Merge branch 'anbangx/fullstack_genomix' into genomix/fullstack_genomix
diff --git a/genomix/genomix-hadoop/pom.xml b/genomix/genomix-hadoop/pom.xml
index 8ca2fa3..f305c49 100755
--- a/genomix/genomix-hadoop/pom.xml
+++ b/genomix/genomix-hadoop/pom.xml
@@ -160,6 +160,8 @@
 			<groupId>edu.uci.ics.hyracks</groupId>
 			<artifactId>genomix-hyracks</artifactId>
 			<version>0.2.6-SNAPSHOT</version>
+			<type>test-jar</type>
+			<scope>test</scope>
 		</dependency>
 		<dependency>
 			<groupId>edu.uci.ics.hyracks</groupId>
diff --git a/genomix/genomix-hyracks/src/test/java/edu/uci/ics/genomix/hyracks/newgraph/test/JobRun.java b/genomix/genomix-hyracks/src/test/java/edu/uci/ics/genomix/hyracks/newgraph/test/JobRun.java
index 87627e1..3a98573 100644
--- a/genomix/genomix-hyracks/src/test/java/edu/uci/ics/genomix/hyracks/newgraph/test/JobRun.java
+++ b/genomix/genomix-hyracks/src/test/java/edu/uci/ics/genomix/hyracks/newgraph/test/JobRun.java
@@ -40,7 +40,7 @@
     private static final String HDFS_INPUT_PATH = "/webmap";
     private static final String HDFS_OUTPUT_PATH = "/webmap_result";
 
-    private static final String DUMPED_RESULT = ACTUAL_RESULT_DIR + HDFS_OUTPUT_PATH + "/merged.txt";
+    private static final String DUMPED_RESULT = ACTUAL_RESULT_DIR + HDFS_OUTPUT_PATH + "/Tips4.txt";
     private static final String HADOOP_CONF_PATH = ACTUAL_RESULT_DIR + File.separator + "conf.xml";;
     private MiniDFSCluster dfsCluster;
     
diff --git a/genomix/genomix-hyracks/src/test/resources/HighSplitRepeatResult.txt b/genomix/genomix-hyracks/src/test/resources/HighSplitRepeatResult.txt
new file mode 100755
index 0000000..dc4395d
--- /dev/null
+++ b/genomix/genomix-hyracks/src/test/resources/HighSplitRepeatResult.txt
@@ -0,0 +1,6 @@
+{[(1-0_0)]	[]	[]	[]	[GCC]	CCA	1.0x}
+{[(2-0_0)]	[GCC]	[]	[]	[]	CGC	1.0x}
+{[(3-0_0)]	[]	[CCG]	[]	[GCC]	CCG	2.0x}
+{[(2-0_0),(3-0_0),(1-0_0)]	[CCG,CCA]	[AGG]	[]	[AGC,CGC]	GCC	3.0x}
+{[(1-0_0)]	[GCC]	[]	[]	[]	AGC	1.0x}
+{[(2-0_0)]	[]	[GCC]	[]	[]	AGG	1.0x}
diff --git a/genomix/genomix-hyracks/src/test/resources/LowSplitRepeatResult.txt b/genomix/genomix-hyracks/src/test/resources/LowSplitRepeatResult.txt
new file mode 100755
index 0000000..f8df8bb
--- /dev/null
+++ b/genomix/genomix-hyracks/src/test/resources/LowSplitRepeatResult.txt
@@ -0,0 +1,6 @@
+{[(1-0_0)]	[]	[]	[]	[GCC]	CCA	1.0x}
+{[(2-0_0)]	[]	[]	[]	[GCC]	CCG	1.0x}
+{[(2-0_0),(3-0_0),(1-0_0)]	[CCG,CCA]	[AGG]	[]	[AGC]	GCC	3.0x}
+{[(2-0_0),(1-0_0)]	[GCC]	[]	[]	[]	AGC	2.0x}
+{[(3-0_0)]	[AGG]	[]	[]	[]	AAG	1.0x}
+{[(3-0_0)]	[]	[GCC]	[]	[AAG]	AGG	1.0x}
diff --git a/genomix/genomix-hyracks/src/test/resources/MidSplitRepeatResult.txt b/genomix/genomix-hyracks/src/test/resources/MidSplitRepeatResult.txt
new file mode 100755
index 0000000..dc4395d
--- /dev/null
+++ b/genomix/genomix-hyracks/src/test/resources/MidSplitRepeatResult.txt
@@ -0,0 +1,6 @@
+{[(1-0_0)]	[]	[]	[]	[GCC]	CCA	1.0x}
+{[(2-0_0)]	[GCC]	[]	[]	[]	CGC	1.0x}
+{[(3-0_0)]	[]	[CCG]	[]	[GCC]	CCG	2.0x}
+{[(2-0_0),(3-0_0),(1-0_0)]	[CCG,CCA]	[AGG]	[]	[AGC,CGC]	GCC	3.0x}
+{[(1-0_0)]	[GCC]	[]	[]	[]	AGC	1.0x}
+{[(2-0_0)]	[]	[GCC]	[]	[]	AGG	1.0x}
diff --git a/genomix/genomix-hyracks/src/test/resources/Tips1Result.txt b/genomix/genomix-hyracks/src/test/resources/Tips1Result.txt
new file mode 100755
index 0000000..3f04844
--- /dev/null
+++ b/genomix/genomix-hyracks/src/test/resources/Tips1Result.txt
@@ -0,0 +1,7 @@
+{[(1-0_0)]	[]	[]	[]	[GCC]	CCA	1.0x}
+{[(1-0_0)]	[AGC]	[]	[]	[]	CAG	1.0x}
+{[(2-0_0)]	[]	[ACG]	[]	[GCC]	CCG	1.0x}
+{[(2-0_0)]	[]	[]	[ACG]	[]	GTA	1.0x}
+{[(2-0_0),(1-0_0)]	[CCG,CCA]	[]	[]	[AGC]	GCC	2.0x}
+{[(1-0_0)]	[GCC]	[]	[]	[CAG]	AGC	1.0x}
+{[(2-0_0)]	[]	[CCG]	[GTA]	[]	ACG	1.0x}
diff --git a/genomix/genomix-hyracks/src/test/resources/Tips2Result.txt b/genomix/genomix-hyracks/src/test/resources/Tips2Result.txt
new file mode 100755
index 0000000..322cc70
--- /dev/null
+++ b/genomix/genomix-hyracks/src/test/resources/Tips2Result.txt
@@ -0,0 +1,7 @@
+{[(2-0_0)]	[GAA]	[]	[CGC]	[]	CGA	1.0x}
+{[(2-0_0),(1-0_0)]	[GCC]	[AGC]	[CGA]	[]	CGC	2.0x}
+{[(1-0_0)]	[AGC]	[]	[]	[ACA]	CAG	1.0x}
+{[(2-0_0)]	[]	[]	[]	[CGA]	GAA	1.0x}
+{[(2-0_0)]	[]	[]	[]	[CGC]	GCC	1.0x}
+{[(1-0_0)]	[CAG]	[]	[]	[]	ACA	1.0x}
+{[(1-0_0)]	[]	[CGC]	[]	[CAG]	AGC	1.0x}
diff --git a/genomix/genomix-hyracks/src/test/resources/Tips3Result.txt b/genomix/genomix-hyracks/src/test/resources/Tips3Result.txt
new file mode 100755
index 0000000..d37d70c
--- /dev/null
+++ b/genomix/genomix-hyracks/src/test/resources/Tips3Result.txt
@@ -0,0 +1,5 @@
+{[(2-0_0)]	[]	[]	[]	[GCC]	CCA	1.0x}
+{[(2-0_0),(1-0_0)]	[AGC]	[]	[]	[]	CAG	2.0x}
+{[(2-0_0),(1-0_0)]	[CCA]	[AGG]	[]	[AGC]	GCC	2.0x}
+{[(2-0_0),(1-0_0)]	[GCC]	[]	[]	[CAG]	AGC	2.0x}
+{[(1-0_0)]	[]	[GCC]	[]	[]	AGG	1.0x}
diff --git a/genomix/genomix-hyracks/src/test/resources/Tips4Result.txt b/genomix/genomix-hyracks/src/test/resources/Tips4Result.txt
new file mode 100755
index 0000000..de3a226
--- /dev/null
+++ b/genomix/genomix-hyracks/src/test/resources/Tips4Result.txt
@@ -0,0 +1,4 @@
+{[(2-0_0),(1-0_0)]	[AGG]	[]	[]	[]	CAG	2.0x}
+{[(1-0_0)]	[]	[]	[GCC]	[]	GCA	1.0x}
+{[(2-0_0),(1-0_0)]	[]	[AGG]	[GCC,GCA]	[]	GCC	3.0x}
+{[(2-0_0),(1-0_0)]	[]	[GCC]	[]	[CAG]	AGG	2.0x}
diff --git a/genomix/genomix-hyracks/src/test/resources/expected/result2 b/genomix/genomix-hyracks/src/test/resources/expected/result2
deleted file mode 100755
index 9296453..0000000
--- a/genomix/genomix-hyracks/src/test/resources/expected/result2
+++ /dev/null
@@ -1,4 +0,0 @@
-AATAG	|A	5
-AGAAG	T|	5
-ATAGA	A|A	5
-TAGAA	A|G	5
diff --git a/genomix/genomix-hyracks/src/test/resources/expected/result_after_generateNode b/genomix/genomix-hyracks/src/test/resources/expected/result_after_generateNode
deleted file mode 100644
index 9334b95..0000000
--- a/genomix/genomix-hyracks/src/test/resources/expected/result_after_generateNode
+++ /dev/null
@@ -1,14 +0,0 @@
-((1,1)	[(1,3)]	[]	[]	[]	AATAGA)
-((1,3)	[(6,1),(1,4)]	[]	[]	[(1,1)]	TAGAA)
-((1,4)	[(6,2)]	[]	[]	[(1,3)]	AGAAG)
-((2,1)	[]	[]	[]	[]	AATAGCTT)
-((3,1)	[(3,3)]	[]	[]	[]	AATAGA)
-((3,3)	[(6,1),(3,4)]	[]	[]	[(3,1)]	TAGAA)
-((3,4)	[(6,2)]	[]	[]	[(3,3)]	AGAAG)
-((4,1)	[]	[]	[]	[]	AATAGCTT)
-((5,1)	[(5,3)]	[]	[]	[]	AATAGA)
-((5,3)	[(6,1),(5,4)]	[]	[]	[(5,1)]	TAGAA)
-((5,4)	[(6,2)]	[]	[]	[(5,3)]	AGAAG)
-((6,1)	[(6,2)]	[]	[]	[(5,3),(3,3),(1,3)]	AGAAG)
-((6,2)	[(6,3)]	[]	[]	[(1,4),(3,4),(5,4),(6,1)]	GAAGA)
-((6,3)	[]	[]	[]	[(6,2)]	AAGAAG)
diff --git a/genomix/genomix-hyracks/src/test/resources/expected/result_after_initial_read b/genomix/genomix-hyracks/src/test/resources/expected/result_after_initial_read
deleted file mode 100644
index 3502e95..0000000
--- a/genomix/genomix-hyracks/src/test/resources/expected/result_after_initial_read
+++ /dev/null
@@ -1,48 +0,0 @@
-AAGAA	(6,3)
-AAGCT	(2,-4)
-AAGCT	(4,-4)
-AATAG	(1,1)
-AATAG	(2,1)
-AATAG	(3,1)
-AATAG	(4,1)
-AATAG	(5,1)
-AGAAG	(1,4)
-AGAAG	(3,4)
-AGAAG	(5,4)
-AGAAG	(6,1)
-AGAAG	(6,4)
-AGCTA	(2,-3)
-AGCTA	(4,-3)
-AGCTT	(2,4)
-AGCTT	(4,4)
-ATAGA	(1,2)
-ATAGA	(3,2)
-ATAGA	(5,2)
-ATAGC	(2,2)
-ATAGC	(4,2)
-CTATT	(1,-1)
-CTATT	(2,-1)
-CTATT	(3,-1)
-CTATT	(4,-1)
-CTATT	(5,-1)
-CTTCT	(1,-4)
-CTTCT	(3,-4)
-CTTCT	(5,-4)
-CTTCT	(6,-1)
-CTTCT	(6,-4)
-GAAGA	(6,2)
-GCTAT	(2,-2)
-GCTAT	(4,-2)
-TAGAA	(1,3)
-TAGAA	(3,3)
-TAGAA	(5,3)
-TAGCT	(2,3)
-TAGCT	(4,3)
-TCTAT	(1,-2)
-TCTAT	(3,-2)
-TCTAT	(5,-2)
-TCTTC	(6,-2)
-TTCTA	(1,-3)
-TTCTA	(3,-3)
-TTCTA	(5,-3)
-TTCTT	(6,-3)
diff --git a/genomix/genomix-hyracks/src/test/resources/expected/result_after_kmer2readId b/genomix/genomix-hyracks/src/test/resources/expected/result_after_kmer2readId
deleted file mode 100644
index b52a848..0000000
--- a/genomix/genomix-hyracks/src/test/resources/expected/result_after_kmer2readId
+++ /dev/null
@@ -1,48 +0,0 @@
-1	-1	[]	
-1	-2	[]	
-1	-3	[]
-1	-4	[(6,-1)]	
-1	1	[]	AATAG
-1	2	[]	ATAGA
-1	3	[]	TAGAA
-1	4	[(6,1)]	AGAAG
-2	-1	[]	
-2	-2	[]	
-2	-3	[]	
-2	-4	[]	
-2	1	[]	AATAG
-2	2	[]	ATAGC
-2	3	[]	TAGCT
-2	4	[]	AGCTT
-3	-1	[]	
-3	-2	[]	
-3	-3	[]
-3	-4	[(6,-1)]	
-3	1	[]	AATAG
-3	2	[]	ATAGA
-3	3	[]	TAGAA
-3	4	[(6,1)]	AGAAG
-4	-1	[]	
-4	-2	[]	
-4	-3	[]	
-4	-4	[]	
-4	1	[]	AATAG
-4	2	[]	ATAGC
-4	3	[]	TAGCT
-4	4	[]	AGCTT
-5	-1	[]	
-5	-2	[]	
-5	-3	[]
-5	-4	[(6,-1)]	
-5	1	[]	AATAG
-5	2	[]	ATAGA
-5	3	[]	TAGAA
-5	4	[(6,1)]	AGAAG
-6	-1	[(1,-4),(3,-4),(5,-4)]	
-6	-2	[]
-6	-3	[]
-6	-4	[]	
-6	1	[(1,4),(3,4),(5,4)]	AGAAG
-6	2	[]	GAAGA
-6	3	[]	AAGAA
-6	4	[]	AGAAG
diff --git a/genomix/genomix-hyracks/src/test/resources/expected/result_after_kmerAggregate b/genomix/genomix-hyracks/src/test/resources/expected/result_after_kmerAggregate
deleted file mode 100644
index 9035f33..0000000
--- a/genomix/genomix-hyracks/src/test/resources/expected/result_after_kmerAggregate
+++ /dev/null
@@ -1,18 +0,0 @@
-AAGAA	[(6,3)]
-AAGCT	[(2,-4),(4,-4)]
-AATAG	[(1,1),(2,1),(3,1),(4,1),(5,1)]
-AGAAG	[(1,4),(3,4),(5,4),(6,1),(6,4)]
-AGCTA	[(2,-3),(4,-3)]
-AGCTT	[(2,4),(4,4)]
-ATAGA	[(1,2),(3,2),(5,2)]
-ATAGC	[(2,2),(4,2)]
-CTATT	[(1,-1),(2,-1),(3,-1),(4,-1),(5,-1)]
-CTTCT	[(1,-4),(3,-4),(5,-4),(6,-1),(6,-4)]
-GAAGA	[(6,2)]
-GCTAT	[(2,-2),(4,-2)]
-TAGAA	[(1,3),(3,3),(5,3)]
-TAGCT	[(2,3),(4,3)]
-TCTAT	[(1,-2),(3,-2),(5,-2)]
-TCTTC	[(6,-2)]
-TTCTA	[(1,-3),(3,-3),(5,-3)]
-TTCTT	[(6,-3)]
diff --git a/genomix/genomix-hyracks/src/test/resources/expected/result_after_readIDAggreage b/genomix/genomix-hyracks/src/test/resources/expected/result_after_readIDAggreage
deleted file mode 100644
index 2cc283d..0000000
--- a/genomix/genomix-hyracks/src/test/resources/expected/result_after_readIDAggreage
+++ /dev/null
@@ -1,6 +0,0 @@
-1	1	[]	AATAG	-1	[]		2	[]	ATAGA	-2	[]		3	[]	TAGAA	-3	[]		4	[(6,1)]	AGAAG	-4	[(6,-1)]		
-2	1	[]	AATAG	-1	[]		2	[]	ATAGC	-2	[]		3	[]	TAGCT	-3	[]		4	[]	AGCTT	-4	[]		
-3	1	[]	AATAG	-1	[]		2	[]	ATAGA	-2	[]		3	[]	TAGAA	-3	[]		4	[(6,1)]	AGAAG	-4	[(6,-1)]		
-4	1	[]	AATAG	-1	[]		2	[]	ATAGC	-2	[]		3	[]	TAGCT	-3	[]		4	[]	AGCTT	-4	[]		
-5	1	[]	AATAG	-1	[]		2	[]	ATAGA	-2	[]		3	[]	TAGAA	-3	[]		4	[(6,1)]	AGAAG	-4	[(6,-1)]		
-6	1	[(3,4),(1,4),(5,4)]	AGAAG	-1	[(1,-4),(3,-4),(5,-4)]		2	[]	GAAGA	-2	[]		3	[]	AAGAA	-3	[]		4	[]	AGAAG	-4	[]		
diff --git a/genomix/genomix-hyracks/src/test/resources/expected/result_reverse b/genomix/genomix-hyracks/src/test/resources/expected/result_reverse
deleted file mode 100644
index cf2712d..0000000
--- a/genomix/genomix-hyracks/src/test/resources/expected/result_reverse
+++ /dev/null
@@ -1,8 +0,0 @@
-AAGAT	G|A	5
-AATAG	|A	5
-AGAAG	T|	5
-AGATA	A|A	5
-ATAGA	A|A	5
-GAAGA	|T	5
-GATAA	A|	5
-TAGAA	A|G	5
diff --git a/genomix/genomix-hyracks/src/test/resources/expected/result_unmerged b/genomix/genomix-hyracks/src/test/resources/expected/result_unmerged
deleted file mode 100644
index f617779..0000000
--- a/genomix/genomix-hyracks/src/test/resources/expected/result_unmerged
+++ /dev/null
@@ -1,24 +0,0 @@
-((1,1)	[(1,2)]	[]	[]	[]	AATAG)
-((1,2)	[(1,3)]	[]	[]	[(1,1)]	ATAGA)
-((1,3)	[(6,1),(1,4)]	[]	[]	[(1,2)]	TAGAA)
-((1,4)	[(6,2)]	[]	[]	[(1,3)]	AGAAG)
-((2,1)	[(2,2)]	[]	[]	[]	AATAG)
-((2,2)	[(2,3)]	[]	[]	[(2,1)]	ATAGC)
-((2,3)	[(2,4)]	[]	[]	[(2,2)]	TAGCT)
-((2,4)	[]	[]	[]	[(2,3)]	AGCTT)
-((3,1)	[(3,2)]	[]	[]	[]	AATAG)
-((3,2)	[(3,3)]	[]	[]	[(3,1)]	ATAGA)
-((3,3)	[(6,1),(3,4)]	[]	[]	[(3,2)]	TAGAA)
-((3,4)	[(6,2)]	[]	[]	[(3,3)]	AGAAG)
-((4,1)	[(4,2)]	[]	[]	[]	AATAG)
-((4,2)	[(4,3)]	[]	[]	[(4,1)]	ATAGC)
-((4,3)	[(4,4)]	[]	[]	[(4,2)]	TAGCT)
-((4,4)	[]	[]	[]	[(4,3)]	AGCTT)
-((5,1)	[(5,2)]	[]	[]	[]	AATAG)
-((5,2)	[(5,3)]	[]	[]	[(5,1)]	ATAGA)
-((5,3)	[(6,1),(5,4)]	[]	[]	[(5,2)]	TAGAA)
-((5,4)	[(6,2)]	[]	[]	[(5,3)]	AGAAG)
-((6,1)	[(6,2)]	[]	[]	[(1,3),(3,3),(5,3)]	AGAAG)
-((6,2)	[(6,3)]	[]	[]	[(3,4),(1,4),(5,4),(6,1)]	GAAGA)
-((6,3)	[(6,4)]	[]	[]	[(6,2)]	AAGAA)
-((6,4)	[]	[]	[]	[(6,3)]	AGAAG)
diff --git a/genomix/genomix-pregelix/pom.xml b/genomix/genomix-pregelix/pom.xml
index f609d3b..95227c5 100644
--- a/genomix/genomix-pregelix/pom.xml
+++ b/genomix/genomix-pregelix/pom.xml
@@ -1,60 +1,61 @@
 <?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>
-  <groupId>edu.uci.ics.pregelix</groupId>
-  <artifactId>genomix-pregelix</artifactId>
-  <packaging>jar</packaging>
-  <version>0.2.6-SNAPSHOT</version>
-  <name>genomix-pregelix</name>
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+	xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+	<modelVersion>4.0.0</modelVersion>
+	<groupId>edu.uci.ics.pregelix</groupId>
+	<artifactId>genomix-pregelix</artifactId>
+	<packaging>jar</packaging>
+	<version>0.2.6-SNAPSHOT</version>
+	<name>genomix-pregelix</name>
 
 	<properties>
 		<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
 	</properties>
 
-  <profiles>
-    <profile>
-      <id>macosx</id>
-      <activation>
-        <os>
-          <name>mac os x</name>
-        </os>
-        <jdk>1.7</jdk>
-      </activation>
-      <properties>
-        <jvm.extraargs>-Djava.nio.channels.spi.SelectorProvider=sun.nio.ch.KQueueSelectorProvider</jvm.extraargs>
-      </properties>
-    </profile>
-  </profiles>
+	<profiles>
+		<profile>
+			<id>macosx</id>
+			<activation>
+				<os>
+					<name>mac os x</name>
+				</os>
+				<jdk>1.7</jdk>
+			</activation>
+			<properties>
+				<jvm.extraargs>-Djava.nio.channels.spi.SelectorProvider=sun.nio.ch.KQueueSelectorProvider</jvm.extraargs>
+			</properties>
+		</profile>
+	</profiles>
 
-  <build>
-        <plugins>
-            <plugin>
-                                <groupId>org.apache.maven.plugins</groupId>
-                                <artifactId>maven-compiler-plugin</artifactId>
-                                <version>2.0.2</version>
-                                <configuration>
-                                        <source>1.7</source>
-                                        <target>1.7</target>
-                                        <fork>true</fork>
-                                </configuration>
-                        </plugin>
-                        <plugin>
-                                <artifactId>maven-assembly-plugin</artifactId>
-                                <configuration>
-                                        <descriptorRefs>
-                                                <descriptorRef>jar-with-dependencies</descriptorRef>
-                                        </descriptorRefs>
-                                </configuration>
-                                <executions>
-                                        <execution>
-                                                <id>make-my-jar-with-dependencies</id>
-                                                <phase>package</phase>
-                                                <goals>
-                                                        <goal>single</goal>
-                                                </goals>
-                                        </execution>
-                                </executions>
-                        </plugin>
+	<build>
+		<plugins>
+			<plugin>
+				<groupId>org.apache.maven.plugins</groupId>
+				<artifactId>maven-compiler-plugin</artifactId>
+				<version>2.0.2</version>
+				<configuration>
+					<source>1.7</source>
+					<target>1.7</target>
+					<fork>true</fork>
+				</configuration>
+			</plugin>
+			<plugin>
+				<artifactId>maven-assembly-plugin</artifactId>
+				<configuration>
+					<descriptorRefs>
+						<descriptorRef>jar-with-dependencies</descriptorRef>
+					</descriptorRefs>
+				</configuration>
+				<executions>
+					<execution>
+						<id>make-my-jar-with-dependencies</id>
+						<phase>package</phase>
+						<goals>
+							<goal>single</goal>
+						</goals>
+					</execution>
+				</executions>
+			</plugin>
 			<plugin>
 				<groupId>org.codehaus.mojo</groupId>
 				<artifactId>appassembler-maven-plugin</artifactId>
@@ -78,207 +79,207 @@
 					</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 -Xmx2047m -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>
-                                                                <include>edu.uci.*</include>
-                                                        </includes>
-                                                </fileset>
-                                        </filesets>
-                                </configuration>
-                        </plugin>
-                </plugins>
-        </build>
+			<plugin>
+				<groupId>org.apache.maven.plugins</groupId>
+				<artifactId>maven-surefire-plugin</artifactId>
+				<version>2.7.2</version>
+				<configuration>
+					<forkMode>pertest</forkMode>
+					<argLine>-enableassertions -Xmx2047m -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>
+								<include>edu.uci.*</include>
+							</includes>
+						</fileset>
+					</filesets>
+				</configuration>
+			</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>pregelix-core</artifactId>
-                	<version>0.2.6-SNAPSHOT</version>
-                	<type>jar</type>
-                	<scope>compile</scope>
-                </dependency>
-                 <dependency>
-                	<groupId>edu.uci.ics.hyracks</groupId>
-                	<artifactId>genomix-data</artifactId>
-                	<version>0.2.6-SNAPSHOT</version>
-                	<type>jar</type>
-                	<scope>compile</scope>
-                </dependency>
-                <dependency>
-					<groupId>edu.uci.ics.hyracks</groupId>
-					<artifactId>hyracks-dataflow-std</artifactId>
-					<version>0.2.6-SNAPSHOT</version>
-					<type>jar</type>
-					<scope>compile</scope>
-				</dependency>
-				<dependency>
-					<groupId>edu.uci.ics.hyracks</groupId>
-					<artifactId>hyracks-api</artifactId>
-					<version>0.2.6-SNAPSHOT</version>
-					<type>jar</type>
-					<scope>compile</scope>
-				</dependency>
-				<dependency>
-					<groupId>edu.uci.ics.hyracks</groupId>
-					<artifactId>hyracks-dataflow-common</artifactId>
-					<version>0.2.6-SNAPSHOT</version>
-					<type>jar</type>
-					<scope>compile</scope>
-				</dependency>
-				<dependency>
-					<groupId>edu.uci.ics.hyracks</groupId>
-					<artifactId>hyracks-data-std</artifactId>
-					<version>0.2.6-SNAPSHOT</version>
-				</dependency>
-				<dependency>
-					<groupId>edu.uci.ics.hyracks</groupId>
-					<artifactId>hyracks-control-cc</artifactId>
-					<version>0.2.6-SNAPSHOT</version>
-					<type>jar</type>
-					<scope>compile</scope>
-				</dependency>
-				<dependency>
-					<groupId>edu.uci.ics.hyracks</groupId>
-					<artifactId>hyracks-control-nc</artifactId>
-					<version>0.2.6-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>0.2.6-SNAPSHOT</version>
-					<scope>test</scope>
-				</dependency>
-				<dependency>
-					<groupId>edu.uci.ics.hyracks</groupId>
-					<artifactId>hyracks-ipc</artifactId>
-					<version>0.2.6-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>0.2.6-SNAPSHOT</version>
-				</dependency>
-				<dependency>
-					<groupId>edu.uci.ics.hyracks</groupId>
-					<artifactId>hyracks-hdfs-core</artifactId>
-					<version>0.2.6-SNAPSHOT</version>
-					<type>test-jar</type>
-					<scope>test</scope>
-				</dependency>
-                <dependency>
-                	<groupId>edu.uci.ics.hyracks</groupId>
-                	<artifactId>genomix-hyracks</artifactId>
-                	<version>0.2.6-SNAPSHOT</version>
-                	<type>jar</type>
-                	<scope>compile</scope>
-                </dependency>
-                <dependency>
-                	<groupId>edu.uci.ics.hyracks</groupId>
-                	<artifactId>genomix-hadoop</artifactId>
-                	<version>0.2.6-SNAPSHOT</version>
-                	<type>jar</type>
-                	<scope>compile</scope>
-                </dependency>
-        </dependencies>
+	<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>pregelix-core</artifactId>
+			<version>0.2.6-SNAPSHOT</version>
+			<type>jar</type>
+			<scope>compile</scope>
+		</dependency>
+		<dependency>
+			<groupId>edu.uci.ics.hyracks</groupId>
+			<artifactId>genomix-data</artifactId>
+			<version>0.2.6-SNAPSHOT</version>
+			<type>jar</type>
+			<scope>compile</scope>
+		</dependency>
+		<dependency>
+			<groupId>edu.uci.ics.hyracks</groupId>
+			<artifactId>hyracks-dataflow-std</artifactId>
+			<version>0.2.6-SNAPSHOT</version>
+			<type>jar</type>
+			<scope>compile</scope>
+		</dependency>
+		<dependency>
+			<groupId>edu.uci.ics.hyracks</groupId>
+			<artifactId>hyracks-api</artifactId>
+			<version>0.2.6-SNAPSHOT</version>
+			<type>jar</type>
+			<scope>compile</scope>
+		</dependency>
+		<dependency>
+			<groupId>edu.uci.ics.hyracks</groupId>
+			<artifactId>hyracks-dataflow-common</artifactId>
+			<version>0.2.6-SNAPSHOT</version>
+			<type>jar</type>
+			<scope>compile</scope>
+		</dependency>
+		<dependency>
+			<groupId>edu.uci.ics.hyracks</groupId>
+			<artifactId>hyracks-data-std</artifactId>
+			<version>0.2.6-SNAPSHOT</version>
+		</dependency>
+		<dependency>
+			<groupId>edu.uci.ics.hyracks</groupId>
+			<artifactId>hyracks-control-cc</artifactId>
+			<version>0.2.6-SNAPSHOT</version>
+			<type>jar</type>
+			<scope>compile</scope>
+		</dependency>
+		<dependency>
+			<groupId>edu.uci.ics.hyracks</groupId>
+			<artifactId>hyracks-control-nc</artifactId>
+			<version>0.2.6-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>0.2.6-SNAPSHOT</version>
+			<scope>test</scope>
+		</dependency>
+		<dependency>
+			<groupId>edu.uci.ics.hyracks</groupId>
+			<artifactId>hyracks-ipc</artifactId>
+			<version>0.2.6-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>0.2.6-SNAPSHOT</version>
+		</dependency>
+		<dependency>
+			<groupId>edu.uci.ics.hyracks</groupId>
+			<artifactId>hyracks-hdfs-core</artifactId>
+			<version>0.2.6-SNAPSHOT</version>
+			<type>test-jar</type>
+			<scope>test</scope>
+		</dependency>
+		<dependency>
+			<groupId>edu.uci.ics.hyracks</groupId>
+			<artifactId>genomix-hyracks</artifactId>
+			<version>0.2.6-SNAPSHOT</version>
+			<type>jar</type>
+			<scope>compile</scope>
+		</dependency>
+		<dependency>
+			<groupId>edu.uci.ics.hyracks</groupId>
+			<artifactId>genomix-hadoop</artifactId>
+			<version>0.2.6-SNAPSHOT</version>
+			<type>jar</type>
+			<scope>compile</scope>
+		</dependency>
+	</dependencies>
 
-  <scm>
-    <connection>scm:svn:https://hyracks.googlecode.com/svn/trunk/fullstack/pregelix</connection>
-    <developerConnection>scm:svn:https://hyracks.googlecode.com/svn/trunk/fullstack/pregelix</developerConnection>
-    <url>http://code.google.com/p/hyracks/source/browse/#svn/trunk/fullstack/pregelix</url>
-  </scm>
+	<scm>
+		<connection>scm:svn:https://hyracks.googlecode.com/svn/trunk/fullstack/pregelix</connection>
+		<developerConnection>scm:svn:https://hyracks.googlecode.com/svn/trunk/fullstack/pregelix</developerConnection>
+		<url>http://code.google.com/p/hyracks/source/browse/#svn/trunk/fullstack/pregelix</url>
+	</scm>
 
-  <distributionManagement>
-    <repository>
-      <id>hyracks-releases</id>
-      <url>http://obelix.ics.uci.edu/nexus/content/repositories/hyracks-releases/</url>
-    </repository>
-    <snapshotRepository>
-      <id>hyracks-snapshots</id>
-      <url>http://obelix.ics.uci.edu/nexus/content/repositories/hyracks-snapshots/</url>
-    </snapshotRepository>
-  </distributionManagement>
+	<distributionManagement>
+		<repository>
+			<id>hyracks-releases</id>
+			<url>http://obelix.ics.uci.edu/nexus/content/repositories/hyracks-releases/</url>
+		</repository>
+		<snapshotRepository>
+			<id>hyracks-snapshots</id>
+			<url>http://obelix.ics.uci.edu/nexus/content/repositories/hyracks-snapshots/</url>
+		</snapshotRepository>
+	</distributionManagement>
 
-  <reporting>
-    <plugins>
-      <plugin>
-        <groupId>org.apache.maven.plugins</groupId>
-        <artifactId>maven-changelog-plugin</artifactId>
-      </plugin>
-    </plugins>
-  </reporting>
+	<reporting>
+		<plugins>
+			<plugin>
+				<groupId>org.apache.maven.plugins</groupId>
+				<artifactId>maven-changelog-plugin</artifactId>
+			</plugin>
+		</plugins>
+	</reporting>
 
-  <repositories>
-    <repository>
-      <id>hyracks-public</id>
-      <url>http://obelix.ics.uci.edu/nexus/content/groups/hyracks-public/</url>
-    </repository>
-    <repository>
-      <id>jboss-public</id>
-      <url>https://repository.jboss.org/nexus/content/groups/public/</url>
-    </repository>
-  </repositories>
+	<repositories>
+		<repository>
+			<id>hyracks-public</id>
+			<url>http://obelix.ics.uci.edu/nexus/content/groups/hyracks-public/</url>
+		</repository>
+		<repository>
+			<id>jboss-public</id>
+			<url>https://repository.jboss.org/nexus/content/groups/public/</url>
+		</repository>
+	</repositories>
 
-  <pluginRepositories>
-    <pluginRepository>
-      <id>hyracks-public</id>
-      <url>http://obelix.ics.uci.edu/nexus/content/groups/hyracks-public/</url>
-      <releases>
-        <updatePolicy>always</updatePolicy>
-      </releases>
-    </pluginRepository>
-  </pluginRepositories>
+	<pluginRepositories>
+		<pluginRepository>
+			<id>hyracks-public</id>
+			<url>http://obelix.ics.uci.edu/nexus/content/groups/hyracks-public/</url>
+			<releases>
+				<updatePolicy>always</updatePolicy>
+			</releases>
+		</pluginRepository>
+	</pluginRepositories>
 </project>