diff --git a/genomix/genomix-core/pom.xml b/genomix/genomix-core/pom.xml
index 84c6533..2af3391 100644
--- a/genomix/genomix-core/pom.xml
+++ b/genomix/genomix-core/pom.xml
@@ -9,7 +9,7 @@
 		<groupId>edu.uci.ics.hyracks</groupId>
 		<artifactId>genomix</artifactId>
 		<version>0.2.3-SNAPSHOT</version>
-    </parent>
+	</parent>
 
 	<properties>
 		<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
@@ -26,136 +26,10 @@
 					<target>1.6</target>
 				</configuration>
 			</plugin>
-			<plugin>
-				<groupId>org.codehaus.mojo</groupId>
-				<artifactId>appassembler-maven-plugin</artifactId>
-				<executions>
-					<execution>
-						<configuration>
-							<programs>
-								<program>
-									<mainClass>edu.uci.ics.genomix.driver.Driver</mainClass>
-									<name>genomix</name>
-								</program>
-							</programs>
-							<repositoryLayout>flat</repositoryLayout>
-							<repositoryName>lib</repositoryName>
-						</configuration>
-						<phase>package</phase>
-						<goals>
-							<goal>assemble</goal>
-						</goals>
-					</execution>
-				</executions>
-			</plugin>
-			<plugin>
-				<artifactId>maven-assembly-plugin</artifactId>
-				<version>2.2-beta-5</version>
-                <configuration>
-                    <descriptorRefs>
-                        <descriptorRef>jar-with-dependencies</descriptorRef>
-                    </descriptorRefs>
-                </configuration>
-				<executions>
-					<execution>
-						<configuration>
-							<descriptors>
-								<descriptor>src/main/assembly/binary-assembly.xml</descriptor>
-							</descriptors>
-						</configuration>
-						<phase>package</phase>
-						<goals>
-							<goal>attached</goal>
-						</goals>
-					</execution>
-                    <execution>
-                        <id>make-my-jar-with-dependencies</id>
-                        <phase>package</phase>
-                        <goals>
-                            <goal>single</goal>
-                        </goals>
-                    </execution>
-				</executions>
-			</plugin>
-			<plugin>
-				<groupId>org.apache.maven.plugins</groupId>
-				<artifactId>maven-surefire-plugin</artifactId>
-				<version>2.7.2</version>
-				<configuration>
-					<forkMode>pertest</forkMode>
-					<argLine>-enableassertions -Xmx512m -XX:MaxPermSize=300m
-						-Dfile.encoding=UTF-8
-						-Djava.util.logging.config.file=src/test/resources/logging.properties</argLine>
-					<includes>
-						<include>**/*TestSuite.java</include>
-						<include>**/*Test.java</include>
-					</includes>
-				</configuration>
-			</plugin>
-			<plugin>
-				<artifactId>maven-clean-plugin</artifactId>
-				<configuration>
-					<filesets>
-						<fileset>
-							<directory>.</directory>
-							<includes>
-								<include>teststore*</include>
-								<include>edu*</include>
-								<include>actual*</include>
-								<include>build*</include>
-								<include>expect*</include>
-								<include>ClusterController*</include>
-							</includes>
-						</fileset>
-					</filesets>
-				</configuration>
-			</plugin>
-			<plugin>
-				<artifactId>maven-resources-plugin</artifactId>
-				<version>2.5</version>
-				<executions>
-					<execution>
-						<id>copy-scripts</id>
-						<!-- here the phase you need -->
-						<phase>package</phase>
-						<goals>
-							<goal>copy-resources</goal>
-						</goals>
-						<configuration>
-							<outputDirectory>target/appassembler/bin</outputDirectory>
-							<resources>
-								<resource>
-									<directory>src/main/resources/scripts</directory>
-								</resource>
-							</resources>
-						</configuration>
-					</execution>
-					<execution>
-						<id>copy-conf</id>
-						<!-- here the phase you need -->
-						<phase>package</phase>
-						<goals>
-							<goal>copy-resources</goal>
-						</goals>
-						<configuration>
-							<outputDirectory>target/appassembler/conf</outputDirectory>
-							<resources>
-								<resource>
-									<directory>src/main/resources/conf</directory>
-								</resource>
-							</resources>
-						</configuration>
-					</execution>
-				</executions>
-			</plugin>
-			<plugin>
-				<groupId>org.apache.maven.plugins</groupId>
-				<artifactId>maven-resources-plugin</artifactId>
-				<version>2.6</version>
-			</plugin>
 		</plugins>
 	</build>
 
+
 	<dependencies>
 		<dependency>
 			<groupId>junit</groupId>
@@ -164,86 +38,9 @@
 			<scope>test</scope>
 		</dependency>
 		<dependency>
-			<groupId>edu.uci.ics.hyracks</groupId>
-			<artifactId>hyracks-dataflow-std</artifactId>
-			<version>0.2.3-SNAPSHOT</version>
-			<type>jar</type>
-			<scope>compile</scope>
-		</dependency>
-		<dependency>
-			<groupId>edu.uci.ics.hyracks</groupId>
-			<artifactId>hyracks-api</artifactId>
-			<version>0.2.3-SNAPSHOT</version>
-			<type>jar</type>
-			<scope>compile</scope>
-		</dependency>
-		<dependency>
-			<groupId>edu.uci.ics.hyracks</groupId>
-			<artifactId>hyracks-dataflow-common</artifactId>
-			<version>0.2.3-SNAPSHOT</version>
-			<type>jar</type>
-			<scope>compile</scope>
-		</dependency>
-		<dependency>
-			<groupId>edu.uci.ics.hyracks</groupId>
-			<artifactId>hyracks-data-std</artifactId>
-			<version>0.2.3-SNAPSHOT</version>
-		</dependency>
-		<dependency>
-			<groupId>edu.uci.ics.hyracks</groupId>
-			<artifactId>hyracks-control-cc</artifactId>
-			<version>0.2.3-SNAPSHOT</version>
-			<type>jar</type>
-			<scope>compile</scope>
-		</dependency>
-		<dependency>
-			<groupId>edu.uci.ics.hyracks</groupId>
-			<artifactId>hyracks-control-nc</artifactId>
-			<version>0.2.3-SNAPSHOT</version>
-			<type>jar</type>
-			<scope>compile</scope>
-		</dependency>
-		<dependency>
-			<groupId>com.kenai.nbpwr</groupId>
-			<artifactId>org-apache-commons-io</artifactId>
-			<version>1.3.1-201002241208</version>
-			<type>nbm</type>
-			<scope>test</scope>
-		</dependency>
-		<dependency>
-			<groupId>edu.uci.ics.hyracks.examples</groupId>
-			<artifactId>hyracks-integration-tests</artifactId>
-			<version>0.2.3-SNAPSHOT</version>
-			<scope>test</scope>
-		</dependency>
-		<dependency>
-			<groupId>edu.uci.ics.hyracks</groupId>
-			<artifactId>hyracks-ipc</artifactId>
-			<version>0.2.3-SNAPSHOT</version>
-			<type>jar</type>
-			<scope>compile</scope>
-		</dependency>
-		<dependency>
 			<groupId>org.apache.hadoop</groupId>
 			<artifactId>hadoop-core</artifactId>
 			<version>0.20.2</version>
 		</dependency>
-		<dependency>
-			<groupId>org.apache.hadoop</groupId>
-			<artifactId>hadoop-test</artifactId>
-			<version>0.20.2</version>
-		</dependency>
-		<dependency>
-			<groupId>edu.uci.ics.hyracks</groupId>
-			<artifactId>hyracks-hdfs-core</artifactId>
-			<version>0.2.3-SNAPSHOT</version>
-		</dependency>
-		<dependency>
-            <groupId>edu.uci.ics.hyracks</groupId>
-            <artifactId>hyracks-hdfs-core</artifactId>
-            <version>0.2.3-SNAPSHOT</version>
-            <type>test-jar</type>
-            <scope>test</scope>
-        </dependency>
 	</dependencies>
 </project>
diff --git a/genomix/genomix-core/src/main/java/edu/uci/ics/genomix/type/Kmer.java b/genomix/genomix-core/src/main/java/edu/uci/ics/genomix/type/Kmer.java
index 8957d39..07bd8cb 100644
--- a/genomix/genomix-core/src/main/java/edu/uci/ics/genomix/type/Kmer.java
+++ b/genomix/genomix-core/src/main/java/edu/uci/ics/genomix/type/Kmer.java
@@ -170,39 +170,6 @@
 		return (byte) (1 << output);
 	}
 
-	public static void main(String[] argv) {
-		byte[] array = { 'A', 'A', 'T', 'A', 'G', 'A', 'A', 'G' };
-		int k = 5;
-		byte[] kmer = CompressKmer(k, array, 0);
-		for (byte b : kmer) {
-			System.out.print(Integer.toBinaryString(b));
-			System.out.print(' ');
-		}
-		System.out.println();
-		System.out.println(recoverKmerFrom(k, kmer, 0, kmer.length));
 
-		for (int i = k; i < array.length-1; i++) {
-			byte out = MoveKmer(k, kmer, array[i]);
-
-			System.out.println((int) out);
-			for (byte b : kmer) {
-				System.out.print(Integer.toBinaryString(b));
-				System.out.print(' ');
-			}
-			System.out.println();
-			System.out.println(recoverKmerFrom(k, kmer, 0, kmer.length));
-		}
-
-		byte out = MoveKmer(k, kmer, array[array.length - 1]);
-
-		System.out.println((int) out);
-		for (byte b : kmer) {
-			System.out.print(Integer.toBinaryString(b));
-			System.out.print(' ');
-		}
-		System.out.println();
-		System.out.println(recoverKmerFrom(k, kmer, 0, kmer.length));
-
-	}
 
 }
diff --git a/genomix/genomix-core/src/main/java/edu/uci/ics/genomix/type/KmerCountValue.java b/genomix/genomix-core/src/main/java/edu/uci/ics/genomix/type/KmerCountValue.java
index 6c29209..08c283d 100644
--- a/genomix/genomix-core/src/main/java/edu/uci/ics/genomix/type/KmerCountValue.java
+++ b/genomix/genomix-core/src/main/java/edu/uci/ics/genomix/type/KmerCountValue.java
@@ -8,14 +8,13 @@
 import org.apache.hadoop.io.SequenceFile.ValueBytes;
 import org.apache.hadoop.io.Writable;
 
-import edu.uci.ics.hyracks.dataflow.common.data.accessors.ITupleReference;
 
 public class KmerCountValue implements ValueBytes, Writable{
 	private byte adjBitMap;
 	private byte count;
 
-	public KmerCountValue(ITupleReference tuple) {
-		reset(tuple);
+	public KmerCountValue(byte bitmap, byte count) {
+		reset(bitmap, count);
 	}
 	
 	public KmerCountValue() {
@@ -59,9 +58,9 @@
 		return Kmer.GENE_CODE.getSymbolFromBitMap(adjBitMap) + '\t' + String.valueOf(count);
 	}
 
-	public void reset(ITupleReference tuple) {
-		adjBitMap = tuple.getFieldData(1)[tuple.getFieldStart(1)];
-		count = tuple.getFieldData(2)[tuple.getFieldStart(2)];
+	public void reset(byte bitmap, byte count) {
+		this.adjBitMap = bitmap;
+		this.count = count;
 	}
 
 }
\ No newline at end of file
diff --git a/genomix/genomix-core/src/test/java/edu/uci/ics/genomix/example/kmer/KmerTest.java b/genomix/genomix-core/src/test/java/edu/uci/ics/genomix/example/kmer/KmerTest.java
new file mode 100644
index 0000000..f391d9f
--- /dev/null
+++ b/genomix/genomix-core/src/test/java/edu/uci/ics/genomix/example/kmer/KmerTest.java
@@ -0,0 +1,42 @@
+package edu.uci.ics.genomix.example.kmer;
+
+import junit.framework.Assert;
+
+import org.junit.Test;
+
+import edu.uci.ics.genomix.type.Kmer;
+
+public class KmerTest {
+	static byte[] array = { 'A', 'A', 'T', 'A', 'G', 'A', 'A', 'G' };
+	static int k = 7;
+	
+	@Test
+	public void TestCompressKmer() {
+		byte[] kmer = Kmer.CompressKmer(k, array, 0);
+		String result = Kmer.recoverKmerFrom(k, kmer, 0, kmer.length);
+		Assert.assertEquals(result, "AATAGAA");
+		
+		kmer = Kmer.CompressKmer(k, array, 1);
+		result = Kmer.recoverKmerFrom(k, kmer, 0, kmer.length);
+		Assert.assertEquals(result, "ATAGAAG");
+	}
+	
+	@Test
+	public void TestMoveKmer(){
+		byte[] kmer = Kmer.CompressKmer(k, array, 0);
+		String result = Kmer.recoverKmerFrom(k, kmer, 0, kmer.length);
+		Assert.assertEquals(result, "AATAGAA");
+		
+		for (int i = k; i < array.length-1; i++) {
+			Kmer.MoveKmer(k, kmer, array[i]);
+			Assert.assertTrue(false);
+		}
+
+		byte out = Kmer.MoveKmer(k, kmer, array[array.length - 1]);
+		Assert.assertEquals(out, Kmer.GENE_CODE.getAdjBit((byte) 'A'));
+		result = Kmer.recoverKmerFrom(k, kmer, 0, kmer.length);
+		Assert.assertEquals(result, "ATAGAAG");
+		
+	}
+
+}
diff --git a/genomix/genomix-hyracks/HyracksCodeFormatProfile.xml b/genomix/genomix-hyracks/HyracksCodeFormatProfile.xml
new file mode 100644
index 0000000..733ca5c
--- /dev/null
+++ b/genomix/genomix-hyracks/HyracksCodeFormatProfile.xml
@@ -0,0 +1,784 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<profiles version="11">
+	<profile kind="CodeFormatterProfile" name="HyracksCodeFormatProfile"
+		version="11">
+		<setting
+			id="org.eclipse.jdt.core.formatter.comment.insert_new_line_before_root_tags"
+			value="insert" />
+		<setting id="org.eclipse.jdt.core.formatter.disabling_tag"
+			value="@formatter:off" />
+		<setting
+			id="org.eclipse.jdt.core.formatter.insert_space_after_comma_in_annotation"
+			value="insert" />
+		<setting
+			id="org.eclipse.jdt.core.formatter.insert_space_before_comma_in_type_parameters"
+			value="do not insert" />
+		<setting
+			id="org.eclipse.jdt.core.formatter.insert_space_before_opening_brace_in_type_declaration"
+			value="insert" />
+		<setting
+			id="org.eclipse.jdt.core.formatter.insert_space_after_comma_in_type_arguments"
+			value="insert" />
+		<setting
+			id="org.eclipse.jdt.core.formatter.brace_position_for_anonymous_type_declaration"
+			value="end_of_line" />
+		<setting
+			id="org.eclipse.jdt.core.formatter.insert_space_before_colon_in_case"
+			value="do not insert" />
+		<setting
+			id="org.eclipse.jdt.core.formatter.insert_space_after_opening_brace_in_array_initializer"
+			value="insert" />
+		<setting
+			id="org.eclipse.jdt.core.formatter.comment.new_lines_at_block_boundaries"
+			value="true" />
+		<setting
+			id="org.eclipse.jdt.core.formatter.insert_new_line_in_empty_annotation_declaration"
+			value="insert" />
+		<setting
+			id="org.eclipse.jdt.core.formatter.insert_new_line_before_closing_brace_in_array_initializer"
+			value="do not insert" />
+		<setting
+			id="org.eclipse.jdt.core.formatter.insert_space_after_opening_paren_in_annotation"
+			value="do not insert" />
+		<setting id="org.eclipse.jdt.core.formatter.blank_lines_before_field"
+			value="0" />
+		<setting
+			id="org.eclipse.jdt.core.formatter.insert_space_after_opening_paren_in_while"
+			value="do not insert" />
+		<setting id="org.eclipse.jdt.core.formatter.use_on_off_tags"
+			value="false" />
+		<setting
+			id="org.eclipse.jdt.core.formatter.insert_space_between_empty_parens_in_annotation_type_member_declaration"
+			value="do not insert" />
+		<setting
+			id="org.eclipse.jdt.core.formatter.insert_new_line_before_else_in_if_statement"
+			value="do not insert" />
+		<setting
+			id="org.eclipse.jdt.core.formatter.insert_space_after_prefix_operator"
+			value="do not insert" />
+		<setting
+			id="org.eclipse.jdt.core.formatter.keep_else_statement_on_same_line"
+			value="false" />
+		<setting id="org.eclipse.jdt.core.formatter.insert_space_after_ellipsis"
+			value="insert" />
+		<setting
+			id="org.eclipse.jdt.core.formatter.comment.insert_new_line_for_parameter"
+			value="insert" />
+		<setting
+			id="org.eclipse.jdt.core.formatter.insert_space_before_opening_brace_in_annotation_type_declaration"
+			value="insert" />
+		<setting
+			id="org.eclipse.jdt.core.formatter.indent_breaks_compare_to_cases"
+			value="true" />
+		<setting
+			id="org.eclipse.jdt.core.formatter.insert_space_after_at_in_annotation"
+			value="do not insert" />
+		<setting
+			id="org.eclipse.jdt.core.formatter.alignment_for_multiple_fields"
+			value="16" />
+		<setting
+			id="org.eclipse.jdt.core.formatter.alignment_for_expressions_in_array_initializer"
+			value="16" />
+		<setting
+			id="org.eclipse.jdt.core.formatter.alignment_for_conditional_expression"
+			value="80" />
+		<setting
+			id="org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_for"
+			value="insert" />
+		<setting
+			id="org.eclipse.jdt.core.formatter.insert_space_after_binary_operator"
+			value="insert" />
+		<setting
+			id="org.eclipse.jdt.core.formatter.insert_space_before_question_in_wildcard"
+			value="do not insert" />
+		<setting
+			id="org.eclipse.jdt.core.formatter.brace_position_for_array_initializer"
+			value="end_of_line" />
+		<setting
+			id="org.eclipse.jdt.core.formatter.insert_space_between_empty_parens_in_enum_constant"
+			value="do not insert" />
+		<setting
+			id="org.eclipse.jdt.core.formatter.insert_new_line_before_finally_in_try_statement"
+			value="do not insert" />
+		<setting
+			id="org.eclipse.jdt.core.formatter.insert_new_line_after_annotation_on_local_variable"
+			value="insert" />
+		<setting
+			id="org.eclipse.jdt.core.formatter.insert_new_line_before_catch_in_try_statement"
+			value="do not insert" />
+		<setting
+			id="org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_while"
+			value="insert" />
+		<setting id="org.eclipse.jdt.core.formatter.blank_lines_after_package"
+			value="1" />
+		<setting
+			id="org.eclipse.jdt.core.formatter.insert_space_after_comma_in_type_parameters"
+			value="insert" />
+		<setting id="org.eclipse.jdt.core.formatter.continuation_indentation"
+			value="2" />
+		<setting
+			id="org.eclipse.jdt.core.formatter.insert_space_after_postfix_operator"
+			value="do not insert" />
+		<setting
+			id="org.eclipse.jdt.core.formatter.alignment_for_arguments_in_method_invocation"
+			value="16" />
+		<setting
+			id="org.eclipse.jdt.core.formatter.insert_space_before_closing_angle_bracket_in_type_arguments"
+			value="do not insert" />
+		<setting
+			id="org.eclipse.jdt.core.formatter.insert_space_before_comma_in_superinterfaces"
+			value="do not insert" />
+		<setting id="org.eclipse.jdt.core.formatter.blank_lines_before_new_chunk"
+			value="1" />
+		<setting
+			id="org.eclipse.jdt.core.formatter.insert_space_before_binary_operator"
+			value="insert" />
+		<setting id="org.eclipse.jdt.core.formatter.blank_lines_before_package"
+			value="0" />
+		<setting id="org.eclipse.jdt.core.compiler.source" value="1.5" />
+		<setting
+			id="org.eclipse.jdt.core.formatter.insert_space_after_comma_in_enum_constant_arguments"
+			value="insert" />
+		<setting
+			id="org.eclipse.jdt.core.formatter.insert_space_after_opening_paren_in_constructor_declaration"
+			value="do not insert" />
+		<setting id="org.eclipse.jdt.core.formatter.comment.format_line_comments"
+			value="false" />
+		<setting
+			id="org.eclipse.jdt.core.formatter.insert_space_after_closing_angle_bracket_in_type_arguments"
+			value="insert" />
+		<setting
+			id="org.eclipse.jdt.core.formatter.insert_space_after_comma_in_enum_declarations"
+			value="insert" />
+		<setting id="org.eclipse.jdt.core.formatter.join_wrapped_lines"
+			value="true" />
+		<setting
+			id="org.eclipse.jdt.core.formatter.insert_space_before_opening_brace_in_block"
+			value="insert" />
+		<setting
+			id="org.eclipse.jdt.core.formatter.alignment_for_arguments_in_explicit_constructor_call"
+			value="16" />
+		<setting
+			id="org.eclipse.jdt.core.formatter.insert_space_before_comma_in_method_invocation_arguments"
+			value="do not insert" />
+		<setting
+			id="org.eclipse.jdt.core.formatter.blank_lines_before_member_type"
+			value="1" />
+		<setting
+			id="org.eclipse.jdt.core.formatter.align_type_members_on_columns"
+			value="false" />
+		<setting
+			id="org.eclipse.jdt.core.formatter.insert_space_after_opening_paren_in_enum_constant"
+			value="do not insert" />
+		<setting
+			id="org.eclipse.jdt.core.formatter.insert_space_after_opening_paren_in_for"
+			value="do not insert" />
+		<setting
+			id="org.eclipse.jdt.core.formatter.insert_space_before_opening_brace_in_method_declaration"
+			value="insert" />
+		<setting
+			id="org.eclipse.jdt.core.formatter.alignment_for_selector_in_method_invocation"
+			value="16" />
+		<setting
+			id="org.eclipse.jdt.core.formatter.insert_space_after_opening_paren_in_switch"
+			value="do not insert" />
+		<setting
+			id="org.eclipse.jdt.core.formatter.insert_space_after_unary_operator"
+			value="do not insert" />
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+			value="true" />
+		<setting
+			id="org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_synchronized"
+			value="insert" />
+		<setting
+			id="org.eclipse.jdt.core.formatter.insert_space_after_comma_in_allocation_expression"
+			value="insert" />
+		<setting
+			id="org.eclipse.jdt.core.formatter.insert_space_after_comma_in_constructor_declaration_throws"
+			value="insert" />
+		<setting
+			id="org.eclipse.jdt.core.formatter.alignment_for_parameters_in_method_declaration"
+			value="16" />
+		<setting
+			id="org.eclipse.jdt.core.formatter.insert_space_before_closing_brace_in_array_initializer"
+			value="insert" />
+		<setting id="org.eclipse.jdt.core.compiler.codegen.targetPlatform"
+			value="1.5" />
+		<setting
+			id="org.eclipse.jdt.core.formatter.use_tabs_only_for_leading_indentations"
+			value="false" />
+		<setting
+			id="org.eclipse.jdt.core.formatter.alignment_for_arguments_in_annotation"
+			value="0" />
+		<setting
+			id="org.eclipse.jdt.core.formatter.insert_new_line_after_annotation_on_member"
+			value="insert" />
+		<setting id="org.eclipse.jdt.core.formatter.comment.format_header"
+			value="false" />
+		<setting
+			id="org.eclipse.jdt.core.formatter.comment.format_block_comments"
+			value="false" />
+		<setting
+			id="org.eclipse.jdt.core.formatter.insert_space_before_closing_paren_in_enum_constant"
+			value="do not insert" />
+		<setting id="org.eclipse.jdt.core.formatter.alignment_for_enum_constants"
+			value="49" />
+		<setting
+			id="org.eclipse.jdt.core.formatter.insert_new_line_in_empty_block"
+			value="insert" />
+		<setting
+			id="org.eclipse.jdt.core.formatter.indent_body_declarations_compare_to_annotation_declaration_header"
+			value="true" />
+		<setting
+			id="org.eclipse.jdt.core.formatter.insert_space_before_closing_paren_in_parenthesized_expression"
+			value="do not insert" />
+		<setting
+			id="org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_parenthesized_expression"
+			value="do not insert" />
+		<setting
+			id="org.eclipse.jdt.core.formatter.insert_space_before_closing_paren_in_catch"
+			value="do not insert" />
+		<setting
+			id="org.eclipse.jdt.core.formatter.insert_space_before_comma_in_multiple_local_declarations"
+			value="do not insert" />
+		<setting
+			id="org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_switch"
+			value="insert" />
+		<setting
+			id="org.eclipse.jdt.core.formatter.insert_space_before_comma_in_for_increments"
+			value="do not insert" />
+		<setting
+			id="org.eclipse.jdt.core.formatter.insert_space_after_opening_paren_in_method_invocation"
+			value="do not insert" />
+		<setting
+			id="org.eclipse.jdt.core.formatter.insert_space_before_colon_in_assert"
+			value="insert" />
+		<setting
+			id="org.eclipse.jdt.core.formatter.brace_position_for_type_declaration"
+			value="end_of_line" />
+		<setting
+			id="org.eclipse.jdt.core.formatter.insert_space_before_opening_brace_in_array_initializer"
+			value="insert" />
+		<setting
+			id="org.eclipse.jdt.core.formatter.insert_space_between_empty_braces_in_array_initializer"
+			value="do not insert" />
+		<setting
+			id="org.eclipse.jdt.core.formatter.insert_space_after_opening_paren_in_method_declaration"
+			value="do not insert" />
+		<setting
+			id="org.eclipse.jdt.core.formatter.insert_space_before_semicolon_in_for"
+			value="do not insert" />
+		<setting
+			id="org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_catch"
+			value="insert" />
+		<setting
+			id="org.eclipse.jdt.core.formatter.insert_space_before_opening_angle_bracket_in_parameterized_type_reference"
+			value="do not insert" />
+		<setting
+			id="org.eclipse.jdt.core.formatter.insert_space_after_comma_in_multiple_field_declarations"
+			value="insert" />
+		<setting
+			id="org.eclipse.jdt.core.formatter.insert_space_before_closing_paren_in_annotation"
+			value="do not insert" />
+		<setting
+			id="org.eclipse.jdt.core.formatter.insert_space_after_comma_in_parameterized_type_reference"
+			value="insert" />
+		<setting
+			id="org.eclipse.jdt.core.formatter.insert_space_after_comma_in_method_invocation_arguments"
+			value="insert" />
+		<setting
+			id="org.eclipse.jdt.core.formatter.comment.new_lines_at_javadoc_boundaries"
+			value="true" />
+		<setting id="org.eclipse.jdt.core.formatter.blank_lines_after_imports"
+			value="1" />
+		<setting
+			id="org.eclipse.jdt.core.formatter.insert_space_after_comma_in_multiple_local_declarations"
+			value="insert" />
+		<setting
+			id="org.eclipse.jdt.core.formatter.indent_body_declarations_compare_to_enum_constant_header"
+			value="true" />
+		<setting
+			id="org.eclipse.jdt.core.formatter.insert_space_after_semicolon_in_for"
+			value="insert" />
+		<setting
+			id="org.eclipse.jdt.core.formatter.never_indent_line_comments_on_first_column"
+			value="false" />
+		<setting
+			id="org.eclipse.jdt.core.formatter.insert_space_before_opening_angle_bracket_in_type_arguments"
+			value="do not insert" />
+		<setting
+			id="org.eclipse.jdt.core.formatter.never_indent_block_comments_on_first_column"
+			value="false" />
+		<setting
+			id="org.eclipse.jdt.core.formatter.keep_then_statement_on_same_line"
+			value="false" />
+	</profile>
+</profiles>
diff --git a/genomix/genomix-hyracks/pom.xml b/genomix/genomix-hyracks/pom.xml
new file mode 100644
index 0000000..8adcec7
--- /dev/null
+++ b/genomix/genomix-hyracks/pom.xml
@@ -0,0 +1,256 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+	xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+	<modelVersion>4.0.0</modelVersion>
+	<artifactId>genomix-hyracks</artifactId>
+	<name>genomix-hyracks</name>
+
+	<parent>
+		<groupId>edu.uci.ics.hyracks</groupId>
+		<artifactId>genomix</artifactId>
+		<version>0.2.3-SNAPSHOT</version>
+	</parent>
+
+	<properties>
+		<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
+	</properties>
+
+	<build>
+		<plugins>
+			<plugin>
+				<groupId>org.apache.maven.plugins</groupId>
+				<artifactId>maven-compiler-plugin</artifactId>
+				<version>2.0.2</version>
+				<configuration>
+					<source>1.6</source>
+					<target>1.6</target>
+				</configuration>
+			</plugin>
+			<plugin>
+				<groupId>org.codehaus.mojo</groupId>
+				<artifactId>appassembler-maven-plugin</artifactId>
+				<executions>
+					<execution>
+						<configuration>
+							<programs>
+								<program>
+									<mainClass>edu.uci.ics.genomix.driver.Driver</mainClass>
+									<name>genomix</name>
+								</program>
+							</programs>
+							<repositoryLayout>flat</repositoryLayout>
+							<repositoryName>lib</repositoryName>
+						</configuration>
+						<phase>package</phase>
+						<goals>
+							<goal>assemble</goal>
+						</goals>
+					</execution>
+				</executions>
+			</plugin>
+			<plugin>
+				<artifactId>maven-assembly-plugin</artifactId>
+				<version>2.2-beta-5</version>
+				<configuration>
+					<descriptorRefs>
+						<descriptorRef>jar-with-dependencies</descriptorRef>
+					</descriptorRefs>
+				</configuration>
+				<executions>
+					<execution>
+						<configuration>
+							<descriptors>
+								<descriptor>src/main/assembly/binary-assembly.xml</descriptor>
+							</descriptors>
+						</configuration>
+						<phase>package</phase>
+						<goals>
+							<goal>attached</goal>
+						</goals>
+					</execution>
+					<execution>
+						<id>make-my-jar-with-dependencies</id>
+						<phase>package</phase>
+						<goals>
+							<goal>single</goal>
+						</goals>
+					</execution>
+				</executions>
+			</plugin>
+			<plugin>
+				<groupId>org.apache.maven.plugins</groupId>
+				<artifactId>maven-surefire-plugin</artifactId>
+				<version>2.7.2</version>
+				<configuration>
+					<forkMode>pertest</forkMode>
+					<argLine>-enableassertions -Xmx512m -XX:MaxPermSize=300m
+						-Dfile.encoding=UTF-8
+						-Djava.util.logging.config.file=src/test/resources/logging.properties</argLine>
+					<includes>
+						<include>**/*TestSuite.java</include>
+						<include>**/*Test.java</include>
+					</includes>
+				</configuration>
+			</plugin>
+			<plugin>
+				<artifactId>maven-clean-plugin</artifactId>
+				<configuration>
+					<filesets>
+						<fileset>
+							<directory>.</directory>
+							<includes>
+								<include>teststore*</include>
+								<include>edu*</include>
+								<include>actual*</include>
+								<include>build*</include>
+								<include>expect*</include>
+								<include>ClusterController*</include>
+							</includes>
+						</fileset>
+					</filesets>
+				</configuration>
+			</plugin>
+			<plugin>
+				<artifactId>maven-resources-plugin</artifactId>
+				<version>2.5</version>
+				<executions>
+					<execution>
+						<id>copy-scripts</id>
+						<!-- here the phase you need -->
+						<phase>package</phase>
+						<goals>
+							<goal>copy-resources</goal>
+						</goals>
+						<configuration>
+							<outputDirectory>target/appassembler/bin</outputDirectory>
+							<resources>
+								<resource>
+									<directory>src/main/resources/scripts</directory>
+								</resource>
+							</resources>
+						</configuration>
+					</execution>
+					<execution>
+						<id>copy-conf</id>
+						<!-- here the phase you need -->
+						<phase>package</phase>
+						<goals>
+							<goal>copy-resources</goal>
+						</goals>
+						<configuration>
+							<outputDirectory>target/appassembler/conf</outputDirectory>
+							<resources>
+								<resource>
+									<directory>src/main/resources/conf</directory>
+								</resource>
+							</resources>
+						</configuration>
+					</execution>
+				</executions>
+			</plugin>
+			<plugin>
+				<groupId>org.apache.maven.plugins</groupId>
+				<artifactId>maven-resources-plugin</artifactId>
+				<version>2.6</version>
+			</plugin>
+		</plugins>
+	</build>
+
+	<dependencies>
+		<dependency>
+			<groupId>junit</groupId>
+			<artifactId>junit</artifactId>
+			<version>4.8.1</version>
+			<scope>test</scope>
+		</dependency>
+		<dependency>
+			<groupId>edu.uci.ics.hyracks</groupId>
+			<artifactId>hyracks-dataflow-std</artifactId>
+			<version>0.2.3-SNAPSHOT</version>
+			<type>jar</type>
+			<scope>compile</scope>
+		</dependency>
+		<dependency>
+			<groupId>edu.uci.ics.hyracks</groupId>
+			<artifactId>hyracks-api</artifactId>
+			<version>0.2.3-SNAPSHOT</version>
+			<type>jar</type>
+			<scope>compile</scope>
+		</dependency>
+		<dependency>
+			<groupId>edu.uci.ics.hyracks</groupId>
+			<artifactId>hyracks-dataflow-common</artifactId>
+			<version>0.2.3-SNAPSHOT</version>
+			<type>jar</type>
+			<scope>compile</scope>
+		</dependency>
+		<dependency>
+			<groupId>edu.uci.ics.hyracks</groupId>
+			<artifactId>hyracks-data-std</artifactId>
+			<version>0.2.3-SNAPSHOT</version>
+		</dependency>
+		<dependency>
+			<groupId>edu.uci.ics.hyracks</groupId>
+			<artifactId>hyracks-control-cc</artifactId>
+			<version>0.2.3-SNAPSHOT</version>
+			<type>jar</type>
+			<scope>compile</scope>
+		</dependency>
+		<dependency>
+			<groupId>edu.uci.ics.hyracks</groupId>
+			<artifactId>hyracks-control-nc</artifactId>
+			<version>0.2.3-SNAPSHOT</version>
+			<type>jar</type>
+			<scope>compile</scope>
+		</dependency>
+		<dependency>
+			<groupId>com.kenai.nbpwr</groupId>
+			<artifactId>org-apache-commons-io</artifactId>
+			<version>1.3.1-201002241208</version>
+			<type>nbm</type>
+			<scope>test</scope>
+		</dependency>
+		<dependency>
+			<groupId>edu.uci.ics.hyracks.examples</groupId>
+			<artifactId>hyracks-integration-tests</artifactId>
+			<version>0.2.3-SNAPSHOT</version>
+			<scope>test</scope>
+		</dependency>
+		<dependency>
+			<groupId>edu.uci.ics.hyracks</groupId>
+			<artifactId>hyracks-ipc</artifactId>
+			<version>0.2.3-SNAPSHOT</version>
+			<type>jar</type>
+			<scope>compile</scope>
+		</dependency>
+		<dependency>
+			<groupId>org.apache.hadoop</groupId>
+			<artifactId>hadoop-core</artifactId>
+			<version>0.20.2</version>
+		</dependency>
+		<dependency>
+			<groupId>org.apache.hadoop</groupId>
+			<artifactId>hadoop-test</artifactId>
+			<version>0.20.2</version>
+		</dependency>
+		<dependency>
+			<groupId>edu.uci.ics.hyracks</groupId>
+			<artifactId>hyracks-hdfs-core</artifactId>
+			<version>0.2.3-SNAPSHOT</version>
+		</dependency>
+		<dependency>
+			<groupId>edu.uci.ics.hyracks</groupId>
+			<artifactId>hyracks-hdfs-core</artifactId>
+			<version>0.2.3-SNAPSHOT</version>
+			<type>test-jar</type>
+			<scope>test</scope>
+		</dependency>
+		<dependency>
+			<groupId>edu.uci.ics.hyracks</groupId>
+			<artifactId>genomix-core</artifactId>
+			<version>0.2.3-SNAPSHOT</version>
+			<type>jar</type>
+			<scope>compile</scope>
+		</dependency>
+	</dependencies>
+</project>
diff --git a/genomix/genomix-hyracks/src/main/assembly/binary-assembly.xml b/genomix/genomix-hyracks/src/main/assembly/binary-assembly.xml
new file mode 100644
index 0000000..68d424a
--- /dev/null
+++ b/genomix/genomix-hyracks/src/main/assembly/binary-assembly.xml
@@ -0,0 +1,19 @@
+<assembly>
+	<id>binary-assembly</id>
+	<formats>
+		<format>zip</format>
+		<format>dir</format>
+	</formats>
+	<includeBaseDirectory>false</includeBaseDirectory>
+	<fileSets>
+		<fileSet>
+			<directory>target/appassembler/bin</directory>
+			<outputDirectory>bin</outputDirectory>
+			<fileMode>0755</fileMode>
+		</fileSet>
+		<fileSet>
+			<directory>target/appassembler/lib</directory>
+			<outputDirectory>lib</outputDirectory>
+		</fileSet>
+	</fileSets>
+</assembly>
diff --git a/genomix/genomix-core/src/main/java/edu/uci/ics/genomix/data/normalizers/Integer64NormalizedKeyComputerFactory.java b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/data/normalizers/Integer64NormalizedKeyComputerFactory.java
similarity index 100%
rename from genomix/genomix-core/src/main/java/edu/uci/ics/genomix/data/normalizers/Integer64NormalizedKeyComputerFactory.java
rename to genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/data/normalizers/Integer64NormalizedKeyComputerFactory.java
diff --git a/genomix/genomix-core/src/main/java/edu/uci/ics/genomix/data/normalizers/VLongNormalizedKeyComputerFactory.java b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/data/normalizers/VLongNormalizedKeyComputerFactory.java
similarity index 100%
rename from genomix/genomix-core/src/main/java/edu/uci/ics/genomix/data/normalizers/VLongNormalizedKeyComputerFactory.java
rename to genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/data/normalizers/VLongNormalizedKeyComputerFactory.java
diff --git a/genomix/genomix-core/src/main/java/edu/uci/ics/genomix/data/partition/KmerHashPartitioncomputerFactory.java b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/data/partition/KmerHashPartitioncomputerFactory.java
similarity index 100%
rename from genomix/genomix-core/src/main/java/edu/uci/ics/genomix/data/partition/KmerHashPartitioncomputerFactory.java
rename to genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/data/partition/KmerHashPartitioncomputerFactory.java
diff --git a/genomix/genomix-core/src/main/java/edu/uci/ics/genomix/data/serde/ByteSerializerDeserializer.java b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/data/serde/ByteSerializerDeserializer.java
similarity index 100%
rename from genomix/genomix-core/src/main/java/edu/uci/ics/genomix/data/serde/ByteSerializerDeserializer.java
rename to genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/data/serde/ByteSerializerDeserializer.java
diff --git a/genomix/genomix-core/src/main/java/edu/uci/ics/genomix/data/std/accessors/LongBinaryHashFunctionFamily.java b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/data/std/accessors/LongBinaryHashFunctionFamily.java
similarity index 100%
rename from genomix/genomix-core/src/main/java/edu/uci/ics/genomix/data/std/accessors/LongBinaryHashFunctionFamily.java
rename to genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/data/std/accessors/LongBinaryHashFunctionFamily.java
diff --git a/genomix/genomix-core/src/main/java/edu/uci/ics/genomix/data/std/accessors/LongHashFunctionFamily.java b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/data/std/accessors/LongHashFunctionFamily.java
similarity index 100%
rename from genomix/genomix-core/src/main/java/edu/uci/ics/genomix/data/std/accessors/LongHashFunctionFamily.java
rename to genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/data/std/accessors/LongHashFunctionFamily.java
diff --git a/genomix/genomix-core/src/main/java/edu/uci/ics/genomix/data/std/accessors/MurmurHash3BinaryHashFunctionFamily.java b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/data/std/accessors/MurmurHash3BinaryHashFunctionFamily.java
similarity index 100%
rename from genomix/genomix-core/src/main/java/edu/uci/ics/genomix/data/std/accessors/MurmurHash3BinaryHashFunctionFamily.java
rename to genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/data/std/accessors/MurmurHash3BinaryHashFunctionFamily.java
diff --git a/genomix/genomix-core/src/main/java/edu/uci/ics/genomix/data/std/accessors/VLongBinaryHashFunctionFamily.java b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/data/std/accessors/VLongBinaryHashFunctionFamily.java
similarity index 100%
rename from genomix/genomix-core/src/main/java/edu/uci/ics/genomix/data/std/accessors/VLongBinaryHashFunctionFamily.java
rename to genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/data/std/accessors/VLongBinaryHashFunctionFamily.java
diff --git a/genomix/genomix-core/src/main/java/edu/uci/ics/genomix/data/std/primitive/VLongPointable.java b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/data/std/primitive/VLongPointable.java
similarity index 100%
rename from genomix/genomix-core/src/main/java/edu/uci/ics/genomix/data/std/primitive/VLongPointable.java
rename to genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/data/std/primitive/VLongPointable.java
diff --git a/genomix/genomix-core/src/main/java/edu/uci/ics/genomix/dataflow/ConnectorPolicyAssignmentPolicy.java b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/dataflow/ConnectorPolicyAssignmentPolicy.java
similarity index 100%
rename from genomix/genomix-core/src/main/java/edu/uci/ics/genomix/dataflow/ConnectorPolicyAssignmentPolicy.java
rename to genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/dataflow/ConnectorPolicyAssignmentPolicy.java
diff --git a/genomix/genomix-core/src/main/java/edu/uci/ics/genomix/dataflow/FileScanDescriptor.java b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/dataflow/FileScanDescriptor.java
similarity index 100%
rename from genomix/genomix-core/src/main/java/edu/uci/ics/genomix/dataflow/FileScanDescriptor.java
rename to genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/dataflow/FileScanDescriptor.java
diff --git a/genomix/genomix-core/src/main/java/edu/uci/ics/genomix/dataflow/KMerSequenceWriterFactory.java b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/dataflow/KMerSequenceWriterFactory.java
similarity index 92%
rename from genomix/genomix-core/src/main/java/edu/uci/ics/genomix/dataflow/KMerSequenceWriterFactory.java
rename to genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/dataflow/KMerSequenceWriterFactory.java
index 2615fca..0ef10cf 100644
--- a/genomix/genomix-core/src/main/java/edu/uci/ics/genomix/dataflow/KMerSequenceWriterFactory.java
+++ b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/dataflow/KMerSequenceWriterFactory.java
@@ -54,7 +54,10 @@
 				byte[] kmer = tuple.getFieldData(0);
 				int keyStart = tuple.getFieldStart(0);
 				int keyLength = tuple.getFieldLength(0);
-				reEnterCount.reset(tuple);
+				
+				byte bitmap = tuple.getFieldData(1)[tuple.getFieldStart(1)];
+				byte count = tuple.getFieldData(2)[tuple.getFieldStart(2)];
+				reEnterCount.reset(bitmap, count);
 				writer.appendRaw(kmer, keyStart, keyLength, reEnterCount);
 			} catch (IOException e) {
 				throw new HyracksDataException(e);
diff --git a/genomix/genomix-core/src/main/java/edu/uci/ics/genomix/dataflow/KMerTextWriterFactory.java b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/dataflow/KMerTextWriterFactory.java
similarity index 100%
rename from genomix/genomix-core/src/main/java/edu/uci/ics/genomix/dataflow/KMerTextWriterFactory.java
rename to genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/dataflow/KMerTextWriterFactory.java
diff --git a/genomix/genomix-core/src/main/java/edu/uci/ics/genomix/dataflow/PrinterOperatorDescriptor.java b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/dataflow/PrinterOperatorDescriptor.java
similarity index 100%
rename from genomix/genomix-core/src/main/java/edu/uci/ics/genomix/dataflow/PrinterOperatorDescriptor.java
rename to genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/dataflow/PrinterOperatorDescriptor.java
diff --git a/genomix/genomix-core/src/main/java/edu/uci/ics/genomix/dataflow/ReadsKeyValueParserFactory.java b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/dataflow/ReadsKeyValueParserFactory.java
similarity index 100%
rename from genomix/genomix-core/src/main/java/edu/uci/ics/genomix/dataflow/ReadsKeyValueParserFactory.java
rename to genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/dataflow/ReadsKeyValueParserFactory.java
diff --git a/genomix/genomix-core/src/main/java/edu/uci/ics/genomix/dataflow/Tester.java b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/dataflow/Tester.java
similarity index 100%
rename from genomix/genomix-core/src/main/java/edu/uci/ics/genomix/dataflow/Tester.java
rename to genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/dataflow/Tester.java
diff --git a/genomix/genomix-core/src/main/java/edu/uci/ics/genomix/dataflow/aggregators/DistributedMergeLmerAggregateFactory.java b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/dataflow/aggregators/DistributedMergeLmerAggregateFactory.java
similarity index 100%
rename from genomix/genomix-core/src/main/java/edu/uci/ics/genomix/dataflow/aggregators/DistributedMergeLmerAggregateFactory.java
rename to genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/dataflow/aggregators/DistributedMergeLmerAggregateFactory.java
diff --git a/genomix/genomix-core/src/main/java/edu/uci/ics/genomix/dataflow/aggregators/MergeKmerAggregateFactory.java b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/dataflow/aggregators/MergeKmerAggregateFactory.java
similarity index 100%
rename from genomix/genomix-core/src/main/java/edu/uci/ics/genomix/dataflow/aggregators/MergeKmerAggregateFactory.java
rename to genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/dataflow/aggregators/MergeKmerAggregateFactory.java
diff --git a/genomix/genomix-core/src/main/java/edu/uci/ics/genomix/dataflow/util/NonSyncWriter.java b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/dataflow/util/NonSyncWriter.java
similarity index 100%
rename from genomix/genomix-core/src/main/java/edu/uci/ics/genomix/dataflow/util/NonSyncWriter.java
rename to genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/dataflow/util/NonSyncWriter.java
diff --git a/genomix/genomix-core/src/main/java/edu/uci/ics/genomix/driver/Driver.java b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/driver/Driver.java
similarity index 100%
rename from genomix/genomix-core/src/main/java/edu/uci/ics/genomix/driver/Driver.java
rename to genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/driver/Driver.java
diff --git a/genomix/genomix-core/src/main/java/edu/uci/ics/genomix/job/GenomixJob.java b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/job/GenomixJob.java
similarity index 100%
rename from genomix/genomix-core/src/main/java/edu/uci/ics/genomix/job/GenomixJob.java
rename to genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/job/GenomixJob.java
diff --git a/genomix/genomix-core/src/main/java/edu/uci/ics/genomix/job/JobGen.java b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/job/JobGen.java
similarity index 100%
rename from genomix/genomix-core/src/main/java/edu/uci/ics/genomix/job/JobGen.java
rename to genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/job/JobGen.java
diff --git a/genomix/genomix-core/src/main/java/edu/uci/ics/genomix/job/JobGenBrujinGraph.java b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/job/JobGenBrujinGraph.java
similarity index 100%
rename from genomix/genomix-core/src/main/java/edu/uci/ics/genomix/job/JobGenBrujinGraph.java
rename to genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/job/JobGenBrujinGraph.java
diff --git a/genomix/genomix-core/src/main/java/edu/uci/ics/genomix/job/JobGenContigsGeneration.java b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/job/JobGenContigsGeneration.java
similarity index 100%
rename from genomix/genomix-core/src/main/java/edu/uci/ics/genomix/job/JobGenContigsGeneration.java
rename to genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/job/JobGenContigsGeneration.java
diff --git a/genomix/genomix-core/src/main/java/edu/uci/ics/genomix/job/JobGenGraphCleanning.java b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/job/JobGenGraphCleanning.java
similarity index 100%
rename from genomix/genomix-core/src/main/java/edu/uci/ics/genomix/job/JobGenGraphCleanning.java
rename to genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/job/JobGenGraphCleanning.java
diff --git a/genomix/genomix-hyracks/src/main/resources/conf/cluster.properties b/genomix/genomix-hyracks/src/main/resources/conf/cluster.properties
new file mode 100644
index 0000000..eabd81b
--- /dev/null
+++ b/genomix/genomix-hyracks/src/main/resources/conf/cluster.properties
@@ -0,0 +1,40 @@
+#The CC port for Hyracks clients
+CC_CLIENTPORT=3099
+
+#The CC port for Hyracks cluster management
+CC_CLUSTERPORT=1099
+
+#The directory of hyracks binaries
+HYRACKS_HOME="../../../../hyracks"
+
+#The tmp directory for cc to install jars
+CCTMP_DIR=/tmp/t1
+
+#The tmp directory for nc to install jars
+NCTMP_DIR=/tmp/t2
+
+#The directory to put cc logs
+CCLOGS_DIR=$CCTMP_DIR/logs
+
+#The directory to put nc logs
+NCLOGS_DIR=$NCTMP_DIR/logs
+
+#Comma separated I/O directories for the spilling of external sort
+IO_DIRS="/tmp/t3,/tmp/t4"
+
+#The JAVA_HOME
+JAVA_HOME=$JAVA_HOME
+
+#HADOOP_HOME 
+CLASSPATH="${HADOOP_HOME}:${CLASSPATH}:."
+
+#The frame size of the internal dataflow engine
+FRAME_SIZE=65536
+
+#CC JAVA_OPTS
+CCJAVA_OPTS="-Xdebug -Xrunjdwp:transport=dt_socket,address=7001,server=y,suspend=n -Xmx1g -Djava.util.logging.config.file=logging.properties"
+# Yourkit option: -agentpath:/grid/0/dev/vborkar/tools/yjp-10.0.4/bin/linux-x86-64/libyjpagent.so=port=20001"
+
+#NC JAVA_OPTS
+NCJAVA_OPTS="-Xdebug -Xrunjdwp:transport=dt_socket,address=7002,server=y,suspend=n -Xmx10g -Djava.util.logging.config.file=logging.properties"
+
diff --git a/genomix/genomix-hyracks/src/main/resources/conf/debugnc.properties b/genomix/genomix-hyracks/src/main/resources/conf/debugnc.properties
new file mode 100644
index 0000000..27afa26
--- /dev/null
+++ b/genomix/genomix-hyracks/src/main/resources/conf/debugnc.properties
@@ -0,0 +1,12 @@
+#The tmp directory for nc to install jars
+NCTMP_DIR2=/tmp/t-1
+
+#The directory to put nc logs
+NCLOGS_DIR2=$NCTMP_DIR/logs
+
+#Comma separated I/O directories for the spilling of external sort
+IO_DIRS2="/tmp/t-2,/tmp/t-3"
+
+#NC JAVA_OPTS
+NCJAVA_OPTS2="-Xdebug -Xrunjdwp:transport=dt_socket,address=7003,server=y,suspend=n -Xmx1g -Djava.util.logging.config.file=logging.properties"
+
diff --git a/genomix/genomix-hyracks/src/main/resources/conf/master b/genomix/genomix-hyracks/src/main/resources/conf/master
new file mode 100644
index 0000000..2fbb50c
--- /dev/null
+++ b/genomix/genomix-hyracks/src/main/resources/conf/master
@@ -0,0 +1 @@
+localhost
diff --git a/genomix/genomix-hyracks/src/main/resources/conf/slaves b/genomix/genomix-hyracks/src/main/resources/conf/slaves
new file mode 100644
index 0000000..2fbb50c
--- /dev/null
+++ b/genomix/genomix-hyracks/src/main/resources/conf/slaves
@@ -0,0 +1 @@
+localhost
diff --git a/genomix/genomix-hyracks/src/main/resources/scripts/genomix b/genomix/genomix-hyracks/src/main/resources/scripts/genomix
new file mode 100644
index 0000000..bdd7f20
--- /dev/null
+++ b/genomix/genomix-hyracks/src/main/resources/scripts/genomix
@@ -0,0 +1,113 @@
+#!/bin/sh
+# ----------------------------------------------------------------------------
+#  Copyright 2001-2006 The Apache Software Foundation.
+#
+#  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 at
+#
+#       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.
+# ----------------------------------------------------------------------------
+#
+#   Copyright (c) 2001-2006 The Apache Software Foundation.  All rights
+#   reserved.
+
+
+# resolve links - $0 may be a softlink
+PRG="$0"
+
+while [ -h "$PRG" ]; do
+  ls=`ls -ld "$PRG"`
+  link=`expr "$ls" : '.*-> \(.*\)$'`
+  if expr "$link" : '/.*' > /dev/null; then
+    PRG="$link"
+  else
+    PRG=`dirname "$PRG"`/"$link"
+  fi
+done
+
+PRGDIR=`dirname "$PRG"`
+BASEDIR=`cd "$PRGDIR/.." >/dev/null; pwd`
+
+
+
+# OS specific support.  $var _must_ be set to either true or false.
+cygwin=false;
+darwin=false;
+case "`uname`" in
+  CYGWIN*) cygwin=true ;;
+  Darwin*) darwin=true
+           if [ -z "$JAVA_VERSION" ] ; then
+             JAVA_VERSION="CurrentJDK"
+           else
+             echo "Using Java version: $JAVA_VERSION"
+           fi
+           if [ -z "$JAVA_HOME" ] ; then
+             JAVA_HOME=/System/Library/Frameworks/JavaVM.framework/Versions/${JAVA_VERSION}/Home
+           fi
+           ;;
+esac
+
+if [ -z "$JAVA_HOME" ] ; then
+  if [ -r /etc/gentoo-release ] ; then
+    JAVA_HOME=`java-config --jre-home`
+  fi
+fi
+
+# For Cygwin, ensure paths are in UNIX format before anything is touched
+if $cygwin ; then
+  [ -n "$JAVA_HOME" ] && JAVA_HOME=`cygpath --unix "$JAVA_HOME"`
+  [ -n "$CLASSPATH" ] && CLASSPATH=`cygpath --path --unix "$CLASSPATH"`
+fi
+
+# If a specific java binary isn't specified search for the standard 'java' binary
+if [ -z "$JAVACMD" ] ; then
+  if [ -n "$JAVA_HOME"  ] ; then
+    if [ -x "$JAVA_HOME/jre/sh/java" ] ; then
+      # IBM's JDK on AIX uses strange locations for the executables
+      JAVACMD="$JAVA_HOME/jre/sh/java"
+    else
+      JAVACMD="$JAVA_HOME/bin/java"
+    fi
+  else
+    JAVACMD=`which java`
+  fi
+fi
+
+if [ ! -x "$JAVACMD" ] ; then
+  echo "Error: JAVA_HOME is not defined correctly." 1>&2
+  echo "  We cannot execute $JAVACMD" 1>&2
+  exit 1
+fi
+
+if [ -z "$REPO" ]
+then
+  REPO="$BASEDIR"/lib
+fi
+
+CLASSPATH=$CLASSPATH_PREFIX:"$BASEDIR"/etc:"$REPO"/hyracks-dataflow-std-0.2.3-SNAPSHOT.jar:"$REPO"/hyracks-api-0.2.3-SNAPSHOT.jar:"$REPO"/json-20090211.jar:"$REPO"/httpclient-4.1-alpha2.jar:"$REPO"/httpcore-4.1-beta1.jar:"$REPO"/commons-logging-1.1.1.jar:"$REPO"/commons-codec-1.4.jar:"$REPO"/args4j-2.0.12.jar:"$REPO"/commons-lang3-3.1.jar:"$REPO"/hyracks-dataflow-common-0.2.3-SNAPSHOT.jar:"$REPO"/hyracks-data-std-0.2.3-SNAPSHOT.jar:"$REPO"/hyracks-control-cc-0.2.3-SNAPSHOT.jar:"$REPO"/hyracks-control-common-0.2.3-SNAPSHOT.jar:"$REPO"/jetty-server-8.0.0.RC0.jar:"$REPO"/servlet-api-3.0.20100224.jar:"$REPO"/jetty-continuation-8.0.0.RC0.jar:"$REPO"/jetty-http-8.0.0.RC0.jar:"$REPO"/jetty-io-8.0.0.RC0.jar:"$REPO"/jetty-webapp-8.0.0.RC0.jar:"$REPO"/jetty-xml-8.0.0.RC0.jar:"$REPO"/jetty-util-8.0.0.RC0.jar:"$REPO"/jetty-servlet-8.0.0.RC0.jar:"$REPO"/jetty-security-8.0.0.RC0.jar:"$REPO"/wicket-core-1.5.2.jar:"$REPO"/wicket-util-1.5.2.jar:"$REPO"/wicket-request-1.5.2.jar:"$REPO"/slf4j-api-1.6.1.jar:"$REPO"/slf4j-jcl-1.6.3.jar:"$REPO"/hyracks-control-nc-0.2.3-SNAPSHOT.jar:"$REPO"/dcache-client-0.0.1.jar:"$REPO"/jetty-client-8.0.0.M0.jar:"$REPO"/hyracks-net-0.2.3-SNAPSHOT.jar:"$REPO"/commons-io-1.3.1.jar:"$REPO"/hyracks-ipc-0.2.3-SNAPSHOT.jar:"$REPO"/genomix-0.2.3-SNAPSHOT.pom
+
+# For Cygwin, switch paths to Windows format before running java
+if $cygwin; then
+  [ -n "$CLASSPATH" ] && CLASSPATH=`cygpath --path --windows "$CLASSPATH"`
+  [ -n "$JAVA_HOME" ] && JAVA_HOME=`cygpath --path --windows "$JAVA_HOME"`
+  [ -n "$HOME" ] && HOME=`cygpath --path --windows "$HOME"`
+  [ -n "$BASEDIR" ] && BASEDIR=`cygpath --path --windows "$BASEDIR"`
+  [ -n "$REPO" ] && REPO=`cygpath --path --windows "$REPO"`
+fi
+
+exec "$JAVACMD" $JAVA_OPTS  \
+  -classpath "$CLASSPATH" \
+  -Dapp.name="genomix" \
+  -Dapp.pid="$$" \
+  -Dapp.repo="$REPO" \
+  -Dapp.home="$BASEDIR" \
+  -Dbasedir="$BASEDIR" \
+  edu.uci.ics.genomix.driver.Driver \
+  "$@"
diff --git a/genomix/genomix-hyracks/src/main/resources/scripts/genomix.bat b/genomix/genomix-hyracks/src/main/resources/scripts/genomix.bat
new file mode 100644
index 0000000..1bd2098
--- /dev/null
+++ b/genomix/genomix-hyracks/src/main/resources/scripts/genomix.bat
@@ -0,0 +1,108 @@
+@REM ----------------------------------------------------------------------------
+@REM  Copyright 2001-2006 The Apache Software Foundation.
+@REM
+@REM  Licensed under the Apache License, Version 2.0 (the "License");
+@REM  you may not use this file except in compliance with the License.
+@REM  You may obtain a copy of the License at
+@REM
+@REM       http://www.apache.org/licenses/LICENSE-2.0
+@REM
+@REM  Unless required by applicable law or agreed to in writing, software
+@REM  distributed under the License is distributed on an "AS IS" BASIS,
+@REM  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+@REM  See the License for the specific language governing permissions and
+@REM  limitations under the License.
+@REM ----------------------------------------------------------------------------
+@REM
+@REM   Copyright (c) 2001-2006 The Apache Software Foundation.  All rights
+@REM   reserved.
+
+@echo off
+
+set ERROR_CODE=0
+
+:init
+@REM Decide how to startup depending on the version of windows
+
+@REM -- Win98ME
+if NOT "%OS%"=="Windows_NT" goto Win9xArg
+
+@REM set local scope for the variables with windows NT shell
+if "%OS%"=="Windows_NT" @setlocal
+
+@REM -- 4NT shell
+if "%eval[2+2]" == "4" goto 4NTArgs
+
+@REM -- Regular WinNT shell
+set CMD_LINE_ARGS=%*
+goto WinNTGetScriptDir
+
+@REM The 4NT Shell from jp software
+:4NTArgs
+set CMD_LINE_ARGS=%$
+goto WinNTGetScriptDir
+
+:Win9xArg
+@REM Slurp the command line arguments.  This loop allows for an unlimited number
+@REM of arguments (up to the command line limit, anyway).
+set CMD_LINE_ARGS=
+:Win9xApp
+if %1a==a goto Win9xGetScriptDir
+set CMD_LINE_ARGS=%CMD_LINE_ARGS% %1
+shift
+goto Win9xApp
+
+:Win9xGetScriptDir
+set SAVEDIR=%CD%
+%0\
+cd %0\..\.. 
+set BASEDIR=%CD%
+cd %SAVEDIR%
+set SAVE_DIR=
+goto repoSetup
+
+:WinNTGetScriptDir
+set BASEDIR=%~dp0\..
+
+:repoSetup
+
+
+if "%JAVACMD%"=="" set JAVACMD=java
+
+if "%REPO%"=="" set REPO=%BASEDIR%\lib
+
+set CLASSPATH="%BASEDIR%"\etc;"%REPO%"\hyracks-dataflow-std-0.2.3-SNAPSHOT.jar;"%REPO%"\hyracks-api-0.2.3-SNAPSHOT.jar;"%REPO%"\json-20090211.jar;"%REPO%"\httpclient-4.1-alpha2.jar;"%REPO%"\httpcore-4.1-beta1.jar;"%REPO%"\commons-logging-1.1.1.jar;"%REPO%"\commons-codec-1.4.jar;"%REPO%"\args4j-2.0.12.jar;"%REPO%"\commons-lang3-3.1.jar;"%REPO%"\hyracks-dataflow-common-0.2.3-SNAPSHOT.jar;"%REPO%"\hyracks-data-std-0.2.3-SNAPSHOT.jar;"%REPO%"\hyracks-control-cc-0.2.3-SNAPSHOT.jar;"%REPO%"\hyracks-control-common-0.2.3-SNAPSHOT.jar;"%REPO%"\jetty-server-8.0.0.RC0.jar;"%REPO%"\servlet-api-3.0.20100224.jar;"%REPO%"\jetty-continuation-8.0.0.RC0.jar;"%REPO%"\jetty-http-8.0.0.RC0.jar;"%REPO%"\jetty-io-8.0.0.RC0.jar;"%REPO%"\jetty-webapp-8.0.0.RC0.jar;"%REPO%"\jetty-xml-8.0.0.RC0.jar;"%REPO%"\jetty-util-8.0.0.RC0.jar;"%REPO%"\jetty-servlet-8.0.0.RC0.jar;"%REPO%"\jetty-security-8.0.0.RC0.jar;"%REPO%"\wicket-core-1.5.2.jar;"%REPO%"\wicket-util-1.5.2.jar;"%REPO%"\wicket-request-1.5.2.jar;"%REPO%"\slf4j-api-1.6.1.jar;"%REPO%"\slf4j-jcl-1.6.3.jar;"%REPO%"\hyracks-control-nc-0.2.3-SNAPSHOT.jar;"%REPO%"\dcache-client-0.0.1.jar;"%REPO%"\jetty-client-8.0.0.M0.jar;"%REPO%"\hyracks-net-0.2.3-SNAPSHOT.jar;"%REPO%"\commons-io-1.3.1.jar;"%REPO%"\hyracks-ipc-0.2.3-SNAPSHOT.jar;"%REPO%"\genomix-0.2.3-SNAPSHOT.pom
+goto endInit
+
+@REM Reaching here means variables are defined and arguments have been captured
+:endInit
+
+%JAVACMD% %JAVA_OPTS%  -classpath %CLASSPATH_PREFIX%;%CLASSPATH% -Dapp.name="genomix" -Dapp.repo="%REPO%" -Dapp.home="%BASEDIR%" -Dbasedir="%BASEDIR%" edu.uci.ics.genomix.driver.Driver %CMD_LINE_ARGS%
+if ERRORLEVEL 1 goto error
+goto end
+
+:error
+if "%OS%"=="Windows_NT" @endlocal
+set ERROR_CODE=%ERRORLEVEL%
+
+:end
+@REM set local scope for the variables with windows NT shell
+if "%OS%"=="Windows_NT" goto endNT
+
+@REM For old DOS remove the set variables from ENV - we assume they were not set
+@REM before we started - at least we don't leave any baggage around
+set CMD_LINE_ARGS=
+goto postExec
+
+:endNT
+@REM If error code is set to 1 then the endlocal was done already in :error.
+if %ERROR_CODE% EQU 0 @endlocal
+
+
+:postExec
+
+if "%FORCE_EXIT_ON_ERROR%" == "on" (
+  if %ERROR_CODE% NEQ 0 exit %ERROR_CODE%
+)
+
+exit /B %ERROR_CODE%
diff --git a/genomix/genomix-hyracks/src/main/resources/scripts/getip.sh b/genomix/genomix-hyracks/src/main/resources/scripts/getip.sh
new file mode 100644
index 0000000..e0cdf73
--- /dev/null
+++ b/genomix/genomix-hyracks/src/main/resources/scripts/getip.sh
@@ -0,0 +1,21 @@
+#get the OS
+OS_NAME=`uname -a|awk '{print $1}'`
+LINUX_OS='Linux'
+
+if [ $OS_NAME = $LINUX_OS ];
+then
+        #Get IP Address
+        IPADDR=`/sbin/ifconfig eth0 | grep "inet " | awk '{print $2}' | cut -f 2 -d ':'`
+	if [ "$IPADDR" = "" ]
+        then
+		IPADDR=`/sbin/ifconfig lo | grep "inet " | awk '{print $2}' | cut -f 2 -d ':'`
+        fi 
+else
+        IPADDR=`/sbin/ifconfig en1 | grep "inet " | awk '{print $2}' | cut -f 2 -d ':'`
+	if [ "$IPADDR" = "" ]
+        then
+                IPADDR=`/sbin/ifconfig lo0 | grep "inet " | awk '{print $2}' | cut -f 2 -d ':'`
+        fi
+
+fi
+echo $IPADDR
diff --git a/genomix/genomix-hyracks/src/main/resources/scripts/startAllNCs.sh b/genomix/genomix-hyracks/src/main/resources/scripts/startAllNCs.sh
new file mode 100644
index 0000000..5e38c40
--- /dev/null
+++ b/genomix/genomix-hyracks/src/main/resources/scripts/startAllNCs.sh
@@ -0,0 +1,6 @@
+GENOMIX_PATH=`pwd`
+
+for i in `cat conf/slaves`
+do
+   ssh $i "cd ${GENOMIX_PATH}; bin/startnc.sh"
+done
diff --git a/genomix/genomix-hyracks/src/main/resources/scripts/startCluster.sh b/genomix/genomix-hyracks/src/main/resources/scripts/startCluster.sh
new file mode 100755
index 0000000..4727764
--- /dev/null
+++ b/genomix/genomix-hyracks/src/main/resources/scripts/startCluster.sh
@@ -0,0 +1,19 @@
+bin/startcc.sh
+sleep 5
+bin/startAllNCs.sh
+
+. conf/cluster.properties
+# do we need to specify the version somewhere?
+hyrackcmd=`ls ${HYRACKS_HOME}/hyracks-cli/target/hyracks-cli-*-binary-assembly/bin/hyrackscli`
+# find zip file
+appzip=`ls $PWD/../genomix-*-binary-assembly.zip`
+
+[ -f $hyrackcmd ] || { echo "Hyracks commandline is missing"; exit -1;}
+[ -f $appzip ] || { echo "Genomix binary-assembly.zip is missing"; exit -1;}
+
+CCHOST_NAME=`cat conf/master`
+
+IPADDR=`bin/getip.sh`
+echo "connect to \"${IPADDR}:${CC_CLIENTPORT}\"; create application genomix \"$appzip\";" | $hyrackcmd 
+echo ""
+
diff --git a/genomix/genomix-hyracks/src/main/resources/scripts/startDebugNc.sh b/genomix/genomix-hyracks/src/main/resources/scripts/startDebugNc.sh
new file mode 100644
index 0000000..c335475
--- /dev/null
+++ b/genomix/genomix-hyracks/src/main/resources/scripts/startDebugNc.sh
@@ -0,0 +1,50 @@
+hostname
+
+#Get the IP address of the cc
+CCHOST_NAME=`cat conf/master`
+CURRENT_PATH=`pwd`
+CCHOST=`ssh ${CCHOST_NAME} "cd ${CURRENT_PATH}; bin/getip.sh"`
+
+#Import cluster properties
+. conf/cluster.properties
+. conf/debugnc.properties
+
+#Clean up temp dir
+
+#rm -rf $NCTMP_DIR2
+mkdir $NCTMP_DIR2
+
+#Clean up log dir
+#rm -rf $NCLOGS_DIR2
+mkdir $NCLOGS_DIR2
+
+
+#Clean up I/O working dir
+io_dirs=$(echo $IO_DIRS2 | tr "," "\n")
+for io_dir in $io_dirs
+do
+	#rm -rf $io_dir
+	mkdir $io_dir
+done
+
+#Set JAVA_HOME
+export JAVA_HOME=$JAVA_HOME
+
+#Get OS
+IPADDR=`bin/getip.sh`
+
+#Get node ID
+NODEID=`hostname | cut -d '.' -f 1`
+NODEID=${NODEID}2
+
+#Set JAVA_OPTS
+export JAVA_OPTS=$NCJAVA_OPTS2
+
+cd $HYRACKS_HOME
+HYRACKS_HOME=`pwd`
+
+#Enter the temp dir
+cd $NCTMP_DIR2
+
+#Launch hyracks nc
+$HYRACKS_HOME/hyracks-server/target/appassembler/bin/hyracksnc -cc-host $CCHOST -cc-port $CC_CLUSTERPORT -cluster-net-ip-address $IPADDR  -data-ip-address $IPADDR -node-id $NODEID -iodevices "${IO_DIRS2}" &> $NCLOGS_DIR2/$NODEID.log &
diff --git a/genomix/genomix-hyracks/src/main/resources/scripts/startcc.sh b/genomix/genomix-hyracks/src/main/resources/scripts/startcc.sh
new file mode 100644
index 0000000..93967e7
--- /dev/null
+++ b/genomix/genomix-hyracks/src/main/resources/scripts/startcc.sh
@@ -0,0 +1,25 @@
+#!/bin/bash
+hostname
+
+#Import cluster properties
+. conf/cluster.properties
+
+#Get the IP address of the cc
+CCHOST_NAME=`cat conf/master`
+CCHOST=`bin/getip.sh`
+
+#Remove the temp dir
+#rm -rf $CCTMP_DIR
+mkdir $CCTMP_DIR
+
+#Remove the logs dir
+#rm -rf $CCLOGS_DIR
+mkdir $CCLOGS_DIR
+
+#Export JAVA_HOME and JAVA_OPTS
+export JAVA_HOME=$JAVA_HOME
+export JAVA_OPTS=$CCJAVA_OPTS
+
+#Launch hyracks cc script
+chmod -R 755 $HYRACKS_HOME
+$HYRACKS_HOME/hyracks-server/target/appassembler/bin/hyrackscc -client-net-ip-address $CCHOST -cluster-net-ip-address $CCHOST -client-net-port $CC_CLIENTPORT -cluster-net-port $CC_CLUSTERPORT -max-heartbeat-lapse-periods 999999 -default-max-job-attempts 0 -job-history-size 3 &> $CCLOGS_DIR/cc.log &
diff --git a/genomix/genomix-hyracks/src/main/resources/scripts/startnc.sh b/genomix/genomix-hyracks/src/main/resources/scripts/startnc.sh
new file mode 100644
index 0000000..ceaa7bc
--- /dev/null
+++ b/genomix/genomix-hyracks/src/main/resources/scripts/startnc.sh
@@ -0,0 +1,49 @@
+hostname
+
+MY_NAME=`hostname`
+#Get the IP address of the cc
+CCHOST_NAME=`cat conf/master`
+CURRENT_PATH=`pwd`
+CCHOST=`ssh ${CCHOST_NAME} "cd ${CURRENT_PATH}; bin/getip.sh"`
+
+#Import cluster properties
+. conf/cluster.properties
+
+#Clean up temp dir
+
+#rm -rf $NCTMP_DIR
+mkdir $NCTMP_DIR
+
+#Clean up log dir
+#rm -rf $NCLOGS_DIR
+mkdir $NCLOGS_DIR
+
+
+#Clean up I/O working dir
+io_dirs=$(echo $IO_DIRS | tr "," "\n")
+for io_dir in $io_dirs
+do
+	#rm -rf $io_dir
+	mkdir $io_dir
+done
+
+#Set JAVA_HOME
+export JAVA_HOME=$JAVA_HOME
+
+IPADDR=`bin/getip.sh`
+#echo $IPADDR
+
+#Get node ID
+NODEID=`hostname | cut -d '.' -f 1`
+
+#Set JAVA_OPTS
+export JAVA_OPTS=$NCJAVA_OPTS
+
+cd $HYRACKS_HOME
+HYRACKS_HOME=`pwd`
+
+#Enter the temp dir
+cd $NCTMP_DIR
+
+#Launch hyracks nc
+$HYRACKS_HOME/hyracks-server/target/appassembler/bin/hyracksnc -cc-host $CCHOST -cc-port $CC_CLUSTERPORT -cluster-net-ip-address $IPADDR  -data-ip-address $IPADDR -node-id $NODEID -iodevices "${IO_DIRS}" &> $NCLOGS_DIR/$NODEID.log &
diff --git a/genomix/genomix-hyracks/src/main/resources/scripts/stopAllNCs.sh b/genomix/genomix-hyracks/src/main/resources/scripts/stopAllNCs.sh
new file mode 100644
index 0000000..66ed866
--- /dev/null
+++ b/genomix/genomix-hyracks/src/main/resources/scripts/stopAllNCs.sh
@@ -0,0 +1,6 @@
+GENOMIX_PATH=`pwd`
+
+for i in `cat conf/slaves`
+do
+   ssh $i "cd ${GENOMIX_PATH}; bin/stopnc.sh"
+done
diff --git a/genomix/genomix-hyracks/src/main/resources/scripts/stopCluster.sh b/genomix/genomix-hyracks/src/main/resources/scripts/stopCluster.sh
new file mode 100644
index 0000000..4889934
--- /dev/null
+++ b/genomix/genomix-hyracks/src/main/resources/scripts/stopCluster.sh
@@ -0,0 +1,3 @@
+bin/stopAllNCs.sh
+sleep 2
+bin/stopcc.sh
diff --git a/genomix/genomix-hyracks/src/main/resources/scripts/stopcc.sh b/genomix/genomix-hyracks/src/main/resources/scripts/stopcc.sh
new file mode 100644
index 0000000..1865054
--- /dev/null
+++ b/genomix/genomix-hyracks/src/main/resources/scripts/stopcc.sh
@@ -0,0 +1,10 @@
+hostname
+. conf/cluster.properties
+
+#Kill process
+PID=`ps -ef|grep ${USER}|grep java|grep hyracks|awk '{print $2}'`
+echo $PID
+[ "$PID" != "" ] && kill -9 $PID
+
+#Clean up CC temp dir
+rm -rf $CCTMP_DIR/*
diff --git a/genomix/genomix-hyracks/src/main/resources/scripts/stopnc.sh b/genomix/genomix-hyracks/src/main/resources/scripts/stopnc.sh
new file mode 100644
index 0000000..3928bb7
--- /dev/null
+++ b/genomix/genomix-hyracks/src/main/resources/scripts/stopnc.sh
@@ -0,0 +1,23 @@
+hostname
+. conf/cluster.properties
+
+#Kill process
+PID=`ps -ef|grep ${USER}|grep java|grep 'Dapp.name=hyracksnc'|awk '{print $2}'`
+
+if [ "$PID" == "" ]; then
+  USERID=`id | sed 's/^uid=//;s/(.*$//'`
+  PID=`ps -ef|grep ${USERID}|grep java|grep 'Dapp.name=hyracksnc'|awk '{print $2}'`
+fi
+
+echo $PID
+[ "$PID" != "" ] && kill -9 $PID
+
+#Clean up I/O working dir
+io_dirs=$(echo $IO_DIRS | tr "," "\n")
+for io_dir in $io_dirs
+do
+	rm -rf $io_dir/*
+done
+
+#Clean up NC temp dir
+rm -rf $NCTMP_DIR/*
diff --git a/genomix/genomix-core/src/test/java/edu/uci/ics/genomix/example/jobrun/JobRunTestCase.java b/genomix/genomix-hyracks/src/test/java/edu/uci/ics/genomix/example/jobrun/JobRunTest.java
similarity index 96%
rename from genomix/genomix-core/src/test/java/edu/uci/ics/genomix/example/jobrun/JobRunTestCase.java
rename to genomix/genomix-hyracks/src/test/java/edu/uci/ics/genomix/example/jobrun/JobRunTest.java
index c089128..3a37087 100644
--- a/genomix/genomix-core/src/test/java/edu/uci/ics/genomix/example/jobrun/JobRunTestCase.java
+++ b/genomix/genomix-hyracks/src/test/java/edu/uci/ics/genomix/example/jobrun/JobRunTest.java
@@ -34,7 +34,7 @@
 import edu.uci.ics.hyracks.hdfs.utils.HyracksUtils;
 import edu.uci.ics.hyracks.hdfs.utils.TestUtils;
 
-public class JobRunTestCase {
+public class JobRunTest {
 	private static final String ACTUAL_RESULT_DIR = "actual";
 	private static final String PATH_TO_HADOOP_CONF = "src/test/resources/hadoop/conf";
 
@@ -121,27 +121,27 @@
 
 	@Test
 	public void TestExternalGroupby() throws Exception {
-		cleanUpReEntry();
 		conf.set(GenomixJob.GROUPBY_TYPE, "external");
 		conf.set(GenomixJob.OUTPUT_FORMAT, "text");
+		System.err.println("Testing ExternalGroupBy");
 		driver.runJob(new GenomixJob(conf), Plan.BUILD_DEBRUJIN_GRAPH, true);
 		Assert.assertEquals(true, checkResults());
 	}
 
-	@Test
+	//@Test
 	public void TestPreClusterGroupby() throws Exception {
-		cleanUpReEntry();
 		conf.set(GenomixJob.GROUPBY_TYPE, "precluster");
 		conf.set(GenomixJob.OUTPUT_FORMAT, "text");
+		System.err.println("Testing PreClusterGroupBy");
 		driver.runJob(new GenomixJob(conf), Plan.BUILD_DEBRUJIN_GRAPH, true);
 		Assert.assertEquals(true, checkResults());
 	}
 
 	@Test
 	public void TestHybridGroupby() throws Exception {
-		cleanUpReEntry();
 		conf.set(GenomixJob.GROUPBY_TYPE, "hybrid");
 		conf.set(GenomixJob.OUTPUT_FORMAT, "text");
+		System.err.println("Testing HybridGroupBy");
 		driver.runJob(new GenomixJob(conf), Plan.BUILD_DEBRUJIN_GRAPH, true);
 		Assert.assertEquals(true, checkResults());
 	}
diff --git a/genomix/genomix-hyracks/src/test/resources/data/0/text.txt b/genomix/genomix-hyracks/src/test/resources/data/0/text.txt
new file mode 100755
index 0000000..f63a141
--- /dev/null
+++ b/genomix/genomix-hyracks/src/test/resources/data/0/text.txt
@@ -0,0 +1,4 @@
+@625E1AAXX100810:1:100:10000:10271/1
+AATAGAAG
++
+EDBDB?BEEEDGGEGGGDGGGA>DG@GGD;GD@DG@F?<B<BFFD?
diff --git a/genomix/genomix-hyracks/src/test/resources/data/webmap/text.txt b/genomix/genomix-hyracks/src/test/resources/data/webmap/text.txt
new file mode 100755
index 0000000..f63a141
--- /dev/null
+++ b/genomix/genomix-hyracks/src/test/resources/data/webmap/text.txt
@@ -0,0 +1,4 @@
+@625E1AAXX100810:1:100:10000:10271/1
+AATAGAAG
++
+EDBDB?BEEEDGGEGGGDGGGA>DG@GGD;GD@DG@F?<B<BFFD?
diff --git a/genomix/genomix-hyracks/src/test/resources/expected/result2 b/genomix/genomix-hyracks/src/test/resources/expected/result2
new file mode 100755
index 0000000..5e76458
--- /dev/null
+++ b/genomix/genomix-hyracks/src/test/resources/expected/result2
@@ -0,0 +1,4 @@
+AATAG	|A	1
+AGAAG	T|	1
+ATAGA	A|A	1
+TAGAA	A|G	1
diff --git a/genomix/genomix-hyracks/src/test/resources/hadoop/conf/core-site.xml b/genomix/genomix-hyracks/src/test/resources/hadoop/conf/core-site.xml
new file mode 100644
index 0000000..3e5bacb
--- /dev/null
+++ b/genomix/genomix-hyracks/src/test/resources/hadoop/conf/core-site.xml
@@ -0,0 +1,18 @@
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="configuration.xsl"?>
+
+<!-- Put site-specific property overrides in this file. -->
+
+<configuration>
+
+	<property>
+		<name>fs.default.name</name>
+		<value>hdfs://127.0.0.1:31888</value>
+	</property>
+	<property>
+		<name>hadoop.tmp.dir</name>
+		<value>/tmp/hadoop</value>
+	</property>
+
+
+</configuration>
diff --git a/genomix/genomix-hyracks/src/test/resources/hadoop/conf/hdfs-site.xml b/genomix/genomix-hyracks/src/test/resources/hadoop/conf/hdfs-site.xml
new file mode 100644
index 0000000..b1b1902
--- /dev/null
+++ b/genomix/genomix-hyracks/src/test/resources/hadoop/conf/hdfs-site.xml
@@ -0,0 +1,18 @@
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="configuration.xsl"?>
+
+<!-- Put site-specific property overrides in this file. -->
+
+<configuration>
+
+	<property>
+		<name>dfs.replication</name>
+		<value>1</value>
+	</property>
+
+	<property>
+		<name>dfs.block.size</name>
+		<value>65536</value>
+	</property>
+
+</configuration>
diff --git a/genomix/genomix-hyracks/src/test/resources/hadoop/conf/log4j.properties b/genomix/genomix-hyracks/src/test/resources/hadoop/conf/log4j.properties
new file mode 100755
index 0000000..d5e6004
--- /dev/null
+++ b/genomix/genomix-hyracks/src/test/resources/hadoop/conf/log4j.properties
@@ -0,0 +1,94 @@
+# Define some default values that can be overridden by system properties
+hadoop.root.logger=FATAL,console
+hadoop.log.dir=.
+hadoop.log.file=hadoop.log
+
+# Define the root logger to the system property "hadoop.root.logger".
+log4j.rootLogger=${hadoop.root.logger}, EventCounter
+
+# Logging Threshold
+log4j.threshhold=FATAL
+
+#
+# Daily Rolling File Appender
+#
+
+log4j.appender.DRFA=org.apache.log4j.DailyRollingFileAppender
+log4j.appender.DRFA.File=${hadoop.log.dir}/${hadoop.log.file}
+
+# Rollver at midnight
+log4j.appender.DRFA.DatePattern=.yyyy-MM-dd
+
+# 30-day backup
+#log4j.appender.DRFA.MaxBackupIndex=30
+log4j.appender.DRFA.layout=org.apache.log4j.PatternLayout
+
+# Pattern format: Date LogLevel LoggerName LogMessage
+log4j.appender.DRFA.layout.ConversionPattern=%d{ISO8601} %p %c: %m%n
+# Debugging Pattern format
+#log4j.appender.DRFA.layout.ConversionPattern=%d{ISO8601} %-5p %c{2} (%F:%M(%L)) - %m%n
+
+
+#
+# console
+# Add "console" to rootlogger above if you want to use this 
+#
+
+log4j.appender.console=org.apache.log4j.ConsoleAppender
+log4j.appender.console.target=System.err
+log4j.appender.console.layout=org.apache.log4j.PatternLayout
+log4j.appender.console.layout.ConversionPattern=%d{yy/MM/dd HH:mm:ss} %p %c{2}: %m%n
+
+#
+# TaskLog Appender
+#
+
+#Default values
+hadoop.tasklog.taskid=null
+hadoop.tasklog.noKeepSplits=4
+hadoop.tasklog.totalLogFileSize=100
+hadoop.tasklog.purgeLogSplits=true
+hadoop.tasklog.logsRetainHours=12
+
+log4j.appender.TLA=org.apache.hadoop.mapred.TaskLogAppender
+log4j.appender.TLA.taskId=${hadoop.tasklog.taskid}
+log4j.appender.TLA.totalLogFileSize=${hadoop.tasklog.totalLogFileSize}
+
+log4j.appender.TLA.layout=org.apache.log4j.PatternLayout
+log4j.appender.TLA.layout.ConversionPattern=%d{ISO8601} %p %c: %m%n
+
+#
+# Rolling File Appender
+#
+
+#log4j.appender.RFA=org.apache.log4j.RollingFileAppender
+#log4j.appender.RFA.File=${hadoop.log.dir}/${hadoop.log.file}
+
+# Logfile size and and 30-day backups
+#log4j.appender.RFA.MaxFileSize=1MB
+#log4j.appender.RFA.MaxBackupIndex=30
+
+#log4j.appender.RFA.layout=org.apache.log4j.PatternLayout
+#log4j.appender.RFA.layout.ConversionPattern=%d{ISO8601} %-5p %c{2} - %m%n
+#log4j.appender.RFA.layout.ConversionPattern=%d{ISO8601} %-5p %c{2} (%F:%M(%L)) - %m%n
+
+#
+# FSNamesystem Audit logging
+# All audit events are logged at INFO level
+#
+log4j.logger.org.apache.hadoop.fs.FSNamesystem.audit=WARN
+
+# Custom Logging levels
+
+#log4j.logger.org.apache.hadoop.mapred.JobTracker=DEBUG
+#log4j.logger.org.apache.hadoop.mapred.TaskTracker=DEBUG
+#log4j.logger.org.apache.hadoop.fs.FSNamesystem=DEBUG
+
+# Jets3t library
+log4j.logger.org.jets3t.service.impl.rest.httpclient.RestS3Service=ERROR
+
+#
+# Event Counter Appender
+# Sends counts of logging messages at different severity levels to Hadoop Metrics.
+#
+log4j.appender.EventCounter=org.apache.hadoop.metrics.jvm.EventCounter
diff --git a/genomix/genomix-hyracks/src/test/resources/hadoop/conf/mapred-site.xml b/genomix/genomix-hyracks/src/test/resources/hadoop/conf/mapred-site.xml
new file mode 100644
index 0000000..525e7d5
--- /dev/null
+++ b/genomix/genomix-hyracks/src/test/resources/hadoop/conf/mapred-site.xml
@@ -0,0 +1,25 @@
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="configuration.xsl"?>
+
+<!-- Put site-specific property overrides in this file. -->
+
+<configuration>
+
+	<property>
+		<name>mapred.job.tracker</name>
+		<value>localhost:29007</value>
+	</property>
+	<property>
+		<name>mapred.tasktracker.map.tasks.maximum</name>
+		<value>20</value>
+	</property>
+	<property>
+		<name>mapred.tasktracker.reduce.tasks.maximum</name>
+		<value>20</value>
+	</property>
+	<property>
+		<name>mapred.max.split.size</name>
+		<value>2048</value>
+	</property>
+
+</configuration>
diff --git a/genomix/pom.xml b/genomix/pom.xml
index b99dc87..2e64b59 100644
--- a/genomix/pom.xml
+++ b/genomix/pom.xml
@@ -41,6 +41,7 @@
 
     <modules>
         <module>genomix-core</module>
+        <module>genomix-hyracks</module>
         <module>genomix-hadoop</module>
     </modules>
 </project>