diff --git a/genomix/genomix-hadoop/target/appassembler/bin/maxclique b/genomix/genomix-hadoop/target/appassembler/bin/maxclique
new file mode 100644
index 0000000..5eab8d0
--- /dev/null
+++ b/genomix/genomix-hadoop/target/appassembler/bin/maxclique
@@ -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"/hadoop-core-0.20.2.jar:"$REPO"/commons-cli-1.2.jar:"$REPO"/xmlenc-0.52.jar:"$REPO"/commons-httpclient-3.0.1.jar:"$REPO"/commons-codec-1.3.jar:"$REPO"/commons-net-1.4.1.jar:"$REPO"/jetty-6.1.14.jar:"$REPO"/jetty-util-6.1.14.jar:"$REPO"/jasper-runtime-5.5.12.jar:"$REPO"/jasper-compiler-5.5.12.jar:"$REPO"/jsp-api-2.1-6.1.14.jar:"$REPO"/jsp-2.1-6.1.14.jar:"$REPO"/ant-1.6.5.jar:"$REPO"/commons-el-1.0.jar:"$REPO"/jets3t-0.7.1.jar:"$REPO"/servlet-api-2.5-6.1.14.jar:"$REPO"/kfs-0.3.jar:"$REPO"/hsqldb-1.8.0.10.jar:"$REPO"/oro-2.0.8.jar:"$REPO"/core-3.1.1.jar:"$REPO"/slf4j-jcl-1.6.3.jar:"$REPO"/commons-logging-1.1.1.jar:"$REPO"/slf4j-api-1.6.3.jar:"$REPO"/args4j-2.0.16.jar:"$REPO"/genomix-hadoop-0.2.3-SNAPSHOT.jar
+
+# 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="maxclique" \
+  -Dapp.pid="$$" \
+  -Dapp.repo="$REPO" \
+  -Dapp.home="$BASEDIR" \
+  -Dbasedir="$BASEDIR" \
+  edu.uci.ics.maxclique.Driver \
+  "$@"
diff --git a/genomix/genomix-hadoop/target/appassembler/bin/maxclique.bat b/genomix/genomix-hadoop/target/appassembler/bin/maxclique.bat
new file mode 100644
index 0000000..6a043d0
--- /dev/null
+++ b/genomix/genomix-hadoop/target/appassembler/bin/maxclique.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%"\hadoop-core-0.20.2.jar;"%REPO%"\commons-cli-1.2.jar;"%REPO%"\xmlenc-0.52.jar;"%REPO%"\commons-httpclient-3.0.1.jar;"%REPO%"\commons-codec-1.3.jar;"%REPO%"\commons-net-1.4.1.jar;"%REPO%"\jetty-6.1.14.jar;"%REPO%"\jetty-util-6.1.14.jar;"%REPO%"\jasper-runtime-5.5.12.jar;"%REPO%"\jasper-compiler-5.5.12.jar;"%REPO%"\jsp-api-2.1-6.1.14.jar;"%REPO%"\jsp-2.1-6.1.14.jar;"%REPO%"\ant-1.6.5.jar;"%REPO%"\commons-el-1.0.jar;"%REPO%"\jets3t-0.7.1.jar;"%REPO%"\servlet-api-2.5-6.1.14.jar;"%REPO%"\kfs-0.3.jar;"%REPO%"\hsqldb-1.8.0.10.jar;"%REPO%"\oro-2.0.8.jar;"%REPO%"\core-3.1.1.jar;"%REPO%"\slf4j-jcl-1.6.3.jar;"%REPO%"\commons-logging-1.1.1.jar;"%REPO%"\slf4j-api-1.6.3.jar;"%REPO%"\args4j-2.0.16.jar;"%REPO%"\genomix-hadoop-0.2.3-SNAPSHOT.jar
+goto endInit
+
+@REM Reaching here means variables are defined and arguments have been captured
+:endInit
+
+%JAVACMD% %JAVA_OPTS%  -classpath %CLASSPATH_PREFIX%;%CLASSPATH% -Dapp.name="maxclique" -Dapp.repo="%REPO%" -Dapp.home="%BASEDIR%" -Dbasedir="%BASEDIR%" edu.uci.ics.maxclique.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-hadoop/target/appassembler/lib/ant-1.6.5.jar b/genomix/genomix-hadoop/target/appassembler/lib/ant-1.6.5.jar
new file mode 100644
index 0000000..3beb3b8
--- /dev/null
+++ b/genomix/genomix-hadoop/target/appassembler/lib/ant-1.6.5.jar
Binary files differ
diff --git a/genomix/genomix-hadoop/target/appassembler/lib/args4j-2.0.16.jar b/genomix/genomix-hadoop/target/appassembler/lib/args4j-2.0.16.jar
new file mode 100644
index 0000000..cfb6a29
--- /dev/null
+++ b/genomix/genomix-hadoop/target/appassembler/lib/args4j-2.0.16.jar
Binary files differ
diff --git a/genomix/genomix-hadoop/target/appassembler/lib/commons-cli-1.2.jar b/genomix/genomix-hadoop/target/appassembler/lib/commons-cli-1.2.jar
new file mode 100644
index 0000000..ce4b9ff
--- /dev/null
+++ b/genomix/genomix-hadoop/target/appassembler/lib/commons-cli-1.2.jar
Binary files differ
diff --git a/genomix/genomix-hadoop/target/appassembler/lib/commons-codec-1.3.jar b/genomix/genomix-hadoop/target/appassembler/lib/commons-codec-1.3.jar
new file mode 100644
index 0000000..957b675
--- /dev/null
+++ b/genomix/genomix-hadoop/target/appassembler/lib/commons-codec-1.3.jar
Binary files differ
diff --git a/genomix/genomix-hadoop/target/appassembler/lib/commons-el-1.0.jar b/genomix/genomix-hadoop/target/appassembler/lib/commons-el-1.0.jar
new file mode 100644
index 0000000..608ed79
--- /dev/null
+++ b/genomix/genomix-hadoop/target/appassembler/lib/commons-el-1.0.jar
Binary files differ
diff --git a/genomix/genomix-hadoop/target/appassembler/lib/commons-httpclient-3.0.1.jar b/genomix/genomix-hadoop/target/appassembler/lib/commons-httpclient-3.0.1.jar
new file mode 100644
index 0000000..cfc777c
--- /dev/null
+++ b/genomix/genomix-hadoop/target/appassembler/lib/commons-httpclient-3.0.1.jar
Binary files differ
diff --git a/genomix/genomix-hadoop/target/appassembler/lib/commons-logging-1.1.1.jar b/genomix/genomix-hadoop/target/appassembler/lib/commons-logging-1.1.1.jar
new file mode 100644
index 0000000..1deef14
--- /dev/null
+++ b/genomix/genomix-hadoop/target/appassembler/lib/commons-logging-1.1.1.jar
Binary files differ
diff --git a/genomix/genomix-hadoop/target/appassembler/lib/commons-net-1.4.1.jar b/genomix/genomix-hadoop/target/appassembler/lib/commons-net-1.4.1.jar
new file mode 100644
index 0000000..9666a92
--- /dev/null
+++ b/genomix/genomix-hadoop/target/appassembler/lib/commons-net-1.4.1.jar
Binary files differ
diff --git a/genomix/genomix-hadoop/target/appassembler/lib/core-3.1.1.jar b/genomix/genomix-hadoop/target/appassembler/lib/core-3.1.1.jar
new file mode 100644
index 0000000..ae0b635
--- /dev/null
+++ b/genomix/genomix-hadoop/target/appassembler/lib/core-3.1.1.jar
Binary files differ
diff --git a/genomix/genomix-hadoop/target/appassembler/lib/genomix-hadoop-0.2.3-SNAPSHOT.jar b/genomix/genomix-hadoop/target/appassembler/lib/genomix-hadoop-0.2.3-SNAPSHOT.jar
new file mode 100644
index 0000000..9188416
--- /dev/null
+++ b/genomix/genomix-hadoop/target/appassembler/lib/genomix-hadoop-0.2.3-SNAPSHOT.jar
Binary files differ
diff --git a/genomix/genomix-hadoop/target/appassembler/lib/hadoop-core-0.20.2.jar b/genomix/genomix-hadoop/target/appassembler/lib/hadoop-core-0.20.2.jar
new file mode 100644
index 0000000..0568eaf
--- /dev/null
+++ b/genomix/genomix-hadoop/target/appassembler/lib/hadoop-core-0.20.2.jar
Binary files differ
diff --git a/genomix/genomix-hadoop/target/appassembler/lib/hsqldb-1.8.0.10.jar b/genomix/genomix-hadoop/target/appassembler/lib/hsqldb-1.8.0.10.jar
new file mode 100644
index 0000000..e010269
--- /dev/null
+++ b/genomix/genomix-hadoop/target/appassembler/lib/hsqldb-1.8.0.10.jar
Binary files differ
diff --git a/genomix/genomix-hadoop/target/appassembler/lib/jasper-compiler-5.5.12.jar b/genomix/genomix-hadoop/target/appassembler/lib/jasper-compiler-5.5.12.jar
new file mode 100644
index 0000000..2a410b4
--- /dev/null
+++ b/genomix/genomix-hadoop/target/appassembler/lib/jasper-compiler-5.5.12.jar
Binary files differ
diff --git a/genomix/genomix-hadoop/target/appassembler/lib/jasper-runtime-5.5.12.jar b/genomix/genomix-hadoop/target/appassembler/lib/jasper-runtime-5.5.12.jar
new file mode 100644
index 0000000..743d906
--- /dev/null
+++ b/genomix/genomix-hadoop/target/appassembler/lib/jasper-runtime-5.5.12.jar
Binary files differ
diff --git a/genomix/genomix-hadoop/target/appassembler/lib/jets3t-0.7.1.jar b/genomix/genomix-hadoop/target/appassembler/lib/jets3t-0.7.1.jar
new file mode 100644
index 0000000..d87e4d1
--- /dev/null
+++ b/genomix/genomix-hadoop/target/appassembler/lib/jets3t-0.7.1.jar
Binary files differ
diff --git a/genomix/genomix-hadoop/target/appassembler/lib/jetty-6.1.14.jar b/genomix/genomix-hadoop/target/appassembler/lib/jetty-6.1.14.jar
new file mode 100644
index 0000000..8c503be
--- /dev/null
+++ b/genomix/genomix-hadoop/target/appassembler/lib/jetty-6.1.14.jar
Binary files differ
diff --git a/genomix/genomix-hadoop/target/appassembler/lib/jetty-util-6.1.14.jar b/genomix/genomix-hadoop/target/appassembler/lib/jetty-util-6.1.14.jar
new file mode 100644
index 0000000..8f924bb
--- /dev/null
+++ b/genomix/genomix-hadoop/target/appassembler/lib/jetty-util-6.1.14.jar
Binary files differ
diff --git a/genomix/genomix-hadoop/target/appassembler/lib/jsp-2.1-6.1.14.jar b/genomix/genomix-hadoop/target/appassembler/lib/jsp-2.1-6.1.14.jar
new file mode 100644
index 0000000..debfe56
--- /dev/null
+++ b/genomix/genomix-hadoop/target/appassembler/lib/jsp-2.1-6.1.14.jar
Binary files differ
diff --git a/genomix/genomix-hadoop/target/appassembler/lib/jsp-api-2.1-6.1.14.jar b/genomix/genomix-hadoop/target/appassembler/lib/jsp-api-2.1-6.1.14.jar
new file mode 100644
index 0000000..1be50ab
--- /dev/null
+++ b/genomix/genomix-hadoop/target/appassembler/lib/jsp-api-2.1-6.1.14.jar
Binary files differ
diff --git a/genomix/genomix-hadoop/target/appassembler/lib/kfs-0.3.jar b/genomix/genomix-hadoop/target/appassembler/lib/kfs-0.3.jar
new file mode 100644
index 0000000..e517c09
--- /dev/null
+++ b/genomix/genomix-hadoop/target/appassembler/lib/kfs-0.3.jar
Binary files differ
diff --git a/genomix/genomix-hadoop/target/appassembler/lib/oro-2.0.8.jar b/genomix/genomix-hadoop/target/appassembler/lib/oro-2.0.8.jar
new file mode 100644
index 0000000..23488d2
--- /dev/null
+++ b/genomix/genomix-hadoop/target/appassembler/lib/oro-2.0.8.jar
Binary files differ
diff --git a/genomix/genomix-hadoop/target/appassembler/lib/servlet-api-2.5-6.1.14.jar b/genomix/genomix-hadoop/target/appassembler/lib/servlet-api-2.5-6.1.14.jar
new file mode 100644
index 0000000..6d7404f
--- /dev/null
+++ b/genomix/genomix-hadoop/target/appassembler/lib/servlet-api-2.5-6.1.14.jar
Binary files differ
diff --git a/genomix/genomix-hadoop/target/appassembler/lib/slf4j-api-1.6.3.jar b/genomix/genomix-hadoop/target/appassembler/lib/slf4j-api-1.6.3.jar
new file mode 100644
index 0000000..08a6c80
--- /dev/null
+++ b/genomix/genomix-hadoop/target/appassembler/lib/slf4j-api-1.6.3.jar
Binary files differ
diff --git a/genomix/genomix-hadoop/target/appassembler/lib/slf4j-jcl-1.6.3.jar b/genomix/genomix-hadoop/target/appassembler/lib/slf4j-jcl-1.6.3.jar
new file mode 100644
index 0000000..c70e2ce
--- /dev/null
+++ b/genomix/genomix-hadoop/target/appassembler/lib/slf4j-jcl-1.6.3.jar
Binary files differ
diff --git a/genomix/genomix-hadoop/target/appassembler/lib/xmlenc-0.52.jar b/genomix/genomix-hadoop/target/appassembler/lib/xmlenc-0.52.jar
new file mode 100644
index 0000000..ec568b4
--- /dev/null
+++ b/genomix/genomix-hadoop/target/appassembler/lib/xmlenc-0.52.jar
Binary files differ
diff --git a/genomix/genomix-hadoop/target/classes/edu/uci/ics/graphbuilding/AdjacentWritable.class b/genomix/genomix-hadoop/target/classes/edu/uci/ics/graphbuilding/AdjacentWritable.class
new file mode 100644
index 0000000..fa276b9
--- /dev/null
+++ b/genomix/genomix-hadoop/target/classes/edu/uci/ics/graphbuilding/AdjacentWritable.class
Binary files differ
diff --git a/genomix/genomix-hadoop/target/classes/edu/uci/ics/graphbuilding/GenomixCombiner.class b/genomix/genomix-hadoop/target/classes/edu/uci/ics/graphbuilding/GenomixCombiner.class
new file mode 100644
index 0000000..7822c22
--- /dev/null
+++ b/genomix/genomix-hadoop/target/classes/edu/uci/ics/graphbuilding/GenomixCombiner.class
Binary files differ
diff --git a/genomix/genomix-hadoop/target/classes/edu/uci/ics/graphbuilding/GenomixDriver$1.class b/genomix/genomix-hadoop/target/classes/edu/uci/ics/graphbuilding/GenomixDriver$1.class
new file mode 100644
index 0000000..8ef8d9b
--- /dev/null
+++ b/genomix/genomix-hadoop/target/classes/edu/uci/ics/graphbuilding/GenomixDriver$1.class
Binary files differ
diff --git a/genomix/genomix-hadoop/target/classes/edu/uci/ics/graphbuilding/GenomixDriver$Options.class b/genomix/genomix-hadoop/target/classes/edu/uci/ics/graphbuilding/GenomixDriver$Options.class
new file mode 100644
index 0000000..c406b17
--- /dev/null
+++ b/genomix/genomix-hadoop/target/classes/edu/uci/ics/graphbuilding/GenomixDriver$Options.class
Binary files differ
diff --git a/genomix/genomix-hadoop/target/classes/edu/uci/ics/graphbuilding/GenomixDriver.class b/genomix/genomix-hadoop/target/classes/edu/uci/ics/graphbuilding/GenomixDriver.class
new file mode 100644
index 0000000..bcb5ff8
--- /dev/null
+++ b/genomix/genomix-hadoop/target/classes/edu/uci/ics/graphbuilding/GenomixDriver.class
Binary files differ
diff --git a/genomix/genomix-hadoop/target/classes/edu/uci/ics/graphbuilding/GenomixMapper$CurrenByte.class b/genomix/genomix-hadoop/target/classes/edu/uci/ics/graphbuilding/GenomixMapper$CurrenByte.class
new file mode 100644
index 0000000..15a44e2
--- /dev/null
+++ b/genomix/genomix-hadoop/target/classes/edu/uci/ics/graphbuilding/GenomixMapper$CurrenByte.class
Binary files differ
diff --git a/genomix/genomix-hadoop/target/classes/edu/uci/ics/graphbuilding/GenomixMapper.class b/genomix/genomix-hadoop/target/classes/edu/uci/ics/graphbuilding/GenomixMapper.class
new file mode 100644
index 0000000..221224f
--- /dev/null
+++ b/genomix/genomix-hadoop/target/classes/edu/uci/ics/graphbuilding/GenomixMapper.class
Binary files differ
diff --git a/genomix/genomix-hadoop/target/classes/edu/uci/ics/graphbuilding/GenomixReducer.class b/genomix/genomix-hadoop/target/classes/edu/uci/ics/graphbuilding/GenomixReducer.class
new file mode 100644
index 0000000..ab1471c
--- /dev/null
+++ b/genomix/genomix-hadoop/target/classes/edu/uci/ics/graphbuilding/GenomixReducer.class
Binary files differ
diff --git a/genomix/genomix-hadoop/target/classes/edu/uci/ics/graphbuilding/KmerBytesWritable$Comparator.class b/genomix/genomix-hadoop/target/classes/edu/uci/ics/graphbuilding/KmerBytesWritable$Comparator.class
new file mode 100644
index 0000000..5abd0a0
--- /dev/null
+++ b/genomix/genomix-hadoop/target/classes/edu/uci/ics/graphbuilding/KmerBytesWritable$Comparator.class
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diff --git a/genomix/genomix-hadoop/target/classes/edu/uci/ics/graphbuilding/KmerBytesWritable.class b/genomix/genomix-hadoop/target/classes/edu/uci/ics/graphbuilding/KmerBytesWritable.class
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diff --git a/genomix/genomix-hadoop/target/classes/edu/uci/ics/graphbuilding/ValueBytesWritable$Comparator.class b/genomix/genomix-hadoop/target/classes/edu/uci/ics/graphbuilding/ValueBytesWritable$Comparator.class
new file mode 100644
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--- /dev/null
+++ b/genomix/genomix-hadoop/target/classes/edu/uci/ics/graphbuilding/ValueBytesWritable$Comparator.class
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diff --git a/genomix/genomix-hadoop/target/classes/edu/uci/ics/graphbuilding/ValueBytesWritable.class b/genomix/genomix-hadoop/target/classes/edu/uci/ics/graphbuilding/ValueBytesWritable.class
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diff --git a/genomix/genomix-hadoop/target/classes/edu/uci/ics/graphbuilding/ValueWritable.class b/genomix/genomix-hadoop/target/classes/edu/uci/ics/graphbuilding/ValueWritable.class
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index 0000000..4bd4fb4
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diff --git a/genomix/genomix-hadoop/target/genomix-hadoop-0.2.3-SNAPSHOT-jar-with-dependencies.jar b/genomix/genomix-hadoop/target/genomix-hadoop-0.2.3-SNAPSHOT-jar-with-dependencies.jar
new file mode 100644
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+++ b/genomix/genomix-hadoop/target/genomix-hadoop-0.2.3-SNAPSHOT-jar-with-dependencies.jar
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diff --git a/genomix/genomix-hadoop/target/genomix-hadoop-0.2.3-SNAPSHOT.jar b/genomix/genomix-hadoop/target/genomix-hadoop-0.2.3-SNAPSHOT.jar
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diff --git a/genomix/genomix-hadoop/target/maven-archiver/pom.properties b/genomix/genomix-hadoop/target/maven-archiver/pom.properties
new file mode 100644
index 0000000..7dbdb75
--- /dev/null
+++ b/genomix/genomix-hadoop/target/maven-archiver/pom.properties
@@ -0,0 +1,5 @@
+#Generated by Maven
+#Wed Feb 20 16:45:32 PST 2013
+version=0.2.3-SNAPSHOT
+groupId=edu.uci.ics.hyracks
+artifactId=genomix-hadoop
diff --git a/genomix/genomix-hadoop/target/surefire-reports/TEST-edu.uci.ics.graphbuilding.GraphBuildingTest.xml b/genomix/genomix-hadoop/target/surefire-reports/TEST-edu.uci.ics.graphbuilding.GraphBuildingTest.xml
new file mode 100644
index 0000000..4a3fe30
--- /dev/null
+++ b/genomix/genomix-hadoop/target/surefire-reports/TEST-edu.uci.ics.graphbuilding.GraphBuildingTest.xml
@@ -0,0 +1,70 @@
+<?xml version="1.0" encoding="UTF-8" ?>
+<testsuite failures="0" time="7.738" errors="0" skipped="0" tests="1" name="edu.uci.ics.graphbuilding.GraphBuildingTest">
+  <properties>
+    <property name="java.runtime.name" value="Java(TM) SE Runtime Environment"/>
+    <property name="sun.boot.library.path" value="/System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Libraries"/>
+    <property name="java.vm.version" value="20.10-b01-428"/>
+    <property name="awt.nativeDoubleBuffering" value="true"/>
+    <property name="gopherProxySet" value="false"/>
+    <property name="mrj.build" value="11M3811"/>
+    <property name="java.vm.vendor" value="Apple Inc."/>
+    <property name="java.vendor.url" value="http://www.apple.com/"/>
+    <property name="path.separator" value=":"/>
+    <property name="java.vm.name" value="Java HotSpot(TM) 64-Bit Server VM"/>
+    <property name="file.encoding.pkg" value="sun.io"/>
+    <property name="java.util.logging.config.file" value="src/test/resources/logging.properties"/>
+    <property name="user.country" value="CN"/>
+    <property name="sun.java.launcher" value="SUN_STANDARD"/>
+    <property name="sun.os.patch.level" value="unknown"/>
+    <property name="java.vm.specification.name" value="Java Virtual Machine Specification"/>
+    <property name="user.dir" value="/Users/hadoop/Desktop/fullstack_genomix/genomix/genomix-hadoop"/>
+    <property name="java.runtime.version" value="1.6.0_35-b10-428-11M3811"/>
+    <property name="java.awt.graphicsenv" value="apple.awt.CGraphicsEnvironment"/>
+    <property name="basedir" value="/Users/hadoop/Desktop/fullstack_genomix/genomix/genomix-hadoop"/>
+    <property name="java.endorsed.dirs" value="/System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Home/lib/endorsed"/>
+    <property name="os.arch" value="x86_64"/>
+    <property name="java.io.tmpdir" value="/var/folders/qw/7w4vv3bx43lchk4nz_4cdpxw0000gp/T/"/>
+    <property name="line.separator" value="
+"/>
+    <property name="java.vm.specification.vendor" value="Sun Microsystems Inc."/>
+    <property name="os.name" value="Mac OS X"/>
+    <property name="sun.jnu.encoding" value="EUC_CN"/>
+    <property name="java.library.path" value=".:/Library/Java/Extensions:/System/Library/Java/Extensions:/usr/lib/java"/>
+    <property name="surefire.test.class.path" value="/Users/hadoop/Desktop/fullstack_genomix/genomix/genomix-hadoop/target/test-classes:/Users/hadoop/Desktop/fullstack_genomix/genomix/genomix-hadoop/target/classes:/Users/hadoop/.m2/repository/junit/junit/4.8.1/junit-4.8.1.jar:/Users/hadoop/.m2/repository/org/apache/hadoop/hadoop-core/0.20.2/hadoop-core-0.20.2.jar:/Users/hadoop/.m2/repository/commons-cli/commons-cli/1.2/commons-cli-1.2.jar:/Users/hadoop/.m2/repository/xmlenc/xmlenc/0.52/xmlenc-0.52.jar:/Users/hadoop/.m2/repository/commons-httpclient/commons-httpclient/3.0.1/commons-httpclient-3.0.1.jar:/Users/hadoop/.m2/repository/commons-codec/commons-codec/1.3/commons-codec-1.3.jar:/Users/hadoop/.m2/repository/commons-net/commons-net/1.4.1/commons-net-1.4.1.jar:/Users/hadoop/.m2/repository/org/mortbay/jetty/jetty/6.1.14/jetty-6.1.14.jar:/Users/hadoop/.m2/repository/org/mortbay/jetty/jetty-util/6.1.14/jetty-util-6.1.14.jar:/Users/hadoop/.m2/repository/tomcat/jasper-runtime/5.5.12/jasper-runtime-5.5.12.jar:/Users/hadoop/.m2/repository/tomcat/jasper-compiler/5.5.12/jasper-compiler-5.5.12.jar:/Users/hadoop/.m2/repository/org/mortbay/jetty/jsp-api-2.1/6.1.14/jsp-api-2.1-6.1.14.jar:/Users/hadoop/.m2/repository/org/mortbay/jetty/jsp-2.1/6.1.14/jsp-2.1-6.1.14.jar:/Users/hadoop/.m2/repository/ant/ant/1.6.5/ant-1.6.5.jar:/Users/hadoop/.m2/repository/commons-el/commons-el/1.0/commons-el-1.0.jar:/Users/hadoop/.m2/repository/net/java/dev/jets3t/jets3t/0.7.1/jets3t-0.7.1.jar:/Users/hadoop/.m2/repository/org/mortbay/jetty/servlet-api-2.5/6.1.14/servlet-api-2.5-6.1.14.jar:/Users/hadoop/.m2/repository/net/sf/kosmosfs/kfs/0.3/kfs-0.3.jar:/Users/hadoop/.m2/repository/hsqldb/hsqldb/1.8.0.10/hsqldb-1.8.0.10.jar:/Users/hadoop/.m2/repository/oro/oro/2.0.8/oro-2.0.8.jar:/Users/hadoop/.m2/repository/org/eclipse/jdt/core/3.1.1/core-3.1.1.jar:/Users/hadoop/.m2/repository/org/apache/hadoop/hadoop-test/0.20.2/hadoop-test-0.20.2.jar:/Users/hadoop/.m2/repository/org/apache/ftpserver/ftplet-api/1.0.0/ftplet-api-1.0.0.jar:/Users/hadoop/.m2/repository/org/apache/mina/mina-core/2.0.0-M5/mina-core-2.0.0-M5.jar:/Users/hadoop/.m2/repository/org/apache/ftpserver/ftpserver-core/1.0.0/ftpserver-core-1.0.0.jar:/Users/hadoop/.m2/repository/org/apache/ftpserver/ftpserver-deprecated/1.0.0-M2/ftpserver-deprecated-1.0.0-M2.jar:/Users/hadoop/.m2/repository/commons-io/commons-io/1.3.1/commons-io-1.3.1.jar:/Users/hadoop/.m2/repository/org/slf4j/slf4j-jcl/1.6.3/slf4j-jcl-1.6.3.jar:/Users/hadoop/.m2/repository/commons-logging/commons-logging/1.1.1/commons-logging-1.1.1.jar:/Users/hadoop/.m2/repository/org/slf4j/slf4j-api/1.6.3/slf4j-api-1.6.3.jar:/Users/hadoop/.m2/repository/args4j/args4j/2.0.16/args4j-2.0.16.jar:"/>
+    <property name="java.specification.name" value="Java Platform API Specification"/>
+    <property name="java.class.version" value="50.0"/>
+    <property name="sun.management.compiler" value="HotSpot 64-Bit Tiered Compilers"/>
+    <property name="os.version" value="10.8.1"/>
+    <property name="http.nonProxyHosts" value="local|*.local|169.254/16|*.169.254/16"/>
+    <property name="user.home" value="/Users/hadoop"/>
+    <property name="user.timezone" value="America/Los_Angeles"/>
+    <property name="java.awt.printerjob" value="apple.awt.CPrinterJob"/>
+    <property name="java.specification.version" value="1.6"/>
+    <property name="file.encoding" value="UTF-8"/>
+    <property name="user.name" value="hadoop"/>
+    <property name="java.class.path" value="/Users/hadoop/Desktop/fullstack_genomix/genomix/genomix-hadoop/target/surefire/surefirebooter2183187004114487162.jar"/>
+    <property name="java.vm.specification.version" value="1.0"/>
+    <property name="sun.arch.data.model" value="64"/>
+    <property name="java.home" value="/System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Home"/>
+    <property name="sun.java.command" value="/Users/hadoop/Desktop/fullstack_genomix/genomix/genomix-hadoop/target/surefire/surefirebooter2183187004114487162.jar /Users/hadoop/Desktop/fullstack_genomix/genomix/genomix-hadoop/target/surefire/surefire4524658770404556182tmp /Users/hadoop/Desktop/fullstack_genomix/genomix/genomix-hadoop/target/surefire/surefire7668612702385218861tmp"/>
+    <property name="java.specification.vendor" value="Sun Microsystems Inc."/>
+    <property name="user.language" value="zh"/>
+    <property name="awt.toolkit" value="apple.awt.CToolkit"/>
+    <property name="java.vm.info" value="mixed mode"/>
+    <property name="hadoop.log.dir" value="logs"/>
+    <property name="java.version" value="1.6.0_35"/>
+    <property name="java.ext.dirs" value="/Library/Java/Extensions:/System/Library/Java/Extensions:/System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Home/lib/ext"/>
+    <property name="sun.boot.class.path" value="/System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Classes/jsfd.jar:/System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Classes/classes.jar:/System/Library/Frameworks/JavaVM.framework/Frameworks/JavaRuntimeSupport.framework/Resources/Java/JavaRuntimeSupport.jar:/System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Classes/ui.jar:/System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Classes/laf.jar:/System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Classes/sunrsasign.jar:/System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Classes/jsse.jar:/System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Classes/jce.jar:/System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Classes/charsets.jar"/>
+    <property name="java.vendor" value="Apple Inc."/>
+    <property name="localRepository" value="/Users/hadoop/.m2/repository"/>
+    <property name="file.separator" value="/"/>
+    <property name="java.vendor.url.bug" value="http://bugreport.apple.com/"/>
+    <property name="sun.cpu.endian" value="little"/>
+    <property name="sun.io.unicode.encoding" value="UnicodeLittle"/>
+    <property name="mrj.version" value="1070.1.6.0_35-428"/>
+    <property name="socksNonProxyHosts" value="local|*.local|169.254/16|*.169.254/16"/>
+    <property name="ftp.nonProxyHosts" value="local|*.local|169.254/16|*.169.254/16"/>
+    <property name="sun.cpu.isalist" value=""/>
+  </properties>
+  <testcase time="7.683" classname="edu.uci.ics.graphbuilding.GraphBuildingTest" name="test"/>
+</testsuite>
\ No newline at end of file
diff --git a/genomix/genomix-hadoop/target/surefire-reports/edu.uci.ics.graphbuilding.GraphBuildingTest.txt b/genomix/genomix-hadoop/target/surefire-reports/edu.uci.ics.graphbuilding.GraphBuildingTest.txt
new file mode 100644
index 0000000..ee383c5
--- /dev/null
+++ b/genomix/genomix-hadoop/target/surefire-reports/edu.uci.ics.graphbuilding.GraphBuildingTest.txt
@@ -0,0 +1,4 @@
+-------------------------------------------------------------------------------
+Test set: edu.uci.ics.graphbuilding.GraphBuildingTest
+-------------------------------------------------------------------------------
+Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 7.737 sec
diff --git a/genomix/genomix-hadoop/target/test-classes/edu/uci/ics/graphbuilding/GraphBuildingTest.class b/genomix/genomix-hadoop/target/test-classes/edu/uci/ics/graphbuilding/GraphBuildingTest.class
new file mode 100644
index 0000000..1609650
--- /dev/null
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Binary files differ
diff --git a/genomix/genomix-hadoop/target/test-classes/edu/uci/ics/utils/TestUtils.class b/genomix/genomix-hadoop/target/test-classes/edu/uci/ics/utils/TestUtils.class
new file mode 100644
index 0000000..1eba8b0
--- /dev/null
+++ b/genomix/genomix-hadoop/target/test-classes/edu/uci/ics/utils/TestUtils.class
Binary files differ