
- *     http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package edu.uci.ics.genomix.hyracks.util;
-
-import java.io.DataOutput;
-import java.io.IOException;
-
-import edu.uci.ics.hyracks.api.comm.IFrameTupleAccessor;
-import edu.uci.ics.hyracks.api.context.IHyracksTaskContext;
-import edu.uci.ics.hyracks.api.dataflow.value.RecordDescriptor;
-import edu.uci.ics.hyracks.api.exceptions.HyracksDataException;
-import edu.uci.ics.hyracks.dataflow.common.comm.io.ArrayTupleBuilder;
-import edu.uci.ics.hyracks.dataflow.common.data.marshalling.IntegerSerializerDeserializer;
-import edu.uci.ics.hyracks.dataflow.std.group.AggregateState;
-import edu.uci.ics.hyracks.dataflow.std.group.IAggregatorDescriptor;
-import edu.uci.ics.hyracks.dataflow.std.group.IAggregatorDescriptorFactory;
-
-public class StatSumAggregateFactory implements IAggregatorDescriptorFactory {
-
-    /**
-	 * 
-	 */
-    private static final long serialVersionUID = 1L;
-
-    public class DistributeAggregatorDescriptor implements IAggregatorDescriptor {
-
-        private final int[] keyFields;
-
-        public DistributeAggregatorDescriptor(int[] keyFields) {
-            this.keyFields = keyFields;
-        }
-
-        @Override
-        public AggregateState createAggregateStates() {
-            // TODO Auto-generated method stub
-            return null;
-        }
-
-        protected int getCount(IFrameTupleAccessor accessor, int tIndex) {
-            int tupleOffset = accessor.getTupleStartOffset(tIndex);
-            int fieldStart = accessor.getFieldStartOffset(tIndex, 1);
-            int countoffset = tupleOffset + accessor.getFieldSlotsLength() + fieldStart;
-            byte[] data = accessor.getBuffer().array();
-            return IntegerSerializerDeserializer.getInt(data, countoffset);
-        }
-
-        @Override
-        public void init(ArrayTupleBuilder tupleBuilder, IFrameTupleAccessor accessor, int tIndex, AggregateState state)
-                throws HyracksDataException {
-            int count = getCount(accessor, tIndex);
-
-            DataOutput fieldOutput = tupleBuilder.getDataOutput();
-            try {
-                fieldOutput.writeInt(count);
-                tupleBuilder.addFieldEndOffset();
-            } catch (IOException e) {
-                throw new HyracksDataException("I/O exception when initializing the aggregator.");
-            }
-        }
-
-        @Override
-        public void reset() {
-            // TODO Auto-generated method stub
-
-        }
-
-        @Override
-        public void aggregate(IFrameTupleAccessor accessor, int tIndex, IFrameTupleAccessor stateAccessor,
-                int stateTupleIndex, AggregateState state) throws HyracksDataException {
-            int count = getCount(accessor, tIndex);
-
-            int statetupleOffset = stateAccessor.getTupleStartOffset(stateTupleIndex);
-            int countfieldStart = stateAccessor.getFieldStartOffset(stateTupleIndex, 1);
-            int countoffset = statetupleOffset + stateAccessor.getFieldSlotsLength() + countfieldStart;
-
-            byte[] data = stateAccessor.getBuffer().array();
-            count += IntegerSerializerDeserializer.getInt(data, countoffset);
-            IntegerSerializerDeserializer.putInt(count, data, countoffset);
-        }
-
-        @Override
-        public void outputPartialResult(ArrayTupleBuilder tupleBuilder, IFrameTupleAccessor accessor, int tIndex,
-                AggregateState state) throws HyracksDataException {
-            int count = getCount(accessor, tIndex);
-            DataOutput fieldOutput = tupleBuilder.getDataOutput();
-            try {
-                fieldOutput.writeInt(count);
-                tupleBuilder.addFieldEndOffset();
-            } catch (IOException e) {
-                throw new HyracksDataException("I/O exception when writing aggregation to the output buffer.");
-            }
-
-        }
-
-        @Override
-        public void outputFinalResult(ArrayTupleBuilder tupleBuilder, IFrameTupleAccessor accessor, int tIndex,
-                AggregateState state) throws HyracksDataException {
-            outputPartialResult(tupleBuilder, accessor, tIndex, state);
-
-        }
-
-        @Override
-        public void close() {
-            // TODO Auto-generated method stub
-
-        }
-
-    }
-
-    @Override
-    public IAggregatorDescriptor createAggregator(IHyracksTaskContext ctx, RecordDescriptor inRecordDescriptor,
-            RecordDescriptor outRecordDescriptor, int[] keyFields, int[] keyFieldsInPartialResults)
-            throws HyracksDataException {
-        // TODO Auto-generated method stub
-        return new DistributeAggregatorDescriptor(keyFields);
-    }
-
-}
diff --git a/genomix/genomix-hyracks/src/test/java/edu/uci/ics/genomix/hyracks/test/JobRunStepByStepTest.java b/genomix/genomix-hyracks/src/test/java/edu/uci/ics/genomix/hyracks/test/JobRunStepByStepTest.java
index ec95aa6..0ee2253 100644
--- a/genomix/genomix-hyracks/src/test/java/edu/uci/ics/genomix/hyracks/test/JobRunStepByStepTest.java
+++ b/genomix/genomix-hyracks/src/test/java/edu/uci/ics/genomix/hyracks/test/JobRunStepByStepTest.java
@@ -1,3 +1,17 @@
+/*
+ * Copyright 2009-2013 by The Regents of the University of California
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * you may obtain a copy of the License from
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
 package edu.uci.ics.genomix.hyracks.test;
 
 import java.io.BufferedWriter;
@@ -94,7 +108,7 @@
         conf.set(GenomixJobConf.OUTPUT_FORMAT, GenomixJobConf.OUTPUT_FORMAT_TEXT);
         conf.set(GenomixJobConf.GROUPBY_TYPE, GenomixJobConf.GROUPBY_TYPE_PRECLUSTER);
         driver.runJob(new GenomixJobConf(conf), Plan.OUTPUT_GROUPBY_READID, true);
-        Assert.assertEquals(true, checkResults(EXPECTED_GROUPBYREADID, new int [] {2,5,8,11,14,17,20,23}));
+        Assert.assertEquals(true, checkResults(EXPECTED_GROUPBYREADID, new int[] { 2, 5, 8, 11, 14, 17, 20, 23 }));
     }
 
     public void TestEndToEnd() throws Exception {
@@ -103,7 +117,7 @@
         cleanUpReEntry();
         conf.set(GenomixJobConf.GROUPBY_TYPE, GenomixJobConf.GROUPBY_TYPE_PRECLUSTER);
         driver.runJob(new GenomixJobConf(conf), Plan.BUILD_DEBRUJIN_GRAPH, true);
-        Assert.assertEquals(true, checkResults(EXPECTED_OUPUT_NODE, new int[] {1,2,3,4}));
+        Assert.assertEquals(true, checkResults(EXPECTED_OUPUT_NODE, new int[] { 1, 2, 3, 4 }));
     }
 
     @Before
@@ -195,7 +209,7 @@
                     if (node == null) {
                         break;
                     }
-                    bw.write(node.toString() );
+                    bw.write(node.toString());
                     System.out.println(node.toString());
                     bw.newLine();
                 }
diff --git a/genomix/genomix-hyracks/src/test/java/edu/uci/ics/genomix/hyracks/test/TestUtils.java b/genomix/genomix-hyracks/src/test/java/edu/uci/ics/genomix/hyracks/test/TestUtils.java
index d22bd0c..cb19d0c 100644
--- a/genomix/genomix-hyracks/src/test/java/edu/uci/ics/genomix/hyracks/test/TestUtils.java
+++ b/genomix/genomix-hyracks/src/test/java/edu/uci/ics/genomix/hyracks/test/TestUtils.java
@@ -1,5 +1,5 @@
 /*
- * Copyright 2009-2012 by The Regents of the University of California
+ * Copyright 2009-2013 by The Regents of the University of California
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
  * you may obtain a copy of the License from
@@ -162,11 +162,11 @@
         }
         return true;
     }
-    
+
     private static boolean containStrings(String lineExpected, String actualLine, int[] poslistField) {
-//        if (lineExpected.equals(actualLine)){
-//            return true;
-//        }
+        if (lineExpected.equals(actualLine)) {
+            return true;
+        }
         String[] fieldsExp = lineExpected.split("\\\t");
         String[] fieldsAct = actualLine.split("\\\t");
         if (fieldsAct.length != fieldsExp.length) {
@@ -180,7 +180,7 @@
                     break;
                 }
             }
-            if (cont){
+            if (cont) {
                 continue;
             }
             if (!fieldsAct[i].equals(fieldsExp[i])) {