From eb52dc6a9b2ccbf1efde9816adbf33b8eda820d4 Mon Sep 17 00:00:00 2001
From: Khalid Shakir <kshakir@broadinstitute.org>
Date: Wed, 29 Jan 2014 13:12:41 -0500
Subject: [PATCH 01/16] Moved build.xml, ivy.xml, ivysettings.xml, ivy
 properties, public/packages/*.xml into private/archive/ant

---
 build.xml                            | 1518 --------------------------
 ivy.xml                              |  117 --
 public/packages/Aligner.xml          |    9 -
 public/packages/CreatePackager.xsl   |  220 ----
 public/packages/GATKEngine.xml       |   62 --
 public/packages/GenomeAnalysisTK.xml |   40 -
 public/packages/PicardPrivate.xml    |   10 -
 public/packages/Queue.xml            |   41 -
 public/packages/QueueEngine.xml      |   78 --
 settings/ivysettings.properties      |    1 -
 settings/ivysettings.xml             |   13 -
 11 files changed, 2109 deletions(-)
 delete mode 100644 build.xml
 delete mode 100644 ivy.xml
 delete mode 100644 public/packages/Aligner.xml
 delete mode 100644 public/packages/CreatePackager.xsl
 delete mode 100644 public/packages/GATKEngine.xml
 delete mode 100644 public/packages/GenomeAnalysisTK.xml
 delete mode 100644 public/packages/PicardPrivate.xml
 delete mode 100644 public/packages/Queue.xml
 delete mode 100644 public/packages/QueueEngine.xml
 delete mode 100644 settings/ivysettings.properties
 delete mode 100644 settings/ivysettings.xml

diff --git a/build.xml b/build.xml
deleted file mode 100644
index fd0801bfb..000000000
--- a/build.xml
+++ /dev/null
@@ -1,1518 +0,0 @@
-<!--
-  ~ Copyright (c) 2012, The Broad Institute
-  ~
-  ~ Permission is hereby granted, free of charge, to any person
-  ~ obtaining a copy of this software and associated documentation
-  ~ files (the "Software"), to deal in the Software without
-  ~ restriction, including without limitation the rights to use,
-  ~ copy, modify, merge, publish, distribute, sublicense, and/or sell
-  ~ copies of the Software, and to permit persons to whom the
-  ~ Software is furnished to do so, subject to the following
-  ~ conditions:
-  ~
-  ~ The above copyright notice and this permission notice shall be
-  ~ included in all copies or substantial portions of the Software.
-  ~ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
-  ~ EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
-  ~ OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
-  ~ NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
-  ~ HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
-  ~ WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
-  ~ FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
-  ~ OTHER DEALINGS IN THE SOFTWARE.
-  -->
-
-<!-- To get a list of the major build targets, run "ant -p" -->
-<project name="Sting" default="dist" basedir="."
-         xmlns:artifact="antlib:org.apache.maven.artifact.ant"
-         xmlns:ivy="antlib:org.apache.ivy.ant">
-    <description>Compile and distribute the Sting toolkit</description>
-
-    <!-- ******************************************************************************** -->
-    <!-- Properties                                                                       -->
-    <!-- ******************************************************************************** -->
-
-    <!-- The system classpath should take precedence over classpaths specified in this file -->
-    <property name="build.sysclasspath" value="first" />
-
-    <!-- Use this prefix to access environment variables -->
-    <property environment="env"/>
-
-    <!-- Build defaults: -->
-    <property name="default.build.target" value="all" />       <!-- can be "all", "public" (public only), or "protected" (public + protected) -->
-    <property name="compile.scala.by.default" value="true" />  <!-- compile Scala by default? "true" or "false" -->
-    <property name="use.contracts.by.default" value="false" /> <!-- should contracts be built by default? "true" or "false -->
-
-    <!-- Top-level directories -->
-    <property name="build.dir" value="build" />
-    <property name="dist.dir" value="dist" />
-    <property name="lib.dir" value="lib" />
-    <property name="public.dir" value="public" />
-    <property name="private.dir" value="private" />
-    <property name="protected.dir" value="protected" />
-    <property name="external.dir" value="external" />
-
-    <!-- Source directories -->
-    <property name="java.public.source.dir" value="${public.dir}/java/src" />
-    <property name="java.private.source.dir" value="${private.dir}/java/src" />
-    <property name="java.protected.source.dir" value="${protected.dir}/java/src" />
-    <property name="scala.public.source.dir" value="${public.dir}/scala/src" />
-    <property name="scala.private.source.dir" value="${private.dir}/scala/src" />
-    <property name="scala.protected.source.dir" value="${protected.dir}/scala/src" />
-    <property name="queue-extensions.source.dir" value="${build.dir}/queue-extensions/src" />
-    <property name="R.public.scripts.dir" value="${public.dir}/R/scripts" />
-    <property name="R.private.scripts.dir" value="${private.dir}/R/scripts" />
-    <property name="R.protected.scripts.dir" value="${protected.dir}/R/scripts" />
-    <property name="R.public.src.dir" value="${public.dir}/R/src" />
-
-    <!-- Build directories -->
-    <property name="java.classes" value="${build.dir}/java/classes" />
-    <property name="scala.classes" value="${build.dir}/scala/classes" />
-    <property name="R.library.dir" value="${public.dir}/R" />  <!-- TODO: Installing libraries back into the source directory: intentionally avoids ant clean?? -->
-    <property name="R.tar.dir" value="${build.dir}/R/src" />
-    <property name="R.package.path" value="org/broadinstitute/sting/utils/R" />
-    <property name="R.script.staging.dir" value="${build.dir}/R/stage" />
-
-    <!-- Packaging system properties -->
-    <property name="package.xml.dir" value="${public.dir}/packages" />
-    <property name="package.output.dir" value="${dist.dir}/packages" />
-    <property name="staging.dir" value="staging" />
-    <property name="default.executable" value="none" />
-
-    <!-- GATKDocs/Javadoc/Scaladoc directories -->
-    <property name="gatkdocs.dir" value="gatkdocs" />
-    <property name="javadoc.dir" value="javadoc" />
-    <property name="scaladoc.dir" value="scaladoc" />
-
-    <!-- Resource file used for help text and version information -->
-    <property name="resource.file" value="StingText.properties" />
-    <property name="resource.path" value="${java.classes}/StingText.properties" />
-
-    <!-- Directory containing cryptographic keys used by the GATK -->
-    <property name="key.dir" value="${public.dir}/keys" />
-
-    <!-- Contracts for Java -->
-    <!-- Disabled by default -->
-    <!-- To enable, run with -Duse.contracts=true -->
-    <property name="java.contracts.dir" value="${build.dir}/java/contracts" />
-    <property name="contracts.version" value="1.0-r139" />
-    <property name="cofoja.jar" value="${lib.dir}/cofoja-${contracts.version}.jar"/>
-    <property name="contract.dump.dir" value="dump" />
-
-    <!-- do we want to halt on failure of a unit test? default to yes (Bamboo uses 'no') -->
-    <property name="halt" value="yes" />
-
-    <!-- should our unit test output go to a file or the screen? false means it goes to the screen (default) true to file -->
-    <property name="usefile" value="false" />
-
-    <!-- To run tests with debugging, use -Dtest.debug=true -Dtest.debug.port=XXXX on the command line -->
-    <property name="test.debug.port" value="5005" />  <!-- override on the command line if desired -->
-    <property name="test.default.maxmemory" value="4g"/>
-
-    <!-- clover parameters -->
-    <property name="clover.jar" location="private/resources/clover/lib/clover.jar"/>
-    <property name="clover.instrument.level" value="method"/>
-    <taskdef resource="cloverlib.xml" classpath="${clover.jar}"/>
-
-    <!-- ******************************************************************************** -->
-    <!-- Filesets and paths                                                               -->
-    <!-- ******************************************************************************** -->
-
-    <!-- All the complexity of selecting among public/private/protected should be up here, not down in the targets -->
-
-    <patternset id="java.source.directories.pattern">
-        <include name="${java.public.source.dir}" />
-        <include name="${java.private.source.dir}" if="include.private" />
-        <include name="${java.protected.source.dir}" if="include.protected" />
-    </patternset>
-
-    <patternset id="java.source.files.pattern">
-        <include name="${java.public.source.dir}/**/*.java" />
-        <include name="${java.private.source.dir}/**/*.java" if="include.private" />
-        <include name="${java.protected.source.dir}/**/*.java" if="include.protected" />
-    </patternset>
-
-    <patternset id="scala.source.directories.pattern">
-        <include name="${scala.public.source.dir}" />
-        <include name="${scala.private.source.dir}" if="include.private" />
-        <include name="${scala.protected.source.dir}" if="include.protected" />
-    </patternset>
-
-    <patternset id="scala.source.files.pattern">
-        <include name="${scala.public.source.dir}/**/*.scala" />
-        <include name="${scala.private.source.dir}/**/*.scala" if="include.private" />
-        <include name="${scala.protected.source.dir}/**/*.scala" if="include.protected" />
-    </patternset>
-
-    <patternset id="R.script.source.directories.pattern">
-        <include name="${R.public.scripts.dir}" />
-        <include name="${R.private.scripts.dir}" if="include.private" />
-        <include name="${R.protected.scripts.dir}" if="include.protected" />
-    </patternset>
-
-    <patternset id="R.script.source.files.pattern">
-        <include name="${R.public.scripts.dir}/**/*.R" />
-        <include name="${R.private.scripts.dir}/**/*.R" if="include.private" />
-        <include name="${R.protected.scripts.dir}/**.*.R" if="include.protected" />
-    </patternset>
-
-    <path id="java.source.path">
-        <dirset dir="${basedir}">
-            <patternset refid="java.source.directories.pattern" />
-        </dirset>
-    </path>
-
-    <path id="scala.source.path">
-        <dirset dir="${basedir}">
-            <patternset refid="scala.source.directories.pattern" />
-        </dirset>
-    </path>
-
-    <path id="R.script.source.path">
-        <dirset dir="${basedir}">
-            <patternset refid="R.script.source.directories.pattern" />
-        </dirset>
-    </path>
-
-    <fileset id="java.source.files" dir="${basedir}">
-        <patternset refid="java.source.files.pattern" />
-    </fileset>
-
-    <fileset id="scala.source.files" dir="${basedir}">
-        <patternset refid="scala.source.files.pattern" />
-    </fileset>
-
-    <fileset id="R.script.source.files" dir="${basedir}">
-        <patternset refid="R.script.source.files.pattern" />
-    </fileset>
-
-    <fileset id="java.class.files" dir="${java.classes}" erroronmissingdir="false">
-        <include name="**/*.class"/>
-    </fileset>
-
-    <patternset id="dependency.mask" includes="*.jar" />
-
-    <path id="external.dependencies">
-        <fileset dir="${lib.dir}" erroronmissingdir="false">
-            <patternset refid="dependency.mask" />
-        </fileset>
-    </path>
-
-    <path id="scala.dependencies">
-        <path refid="external.dependencies" />
-        <pathelement location="${java.classes}" />
-        <!-- Need the resources as we will be running a command line program which needs the help text. -->
-        <pathelement location="${resource.path}" />
-        <!-- Add any previously compiled scala classes to the path. -->
-        <pathelement location="${scala.classes}" />
-    </path>
-
-    <path id="build.results">
-        <!-- Ensure that GenomeAnalysisTK.jar comes first in the path, as it contains overrides for certain classes in our dependencies -->
-        <pathelement location="${dist.dir}/GenomeAnalysisTK.jar" />
-        <!-- After GenomeAnalysisTK.jar we include all of the other jars in the dist directory -->
-        <fileset dir="${dist.dir}" erroronmissingdir="false">
-            <patternset refid="dependency.mask" />
-            <exclude name="GenomeAnalysisTK.jar" />
-        </fileset>
-    </path>
-
-    <fileset id="external.source.files" dir="${external.dir}" erroronmissingdir="false">
-        <include name="**/*.java" />
-    </fileset>
-
-    <path id="external.build.dir">
-        <path path="${java.classes}" />
-    </path>
-
-    <path id="external.dist.dir">
-        <path path="${dist.dir}" />
-    </path>
-
-    <!-- GATK dependencies consist of 3rd party plugins plus compiled GATK classes -->
-    <path id="external.gatk.classpath">
-        <path path="${java.classes}"/>
-        <path refid="external.dependencies" />
-    </path>
-
-    <!-- the path for resources that need to go into the GATK jar;
-         any additional resources should go into this set. -->
-    <path id="gatk.resources">
-        <fileset dir="${java.public.source.dir}">
-            <include name="**/resources/*" />
-            <include name="**/templates/*" />
-        </fileset>
-        <fileset dir="${java.private.source.dir}" erroronmissingdir="false">
-            <include name="**/resources/*" if="include.private" />
-            <include name="**/templates/*" if="include.private" />
-        </fileset>
-        <fileset dir="${java.protected.source.dir}" erroronmissingdir="false">
-            <include name="**/resources/*" if="include.protected" />
-            <include name="**/templates/*" if="include.protected" />
-        </fileset>
-    </path>
-
-    <!-- ******************************************************************************** -->
-    <!-- Ivy Retrieve                                                                     -->
-    <!-- ******************************************************************************** -->
-
-    <target name="init.resolve" unless="init.resolve.done">
-        <!-- ivy properties -->
-        <property name="ivy.install.version" value="2.2.0"/>
-        <property name="ivy.home" value="${user.home}/.ant"/>
-        <property name="ivy.jar.dir" value="${ivy.home}/${lib.dir}"/>
-        <property name="ivy.jar.file" value="ivy-${ivy.install.version}.jar"/>
-        <property name="ivy.settings.dir" value="settings"/>
-        <property file="${ivy.settings.dir}/ivysettings.properties"/>
-        <property name="maven-ant-tasks.install.version" value="2.1.3"/>
-        <property name="maven-ant-tasks.jar.file" value="maven-ant-tasks-${maven-ant-tasks.install.version}.jar"/>
-
-        <mkdir dir="${lib.dir}"/>
-        <mkdir dir="${ivy.jar.dir}"/>
-
-        <!-- Comment out the following lines to build the GATK without a network connection, assuming you have all of the libraries cached already -->
-
-        <get src="http://repo1.maven.org/maven2/org/apache/ivy/ivy/${ivy.install.version}/${ivy.jar.file}"
-             dest="${ivy.jar.dir}/${ivy.jar.file}"
-             usetimestamp="true"/>
-        <taskdef resource="org/apache/ivy/ant/antlib.xml"
-                 uri="antlib:org.apache.ivy.ant"
-                 classpath="${ivy.jar.dir}/${ivy.jar.file}"/>
-
-        <get src="http://repo1.maven.org/maven2/org/apache/maven/maven-ant-tasks/${maven-ant-tasks.install.version}/${maven-ant-tasks.jar.file}"
-             dest="${ivy.jar.dir}/${maven-ant-tasks.jar.file}"
-             usetimestamp="true"/>
-        <taskdef resource="org/apache/maven/artifact/ant/antlib.xml"
-                 uri="antlib:antlib:org.apache.maven.artifact.ant"
-                 classpath="${ivy.jar.dir}/${maven-ant-tasks.jar.file}"/>
-
-        <!-- End network lines -->
-
-        <ivy:settings file="${ivy.settings.dir}/ivysettings.xml"/>
-        <property name="init.resolve.done" value="true"/>
-    </target>
-
-    <target name="resolve" depends="init.resolve,init" description="Locate and download library dependencies">
-        <property name="ivy.conf" value="default"/>
-        <ivy:retrieve file="ivy.xml" conf="${ivy.conf}" />
-        <!-- Remove old versions of ivy jars AFTER the ivy:retrieve has been class loaded. -->
-        <delete file="${ivy.jar.dir}/ivy-2.0.0.jar"/>
-        <delete file="${ivy.jar.dir}/ivy-2.2.0-rc1.jar"/>
-    </target>
-
-
-    <!-- ******************************************************************************** -->
-    <!-- Initialization                                                                   -->
-    <!-- ******************************************************************************** -->
-
-    <!-- Targets for generating the build version -->
-    <target name="git.describe">
-      <exec executable="git" outputproperty="git.describe.output" resultproperty="git.describe.exit.value" failonerror="false">
-        <arg line="describe --long" />
-      </exec>
-      <condition property="git.describe.succeeded">
-        <equals arg1="${git.describe.exit.value}" arg2="0" />
-      </condition>
-    </target>
-
-    <target name="tagged.build.version" depends="git.describe" if="git.describe.succeeded">
-        <property name="build.version" value="${git.describe.output}" />
-    </target>
-
-    <target name="git.rev-parse" depends="git.describe" unless="git.describe.succeeded">
-      <exec executable="git" outputproperty="git.rev-parse.output" resultproperty="git.rev-parse.exit.value" failonerror="false">
-        <arg line="rev-parse --short HEAD" />
-      </exec>
-      <condition property="git.rev-parse.succeeded">
-        <equals arg1="${git.rev-parse.exit.value}" arg2="0" />
-      </condition>
-    </target>
-
-    <target name="untagged.build.version" depends="git.rev-parse" if="git.rev-parse.succeeded">
-        <property name="build.version" value="${git.rev-parse.output}" />
-    </target>
-
-    <target name="generate.build.version" depends="tagged.build.version, untagged.build.version">
-        <!-- Set build.version to exported if no other value has been set -->
-        <property name="build.version" value="exported" />
-    </target>
-
-
-    <!-- INIT OVERRIDES: call these targets BEFORE init to override build defaults -->
-    <target name="init.build.publiconly">
-        <property name="build.target" value="public" />
-    </target>
-
-    <target name="init.build.publicprotectedonly">
-        <property name="build.target" value="protected" />
-    </target>
-
-    <target name="init.build.all">
-        <property name="build.target" value="all" />
-    </target>
-
-    <target name="init.javaonly">
-        <property name="compile.scala" value="false" />
-    </target>
-
-    <target name="init.javaandscala">
-        <property name="compile.scala" value="true" />
-    </target>
-
-    <target name="init.usecontracts">
-        <property name="use.contracts" value="true" />
-    </target>
-
-
-    <!-- INIT -->
-    <target name="init" depends="generate.build.version">
-        <tstamp>
-            <format property="build.timestamp" pattern="yyyy/MM/dd HH:mm:ss"/>
-        </tstamp>
-
-        <!-- These properties should be overridden before init is called if the defaults are not desired -->
-        <property name="build.target" value="${default.build.target}" />
-        <property name="compile.scala" value="${compile.scala.by.default}" />
-        <property name="use.contracts" value="${use.contracts.by.default}" />
-        <property name="executable" value="${default.executable}" />
-
-        <!-- Determine what should be built -->
-        <condition property="include.scala">
-            <equals arg1="${compile.scala}" arg2="true" />
-        </condition>
-
-        <condition property="include.private">
-            <and>
-                <available file="${private.dir}" />
-                <equals arg1="${build.target}" arg2="all" />
-            </and>
-        </condition>
-
-        <condition property="include.protected">
-            <and>
-                <available file="${protected.dir}" />
-                <or>
-                    <equals arg1="${build.target}" arg2="all" />
-                    <equals arg1="${build.target}" arg2="protected" />
-                </or>
-            </and>
-        </condition>
-
-        <condition property="include.contracts">
-            <equals arg1="${use.contracts}" arg2="true" />
-        </condition>
-
-        <condition property="include.external">
-            <available file="${external.dir}"/>
-        </condition>
-
-        <!-- Construct display strings for the build properties print out -->
-
-        <condition property="include.scala.display.string" value="yes" else="no">
-            <isset property="include.scala" />
-        </condition>
-
-        <condition property="include.private.display.string" value="yes" else="no">
-            <isset property="include.private" />
-        </condition>
-
-        <condition property="include.protected.display.string" value="yes" else="no">
-            <isset property="include.protected" />
-        </condition>
-
-        <condition property="include.external.display.string" value="yes" else="no">
-            <isset property="include.external" />
-        </condition>
-
-        <condition property="include.contracts.display.string" value="yes" else="no">
-            <isset property="include.contracts" />
-        </condition>
-
-        <!-- Print out build properties -->
-        <echo message="BUILD PROPERTIES" />
-        <echo message="Include Scala?     : ${include.scala.display.string}" />
-        <echo message="Include Private?   : ${include.private.display.string}" />
-        <echo message="Include Protected? : ${include.protected.display.string}" />
-        <echo message="Include External?  : ${include.external.display.string}" />
-        <echo message="Include Contracts? : ${include.contracts.display.string}" />
-        <echo message="Source revision    : ${build.version}" />
-        <echo message="Build time         : ${build.timestamp}" />
-
-        <!-- Create the build directory structure used by compile -->
-        <mkdir dir="${build.dir}"/>
-        <mkdir dir="${lib.dir}"/>
-        <mkdir dir="${java.classes}"/>
-        <mkdir dir="${java.contracts.dir}"/>
-    </target>
-
-
-    <!-- ******************************************************************************** -->
-    <!-- Java Compilation                                                                 -->
-    <!-- ******************************************************************************** -->
-
-    <target name="gatk.compile.internal.source" depends="init,resolve">
-        <javac fork="true" memoryMaximumSize="512m" destdir="${java.classes}" debug="true" debuglevel="lines,vars,source" classpathref="external.dependencies" tempdir="${java.io.tmpdir}">
-            <src refid="java.source.path" />
-            <compilerarg value="-proc:none" />
-        </javac>
-    </target>
-
-    <target name="gatk.compile.external.source" depends="gatk.compile.internal.source" if="include.external">
-        <subant target="compile" genericantfile="build.xml">
-            <property name="build.dir" refid="external.build.dir" />
-            <property name="dist.dir" refid="external.dist.dir" />
-            <property name="gatk.classpath" refid="external.gatk.classpath" />
-            <fileset dir="${external.dir}" includes="*/build.xml" erroronmissingdir="false" />
-        </subant>
-    </target>
-
-    <target name="gatk.compile.source" depends="gatk.compile.internal.source,gatk.compile.external.source" />
-
-    <target name="gatk.contracts" depends="gatk.compile.source" if="include.contracts">
-        <javac fork="true" memoryMaximumSize="512m" destdir="${java.contracts.dir}" debug="true" debuglevel="lines,vars,source" tempdir="${java.io.tmpdir}" >
-            <src refid="java.source.path" />
-            <classpath>
-                <path refid="external.dependencies" />
-                <pathelement path="${java.classes}" />
-            </classpath>
-            <compilerarg value="-Acom.google.java.contract.debug"/>
-            <compilerarg value="-Acom.google.java.contract.dump=${contract.dump.dir}"/>
-            <compilerarg value="-proc:only"/>
-        </javac>
-    </target>
-
-    <target name="gatk.compile" depends="init,resolve,gatk.compile.source,gatk.contracts" />
-
-
-    <!-- ******************************************************************************** -->
-    <!-- Scala Compilation                                                                -->
-    <!-- ******************************************************************************** -->
-
-    <target name="init.queue-extensions.generate" depends="gatk.compile">
-        <condition property="uptodate.queue-extensions.generate">
-            <or>
-                <not>
-                    <isset property="include.scala"/>
-                </not>
-                <uptodate targetfile="${queue-extensions.source.dir}">
-                    <srcfiles refid="java.class.files"/>
-                    <srcfiles file="${queue-extensions.gatk.jar}"/>
-                </uptodate>
-            </or>
-        </condition>
-    </target>
-
-    <!-- NOTE: Extracting help first to avoid "Unable to load help text.  Help output will be sparse." warning message. -->
-    <target name="queue-extensions.generate" depends="gatk.compile,extracthelp,init.queue-extensions.generate" unless="uptodate.queue-extensions.generate">
-        <mkdir dir="${queue-extensions.source.dir}"/>
-        <echo>Generating Queue GATK extensions...</echo>
-        <java fork="true" failonerror="true" classname="org.broadinstitute.sting.queue.extensions.gatk.GATKExtensionsGenerator" >
-            <arg value="-outDir" />
-            <arg path="${queue-extensions.source.dir}" />
-            <arg value="-l" />
-            <arg value="WARN" />
-            <classpath>
-                <file file="${queue-extensions.gatk.jar}"/>
-                <path refid="scala.dependencies"/>
-            </classpath>
-        </java>
-        <touch>
-            <file file="${queue-extensions.source.dir}"/>
-        </touch>
-    </target>
-
-    <target name="init.scala.compile" depends="resolve">
-        <path id="scala.classpath">
-            <fileset dir="${lib.dir}">
-                <include name="scala-compiler-*.jar"/>
-                <include name="scala-library-*.jar"/>
-                <include name="scala-reflect-*.jar"/>
-            </fileset>
-        </path>
-        <taskdef resource="scala/tools/ant/antlib.xml">
-            <classpath refid="scala.classpath"/>
-        </taskdef>
-    </target>
-
-    <!-- Scala depends on the java compile -->
-    <target name="scala.compile" depends="init,resolve,gatk.compile,queue-extensions.generate,init.scala.compile" if="include.scala">
-        <mkdir dir="${scala.classes}"/>
-        <echo>Building Scala...</echo>
-        <scalac fork="true" jvmargs="-Xmx512m" destdir="${scala.classes}" classpathref="scala.dependencies" deprecation="yes" unchecked="yes" addparams="-feature">
-            <src refid="scala.source.path" />
-            <src path="${queue-extensions.source.dir}" />
-            <include name="**/*.scala" />
-        </scalac>
-    </target>
-
-
-    <!-- ******************************************************************************** -->
-    <!-- Sting Resource File Generation                                                   -->
-    <!-- ******************************************************************************** -->
-
-    <target name="init.extracthelp" depends="gatk.compile">
-        <loadfile property="properties.version" srcfile="${basedir}/${resource.path}" failonerror="false" quiet="true">
-            <filterchain>
-                <linecontains>
-                    <contains value="org.broadinstitute.sting.gatk.CommandLineGATK.version"/>
-                </linecontains>
-                <tokenfilter>
-                    <replaceregex pattern="^.*\.(.*?)$" replace="\1"/>
-                </tokenfilter>
-                <striplinebreaks/>
-            </filterchain>
-        </loadfile>
-
-        <!-- This fileset will contain only source files modified since the resource file was last generated,
-             or all source files if the resource file doesn't exist -->
-        <fileset dir="${basedir}" id="modified.source.files">
-            <patternset refid="java.source.files.pattern" />
-            <include name="${external.dir}/**/*.java"/>
-            <depend targetdir="${basedir}">
-                <mapper type="merge" to="${resource.path}"/>
-            </depend>
-        </fileset>
-
-        <!-- Set the sources.modified property only if our fileset of modified source files is non-empty -->
-        <pathconvert refid="modified.source.files" property="sources.modified" setonempty="false"/>
-
-        <!-- Due to a limitation in the doclet API, we always need to pass package-info files to javadoc -->
-        <fileset dir="${basedir}" id="package.info.files">
-            <include name="${java.public.source.dir}/**/package-info.java"/>
-            <include name="${java.private.source.dir}/**/package-info.java" if="include.private" />
-            <include name="${java.protected.source.dir}/**/package-info.java" if="include.protected" />
-            <include name="${external.dir}/**/package-info.java"/>
-        </fileset>
-
-        <condition property="uptodate.extracthelp">
-            <or>
-                <isset property="disable.help"/>
-                <and>
-                    <not>
-                        <isset property="sources.modified"/>
-                    </not>
-                    <equals arg1="${properties.version}" arg2="${build.version}"/>
-                </and>
-            </or>
-        </condition>
-    </target>
-
-    <target name="extracthelp" depends="init.extracthelp" unless="uptodate.extracthelp">
-        <path id="doclet.classpath">
-            <path refid="external.dependencies" />
-            <pathelement location="${java.classes}" />
-	    <pathelement location="${clover.jar}" />
-        </path>
-
-        <javadoc doclet="org.broadinstitute.sting.utils.help.ResourceBundleExtractorDoclet"
-                 docletpathref="doclet.classpath"
-                 classpathref="external.dependencies"
-                 classpath="${java.classes}"
-		 maxmemory="2g"
-                 additionalparam="-build-timestamp &quot;${build.timestamp}&quot; -absolute-version ${build.version} -out ${basedir}/${resource.path} -quiet">
-            <sourcefiles>
-                <union>
-                    <fileset refid="modified.source.files"/>
-                    <fileset refid="package.info.files"/>
-                </union>
-            </sourcefiles>
-        </javadoc>
-    </target>
-
-
-    <!-- ******************************************************************************** -->
-    <!-- Build Jars                                                                       -->
-    <!-- ******************************************************************************** -->
-
-    <target name="sting.compile" depends="gatk.compile, scala.compile" />
-
-    <target name="init.jar" depends="sting.compile,extracthelp">
-        <mkdir dir="${dist.dir}"/>
-        <copy todir="${dist.dir}">
-            <fileset dir="${lib.dir}" includes="*.jar"/>
-        </copy>
-    </target>
-
-    <target name="R.public.tar">
-        <mkdir dir="${R.tar.dir}/${R.package.path}" />
-        <tar compression="gzip" basedir="${R.public.src.dir}/${R.package.path}" includes="gsalib/**" destfile="${R.tar.dir}/${R.package.path}/gsalib.tar.gz" />
-    </target>
-
-    <target name="R.script.stage">
-        <mkdir dir="${R.script.staging.dir}" />
-        <copy todir="${R.script.staging.dir}" overwrite="true">
-            <fileset refid="R.script.source.files" />
-            <!-- remove the initial path components (eg., public/R/scripts) when doing the copy -->
-            <!-- ant 1.8.2 has a cutdirsmapper, but ant versions < 1.8.2 are too common to use it -->
-            <mapper type="regexp" from="^(${R.public.scripts.dir}|${R.private.scripts.dir}|${R.protected.scripts.dir})/(.*)" to="\2" />
-        </copy>
-    </target>
-
-    <target name="sting-utils.jar" depends="gatk.compile, init.jar, R.public.tar, R.script.stage">
-        <jar jarfile="${dist.dir}/StingUtils.jar">
-            <fileset dir="${java.classes}" includes="**/sting/utils/**/*.class"/>
-            <fileset dir="${java.classes}" includes="**/sting/commandline/**/*.class"/>
-            <fileset dir="${java.classes}" includes="**/sting/pipeline/**/*.class"/>
-            <fileset dir="${java.classes}" includes="**/sting/tools/**/*.class"/>
-            <fileset dir="${java.classes}" includes="**/sting/jna/**/*.class"/>
-            <fileset dir="${java.classes}" includes="net/sf/picard/**/*.class"/>
-            <fileset dir="${java.classes}" includes="net/sf/samtools/**/*.class"/>
-            <fileset dir="${R.tar.dir}">
-                <include name="**/${R.package.path}/**/*.tar.gz"/>
-            </fileset>
-            <fileset dir="${R.script.staging.dir}">
-                <include name="**/sting/utils/**/*.R"/>
-            </fileset>
-            <manifest>
-                <attribute name="Premain-Class" value="org.broadinstitute.sting.utils.instrumentation.Sizeof" />
-            </manifest>
-        </jar>
-    </target>
-
-    <target name="na12878kb.jar" depends="gatk.compile,init.jar">
-        <jar jarfile="${dist.dir}/na12878kb.jar">
-            <fileset dir="${java.classes}">
-              <include name="org/broadinstitute/sting/utils/GenomeLocParser*.class"/>
-              <include name="org/broadinstitute/sting/utils/GenomeLoc.class"/>
-              <include name="org/broadinstitute/sting/utils/HasGenomeLocation.class"/>
-              <include name="org/broadinstitute/sting/utils/BaseUtils*.class"/>
-              <include name="org/broadinstitute/sting/utils/Utils.class"/>
-              <include name="org/broadinstitute/sting/utils/MRUCaching*.class"/>
-              <include name="org/broadinstitute/sting/utils/exceptions/**/*.class"/>
-              <include name="org/broadinstitute/sting/gatk/walkers/na12878kb/core/**/*.class"/>
-              <include name="net/sf/picard/reference/FastaSequenceFile.class"/>
-            </fileset>
-	    <fileset dir="${java.private.source.dir}">
-              <include name="org/broadinstitute/sting/gatk/walkers/na12878kb/core/resources/**/*"/>
-	    </fileset>
-        </jar>
-    </target>
-
-    <target name="gatk.jar" depends="gatk.compile, init.jar, R.script.stage">
-        <jar jarfile="${dist.dir}/GenomeAnalysisTK.jar">
-            <path refid="gatk.resources"/>
-            <fileset dir="${java.contracts.dir}" />
-            <fileset dir="${java.classes}">
-	          <include name="${resource.file}" />
-              <include name="**/sting/gatk/**/*.class" />
-              <include name="**/sting/alignment/**/*.class"/>
-            </fileset>
-            <fileset dir="${R.script.staging.dir}">
-                <include name="**/sting/gatk/**/*.R"/>
-                <include name="**/sting/alignment/**/*.R"/>
-            </fileset>
-            <fileset dir="${key.dir}">
-                <include name="**/*.key"/>
-            </fileset>
-            <manifest>
-                <attribute name="Main-Class" value="org.broadinstitute.sting.gatk.CommandLineGATK" />
-            </manifest>
-        </jar>
-
-        <jar jarfile="${dist.dir}/Aligner.jar">
-            <fileset dir="${java.classes}" includes="**/sting/alignment/**/*.class" />
-        </jar>
-
-        <subant target="dist" genericantfile="build.xml">
-            <property name="build.dir" refid="external.build.dir" />
-            <property name="dist.dir" refid="external.dist.dir" />
-            <property name="gatk.classpath" refid="external.gatk.classpath" />
-            <fileset dir="${external.dir}" includes="*/build.xml" erroronmissingdir="false" />
-        </subant>
-    </target>
-
-    <target name="scala.jar" depends="scala.compile, init.jar" if="include.scala">
-        <jar jarfile="${dist.dir}/GATKScala.jar">
-          <fileset dir="${scala.classes}">
-            <include name="org/broadinstitute/sting/scala/**/*.class"/>
-          </fileset>
-        </jar>
-    </target>
-
-    <target name="queue.jar" depends="scala.compile, init.jar, R.script.stage" if="include.scala">
-        <jar jarfile="${dist.dir}/Queue.jar">
-            <fileset dir="${scala.classes}">
-                <include name="org/broadinstitute/sting/queue/**/*.class"/>
-            </fileset>
-            <fileset dir="${java.classes}">
-              <include name="org/broadinstitute/sting/queue/**/*.class" />
-            </fileset>
-            <fileset dir="${R.script.staging.dir}">
-                <include name="org/broadinstitute/sting/queue/**/*.R"/>
-            </fileset>
-            <manifest>
-                <attribute name="Main-Class" value="org.broadinstitute.sting.queue.QCommandLine" />
-            </manifest>
-        </jar>
-    </target>
-
-    <target name="sting.jar" depends="sting-utils.jar, gatk.jar, queue.jar" />
-
-    <target name="init.manifests" depends="sting.jar">
-        <pathconvert property="jar.classpath" pathsep=" ">
-            <flattenmapper/>
-            <fileset dir="${dist.dir}" includes="*.jar"/>
-            <filelist files="GATKScala.jar"/>
-        </pathconvert>
-    </target>
-
-    <target name="sting-utils.manifests" depends="sting-utils.jar, init.manifests">
-        <jar jarfile="${dist.dir}/StingUtils.jar" update="true">
-            <manifest>
-                <attribute name="Class-Path" value="${jar.classpath}"/>
-            </manifest>
-        </jar>
-    </target>
-
-    <target name="gatk.manifests" depends="gatk.jar, init.manifests">
-        <jar jarfile="${dist.dir}/GenomeAnalysisTK.jar" update="true">
-            <manifest>
-                <attribute name="Class-Path" value="${jar.classpath}"/>
-            </manifest>
-        </jar>
-    </target>
-
-    <target name="queue.manifests" depends="queue.jar, init.manifests" if="include.scala">
-        <jar jarfile="${dist.dir}/Queue.jar" update="true" >
-            <manifest>
-                <attribute name="Class-Path" value="${jar.classpath}" />
-            </manifest>
-        </jar>
-    </target>
-
-    <target name="sting.manifests" depends="sting-utils.manifests, gatk.manifests, queue.manifests" />
-
-
-    <!-- ******************************************************************************** -->
-    <!-- Top-Level Build Targets                                                          -->
-    <!-- ******************************************************************************** -->
-
-    <target name="dist" depends="sting.manifests" description="Build the GATK and Queue" />
-
-    <target name="gatk" depends="init.javaonly, sting.manifests" description="Build the GATK only" />
-
-    <target name="queue" depends="dist" />  <!-- Obsolete target. Now just an alias for dist -->
-
-    <target name="scala" depends="scala.jar" />
-
-
-    <!-- ******************************************************************************** -->
-    <!-- GATKDocs                                                                          -->
-    <!-- ******************************************************************************** -->
-
-    <target name="gatkdocs" depends="gatk.compile" description="Generate GATK HTML documentation">
-        <path id="doclet.classpath">
-            <path refid="external.dependencies" />
-            <pathelement location="${java.classes}" />
-        </path>
-
-        <!-- Run with -Dgatkdocs.include.hidden=true to include documentation for hidden features -->
-        <condition property="gatkdocs.include.hidden.arg" value="-include-hidden" else="">
-            <isset property="gatkdocs.include.hidden" />
-        </condition>
-
-        <javadoc doclet="org.broadinstitute.sting.utils.help.GATKDoclet"
-                 docletpathref="doclet.classpath"
-                 classpathref="external.dependencies"
-                 classpath="${java.classes}"
-		 maxmemory="2g"
-                 additionalparam="${gatkdocs.include.hidden.arg} -private -build-timestamp &quot;${build.timestamp}&quot; -absolute-version ${build.version} -quiet"> <!-- -test to only do DocumentationTest walker -->
-            <sourcefiles>
-                <fileset refid="java.source.files"/>
-            </sourcefiles>
-        </javadoc>
-    </target>
-
-
-    <!-- ******************************************************************************** -->
-    <!-- Javadoc                                                                          -->
-    <!-- ******************************************************************************** -->
-
-    <target name="init.javadoc">
-        <mkdir dir="${javadoc.dir}" />
-    </target>
-
-    <target name="javadoc" depends="init.javadoc,resolve" description="Generate Javadoc">
-        <javadoc destdir="${javadoc.dir}" classpathref="external.dependencies">
-            <fileset refid="java.source.files" />
-            <sourcepath path="${external.dir}" />
-        </javadoc>
-    </target>
-
-
-    <!-- ******************************************************************************** -->
-    <!-- Scaladoc                                                                         -->
-    <!-- ******************************************************************************** -->
-
-    <target name="init.scaladoc">
-        <mkdir dir="${scaladoc.dir}" />
-    </target>
-
-    <!-- NOTE: the scaladoc target requires that the environment variable ANT_OPTS has been set to "-Xmx1G" -->
-
-    <target name="scaladoc" depends="resolve,queue-extensions.generate,init.scala.compile,scala.compile,init.scaladoc" description="Generate Scaladoc">
-        <scaladoc srcdir="${basedir}" destdir="${scaladoc.dir}" classpathref="scala.dependencies" deprecation="yes" unchecked="yes">
-            <patternset refid="scala.source.files.pattern" />
-            <include name="${queue-extensions.source.dir}/**/*.scala" />
-        </scaladoc>
-    </target>
-
-
-    <!-- ******************************************************************************** -->
-    <!-- Release-related tasks                                                            -->
-    <!-- ******************************************************************************** -->
-
-    <target name="init.executable.gatkfull" depends="init.build.publicprotectedonly, init.javaonly">
-        <property name="executable" value="GenomeAnalysisTK" />
-    </target>
-
-    <target name="init.executable.gatkall" depends="init.build.all, init.javaonly">
-        <property name="executable" value="GenomeAnalysisTK" />
-    </target>
-
-    <target name="init.executable.queuefull" depends="init.build.publicprotectedonly, init.javaandscala">
-        <property name="executable" value="Queue" />
-    </target>
-
-    <target name="init.executable.queueall" depends="init.build.all, init.javaandscala">
-        <property name="executable" value="Queue" />
-    </target>
-
-    <target name="require.executable">
-        <condition property="no.executable.defined">
-            <or>
-                <equals arg1="${executable}" arg2="none" />
-                <equals arg1="${executable}" arg2="$${executable}" />
-            </or>
-        </condition>
-        <fail message="No executable defined. Call a more specific packaging/release target, or define an executable manually" if="no.executable.defined" />
-    </target>
-
-    <target name="require.bcel">
-        <fileset id="bcel.jar" dir="${user.home}/.ant/lib">
-            <include name="bcel-*.jar" />
-        </fileset>
-        <pathconvert refid="bcel.jar" property="bcel.jar.installed" setonempty="false" />
-
-        <fileset id="ant.bcel.jar" dir="${user.home}/.ant/lib">
-            <include name="ant-apache-bcel-*.jar" />
-        </fileset>
-        <pathconvert refid="ant.bcel.jar" property="ant.bcel.jar.installed" setonempty="false" />
-
-        <condition property="bcel.installed">
-            <and>
-                <isset property="bcel.jar.installed" />
-                <isset property="ant.bcel.jar.installed" />
-            </and>
-        </condition>
-        <fail unless="bcel.installed"
-              message="Required bcel libraries for GATK packaging not installed in ${user.home}/.ant/lib/${line.separator}The bcel jar can be found in the lib directory of a GATK clone after compiling, and the ant-apache-bcel jar can be downloaded from here: http://repo1.maven.org/maven2/ant/ant-apache-bcel/1.6.5/ant-apache-bcel-1.6.5.jar${line.separator}Please copy these two jar files to ${user.home}/.ant/lib/" />
-    </target>
-
-    <!-- Unzip all classes from their current locations and assemble them in a staging directory -->
-    <target name="stage">
-        <mkdir dir="${staging.dir}"/>
-        <!--
-            HACK: Create the edu directory before EDU on case-insensitive mac filesystems.
-            The ivy dependency colt -> concurrent contains an EDU.oswego package which
-            BCEL doesn't even pull in but messes up edu.mit.broad.
-          -->
-        <mkdir dir="${staging.dir}/edu"/>
-        <unjar dest="${staging.dir}" overwrite="false">
-          <fileset dir="${dist.dir}">
-            <patternset refid="dependency.mask" />
-          </fileset>
-        </unjar>
-
-        <!-- HACK: The GATK jar itself contains overrides for some core classes.  Make sure the GATK.jar is unrolled last. -->
-        <unjar dest="${staging.dir}" overwrite="true">
-          <fileset dir="${dist.dir}" includes="**/GenomeAnalysisTK.jar"/>
-        </unjar>
-    </target>
-
-
-    <!-- Build a package consisting of all supporting files. Don't call this target directly. Call one of the specific packaging targets below -->
-    <target name="package" depends="require.clean,require.bcel,dist,stage,require.executable">
-      <mkdir dir="${package.output.dir}" />
-      <xslt destdir="${package.output.dir}" style="${package.xml.dir}/CreatePackager.xsl" useImplicitFileset="false">
-          <flattenmapper/>
-          <fileset dir="${package.xml.dir}">
-              <include name="${executable}.xml" />
-          </fileset>
-          <fileset dir="${external.dir}" erroronmissingdir="false">
-              <include name="*/${executable}.xml" />
-          </fileset>
-      </xslt>
-      <ant antfile="${package.output.dir}/${executable}.xml" target="package" />
-    </target>
-
-    <!-- Package specific versions of the GATK/Queue. ALWAYS do an ant clean before invoking these! -->
-
-    <!-- GATK "full" == public + protected, ie., the standard binary release of the GATK  -->
-    <target name="package.gatk.full" depends="init.executable.gatkfull,package" description="Create a standalone GATK jar with public and protected code" />
-
-    <!-- GATK "all" == public + protected + private. Should never be publicly released -->
-    <target name="package.gatk.all" depends="init.executable.gatkall,package" description="Create a standalone GATK jar with public, protected, and private code" />
-
-    <target name="package.queue.full" depends="init.executable.queuefull,package" description="Create a standalone Queue jar with public and protected code" />
-
-    <target name="package.queue.all" depends="init.executable.queueall,package" description="Create a standalone Queue jar with public, protected, and private code" />
-
-    <!-- Release a build. Don't call this target directly. Call one of the specific release targets below -->
-    <target name="release" depends="require.executable">
-        <ant antfile="${package.output.dir}/${executable}.xml" target="release" />
-    </target>
-
-    <!-- Release specific versions of the GATK/Queue. ALWAYS do an ant clean before invoking these! -->
-    <target name="release.gatk.full" depends="package.gatk.full,release" />
-
-    <target name="release.queue.full" depends="package.queue.full,release" />
-
-    <!-- Build a subset of picard with only those classes we need by completely abusing the packaging system -->
-    <!-- TODO: Reuse as much as possible of the 'stage' and 'package' targets -->
-    <target name="build-picard-private" depends="resolve">
-      <!-- Build out a classpath -->
-      <pathconvert property="required.picard.jars" pathsep=":">
-        <fileset dir="${basedir}">
-	     <include name="${staging.dir}" />
-	     <include name="${lib.dir}/picard-*.*.*.jar" />
-	     <include name="${lib.dir}/sam-*.jar" />
-	   </fileset>
-      </pathconvert>
-      <echo message="required.picard.jars=${required.picard.jars}" />
-
-      <!-- Stage picard-private -->
-      <delete dir="${staging.dir}" />
-      <mkdir dir="${staging.dir}" />
-      <unjar src="${picard.dist.dir}/picard-private.jar" dest="${staging.dir}" overwrite="true" />
-
-      <!-- Use the packaging system to extract parts of picard-private we need -->
-      <mkdir dir="${package.output.dir}" />
-      <xslt in="${package.xml.dir}/PicardPrivate.xml" out="${package.output.dir}/BuildPicardPrivate.xml" style="${package.xml.dir}/CreatePackager.xsl" />
-      <ant antfile="${package.output.dir}/BuildPicardPrivate.xml">
-	    <property name="additional.jars" value="${required.picard.jars}" />
-      </ant>
-    </target>
-
-    <!-- Maven install a package consisting of all supporting files. Don't call this target directly. Call one of the specific packaging targets below -->
-    <target name="mvninstall" depends="package">
-        <property name="mvn.build.version" value="0.0.2" />
-        <!--
-        We should use the build version or better yet a git tag version, but tags are currently missing. Alternatively how do we then depend on the LATEST?
-        <property name="mvn.build.version" value="${build.version}" />
-        -->
-        <artifact:pom id="${executable}.pom" groupId="org.broadinstitute.sting" artifactId="${executable}" version="${mvn.build.version}" name="${executable}" />
-        <artifact:writepom pomRefId="${executable}.pom" file="${package.output.dir}/${executable}-${build.version}/${executable}.pom.xml"/>
-        <artifact:install file="${package.output.dir}/${executable}-${build.version}/${executable}.jar">
-            <artifact:pom file="${package.output.dir}/${executable}-${build.version}/${executable}.pom.xml" />
-        </artifact:install>
-    </target>
-
-    <!-- Maven install specific versions of the GATK/Queue. ALWAYS do an ant clean before invoking these! -->
-    <target name="mvninstall.gatk.full" depends="package.gatk.full,mvninstall" />
-
-    <target name="mvninstall.queue.all" depends="package.queue.all,mvninstall" />
-
-    <target name="mvninstall.queue.full" depends="package.queue.full,mvninstall" />
-
-    <!-- ******************************************************************************** -->
-    <!-- Clean                                                                            -->
-    <!-- ******************************************************************************** -->
-
-    <target name="clean.gatkdocs">
-        <delete dir="${gatkdocs.dir}"/>
-    </target>
-
-    <target name="clean.javadoc">
-        <delete dir="${javadoc.dir}" />
-    </target>
-
-    <target name="clean.scaladoc">
-        <delete dir="${scaladoc.dir}" />
-    </target>
-
-    <target name="-check.clover">
-      <available property="clover.installed" classname="com.cenqua.clover.CloverInstr" />
-    </target>
-
-    <target name="clean.clover" depends="-check.clover" if="clover.installed">
-      <clover-clean/>
-    </target>
-
-    <target name="clean.gsalib">
-        <!-- Currently not cleaning out the lib during 'ant clean' -->
-      <exec executable="R" failonerror="false">
-        <arg line="R CMD REMOVE gsalib" />
-      </exec>
-    </target>
-
-    <target name="clean" description="Clean up old build-related directories" depends="clean.javadoc,clean.scaladoc,clean.gatkdocs,clean.clover">
-        <delete dir="${build.dir}"/>
-        <delete dir="${lib.dir}"/>
-        <delete dir="${contract.dump.dir}"/>
-        <delete dir="${staging.dir}"/>
-        <delete dir="${dist.dir}"/>
-        <delete dir="${pipelinetest.dir}"/>
-        <delete dir="${integration.tests.dir}"/>
-    </target>
-
-    <!-- Depend on this target if your target requires a clean working directory but you don't want to depend on clean directly -->
-    <target name="require.clean">
-        <condition property="not.clean">
-            <or>
-                <available file="${build.dir}" />
-                <available file="${lib.dir}" />
-                <available file="${contract.dump.dir}" />
-                <available file="${staging.dir}" />
-                <available file="${dist.dir}" />
-                <available file="${pipelinetest.dir}" />
-                <available file="${integration.tests.dir}" />
-                <available file="${javadoc.dir}" />
-                <available file="${scaladoc.dir}" />
-                <available file="${gatkdocs.dir}" />
-            </or>
-        </condition>
-        <fail message="Selected build target requires a clean working directory. Run ant clean and then try again." if="not.clean" />
-    </target>
-
-
-    <!-- ******************************************************************************** -->
-    <!-- gsalib                                                                           -->
-    <!-- ******************************************************************************** -->
-
-    <!-- Build gsalib R module -->
-    <target name="gsalib" description="Build the gsalib R module">
-      <exec executable="R" failonerror="true">
-        <arg line="R CMD INSTALL --preclean ${R.public.src.dir}/${R.package.path}/gsalib" />
-      </exec>
-    </target>
-
-
-    <!-- ***************************************************************************** -->
-    <!-- ***********               Tests and associated tasks                ********* -->
-    <!-- ***************************************************************************** -->
-
-    <!-- Properties and Paths -->
-
-    <property name="java.test.classes" value="${build.dir}/java/testclasses"/>
-    <property name="java.public.test.sources" value="${public.dir}/java/test"/>
-    <property name="java.private.test.sources" value="${private.dir}/java/test"/>
-    <property name="java.protected.test.sources" value="${protected.dir}/java/test"/>
-    <property name="scala.test.classes" value="${build.dir}/scala/testclasses"/>
-    <property name="scala.public.test.sources" value="${public.dir}/scala/test"/>
-    <property name="scala.private.test.sources" value="${private.dir}/scala/test"/>
-    <property name="scala.protected.test.sources" value="${protected.dir}/scala/test"/>
-    <property name="integration.tests.dir" value="integrationtests" />
-    <property name="pipelinetest.dir" value="pipelinetests" />
-    <property name="report" value="${build.dir}/report"/>
-    <property name="iwww.report.dir" value="${user.home}/private_html/report"/>
-    <property name="test.output" value="${dist.dir}/test"/>
-    <property name="testng.jar" value="${lib.dir}/testng-6.8.jar"/>
-
-    <path id="java.test.source.path">
-        <dirset dir="${basedir}">
-            <include name="${java.public.test.sources}" />
-            <include name="${java.private.test.sources}" if="include.private" />
-            <include name="${java.protected.test.sources}" if="include.protected" />
-        </dirset>
-    </path>
-
-    <path id="scala.test.source.path">
-        <dirset dir="${basedir}">
-            <include name="${scala.public.test.sources}" />
-            <include name="${scala.private.test.sources}" if="include.private" />
-            <include name="${scala.protected.test.sources}" if="include.protected" />
-        </dirset>
-    </path>
-
-    <path id="testng.dependencies">
-        <fileset dir="${lib.dir}">
-            <include name="jcommander*.jar"/>
-            <include name="guice*.jar"/>
-            <include name="junit*.jar"/>
-            <include name="bsh*.jar"/>
-            <include name="snakeyaml*.jar"/>
-            <include name="reportng*.jar"/>
-        </fileset>
-    </path>
-
-    <path id="testng.default.classpath">
-        <path refid="build.results" />
-        <pathelement path="${clover.jar}"/>
-        <pathelement location="${java.contracts.dir}" />
-        <pathelement location="${java.test.classes}" />
-        <pathelement location="${scala.test.classes}" />
-    </path>
-
-    <!-- Test targets -->
-
-    <target name="clover.report">
-      <clover-report coverageCacheSize="nocache">
-      <current outfile="clover_html" title="GATK clover report" showUniqueCoverage="false" numThreads="4">
-	  <format type="html" filter="catch,static,property"/>
-	  <fileset dir="public">
-	    <patternset id="clover.excludes">
-	      <exclude name="**/*UnitTest.java"/>
-	      <exclude name="**/*TestProvider*.java"/>
-	      <exclude name="**/*PerformanceTest.java"/>
-	      <exclude name="**/*Benchmark.java"/>
-	      <exclude name="**/*LargeScaleTest.java"/>
-	      <exclude name="**/*IntegrationTest.java"/>
-	      <exclude name="**/jna/**/*.java"/>
-	      <exclude name="**/queue/extensions/**/*.java"/>
-	      <exclude name="**/sting/utils/help/*.java"/>
-	      <exclude name="**/sting/tools/*.java"/>
-	      <exclude name="**/datasources/reads/utilities/*.java"/>
-	      <exclude name="**/sting/alignment/**/*.java"/>
-	      <exclude name="**/examples/**/*.java"/>
-	    </patternset>
-	  </fileset>
-	  <fileset dir="private">
-	    <patternset refid="clover.excludes" />
-	  </fileset>
-	  <fileset dir="protected">
-	    <patternset refid="clover.excludes" />
-	  </fileset>
-	</current>
-      </clover-report>
-    </target>
-
-    <target name="with.clover">
-      <clover-setup fullyQualifyJavaLang="true" instrumentationLevel="${clover.instrument.level}">
-      </clover-setup>
-      <property name="compile.scala" value="false" /> <!-- currently doesn't work with scala -->
-      <property name="test.maxmemory" value="32g"/>  <!-- clover requires lots of memory -->
-      <echo message="Clover instrument level: ${clover.instrument.level}" />
-    </target>
-
-    <target name="test.init.compile">
-        <mkdir dir="${java.test.classes}"/>
-        <mkdir dir="${scala.test.classes}"/>
-    </target>
-
-   <target name="test.java.internal.compile" depends="dist,test.init.compile">
-        <echo message="Sting: Compiling java test cases!"/>
-        <javac fork="true" memoryMaximumSize="512m" destdir="${java.test.classes}" debug="true" optimize="on" tempdir="${java.io.tmpdir}">
-            <src refid="java.test.source.path" />
-            <classpath>
-                <path refid="build.results" />
-                <pathelement location="${java.contracts.dir}"/>
-            </classpath>
-            <compilerarg value="-proc:none"/>
-        </javac>
-    </target>
-
-    <target name="test.java.external.compile" depends="dist,test.init.compile,test.java.internal.compile" if="include.external">
-        <echo message="Sting: Compiling external java test cases!"/>
-        <javac fork="true" memoryMaximumSize="512m" destdir="${java.test.classes}" debug="true" optimize="on" tempdir="${java.io.tmpdir}" srcdir="${external.dir}">
-            <include name="*/test/**/*.java"/>
-            <classpath>
-                <path refid="build.results" />
-                <pathelement location="${java.test.classes}"/>
-                <pathelement location="${java.contracts.dir}"/>
-            </classpath>
-            <compilerarg value="-proc:none"/>
-        </javac>
-    </target>
-
-    <target name="test.java.compile" depends="test.java.internal.compile, test.java.external.compile"/>
-
-    <target name="test.scala.compile" depends="test.java.compile,scala.compile" if="include.scala">
-        <echo message="Scala: Compiling test cases!"/>
-        <scalac fork="true" jvmargs="-Xmx512m" destdir="${scala.test.classes}" deprecation="yes" unchecked="yes" addparams="-feature">
-	        <src refid="scala.test.source.path" />
-            <classpath>
-                <path refid="build.results"/>
-                <pathelement location="${java.test.classes}"/>
-            </classpath>
-        </scalac>
-    </target>
-
-    <!-- NOTE: contracts disabled for all tests now, since contracts don't work with Java 7 -->
-    <target name="test.compile" depends="dist,test.java.compile,test.scala.compile" />
-
-
-    <!-- Run test macro -->
-    <macrodef name="run-test">
-        <attribute name="testtype"/>
-        <attribute name="outputdir"/>
-        <attribute name="runfailed"/>
-
-        <sequential>
-            <condition property="run.failed.tests">
-                <equals arg1="@{runfailed}" arg2="true"/>
-            </condition>
-
-            <!-- Get the pipeline run type.  Default to dry.  -->
-            <condition property="pipeline.run" value="dry" else="${pipeline.run}">
-                <equals arg1="${pipeline.run}" arg2="$${pipeline.run}" />
-            </condition>
-
-            <condition property="cofoja.jvm.args" value="-javaagent:${cofoja.jar} -Dcom.google.java.contract.log.contract=false" else="">
-                <isset property="include.contracts" />
-            </condition>
-
-            <condition property="debug.jvm.args" value="-Xdebug -Xrunjdwp:transport=dt_socket,server=y,suspend=y,address=${test.debug.port}" else="">
-                <isset property="test.debug" />
-            </condition>
-
-            <mkdir dir="@{outputdir}"/>
-
-            <echo message="" />
-            <echo message="Test Classpath ID: ${testng.classpath}" />
-            <property name="test.classpath.display.string" refid="${testng.classpath}" />
-            <echo message="Test Classpath: ${test.classpath.display.string}" />
-            <echo message="" />
-            <echo message="Sting: Running @{testtype} test cases!"/>
-            <echo message="Test Memory : ${test.maxmemory}" />
-
-	    <!-- no test is allowed to run for more than 10 hours -->
-            <taskdef resource="testngtasks" classpath="${testng.jar}"/>
-            <testng outputDir="@{outputdir}"
-                    classpathref="${testng.classpath}"
-                    haltOnFailure="false" failureProperty="test.failure"
-                    verbose="2"
-		            timeout="36000000"
-                    workingDir="${basedir}"
-                    useDefaultListeners="false"
-                    listeners="org.testng.reporters.FailedReporter,org.testng.reporters.JUnitXMLReporter,org.broadinstitute.sting.TestNGTestTransformer,org.broadinstitute.sting.StingTextReporter,org.uncommons.reportng.HTMLReporter">
-                <jvmarg value="-Xmx${test.maxmemory}" />
-                <jvmarg value="-ea" />
-                <jvmarg value="-Dclover.pertest.coverage=diff" />
-                <jvmarg value="-Djava.awt.headless=true" />
-                <jvmarg value="-Dpipeline.run=${pipeline.run}" />
-                <jvmarg value="-Djava.io.tmpdir=${java.io.tmpdir}" />
-                <jvmarg line="${cofoja.jvm.args}"/>
-                <jvmarg line="${debug.jvm.args}"/>
-
-                <!-- NOTE: To run tests with debugging, use -Dtest.debug=true -Dtest.debug.port=XXXX on the command line -->
-
-                <classfileset dir="${java.test.classes}" includes="**/@{testtype}.class"/>
-                <classfileset dir="${java.external.test.classes}" erroronmissingdir="false">
-                    <include name="**/@{testtype}.class" if="include.external"/>
-                </classfileset>
-                <classfileset dir="${scala.test.classes}" erroronmissingdir="false">
-                    <include name="**/@{testtype}*.class" if="include.scala"/>
-                </classfileset>
-
-                <xmlfileset dir="${basedir}">
-                    <include name="@{testtype}" if="run.failed.tests"/>
-                </xmlfileset>
-            </testng>
-
-            <!-- generate a report for Bamboo or Hudson to read in -->
-            <junitreport todir="@{outputdir}">
-                <fileset dir="@{outputdir}">
-                    <include name="*/*.xml"/>
-                </fileset>
-                <report format="noframes" todir="@{outputdir}"/>
-            </junitreport>
-
-	    <!-- copy the report to our private_html directory for easy viewing in a broswer -->
-            <mkdir dir="${iwww.report.dir}/@{testtype}"/>
-            <copy todir="${iwww.report.dir}/@{testtype}" verbose="false">
-              <fileset dir="@{outputdir}"/>
-            </copy>
-
-            <fail message="test failed" if="test.failure" />
-        </sequential>
-    </macrodef>
-
-
-    <target name="test.init">
-        <property name="testng.classpath" value="testng.default.classpath" />
-        <property name="test.maxmemory" value="${test.default.maxmemory}"/>
-    </target>
-
-    <target name="init.testgatkjar">
-        <path id="gatk.binary.release.tests.classpath">
-            <path refid="testng.dependencies" />
-            <path>
-                <fileset dir="${package.output.dir}">
-                    <include name="**/${executable}.jar" />
-                </fileset>
-            </path>
-            <pathelement location="${java.contracts.dir}" />
-            <pathelement location="${java.test.classes}" />
-            <pathelement location="${scala.test.classes}" />
-            <pathelement location="${scala.classes}" />
-            <path>
-                <fileset dir="${lib.dir}">
-                    <include name="scala*.jar"/>
-                    <include name="jna*.jar"/>
-                    <include name="cofoja*.jar"/>
-                </fileset>
-            </path>
-        </path>
-        <property name="testng.classpath" value="gatk.binary.release.tests.classpath" />
-    </target>
-
-    <target name="init.testqueuejar">
-        <path id="queue.binary.release.tests.classpath">
-            <path refid="testng.dependencies" />
-            <path>
-                <fileset dir="${package.output.dir}">
-                    <include name="**/${executable}.jar" />
-                </fileset>
-            </path>
-            <pathelement location="${java.contracts.dir}" />
-            <pathelement location="${java.test.classes}" />
-            <pathelement location="${scala.test.classes}" />
-            <path>
-                <fileset dir="${lib.dir}">
-                    <include name="cofoja*.jar"/>
-                </fileset>
-            </path>
-        </path>
-        <property name="testng.classpath" value="queue.binary.release.tests.classpath" />
-    </target>
-
-
-    <target name="committests" depends="unittest,integrationtest,pipelinetest" description="Run unit tests, integration tests, and do a dry-run of the pipeline tests" />
-
-    <!-- Order of the dependencies is significant in the *.release.tests targets -->
-    <target name="gatkfull.binary.release.tests" depends="package.gatk.full,init.testgatkjar,unittest,integrationtest" />
-
-    <target name="queuefull.binary.release.tests" depends="package.queue.full,init.testqueuejar,pipelinetest" />
-
-    <!-- Our four different test types: UnitTest, IntegrationTest, LargeScaleTest, PipelineTest -->
-    <target name="unittest" depends="test.compile,test.init" description="Run unit tests">
-        <condition property="ttype" value="*UnitTest" else="${single}">
-            <not><isset property="single"/></not>
-        </condition>
-        <run-test testtype="${ttype}" outputdir="${report}/${ttype}" runfailed="false"/>
-    </target>
-
-    <!-- Keep the alias "test" for "unittest" for backwards compatibility -->
-    <target name="test" depends="unittest" />
-
-    <target name="integrationtest" depends="test.compile,test.init" description="Run integration tests">
-        <condition property="itype" value="*IntegrationTest" else="${single}">
-            <not><isset property="single"/></not>
-        </condition>
-        <run-test testtype="${itype}" outputdir="${report}/${itype}" runfailed="false"/>
-    </target>
-
-    <target name="largescaletest" depends="test.compile,test.init" description="Run large-scale tests">
-       <condition property="ptype" value="*LargeScaleTest" else="${single}">
-            <not><isset property="single"/></not>
-        </condition>
-        <run-test testtype="${ptype}" outputdir="${report}/${ptype}" runfailed="false"/>
-    </target>
-
-    <target name="pipelinetest" depends="test.compile,test.init" description="Dry-run pipeline tests">
-        <condition property="pipetype" value="*PipelineTest" else="${single}">
-            <not><isset property="single"/></not>
-        </condition>
-        <run-test testtype="${pipetype}" outputdir="${report}/${pipetype}" runfailed="false"/>
-    </target>
-
-    <target name="pipelinetestrun" depends="test.compile,test.init" description="Run pipeline tests">
-        <property name="pipeline.run" value="run"/>
-        <condition property="pipetype" value="*PipelineTest" else="${single}">
-            <not><isset property="single"/></not>
-        </condition>
-        <run-test testtype="${pipetype}" outputdir="${report}/${pipetype}" runfailed="false"/>
-    </target>
-
-    <target name="knowledgebasetest" depends="test.compile,test.init" description="Run knowledge base tests">
-        <condition property="ktype" value="*KnowledgeBaseTest" else="${single}">
-            <not><isset property="single"/></not>
-        </condition>
-        <run-test testtype="${ktype}" outputdir="${report}/${ktype}" runfailed="false"/>
-    </target>
-
-    <target name="failed-unit" depends="test.compile,test.init">
-        <run-test testtype="${report}/*UnitTest/testng-failed.xml" outputdir="${report}/failed_rerun" runfailed="true"/>
-    </target>
-
-    <target name="failed-integration" depends="test.compile,test.init">
-        <run-test testtype="${report}/*IntegrationTest/testng-failed.xml" outputdir="${report}/failed_rerun" runfailed="true"/>
-    </target>
-
-    <target name="failed-largescale" depends="test.compile,test.init">
-        <run-test testtype="${report}/*LargeScaleTest/testng-failed.xml" outputdir="${report}/failed_rerun" runfailed="true"/>
-    </target>
-
-    <target name="failed-pipeline" depends="test.compile,test.init">
-        <run-test testtype="${report}/*PipelineTest/testng-failed.xml" outputdir="${report}/failed_rerun" runfailed="true"/>
-    </target>
-
-
-    <!-- Fast test target that cuts major corners for speed. Requires that a full build has been done first. Java-only, single test class only -->
-    <!-- Usage: ant fasttest -Dsingle=TestClass -->
-    <target name="fasttest" depends="init.javaonly,init" description="Quickly run a single test">
-	<property name="test.maxmemory" value="${test.default.maxmemory}"/>
-        <condition property="not.clean">
-            <and>
-                <available file="${build.dir}" />
-                <available file="${lib.dir}" />
-                <available file="${dist.dir}" />
-                <available file="${java.test.classes}" />
-            </and>
-        </condition>
-        <fail message="fasttest requires a NON-CLEAN working directory (INCLUDING test classes). Do a full test build using ant test.compile first." unless="not.clean" />
-
-        <condition property="no.single.test.specified">
-            <equals arg1="${single}" arg2="$${single}" />
-        </condition>
-        <fail message="Must specify a specific test. Usage: ant fasttest -Dsingle=TestClass" if="no.single.test.specified" />
-
-        <javac fork="true" memoryMaximumSize="512m" destdir="${java.classes}" debug="true" debuglevel="lines,vars,source" classpathref="external.dependencies" tempdir="${java.io.tmpdir}">
-            <src refid="java.source.path" />
-            <compilerarg value="-proc:none" />
-        </javac>
-
-        <javac fork="true" memoryMaximumSize="512m" destdir="${java.test.classes}" debug="true" optimize="on" tempdir="${java.io.tmpdir}">
-            <src refid="java.test.source.path" />
-            <classpath>
-                <pathelement location="${java.classes}"/>
-                <path refid="external.dependencies" />
-            </classpath>
-            <compilerarg value="-proc:none"/>
-        </javac>
-
-        <!-- fasttest uses the unpackaged class files in its test classpath to avoid having to rebuild the jars in dist/ -->
-        <path id="testng.fasttest.classpath">
-            <pathelement location="${java.classes}" />
-            <pathelement location="${scala.classes}" />
-            <pathelement location="${java.contracts.dir}" />
-            <pathelement location="${java.test.classes}" />
-            <pathelement location="${scala.test.classes}" />
-            <pathelement location="${R.tar.dir}" />
-            <path refid="R.script.source.path" />
-            <pathelement location="${key.dir}" />
-            <path refid="external.dependencies" />
-            <path refid="java.source.path" />  <!-- Terrible hack to allow fasttest to see resource files stored in the source tree -->
-        </path>
-        <property name="testng.classpath" value="testng.fasttest.classpath" />
-
-        <run-test testtype="${single}" outputdir="${report}/${single}" runfailed="false"/>
-    </target>
-
-    <!-- A target that runs a test without doing ANY compilation or any extra work at all -->
-    <!-- Intended to enable parallel tests that share the same working directory and build -->
-    <target name="runtestonly">
-        <condition property="not.clean">
-            <and>
-                <available file="${build.dir}" />
-                <available file="${lib.dir}" />
-                <available file="${dist.dir}" />
-                <available file="${java.test.classes}" />
-            </and>
-        </condition>
-        <fail message="runtestonly target requires a NON-CLEAN working directory (INCLUDING test classes). Do a full test build using ant test.compile first." unless="not.clean" />
-
-        <condition property="no.single.test.specified">
-            <equals arg1="${single}" arg2="$${single}" />
-        </condition>
-        <fail message="Must specify a specific test. Usage: ant runtestonly -Dsingle=TestClass" if="no.single.test.specified" />
-
-        <property name="testng.classpath" value="testng.default.classpath" />
-        <property name="test.maxmemory" value="${test.default.maxmemory}"/>
-        <property name="include.scala" value="true" />
-
-        <run-test testtype="${single}" outputdir="${report}/${single}" runfailed="false"/>
-    </target>
-
-</project>
diff --git a/ivy.xml b/ivy.xml
deleted file mode 100644
index 2e45247ab..000000000
--- a/ivy.xml
+++ /dev/null
@@ -1,117 +0,0 @@
-<!--
-  ~ Copyright (c) 2012, The Broad Institute
-  ~
-  ~ Permission is hereby granted, free of charge, to any person
-  ~ obtaining a copy of this software and associated documentation
-  ~ files (the "Software"), to deal in the Software without
-  ~ restriction, including without limitation the rights to use,
-  ~ copy, modify, merge, publish, distribute, sublicense, and/or sell
-  ~ copies of the Software, and to permit persons to whom the
-  ~ Software is furnished to do so, subject to the following
-  ~ conditions:
-  ~
-  ~ The above copyright notice and this permission notice shall be
-  ~ included in all copies or substantial portions of the Software.
-  ~ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
-  ~ EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
-  ~ OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
-  ~ NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
-  ~ HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
-  ~ WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
-  ~ FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
-  ~ OTHER DEALINGS IN THE SOFTWARE.
-  -->
-
-<ivy-module version="1.0">
-    <info organisation="org.broadinstitute" module="Sting"/>
-    <configurations>
-        <conf name="default" description="the core dependencies for the GATK"/>
-    </configurations>
-    <dependencies defaultconf="default">
-        <dependency org="net.sf" name="sam" rev="latest.integration"/>
-        <dependency org="net.sf" name="picard" rev="latest.integration"/>
-        <dependency org="edu.mit.broad" name="picard-private-parts" rev="latest.integration"/>
-
-        <!-- Tribble -->
-        <dependency org="org.broad" name="tribble" rev="latest.integration"/>
-
-        <!-- Variant -->
-        <dependency org="org.broadinstitute" name="variant" rev="latest.integration"/>
-
-        <dependency org="log4j" name="log4j" rev="1.2.15"/>
-        <dependency org="javax.mail" name="mail" rev="1.4.4"/>
-        <dependency org="colt" name="colt" rev="1.2.0"/>
-        <dependency org="it.unimi.dsi" name="fastutil" rev="6.5.3" />
-
-        <!-- <dependency org="jboss" name="javassist" rev="3.7.ga"/> -->
-        <dependency org="org.simpleframework" name="simple-xml" rev="2.0.4"/>
-        <dependency org="org.apache.bcel" name="bcel" rev="5.2"/>
-
-        <!-- Dependencies for reflections mvn repository -->
-        <dependency org="org.reflections" name="reflections" rev="0.9.8"/>
-        <dependency org="org.slf4j" name="slf4j-log4j12" rev="1.6.1"/>
-
-        <!-- Matrix package from math.nist.gov -->
-        <dependency org="gov.nist" name="Jama" rev="1.0.2"/>
-
-        <!-- Dependencies for the graph aligner -->
-        <dependency org="net.sf.jgrapht" name="jgrapht" rev="0.8.3"/>
-
-        <!-- Dependencies for the html walker documention -->
-        <dependency org="org.freemarker" name="freemarker" rev="2.3.18"/>
-
-        <!-- Commons Dependencies -->
-        <dependency org="org.apache.commons" name="commons-email" rev="1.2"/>
-        <dependency org="org.apache.commons" name="commons-jexl" rev="2.1.1"/>
-        <dependency org="commons-lang" name="commons-lang" rev="2.5"/>
-        <dependency org="commons-logging" name="commons-logging" rev="1.1.1"/>
-        <dependency org="commons-io" name="commons-io" rev="2.1"/>
-        <dependency org="commons-collections" name="commons-collections" rev="3.2.1"/>
-        <dependency org="org.apache.commons" name="commons-math" rev="2.2"/>
-
-        <!-- Lucene core utilities -->
-        <!-- <dependency org="org.apache.lucene" name="lucene-core" rev="3.0.3"/> -->
-
-        <!-- Dependencies for LSF, DRMAA, and other C libraries -->
-        <dependency org="net.java.dev.jna" name="jna" rev="3.2.7"/>
-
-        <!-- Dependencies for amazon.com S3 support -->
-        <dependency org="net.java.dev.jets3t" name="jets3t" rev="0.8.1"/>
-
-        <!-- Dependencies for GridEngine -->
-        <dependency org="net.sf.gridscheduler" name="drmaa" rev="latest.integration"/>
-
-        <!-- Scala dependancies -->
-        <dependency org="org.scala-lang" name="scala-compiler" rev="2.10.2"/>
-        <dependency org="org.scala-lang" name="scala-library" rev="2.10.2"/>
-
-        <!-- testing and evaluation dependencies -->
-        <dependency org="org.testng" name="testng" rev="6.8"/>
-        <dependency org="org.uncommons" name="reportng" rev="1.1.2"/>
-        <dependency org="com.google.caliper" name="caliper" rev="0.5-rc1"/>
-		<dependency org="com.google.inject" name="guice" rev="3.0"/>
-
-        <!-- Contracts for Java and dependencies -->
-        <dependency org="com.google.code.cofoja" name="cofoja" rev="1.0-r139"/>
-        <dependency org="asm" name="asm-all" rev="3.3.1"/>
-
-        <!-- POI, for reading pipeline files -->
-        <dependency org="org.apache.poi" name="poi" rev="3.8-beta3"/>
-        <dependency org="org.apache.poi" name="poi-ooxml" rev="3.8-beta3"/>
-
-        <!-- snpEff annotator for pipelines -->
-        <dependency org="net.sf.snpeff" name="snpeff" rev="2.0.5"/>
-
-        <!-- MongoDB for the GXDB project -->
-        <dependency org="org.mongodb" name="mongo-java-driver" rev="2.7.3"/>
-
-        <!-- GSON and HTTP for talking to the REST API on Vanilla Forums -->
-        <dependency org="com.google.code.gson" name="gson" rev="2.2.2"/>
-        <dependency org="org.apache.httpcomponents" name="httpclient" rev="4.1.1"/>
-
-        <!-- Exclude dependencies on sun libraries where the downloads aren't available but included in the jvm. -->
-        <exclude org="javax.servlet"/>
-        <exclude org="javax.jms"/>
-        <exclude org="com.sun.*"/>
-    </dependencies>
-</ivy-module>
diff --git a/public/packages/Aligner.xml b/public/packages/Aligner.xml
deleted file mode 100644
index 031dfacfd..000000000
--- a/public/packages/Aligner.xml
+++ /dev/null
@@ -1,9 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<package name="Aligner">
-  <executable name="Aligner">
-    <dependencies>
-      <!-- BWA/C aligner implementation -->
-      <class name="org.broadinstitute.sting.alignment.bwa.c.BWACAligner" />
-    </dependencies>
-  </executable>
-</package>
diff --git a/public/packages/CreatePackager.xsl b/public/packages/CreatePackager.xsl
deleted file mode 100644
index a89b6bb35..000000000
--- a/public/packages/CreatePackager.xsl
+++ /dev/null
@@ -1,220 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<xsl:stylesheet version="1.0" xmlns:xsl="http://www.w3.org/1999/XSL/Transform">
-
-  <xsl:variable name="ant.basedir" select="'${basedir}'" />
-  <xsl:variable name="sting.dir" select="'${sting.dir}/'" />
-  <xsl:variable name="classpath" select="'${sting.dir}/staging:${additional.jars}'" />
-  <xsl:variable name="dist.dir" select="'${sting.dir}/dist'" />
-  <xsl:variable name="staging.dir" select="'${sting.dir}/staging'" />
-  <xsl:variable name="package.basename" select="'${package.basename}'" />
-  <xsl:variable name="package.dir" select="'${package.dir}'" />
-  <xsl:variable name="package.filename" select="'${package.filename}'" />
-  <xsl:variable name="resources.dir" select="'${package.dir}/resources'" />
-  
-<xsl:template match="package">
-  <xsl:output method="xml" indent="yes"/>
-
-  <project name="{@name}" default="package">
-
-    <property name="sting.dir" value="{$ant.basedir}" />
-    <!-- Read version information out of the xml file -->
-    <xsl:choose>
-      <xsl:when test="version/@property">
-	<xsl:variable name="version.property" select="concat('${',version/@property,'}')" />
-	<property file="{$staging.dir}/{version/@file}" />
-	<property name="package.basename" value="{concat(@name,'-',$version.property)}" />
-      </xsl:when>
-      <xsl:otherwise>
-	<property name="package.basename" value="{@name}" />
-      </xsl:otherwise>
-    </xsl:choose>
-    <property name="package.dir" value="{concat($dist.dir,'/packages/',$package.basename)}" />
-    <property name="package.filename" value="{concat($package.basename,'.tar.bz2')}" />
-
-    <target name="package">
-      <!-- Verify that all classes specified are present -->
-      <xsl:for-each select="//class">
-	<available property="is.{@name}.present" classpath="{$classpath}" classname="{@name}"/>
-	<fail message="Class {@name} not found" unless="is.{@name}.present" />
-      </xsl:for-each>
-      <xsl:for-each select="//resource-bundle">
-	<available property="is.{@file}.present" file="{$staging.dir}/{@file}"/>
-	<fail message="Resource bundle {@file} not found" unless="is.{@file}.present" />
-      </xsl:for-each>
-
-      <!-- Verify that all files specified are present -->
-      <xsl:for-each select="//dependencies/file">
-        <xsl:choose>
-          <xsl:when test="@name">
-            <available property="is.{@name}.present" file="{$staging.dir}/{@name}" type="file"/>
-            <fail message="File dependency {@name} not found" unless="is.{@name}.present" />
-          </xsl:when>
-          <xsl:when test="@path">
-            <available property="is.{@path}.present" file="{$staging.dir}/{@path}" type="file"/>
-            <fail message="File dependency {@path} not found" unless="is.{@path}.present" />
-          </xsl:when>
-          <xsl:otherwise>
-            <fail message="File dependency must specify a name or a path"/>
-          </xsl:otherwise>
-        </xsl:choose>
-      </xsl:for-each>
-      <xsl:for-each select="//dependencies/dir">
-        <available property="is.{@name}.present" file="{$staging.dir}/{@name}" type="dir"/>
-        <fail message="Directory {@name} not found" unless="is.{@name}.present" />
-      </xsl:for-each>
-
-      <!-- Create an output directory for the package -->
-      <mkdir dir="{$package.dir}"/>
-
-      <!-- Create the executable sections -->
-      <xsl:apply-templates select="executable" />
-
-      <!-- Add in other modules -->
-      <xsl:for-each select="modules/module">
-	<xsl:apply-templates select="document(@file)/package/executable" />
-      </xsl:for-each>
-
-      <!-- Include various resource files explicitly specified in this file and in all other modules -->
-      <xsl:apply-templates select="resources" />
-      <xsl:for-each select="//modules/module">
-	<xsl:apply-templates select="document(@file)/package/resources" />
-      </xsl:for-each>
-
-      <!-- Bundle the package into a single zip file -->
-      <tar destfile="{$dist.dir}/packages/{$package.filename}" compression="bzip2">
-        <fileset dir="{$dist.dir}/packages" includes="{$package.basename}/**"/>
-      </tar>
-    </target>
-
-    <target name="release">
-      <xsl:for-each select="release/executable">
-	<copy todir="{@directory}/{$package.basename}"><fileset dir="{$package.dir}" /></copy>
-	<xsl:if test="@symlink">
-	  <symlink link="{@directory}/{@symlink}" resource="{$package.basename}" overwrite="true" />	
-	</xsl:if>
-      </xsl:for-each>
-      <xsl:for-each select="release/archive">
-	<copy file="{$dist.dir}/packages/{$package.filename}" todir="{@directory}" />
-	<xsl:if test="@symlink">
-	  <symlink link="{@directory}/{@symlink}" resource="{$package.filename}" overwrite="true" />	
-	</xsl:if>
-      </xsl:for-each>
-    </target>
-  </project>
-</xsl:template>
-
-<!-- Create a symlink for the given file in the given target directory -->
-<xsl:template name="symlink">
-  <xsl:param name="file.name" />
-  <xsl:param name="target.dir" />
-  <xsl:variable name="short.name">
-    <xsl:call-template name="get-short-name">
-      <xsl:with-param name="string" select="$file.name" />
-    </xsl:call-template>
-  </xsl:variable>
-  <xsl:variable name="full.path">
-    <xsl:call-template name="get-full-path">
-      <xsl:with-param name="working-dir" select="$sting.dir"/>
-      <xsl:with-param name="file" select="$file.name" />
-    </xsl:call-template>
-  </xsl:variable>
-  <available property="is.{$short.name}.present" file="{$file.name}"/>
-  <fail message="File {$file.name} not found" unless="is.{$short.name}.present" />
-  <delete file="{$target.dir}/{$short.name}" />
-  <symlink link="{$target.dir}/{$short.name}" resource="{$full.path}" overwrite="true" />
-</xsl:template>
-
-<!-- Transform an executable tag into an ant 'jar' task with nested fileset -->
-<xsl:template match="executable">
-  <!-- Create a jar file containing the specified classes / packages and all their dependencies -->
-  <jar jarfile="{$package.dir}/{@name}.jar">
-    <classfileset dir="{$staging.dir}">
-      <root classname="{main-class/@name}"/>
-    </classfileset>
-    <xsl:for-each select="resource-bundle">
-      <fileset file="{$staging.dir}/{@file}" />
-    </xsl:for-each>
-    <xsl:for-each select="modules/module">
-      <xsl:apply-templates select="document(@file)/package/executable/dependencies" />
-    </xsl:for-each>
-    <xsl:apply-templates select="dependencies" />
-    <manifest>
-      <attribute name="Main-Class" value="{main-class/@name}"/>
-    </manifest>
-  </jar>
-</xsl:template>
-
-<!-- Transform a resource file into a symlink operation -->
-<xsl:template match="resources">
-  <xsl:for-each select="file">
-    <mkdir dir="{$resources.dir}"/>
-    <xsl:call-template name="symlink">
-      <xsl:with-param name="file.name" select="@name" />
-      <xsl:with-param name="target.dir" select="$resources.dir" />
-    </xsl:call-template>
-  </xsl:for-each>
-</xsl:template>
-
-<!-- Transform a dependency list into a fileset for embedding in a jar -->
-<xsl:template match="dependencies">
-  <classfileset dir="{$staging.dir}">
-    <xsl:for-each select="package">
-      <rootfileset dir="{$staging.dir}" includes="{concat(translate(@name,'.','/'),'/','*.class')}" />
-    </xsl:for-each>
-    <xsl:for-each select="class">
-      <root classname="{@name}" />
-    </xsl:for-each>
-  </classfileset>
-  <xsl:for-each select="file">
-    <xsl:choose>
-      <xsl:when test="@name">
-        <fileset file="{$staging.dir}/{@name}" />
-      </xsl:when>
-      <xsl:when test="@path">
-        <fileset dir="{$staging.dir}">
-          <xsl:attribute name="includes">
-            <xsl:value-of select="@path"/>
-          </xsl:attribute>
-        </fileset>
-      </xsl:when>
-    </xsl:choose>
-  </xsl:for-each>
-  <xsl:for-each select="dir">
-    <xsl:variable name="includes">
-      <xsl:choose>
-        <xsl:when test="@includes = ''">
-          <xsl:value-of select="concat(@name,'/**')"/>
-        </xsl:when>
-        <xsl:otherwise>
-          <xsl:value-of select="concat(@name,'/',@includes)"/>
-        </xsl:otherwise>
-      </xsl:choose>
-    </xsl:variable>
-    <fileset dir="{$staging.dir}" includes="{$includes}"/>
-  </xsl:for-each>
-</xsl:template>
-
-<!-- Determine the short name (filename w/o directory structure of the given filename -->
-<xsl:template name="get-short-name">
-  <xsl:param name="string"/>
-  <xsl:choose>
-    <xsl:when test="contains($string,'/')">
-      <xsl:call-template name="get-short-name">
-        <xsl:with-param name="string" select="substring-after($string,'/')" />
-      </xsl:call-template>
-    </xsl:when>
-    <xsl:otherwise><xsl:value-of select="$string"/></xsl:otherwise>
-  </xsl:choose>    
-</xsl:template>
-
-<!-- Determine the full path of the given filename.  Take into account absolute / relative paths -->
-<xsl:template name="get-full-path">
-  <xsl:param name="working-dir"/>
-  <xsl:param name="file"/>
-  <xsl:choose>
-    <xsl:when test="starts-with($file,'/')"><xsl:value-of select="$file"/></xsl:when>
-    <xsl:otherwise><xsl:value-of select="concat($working-dir,$file)"/></xsl:otherwise>
-  </xsl:choose>
-</xsl:template>
-
-</xsl:stylesheet>
diff --git a/public/packages/GATKEngine.xml b/public/packages/GATKEngine.xml
deleted file mode 100644
index 08d2e1c2c..000000000
--- a/public/packages/GATKEngine.xml
+++ /dev/null
@@ -1,62 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!--
-  ~ Copyright (c) 2011, The Broad Institute
-  ~
-  ~ Permission is hereby granted, free of charge, to any person
-  ~ obtaining a copy of this software and associated documentation
-  ~ files (the "Software"), to deal in the Software without
-  ~ restriction, including without limitation the rights to use,
-  ~ copy, modify, merge, publish, distribute, sublicense, and/or sell
-  ~ copies of the Software, and to permit persons to whom the
-  ~ Software is furnished to do so, subject to the following
-  ~ conditions:
-  ~
-  ~ The above copyright notice and this permission notice shall be
-  ~ included in all copies or substantial portions of the Software.
-  ~ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
-  ~ EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
-  ~ OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
-  ~ NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
-  ~ HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
-  ~ WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
-  ~ FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
-  ~ OTHER DEALINGS IN THE SOFTWARE.
-  -->
-
-<package name="GATKEngine">
-  <executable name="GATKEngine">
-    <dependencies>
-      <!-- Package everything in org.broadinstitute.sting -->
-      <package name="org.broadinstitute.sting.**" />
-      <!-- Tribble codecs -->
-      <package name="org.broad.tribble.**" />
-      <!-- The variant package (VCF, BCF, and VariantContext) -->
-      <package name="org.broadinstitute.variant.**" />
-      <!-- Workaround - depend on the logger impl required by JEXL -->
-      <package name="org.apache.commons.logging.impl" />
-      <!-- R packages -->
-      <dir name="org/broadinstitute/sting/utils/R" includes="**/*.tar.gz" />
-      <!-- All R scripts in org.broadinstitute.sting -->
-      <dir name="org/broadinstitute/sting" includes="**/*.R" />
-      <!-- Resources in org.broadinstitute.sting -->
-      <dir name="org/broadinstitute/sting" includes="**/resources/*" />
-      <dir name="org/broadinstitute/sting" includes="**/templates/*" />
-      <!-- The GATK public key -->
-      <file path="GATK_public.key" />
-    </dependencies>
-  </executable>
-  <resources>
-    <!-- Sample reads and reference files -->
-    <file name="public/testdata/exampleBAM.bam" />
-    <file name="public/testdata/exampleBAM.bam.bai" />
-    <file name="public/testdata/exampleFASTA.fasta" />
-    <file name="public/testdata/exampleFASTA.fasta.fai" />
-    <file name="public/testdata/exampleFASTA.dict" />
-    <!-- GATK sample code and build scripts -->
-    <file name="public/java/src/org/broadinstitute/sting/gatk/walkers/qc/Pileup.java" />
-    <file name="public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountLoci.java" />
-    <file name="public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountReads.java" />
-    <file name="public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CheckPileup.java" />
-    <file name="public/java/src/org/broadinstitute/sting/gatk/walkers/readutils/PrintReads.java" />
-  </resources>
-</package>
diff --git a/public/packages/GenomeAnalysisTK.xml b/public/packages/GenomeAnalysisTK.xml
deleted file mode 100644
index e95c992b6..000000000
--- a/public/packages/GenomeAnalysisTK.xml
+++ /dev/null
@@ -1,40 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!--
-  ~ Copyright (c) 2012, The Broad Institute
-  ~
-  ~ Permission is hereby granted, free of charge, to any person
-  ~ obtaining a copy of this software and associated documentation
-  ~ files (the "Software"), to deal in the Software without
-  ~ restriction, including without limitation the rights to use,
-  ~ copy, modify, merge, publish, distribute, sublicense, and/or sell
-  ~ copies of the Software, and to permit persons to whom the
-  ~ Software is furnished to do so, subject to the following
-  ~ conditions:
-  ~
-  ~ The above copyright notice and this permission notice shall be
-  ~ included in all copies or substantial portions of the Software.
-  ~ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
-  ~ EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
-  ~ OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
-  ~ NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
-  ~ HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
-  ~ WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
-  ~ FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
-  ~ OTHER DEALINGS IN THE SOFTWARE.
-  -->
-
-<!-- The full release of the GATK contains both public and protected tools (but nothing from private) -->
-<package name="GenomeAnalysisTK">
-  <version file="StingText.properties" property="org.broadinstitute.sting.gatk.version" />
-  <executable name="GenomeAnalysisTK">
-    <main-class name="org.broadinstitute.sting.gatk.CommandLineGATK" />
-    <resource-bundle file="StingText.properties" />
-    <modules>
-      <module file="GATKEngine.xml"/>
-    </modules>
-  </executable>
-  <release>
-    <executable directory="/humgen/gsa-hpprojects/GATK/bin" symlink="current" />
-    <archive directory="/humgen/gsa-hpprojects/GATK/bin" symlink="GenomeAnalysisTK-latest.tar.bz2" />
-  </release>
-</package>
diff --git a/public/packages/PicardPrivate.xml b/public/packages/PicardPrivate.xml
deleted file mode 100644
index d898a5d07..000000000
--- a/public/packages/PicardPrivate.xml
+++ /dev/null
@@ -1,10 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<package name="picard-private-parts">
-  <executable name="picard-private-parts">
-    <dependencies>
-      <class name="edu.mit.broad.picard.util.PicardAggregationFsUtil" />
-      <class name="edu.mit.broad.picard.genotype.fingerprint.v2.FingerprintingSummaryMetrics" />
-      <class name="edu.mit.broad.picard.genotype.concordance.DbSnpMatchMetrics" />
-    </dependencies>
-  </executable>
-</package>
diff --git a/public/packages/Queue.xml b/public/packages/Queue.xml
deleted file mode 100644
index 621a549d5..000000000
--- a/public/packages/Queue.xml
+++ /dev/null
@@ -1,41 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!--
-  ~ Copyright (c) 2011, The Broad Institute
-  ~
-  ~ Permission is hereby granted, free of charge, to any person
-  ~ obtaining a copy of this software and associated documentation
-  ~ files (the "Software"), to deal in the Software without
-  ~ restriction, including without limitation the rights to use,
-  ~ copy, modify, merge, publish, distribute, sublicense, and/or sell
-  ~ copies of the Software, and to permit persons to whom the
-  ~ Software is furnished to do so, subject to the following
-  ~ conditions:
-  ~
-  ~ The above copyright notice and this permission notice shall be
-  ~ included in all copies or substantial portions of the Software.
-  ~ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
-  ~ EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
-  ~ OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
-  ~ NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
-  ~ HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
-  ~ WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
-  ~ FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
-  ~ OTHER DEALINGS IN THE SOFTWARE.
-  -->
-
-<!-- The full release of Queue contains both public and protected tools (but nothing from private) -->
-<package name="Queue">
-    <version file="StingText.properties" property="org.broadinstitute.sting.queue.version" />
-    <executable name="Queue">
-        <main-class name="org.broadinstitute.sting.queue.QCommandLine" />
-        <resource-bundle file="StingText.properties" />
-        <modules>
-            <module file="QueueEngine.xml"/>
-            <module file="GATKEngine.xml"/>
-        </modules>
-    </executable>
-    <release>
-        <executable directory="/humgen/gsa-hpprojects/Queue/bin" symlink="current" />
-        <archive directory="/humgen/gsa-hpprojects/Queue/bin" symlink="Queue-latest.tar.bz2" />
-    </release>
-</package>
diff --git a/public/packages/QueueEngine.xml b/public/packages/QueueEngine.xml
deleted file mode 100644
index af3e20219..000000000
--- a/public/packages/QueueEngine.xml
+++ /dev/null
@@ -1,78 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!--
-  ~ Copyright (c) 2012, The Broad Institute
-  ~
-  ~ Permission is hereby granted, free of charge, to any person
-  ~ obtaining a copy of this software and associated documentation
-  ~ files (the "Software"), to deal in the Software without
-  ~ restriction, including without limitation the rights to use,
-  ~ copy, modify, merge, publish, distribute, sublicense, and/or sell
-  ~ copies of the Software, and to permit persons to whom the
-  ~ Software is furnished to do so, subject to the following
-  ~ conditions:
-  ~
-  ~ The above copyright notice and this permission notice shall be
-  ~ included in all copies or substantial portions of the Software.
-  ~ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
-  ~ EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
-  ~ OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
-  ~ NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
-  ~ HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
-  ~ WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
-  ~ FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
-  ~ OTHER DEALINGS IN THE SOFTWARE.
-  -->
-
-<package name="QueueEngine">
-    <executable name="QueueEngine">
-        <dependencies>
-            <!-- Queue -->
-            <package name="org.broadinstitute.sting.queue.**" />
-
-            <!-- Pipeline + Utils -->
-            <package name="org.broadinstitute.sting.pipeline.**" />
-            <package name="org.broadinstitute.sting.utils.**" />
-
-            <!-- Scala -->
-            <package name="scala.**" />
-
-            <!-- Picard -->
-            <package name="net.sf.picard.**" />
-            <package name="edu.mit.broad.picard.**" />
-
-            <!-- JavaMail -->
-            <package name="javax.activation.**" />
-            <package name="javax.mail.**" />
-            <package name="com.sun.activation.**" />
-            <package name="com.sun.mail.**" />
-            <file path="META-INF/javamail.charset.map" />
-            <file path="META-INF/javamail.default.address.map" />
-            <file path="META-INF/javamail.default.providers" />
-            <file path="META-INF/mailcap" />
-            <file path="META-INF/mailcap.default" />
-            <file path="META-INF/mimetypes.default" />
-
-            <!-- JNA, including embedded native libraries -->
-            <dir name="com/sun/jna" />
-
-            <!-- Contracts for Java -->
-            <package name="com.google.java.contract.**" />
-
-            <!-- snpEff -->
-            <package name="ca.mcgill.mcb.pcingola.**" />
-            <file path="snpEff_genes.ftl" />
-            <file path="snpEff_summary.ftl" />
-            
-            <!-- R scripts -->
-            <dir name="org/broadinstitute/sting/queue" includes="**/*.R" />
-        </dependencies>
-    </executable>
-    <resources>
-        <!-- Sample QScripts -->
-        <file name="public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/ExampleCountReads.scala" />
-        <file name="public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/ExampleCountLoci.scala" />
-        <file name="public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/ExampleUnifiedGenotyper.scala" />
-        <file name="public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/ExampleReadFilter.scala" />
-        <file name="public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples/ExampleCustomWalker.scala" />
-    </resources>
-</package>
diff --git a/settings/ivysettings.properties b/settings/ivysettings.properties
deleted file mode 100644
index 8a67434f9..000000000
--- a/settings/ivysettings.properties
+++ /dev/null
@@ -1 +0,0 @@
-repository.dir=${ivy.settings.dir}/repository
diff --git a/settings/ivysettings.xml b/settings/ivysettings.xml
deleted file mode 100644
index ce7667140..000000000
--- a/settings/ivysettings.xml
+++ /dev/null
@@ -1,13 +0,0 @@
-<ivysettings>
-  <properties file="${ivy.settings.dir}/ivysettings.properties"/>
-  <settings defaultResolver="chain"/>
-  <resolvers>
-    <chain name="chain">
-      <filesystem name="projects">
-	<artifact pattern="${repository.dir}/[organisation]/[artifact]-[revision].[ext]" />
-	<ivy pattern="${repository.dir}/[organisation]/[module]-[revision].xml" />
-      </filesystem>
-      <ibiblio name="maven" root="http://repo1.maven.org/maven2" m2compatible="true" />
-    </chain>
-  </resolvers>
-</ivysettings>

From faaef236ea0cbf0ad45b8b624ef51a9feeaab44c Mon Sep 17 00:00:00 2001
From: Khalid Shakir <kshakir@broadinstitute.org>
Date: Wed, 29 Jan 2014 13:25:35 -0500
Subject: [PATCH 02/16] Moved gsalib, R and other resources, Queue GATK
 extensions generator, Queue version java files.

---
 .../src/main/resources}/GATK_public.key             | Bin
 .../gatk/phonehome/resources/GATK_AWS_access.key    | Bin
 .../gatk/phonehome/resources/GATK_AWS_secret.key    | Bin
 .../walkers/variantrecalibration/plot_Tranches.R    |   0
 .../broadinstitute/sting/utils/recalibration/BQSR.R |   0
 .../extensions/gatk/ArgumentDefinitionField.java    |   0
 .../sting/queue/extensions/gatk/ArgumentField.java  |   0
 .../extensions/gatk/GATKExtensionsGenerator.java    |   0
 .../queue/extensions/gatk/ReadFilterField.java      |   0
 .../utils/R/gsalib => gsalib/src/R}/DESCRIPTION     |   0
 .../sting/utils/R/gsalib => gsalib/src/R}/NAMESPACE |   0
 .../utils/R/gsalib => gsalib/src/R}/R/gsa.error.R   |   0
 .../utils/R/gsalib => gsalib/src/R}/R/gsa.getargs.R |   0
 .../utils/R/gsalib => gsalib/src/R}/R/gsa.message.R |   0
 .../R/gsalib => gsalib/src/R}/R/gsa.plot.venn.R     |   0
 .../R/gsalib => gsalib/src/R}/R/gsa.read.eval.R     |   0
 .../gsalib => gsalib/src/R}/R/gsa.read.gatkreport.R |   0
 .../src/R}/R/gsa.read.squidmetrics.R                |   0
 .../R/gsalib => gsalib/src/R}/R/gsa.read.vcf.R      |   0
 .../gsalib => gsalib/src/R}/R/gsa.variantqc.utils.R |   0
 .../utils/R/gsalib => gsalib/src/R}/R/gsa.warn.R    |   0
 .../R/gsalib => gsalib/src/R}/Read-and-delete-me    |   0
 .../R/gsalib => gsalib/src/R}/man/gsa.error.Rd      |   0
 .../R/gsalib => gsalib/src/R}/man/gsa.getargs.Rd    |   0
 .../R/gsalib => gsalib/src/R}/man/gsa.message.Rd    |   0
 .../R/gsalib => gsalib/src/R}/man/gsa.plot.venn.Rd  |   0
 .../R/gsalib => gsalib/src/R}/man/gsa.read.eval.Rd  |   0
 .../src/R}/man/gsa.read.gatkreport.Rd               |   0
 .../src/R}/man/gsa.read.squidmetrics.Rd             |   0
 .../R/gsalib => gsalib/src/R}/man/gsa.read.vcf.Rd   |   0
 .../utils/R/gsalib => gsalib/src/R}/man/gsa.warn.Rd |   0
 .../R/gsalib => gsalib/src/R}/man/gsalib-package.Rd |   0
 .../broadinstitute/sting/queue/QueueVersion.java    |   0
 .../broadinstitute/sting/queue/package-info.java    |   0
 .../sting/queue/util/queueJobReport.R               |   0
 35 files changed, 0 insertions(+), 0 deletions(-)
 rename public/{keys => gatk-framework/src/main/resources}/GATK_public.key (100%)
 rename public/{java/src => gatk-framework/src/main/resources}/org/broadinstitute/sting/gatk/phonehome/resources/GATK_AWS_access.key (100%)
 rename public/{java/src => gatk-framework/src/main/resources}/org/broadinstitute/sting/gatk/phonehome/resources/GATK_AWS_secret.key (100%)
 rename public/{R/scripts => gatk-framework/src/main/resources}/org/broadinstitute/sting/gatk/walkers/variantrecalibration/plot_Tranches.R (100%)
 rename public/{R/scripts => gatk-framework/src/main/resources}/org/broadinstitute/sting/utils/recalibration/BQSR.R (100%)
 rename public/{java/src => gatk-queue-extgen/src/main/java}/org/broadinstitute/sting/queue/extensions/gatk/ArgumentDefinitionField.java (100%)
 rename public/{java/src => gatk-queue-extgen/src/main/java}/org/broadinstitute/sting/queue/extensions/gatk/ArgumentField.java (100%)
 rename public/{java/src => gatk-queue-extgen/src/main/java}/org/broadinstitute/sting/queue/extensions/gatk/GATKExtensionsGenerator.java (100%)
 rename public/{java/src => gatk-queue-extgen/src/main/java}/org/broadinstitute/sting/queue/extensions/gatk/ReadFilterField.java (100%)
 rename public/{R/src/org/broadinstitute/sting/utils/R/gsalib => gsalib/src/R}/DESCRIPTION (100%)
 rename public/{R/src/org/broadinstitute/sting/utils/R/gsalib => gsalib/src/R}/NAMESPACE (100%)
 rename public/{R/src/org/broadinstitute/sting/utils/R/gsalib => gsalib/src/R}/R/gsa.error.R (100%)
 rename public/{R/src/org/broadinstitute/sting/utils/R/gsalib => gsalib/src/R}/R/gsa.getargs.R (100%)
 rename public/{R/src/org/broadinstitute/sting/utils/R/gsalib => gsalib/src/R}/R/gsa.message.R (100%)
 rename public/{R/src/org/broadinstitute/sting/utils/R/gsalib => gsalib/src/R}/R/gsa.plot.venn.R (100%)
 rename public/{R/src/org/broadinstitute/sting/utils/R/gsalib => gsalib/src/R}/R/gsa.read.eval.R (100%)
 rename public/{R/src/org/broadinstitute/sting/utils/R/gsalib => gsalib/src/R}/R/gsa.read.gatkreport.R (100%)
 rename public/{R/src/org/broadinstitute/sting/utils/R/gsalib => gsalib/src/R}/R/gsa.read.squidmetrics.R (100%)
 rename public/{R/src/org/broadinstitute/sting/utils/R/gsalib => gsalib/src/R}/R/gsa.read.vcf.R (100%)
 rename public/{R/src/org/broadinstitute/sting/utils/R/gsalib => gsalib/src/R}/R/gsa.variantqc.utils.R (100%)
 rename public/{R/src/org/broadinstitute/sting/utils/R/gsalib => gsalib/src/R}/R/gsa.warn.R (100%)
 rename public/{R/src/org/broadinstitute/sting/utils/R/gsalib => gsalib/src/R}/Read-and-delete-me (100%)
 rename public/{R/src/org/broadinstitute/sting/utils/R/gsalib => gsalib/src/R}/man/gsa.error.Rd (100%)
 rename public/{R/src/org/broadinstitute/sting/utils/R/gsalib => gsalib/src/R}/man/gsa.getargs.Rd (100%)
 rename public/{R/src/org/broadinstitute/sting/utils/R/gsalib => gsalib/src/R}/man/gsa.message.Rd (100%)
 rename public/{R/src/org/broadinstitute/sting/utils/R/gsalib => gsalib/src/R}/man/gsa.plot.venn.Rd (100%)
 rename public/{R/src/org/broadinstitute/sting/utils/R/gsalib => gsalib/src/R}/man/gsa.read.eval.Rd (100%)
 rename public/{R/src/org/broadinstitute/sting/utils/R/gsalib => gsalib/src/R}/man/gsa.read.gatkreport.Rd (100%)
 rename public/{R/src/org/broadinstitute/sting/utils/R/gsalib => gsalib/src/R}/man/gsa.read.squidmetrics.Rd (100%)
 rename public/{R/src/org/broadinstitute/sting/utils/R/gsalib => gsalib/src/R}/man/gsa.read.vcf.Rd (100%)
 rename public/{R/src/org/broadinstitute/sting/utils/R/gsalib => gsalib/src/R}/man/gsa.warn.Rd (100%)
 rename public/{R/src/org/broadinstitute/sting/utils/R/gsalib => gsalib/src/R}/man/gsalib-package.Rd (100%)
 rename public/{java/src => queue-framework/src/main/java}/org/broadinstitute/sting/queue/QueueVersion.java (100%)
 rename public/{java/src => queue-framework/src/main/java}/org/broadinstitute/sting/queue/package-info.java (100%)
 rename public/{R/scripts => queue-framework/src/main/resources}/org/broadinstitute/sting/queue/util/queueJobReport.R (100%)

diff --git a/public/keys/GATK_public.key b/public/gatk-framework/src/main/resources/GATK_public.key
similarity index 100%
rename from public/keys/GATK_public.key
rename to public/gatk-framework/src/main/resources/GATK_public.key
diff --git a/public/java/src/org/broadinstitute/sting/gatk/phonehome/resources/GATK_AWS_access.key b/public/gatk-framework/src/main/resources/org/broadinstitute/sting/gatk/phonehome/resources/GATK_AWS_access.key
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/phonehome/resources/GATK_AWS_access.key
rename to public/gatk-framework/src/main/resources/org/broadinstitute/sting/gatk/phonehome/resources/GATK_AWS_access.key
diff --git a/public/java/src/org/broadinstitute/sting/gatk/phonehome/resources/GATK_AWS_secret.key b/public/gatk-framework/src/main/resources/org/broadinstitute/sting/gatk/phonehome/resources/GATK_AWS_secret.key
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/gatk/phonehome/resources/GATK_AWS_secret.key
rename to public/gatk-framework/src/main/resources/org/broadinstitute/sting/gatk/phonehome/resources/GATK_AWS_secret.key
diff --git a/public/R/scripts/org/broadinstitute/sting/gatk/walkers/variantrecalibration/plot_Tranches.R b/public/gatk-framework/src/main/resources/org/broadinstitute/sting/gatk/walkers/variantrecalibration/plot_Tranches.R
similarity index 100%
rename from public/R/scripts/org/broadinstitute/sting/gatk/walkers/variantrecalibration/plot_Tranches.R
rename to public/gatk-framework/src/main/resources/org/broadinstitute/sting/gatk/walkers/variantrecalibration/plot_Tranches.R
diff --git a/public/R/scripts/org/broadinstitute/sting/utils/recalibration/BQSR.R b/public/gatk-framework/src/main/resources/org/broadinstitute/sting/utils/recalibration/BQSR.R
similarity index 100%
rename from public/R/scripts/org/broadinstitute/sting/utils/recalibration/BQSR.R
rename to public/gatk-framework/src/main/resources/org/broadinstitute/sting/utils/recalibration/BQSR.R
diff --git a/public/java/src/org/broadinstitute/sting/queue/extensions/gatk/ArgumentDefinitionField.java b/public/gatk-queue-extgen/src/main/java/org/broadinstitute/sting/queue/extensions/gatk/ArgumentDefinitionField.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/queue/extensions/gatk/ArgumentDefinitionField.java
rename to public/gatk-queue-extgen/src/main/java/org/broadinstitute/sting/queue/extensions/gatk/ArgumentDefinitionField.java
diff --git a/public/java/src/org/broadinstitute/sting/queue/extensions/gatk/ArgumentField.java b/public/gatk-queue-extgen/src/main/java/org/broadinstitute/sting/queue/extensions/gatk/ArgumentField.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/queue/extensions/gatk/ArgumentField.java
rename to public/gatk-queue-extgen/src/main/java/org/broadinstitute/sting/queue/extensions/gatk/ArgumentField.java
diff --git a/public/java/src/org/broadinstitute/sting/queue/extensions/gatk/GATKExtensionsGenerator.java b/public/gatk-queue-extgen/src/main/java/org/broadinstitute/sting/queue/extensions/gatk/GATKExtensionsGenerator.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/queue/extensions/gatk/GATKExtensionsGenerator.java
rename to public/gatk-queue-extgen/src/main/java/org/broadinstitute/sting/queue/extensions/gatk/GATKExtensionsGenerator.java
diff --git a/public/java/src/org/broadinstitute/sting/queue/extensions/gatk/ReadFilterField.java b/public/gatk-queue-extgen/src/main/java/org/broadinstitute/sting/queue/extensions/gatk/ReadFilterField.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/queue/extensions/gatk/ReadFilterField.java
rename to public/gatk-queue-extgen/src/main/java/org/broadinstitute/sting/queue/extensions/gatk/ReadFilterField.java
diff --git a/public/R/src/org/broadinstitute/sting/utils/R/gsalib/DESCRIPTION b/public/gsalib/src/R/DESCRIPTION
similarity index 100%
rename from public/R/src/org/broadinstitute/sting/utils/R/gsalib/DESCRIPTION
rename to public/gsalib/src/R/DESCRIPTION
diff --git a/public/R/src/org/broadinstitute/sting/utils/R/gsalib/NAMESPACE b/public/gsalib/src/R/NAMESPACE
similarity index 100%
rename from public/R/src/org/broadinstitute/sting/utils/R/gsalib/NAMESPACE
rename to public/gsalib/src/R/NAMESPACE
diff --git a/public/R/src/org/broadinstitute/sting/utils/R/gsalib/R/gsa.error.R b/public/gsalib/src/R/R/gsa.error.R
similarity index 100%
rename from public/R/src/org/broadinstitute/sting/utils/R/gsalib/R/gsa.error.R
rename to public/gsalib/src/R/R/gsa.error.R
diff --git a/public/R/src/org/broadinstitute/sting/utils/R/gsalib/R/gsa.getargs.R b/public/gsalib/src/R/R/gsa.getargs.R
similarity index 100%
rename from public/R/src/org/broadinstitute/sting/utils/R/gsalib/R/gsa.getargs.R
rename to public/gsalib/src/R/R/gsa.getargs.R
diff --git a/public/R/src/org/broadinstitute/sting/utils/R/gsalib/R/gsa.message.R b/public/gsalib/src/R/R/gsa.message.R
similarity index 100%
rename from public/R/src/org/broadinstitute/sting/utils/R/gsalib/R/gsa.message.R
rename to public/gsalib/src/R/R/gsa.message.R
diff --git a/public/R/src/org/broadinstitute/sting/utils/R/gsalib/R/gsa.plot.venn.R b/public/gsalib/src/R/R/gsa.plot.venn.R
similarity index 100%
rename from public/R/src/org/broadinstitute/sting/utils/R/gsalib/R/gsa.plot.venn.R
rename to public/gsalib/src/R/R/gsa.plot.venn.R
diff --git a/public/R/src/org/broadinstitute/sting/utils/R/gsalib/R/gsa.read.eval.R b/public/gsalib/src/R/R/gsa.read.eval.R
similarity index 100%
rename from public/R/src/org/broadinstitute/sting/utils/R/gsalib/R/gsa.read.eval.R
rename to public/gsalib/src/R/R/gsa.read.eval.R
diff --git a/public/R/src/org/broadinstitute/sting/utils/R/gsalib/R/gsa.read.gatkreport.R b/public/gsalib/src/R/R/gsa.read.gatkreport.R
similarity index 100%
rename from public/R/src/org/broadinstitute/sting/utils/R/gsalib/R/gsa.read.gatkreport.R
rename to public/gsalib/src/R/R/gsa.read.gatkreport.R
diff --git a/public/R/src/org/broadinstitute/sting/utils/R/gsalib/R/gsa.read.squidmetrics.R b/public/gsalib/src/R/R/gsa.read.squidmetrics.R
similarity index 100%
rename from public/R/src/org/broadinstitute/sting/utils/R/gsalib/R/gsa.read.squidmetrics.R
rename to public/gsalib/src/R/R/gsa.read.squidmetrics.R
diff --git a/public/R/src/org/broadinstitute/sting/utils/R/gsalib/R/gsa.read.vcf.R b/public/gsalib/src/R/R/gsa.read.vcf.R
similarity index 100%
rename from public/R/src/org/broadinstitute/sting/utils/R/gsalib/R/gsa.read.vcf.R
rename to public/gsalib/src/R/R/gsa.read.vcf.R
diff --git a/public/R/src/org/broadinstitute/sting/utils/R/gsalib/R/gsa.variantqc.utils.R b/public/gsalib/src/R/R/gsa.variantqc.utils.R
similarity index 100%
rename from public/R/src/org/broadinstitute/sting/utils/R/gsalib/R/gsa.variantqc.utils.R
rename to public/gsalib/src/R/R/gsa.variantqc.utils.R
diff --git a/public/R/src/org/broadinstitute/sting/utils/R/gsalib/R/gsa.warn.R b/public/gsalib/src/R/R/gsa.warn.R
similarity index 100%
rename from public/R/src/org/broadinstitute/sting/utils/R/gsalib/R/gsa.warn.R
rename to public/gsalib/src/R/R/gsa.warn.R
diff --git a/public/R/src/org/broadinstitute/sting/utils/R/gsalib/Read-and-delete-me b/public/gsalib/src/R/Read-and-delete-me
similarity index 100%
rename from public/R/src/org/broadinstitute/sting/utils/R/gsalib/Read-and-delete-me
rename to public/gsalib/src/R/Read-and-delete-me
diff --git a/public/R/src/org/broadinstitute/sting/utils/R/gsalib/man/gsa.error.Rd b/public/gsalib/src/R/man/gsa.error.Rd
similarity index 100%
rename from public/R/src/org/broadinstitute/sting/utils/R/gsalib/man/gsa.error.Rd
rename to public/gsalib/src/R/man/gsa.error.Rd
diff --git a/public/R/src/org/broadinstitute/sting/utils/R/gsalib/man/gsa.getargs.Rd b/public/gsalib/src/R/man/gsa.getargs.Rd
similarity index 100%
rename from public/R/src/org/broadinstitute/sting/utils/R/gsalib/man/gsa.getargs.Rd
rename to public/gsalib/src/R/man/gsa.getargs.Rd
diff --git a/public/R/src/org/broadinstitute/sting/utils/R/gsalib/man/gsa.message.Rd b/public/gsalib/src/R/man/gsa.message.Rd
similarity index 100%
rename from public/R/src/org/broadinstitute/sting/utils/R/gsalib/man/gsa.message.Rd
rename to public/gsalib/src/R/man/gsa.message.Rd
diff --git a/public/R/src/org/broadinstitute/sting/utils/R/gsalib/man/gsa.plot.venn.Rd b/public/gsalib/src/R/man/gsa.plot.venn.Rd
similarity index 100%
rename from public/R/src/org/broadinstitute/sting/utils/R/gsalib/man/gsa.plot.venn.Rd
rename to public/gsalib/src/R/man/gsa.plot.venn.Rd
diff --git a/public/R/src/org/broadinstitute/sting/utils/R/gsalib/man/gsa.read.eval.Rd b/public/gsalib/src/R/man/gsa.read.eval.Rd
similarity index 100%
rename from public/R/src/org/broadinstitute/sting/utils/R/gsalib/man/gsa.read.eval.Rd
rename to public/gsalib/src/R/man/gsa.read.eval.Rd
diff --git a/public/R/src/org/broadinstitute/sting/utils/R/gsalib/man/gsa.read.gatkreport.Rd b/public/gsalib/src/R/man/gsa.read.gatkreport.Rd
similarity index 100%
rename from public/R/src/org/broadinstitute/sting/utils/R/gsalib/man/gsa.read.gatkreport.Rd
rename to public/gsalib/src/R/man/gsa.read.gatkreport.Rd
diff --git a/public/R/src/org/broadinstitute/sting/utils/R/gsalib/man/gsa.read.squidmetrics.Rd b/public/gsalib/src/R/man/gsa.read.squidmetrics.Rd
similarity index 100%
rename from public/R/src/org/broadinstitute/sting/utils/R/gsalib/man/gsa.read.squidmetrics.Rd
rename to public/gsalib/src/R/man/gsa.read.squidmetrics.Rd
diff --git a/public/R/src/org/broadinstitute/sting/utils/R/gsalib/man/gsa.read.vcf.Rd b/public/gsalib/src/R/man/gsa.read.vcf.Rd
similarity index 100%
rename from public/R/src/org/broadinstitute/sting/utils/R/gsalib/man/gsa.read.vcf.Rd
rename to public/gsalib/src/R/man/gsa.read.vcf.Rd
diff --git a/public/R/src/org/broadinstitute/sting/utils/R/gsalib/man/gsa.warn.Rd b/public/gsalib/src/R/man/gsa.warn.Rd
similarity index 100%
rename from public/R/src/org/broadinstitute/sting/utils/R/gsalib/man/gsa.warn.Rd
rename to public/gsalib/src/R/man/gsa.warn.Rd
diff --git a/public/R/src/org/broadinstitute/sting/utils/R/gsalib/man/gsalib-package.Rd b/public/gsalib/src/R/man/gsalib-package.Rd
similarity index 100%
rename from public/R/src/org/broadinstitute/sting/utils/R/gsalib/man/gsalib-package.Rd
rename to public/gsalib/src/R/man/gsalib-package.Rd
diff --git a/public/java/src/org/broadinstitute/sting/queue/QueueVersion.java b/public/queue-framework/src/main/java/org/broadinstitute/sting/queue/QueueVersion.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/queue/QueueVersion.java
rename to public/queue-framework/src/main/java/org/broadinstitute/sting/queue/QueueVersion.java
diff --git a/public/java/src/org/broadinstitute/sting/queue/package-info.java b/public/queue-framework/src/main/java/org/broadinstitute/sting/queue/package-info.java
similarity index 100%
rename from public/java/src/org/broadinstitute/sting/queue/package-info.java
rename to public/queue-framework/src/main/java/org/broadinstitute/sting/queue/package-info.java
diff --git a/public/R/scripts/org/broadinstitute/sting/queue/util/queueJobReport.R b/public/queue-framework/src/main/resources/org/broadinstitute/sting/queue/util/queueJobReport.R
similarity index 100%
rename from public/R/scripts/org/broadinstitute/sting/queue/util/queueJobReport.R
rename to public/queue-framework/src/main/resources/org/broadinstitute/sting/queue/util/queueJobReport.R

From 1e25a758f57b74c538afd7da6ba4798e0d2f1590 Mon Sep 17 00:00:00 2001
From: Khalid Shakir <kshakir@broadinstitute.org>
Date: Wed, 29 Jan 2014 13:36:16 -0500
Subject: [PATCH 03/16] Moved files to maven directories. Here are the git
 moved directories in case other files need to be moved during a merge:  
 git-mv private/java/src/        private/gatk-private/src/main/java/   git-mv
 private/R/scripts/       private/gatk-private/src/main/resources/   git-mv
 private/java/test/       private/gatk-private/src/test/java/   git-mv
 private/testdata/        private/gatk-private/src/test/resources/   git-mv
 private/scala/qscript/   private/queue-private/src/main/qscripts/   git-mv
 private/scala/src/       private/queue-private/src/main/scala/   git-mv
 protected/java/src/      protected/gatk-protected/src/main/java/   git-mv
 protected/java/test/     protected/gatk-protected/src/test/java/   git-mv
 public/java/src/         public/gatk-framework/src/main/java/   git-mv
 public/java/test/        public/gatk-framework/src/test/java/   git-mv
 public/testdata/         public/gatk-framework/src/test/resources/   git-mv
 public/scala/qscript/    public/queue-framework/src/main/qscripts/   git-mv
 public/scala/src/        public/queue-framework/src/main/scala/   git-mv
 public/scala/test/       public/queue-framework/src/test/scala/

---
 .../arguments/StandardCallerArgumentCollection.java |   0
 .../walkers/annotator/BaseQualityRankSumTest.java   |   0
 .../gatk/walkers/annotator/ChromosomeCounts.java    |   0
 .../gatk/walkers/annotator/ClippingRankSumTest.java |   0
 .../sting/gatk/walkers/annotator/Coverage.java      |   0
 .../walkers/annotator/DepthPerAlleleBySample.java   |   0
 .../gatk/walkers/annotator/DepthPerSampleHC.java    |   0
 .../sting/gatk/walkers/annotator/FisherStrand.java  |   0
 .../sting/gatk/walkers/annotator/GCContent.java     |   0
 .../gatk/walkers/annotator/HaplotypeScore.java      |   0
 .../sting/gatk/walkers/annotator/HardyWeinberg.java |   0
 .../gatk/walkers/annotator/HomopolymerRun.java      |   0
 .../gatk/walkers/annotator/InbreedingCoeff.java     |   0
 .../walkers/annotator/LikelihoodRankSumTest.java    |   0
 .../gatk/walkers/annotator/MVLikelihoodRatio.java   |   0
 .../annotator/MappingQualityRankSumTest.java        |   0
 .../gatk/walkers/annotator/MappingQualityZero.java  |   0
 .../sting/gatk/walkers/annotator/QualByDepth.java   |   0
 .../gatk/walkers/annotator/RMSMappingQuality.java   |   0
 .../sting/gatk/walkers/annotator/RankSumTest.java   |   0
 .../gatk/walkers/annotator/ReadPosRankSumTest.java  |   0
 .../sting/gatk/walkers/annotator/SampleList.java    |   0
 .../gatk/walkers/annotator/SpanningDeletions.java   |   0
 .../gatk/walkers/annotator/StrandBiasBySample.java  |   0
 .../walkers/annotator/TandemRepeatAnnotator.java    |   0
 .../annotator/TransmissionDisequilibriumTest.java   |   0
 .../sting/gatk/walkers/annotator/VariantType.java   |   0
 .../sting/gatk/walkers/bqsr/AnalyzeCovariates.java  |   0
 .../sting/gatk/walkers/bqsr/BQSRGatherer.java       |   0
 .../sting/gatk/walkers/bqsr/BaseRecalibrator.java   |   0
 .../gatk/walkers/bqsr/ReadRecalibrationInfo.java    |   0
 .../bqsr/RecalibrationArgumentCollection.java       |   0
 .../gatk/walkers/bqsr/RecalibrationEngine.java      |   0
 .../compression/reducereads/BaseAndQualsCounts.java |   0
 .../walkers/compression/reducereads/BaseCounts.java |   0
 .../walkers/compression/reducereads/BaseIndex.java  |   0
 .../compression/reducereads/CompressionStash.java   |   0
 .../walkers/compression/reducereads/Compressor.java |   0
 .../compression/reducereads/FinishedGenomeLoc.java  |   0
 .../compression/reducereads/HeaderElement.java      |   0
 .../reducereads/MultiSampleCompressor.java          |   0
 .../compression/reducereads/ReduceReads.java        |   0
 .../compression/reducereads/ReduceReadsStash.java   |   0
 .../reducereads/SingleSampleCompressor.java         |   0
 .../compression/reducereads/SlidingWindow.java      |   0
 .../compression/reducereads/SyntheticRead.java      |   0
 .../diagnostics/BaseCoverageDistribution.java       |   0
 .../walkers/diagnostics/FindCoveredIntervals.java   |   0
 .../diagnosetargets/AbstractStratification.java     |   0
 .../diagnostics/diagnosetargets/CallableStatus.java |   0
 .../diagnosetargets/DiagnoseTargets.java            |   0
 .../diagnostics/diagnosetargets/IntervalMetric.java |   0
 .../diagnosetargets/IntervalStratification.java     |   0
 .../diagnostics/diagnosetargets/LocusMetric.java    |   0
 .../diagnosetargets/LocusMetricCoverageGap.java     |   0
 .../LocusMetricExcessiveCoverage.java               |   0
 .../diagnosetargets/LocusMetricLowCoverage.java     |   0
 .../diagnosetargets/LocusMetricPoorQuality.java     |   0
 .../diagnosetargets/LocusStratification.java        |   0
 .../walkers/diagnostics/diagnosetargets/Metric.java |   0
 .../diagnostics/diagnosetargets/PluginUtils.java    |   0
 .../diagnostics/diagnosetargets/SampleMetric.java   |   0
 .../diagnosetargets/SampleMetricBadMates.java       |   0
 .../diagnosetargets/SampleMetricNoReads.java        |   0
 .../diagnosetargets/SampleStratification.java       |   0
 .../diagnostics/diagnosetargets/ThresHolder.java    |   0
 .../gatk/walkers/diagnostics/missing/Metrics.java   |   0
 .../missing/QualifyMissingIntervals.java            |   0
 .../gatk/walkers/genotyper/BaseMismatchModel.java   |   0
 .../walkers/genotyper/ConsensusAlleleCounter.java   |   0
 .../genotyper/DiploidSNPGenotypeLikelihoods.java    |   0
 .../sting/gatk/walkers/genotyper/ErrorModel.java    |   0
 .../genotyper/GeneralPloidyGenotypeLikelihoods.java |   0
 ...alPloidyGenotypeLikelihoodsCalculationModel.java |   0
 .../GeneralPloidyIndelGenotypeLikelihoods.java      |   0
 ...idyIndelGenotypeLikelihoodsCalculationModel.java |   0
 .../GeneralPloidySNPGenotypeLikelihoods.java        |   0
 ...loidySNPGenotypeLikelihoodsCalculationModel.java |   0
 .../GenotypeLikelihoodsCalculationModel.java        |   0
 .../gatk/walkers/genotyper/GenotypePriors.java      |   0
 .../IndelGenotypeLikelihoodsCalculationModel.java   |   0
 .../gatk/walkers/genotyper/PoolGenotypePriors.java  |   0
 .../gatk/walkers/genotyper/ProbabilityVector.java   |   0
 .../SNPGenotypeLikelihoodsCalculationModel.java     |   0
 .../genotyper/UnifiedArgumentCollection.java        |   0
 .../gatk/walkers/genotyper/UnifiedGenotyper.java    |   0
 .../walkers/genotyper/UnifiedGenotyperEngine.java   |   0
 .../gatk/walkers/genotyper/VariantCallContext.java  |   0
 .../sting/gatk/walkers/genotyper/afcalc/AFCalc.java |   0
 .../walkers/genotyper/afcalc/AFCalcFactory.java     |   0
 .../genotyper/afcalc/AFCalcPerformanceTest.java     |   0
 .../gatk/walkers/genotyper/afcalc/AFCalcResult.java |   0
 .../walkers/genotyper/afcalc/AFCalcTestBuilder.java |   0
 .../genotyper/afcalc/DiploidExactAFCalc.java        |   0
 .../walkers/genotyper/afcalc/ExactACcounts.java     |   0
 .../gatk/walkers/genotyper/afcalc/ExactACset.java   |   0
 .../gatk/walkers/genotyper/afcalc/ExactAFCalc.java  |   0
 .../walkers/genotyper/afcalc/ExactCallLogger.java   |   0
 .../genotyper/afcalc/GeneralPloidyExactAFCalc.java  |   0
 .../IndependentAllelesDiploidExactAFCalc.java       |   0
 .../afcalc/OriginalDiploidExactAFCalc.java          |   0
 .../afcalc/ReferenceDiploidExactAFCalc.java         |   0
 .../gatk/walkers/genotyper/afcalc/StateTracker.java |   0
 .../haplotypecaller/ActiveRegionTrimmer.java        |   0
 .../walkers/haplotypecaller/AssemblyResult.java     |   0
 .../walkers/haplotypecaller/AssemblyResultSet.java  |   0
 .../gatk/walkers/haplotypecaller/EventBlock.java    |   0
 .../walkers/haplotypecaller/EventBlockFinder.java   |   0
 .../walkers/haplotypecaller/GenotypingEngine.java   |   0
 .../GraphBasedLikelihoodCalculationEngine.java      |   0
 ...aphBasedLikelihoodCalculationEngineInstance.java |   0
 .../walkers/haplotypecaller/HaplotypeCaller.java    |   0
 .../walkers/haplotypecaller/HaplotypeResolver.java  |   0
 .../walkers/haplotypecaller/HaplotypeRoute.java     |   0
 .../HeterogeneousKmerSizeResolution.java            |   0
 .../gatk/walkers/haplotypecaller/KMerCounter.java   |   0
 .../sting/gatk/walkers/haplotypecaller/Kmer.java    |   0
 .../gatk/walkers/haplotypecaller/KmerSequence.java  |   0
 .../haplotypecaller/KmerSequenceGraphMap.java       |   0
 .../LikelihoodCalculationEngine.java                |   0
 .../haplotypecaller/LocalAssemblyEngine.java        |   0
 .../PairHMMLikelihoodCalculationEngine.java         |   0
 .../RandomLikelihoodCalculationEngine.java          |   0
 .../gatk/walkers/haplotypecaller/ReadAnchoring.java |   0
 .../gatk/walkers/haplotypecaller/ReadCost.java      |   0
 .../walkers/haplotypecaller/ReadErrorCorrector.java |   0
 .../haplotypecaller/ReadSegmentComparator.java      |   0
 .../walkers/haplotypecaller/ReadSegmentCost.java    |   0
 .../walkers/haplotypecaller/RefVsAnyResult.java     |   0
 .../haplotypecaller/ReferenceConfidenceModel.java   |   0
 .../walkers/haplotypecaller/graphs/BaseEdge.java    |   0
 .../walkers/haplotypecaller/graphs/BaseGraph.java   |   0
 .../haplotypecaller/graphs/BaseGraphIterator.java   |   0
 .../walkers/haplotypecaller/graphs/BaseVertex.java  |   0
 .../graphs/CommonSuffixSplitter.java                |   0
 .../haplotypecaller/graphs/DeBruijnVertex.java      |   0
 .../walkers/haplotypecaller/graphs/GraphUtils.java  |   0
 .../walkers/haplotypecaller/graphs/KBestPaths.java  |   0
 .../haplotypecaller/graphs/KmerSearchableGraph.java |   0
 .../graphs/LowWeightChainPruner.java                |   0
 .../haplotypecaller/graphs/MultiSampleEdge.java     |   0
 .../gatk/walkers/haplotypecaller/graphs/Path.java   |   0
 .../gatk/walkers/haplotypecaller/graphs/Route.java  |   0
 .../walkers/haplotypecaller/graphs/RouteFinder.java |   0
 .../walkers/haplotypecaller/graphs/SeqGraph.java    |   0
 .../walkers/haplotypecaller/graphs/SeqVertex.java   |   0
 .../graphs/SharedSequenceMerger.java                |   0
 .../graphs/SharedVertexSequenceSplitter.java        |   0
 .../walkers/haplotypecaller/graphs/TestGraph.java   |   0
 .../walkers/haplotypecaller/graphs/VertexOrder.java |   0
 .../readthreading/HaplotypeGraph.java               |   0
 .../readthreading/MultiDeBruijnVertex.java          |   0
 .../readthreading/ReadThreadingAssembler.java       |   0
 .../readthreading/ReadThreadingGraph.java           |   0
 .../readthreading/SequenceForKmers.java             |   0
 .../indels/ConstrainedMateFixingManager.java        |   0
 .../walkers/indels/HaplotypeIndelErrorModel.java    |   0
 .../sting/gatk/walkers/indels/IndelRealigner.java   |   0
 .../sting/gatk/walkers/indels/LeftAlignIndels.java  |   0
 .../gatk/walkers/indels/PairHMMIndelErrorModel.java |   0
 .../sting/gatk/walkers/indels/ReadBin.java          |   0
 .../gatk/walkers/indels/RealignerTargetCreator.java |   0
 .../sting/gatk/walkers/phasing/AllelePair.java      |   0
 .../sting/gatk/walkers/phasing/BaseArray.java       |   0
 .../gatk/walkers/phasing/CardinalityCounter.java    |   0
 .../phasing/CloneableIteratorLinkedList.java        |   0
 .../sting/gatk/walkers/phasing/DisjointSet.java     |   0
 .../sting/gatk/walkers/phasing/Haplotype.java       |   0
 .../MergeSegregatingAlternateAllelesVCFWriter.java  |   0
 .../gatk/walkers/phasing/PhaseByTransmission.java   |   0
 .../sting/gatk/walkers/phasing/PhasingGraph.java    |   0
 .../gatk/walkers/phasing/PhasingGraphEdge.java      |   0
 .../sting/gatk/walkers/phasing/PhasingRead.java     |   0
 .../sting/gatk/walkers/phasing/PhasingUtils.java    |   0
 .../walkers/phasing/PreciseNonNegativeDouble.java   |   0
 .../gatk/walkers/phasing/ReadBackedPhasing.java     |   0
 .../sting/gatk/walkers/phasing/ReadBase.java        |   0
 .../gatk/walkers/phasing/ReadBasesAtPosition.java   |   0
 .../sting/gatk/walkers/phasing/SNPallelePair.java   |   0
 .../gatk/walkers/qc/AssessReducedCoverage.java      |   0
 .../sting/gatk/walkers/qc/AssessReducedQuals.java   |   0
 .../sting/gatk/walkers/rnaseq/SplitNCigarReads.java |   0
 .../simulatereads/SimulateReadsForVariants.java     |   0
 .../walkers/validation/GenotypeAndValidate.java     |   0
 .../FrequencyModeSelector.java                      |   0
 .../GLBasedSampleSelector.java                      |   0
 .../GTBasedSampleSelector.java                      |   0
 .../validationsiteselector/GenomeEvent.java         |   0
 .../KeepAFSpectrumFrequencySelector.java            |   0
 .../validationsiteselector/NullSampleSelector.java  |   0
 .../validationsiteselector/SampleSelector.java      |   0
 .../UniformSamplingFrequencySelector.java           |   0
 .../ValidationSiteSelector.java                     |   0
 .../variantrecalibration/ApplyRecalibration.java    |   0
 .../variantrecalibration/GaussianMixtureModel.java  |   0
 .../variantrecalibration/MultivariateGaussian.java  |   0
 .../walkers/variantrecalibration/TrainingSet.java   |   0
 .../gatk/walkers/variantrecalibration/Tranche.java  |   0
 .../variantrecalibration/TrancheManager.java        |   0
 .../variantrecalibration/VariantDataManager.java    |   0
 .../walkers/variantrecalibration/VariantDatum.java  |   0
 .../variantrecalibration/VariantRecalibrator.java   |   0
 .../VariantRecalibratorArgumentCollection.java      |   0
 .../VariantRecalibratorEngine.java                  |   0
 .../variantutils/CalculateGenotypePosteriors.java   |   0
 .../CombineReferenceCalculationVariants.java        |   0
 .../variantutils/PosteriorLikelihoodsUtils.java     |   0
 .../walkers/variantutils/RegenotypeVariants.java    |   0
 .../org/broadinstitute/sting/package-info.java      |   0
 .../sting/utils/SequenceComplexity.java             |   0
 .../sting/utils/collections/CountSet.java           |   0
 .../broadinstitute/sting/utils/gvcf/GVCFWriter.java |   0
 .../sting/utils/gvcf/HomRefBlock.java               |   0
 .../utils/haplotype/HaplotypeLDCalculator.java      |   0
 .../sting/utils/haplotype/LDMerger.java             |   0
 .../haplotype/MergeVariantsAcrossHaplotypes.java    |   0
 .../haplotypeBAMWriter/AllHaplotypeBAMWriter.java   |   0
 .../CalledHaplotypeBAMWriter.java                   |   0
 .../haplotypeBAMWriter/HaplotypeBAMWriter.java      |   0
 .../utils/haplotypeBAMWriter/ReadDestination.java   |   0
 .../sting/utils/pairhmm/ArrayLoglessPairHMM.java    |   0
 .../sting/utils/pairhmm/CnyPairHMM.java             |   0
 .../sting/utils/pairhmm/FastLoglessPairHMM.java     |   0
 .../sting/utils/pairhmm/FlexibleHMM.java            |   0
 .../sting/utils/pairhmm/LoglessPairHMM.java         |   0
 .../utils/recalibration/BQSRReadTransformer.java    |   0
 .../utils/recalibration/BaseRecalibration.java      |   0
 .../sting/utils/recalibration/QualQuantizer.java    |   0
 .../sting/utils/recalibration/QuantizationInfo.java |   0
 .../sting/utils/recalibration/ReadCovariates.java   |   0
 .../sting/utils/recalibration/RecalDatum.java       |   0
 .../sting/utils/recalibration/RecalDatumNode.java   |   0
 .../sting/utils/recalibration/RecalUtils.java       |   0
 .../utils/recalibration/RecalibrationReport.java    |   0
 .../utils/recalibration/RecalibrationTables.java    |   0
 .../recalibration/covariates/ContextCovariate.java  |   0
 .../utils/recalibration/covariates/Covariate.java   |   0
 .../recalibration/covariates/CycleCovariate.java    |   0
 .../covariates/ExperimentalCovariate.java           |   0
 .../covariates/QualityScoreCovariate.java           |   0
 .../covariates/ReadGroupCovariate.java              |   0
 .../recalibration/covariates/RepeatCovariate.java   |   0
 .../covariates/RepeatLengthCovariate.java           |   0
 .../covariates/RepeatUnitAndLengthCovariate.java    |   0
 .../covariates/RepeatUnitCovariate.java             |   0
 .../recalibration/covariates/RequiredCovariate.java |   0
 .../recalibration/covariates/StandardCovariate.java |   0
 .../sting/utils/sam/ClippedGATKSAMRecord.java       |   0
 .../gatk/walkers/WalkerTestIntegrationTest.java     |   0
 .../gatk/walkers/annotator/RankSumUnitTest.java     |   0
 .../gatk/walkers/annotator/SnpEffUnitTest.java      |   0
 .../annotator/VariantAnnotatorIntegrationTest.java  |   0
 .../annotator/VariantOverlapAnnotatorUnitTest.java  |   0
 .../gatk/walkers/beagle/BeagleIntegrationTest.java  |   0
 .../bqsr/AnalyzeCovariatesIntegrationTest.java      |   0
 .../gatk/walkers/bqsr/BQSRGathererUnitTest.java     |   0
 .../gatk/walkers/bqsr/BQSRIntegrationTest.java      |   0
 .../walkers/bqsr/ReadRecalibrationInfoUnitTest.java |   0
 .../compression/reducereads/BaseCountsUnitTest.java |   0
 .../reducereads/HeaderElementUnitTest.java          |   0
 .../reducereads/ReduceReadsIntegrationTest.java     |   0
 .../reducereads/ReduceReadsUnitTest.java            |   0
 .../reducereads/SlidingWindowUnitTest.java          |   0
 .../BaseCoverageDistributionIntegrationTest.java    |   0
 .../ErrorRatePerCycleIntegrationTest.java           |   0
 .../ReadGroupPropertiesIntegrationTest.java         |   0
 .../DiagnoseTargetsIntegrationTest.java             |   0
 .../diagnosetargets/LocusStatisticsUnitTest.java    |   0
 .../missing/QualifyMissingIntervalsUnitTest.java    |   0
 .../gatk/walkers/diffengine/DiffEngineUnitTest.java |   0
 .../gatk/walkers/diffengine/DiffNodeUnitTest.java   |   0
 .../diffengine/DiffObjectsIntegrationTest.java      |   0
 .../walkers/diffengine/DiffableReaderUnitTest.java  |   0
 .../gatk/walkers/diffengine/DifferenceUnitTest.java |   0
 .../FastaAlternateReferenceIntegrationTest.java     |   0
 .../filters/VariantFiltrationIntegrationTest.java   |   0
 .../genotyper/ArtificialReadPileupTestProvider.java |   0
 .../BiasedDownsamplingIntegrationTest.java          |   0
 .../GeneralPloidyGenotypeLikelihoodsUnitTest.java   |   0
 .../genotyper/IndelGenotypeLikelihoodsUnitTest.java |   0
 .../genotyper/UnifiedGenotyperEngineUnitTest.java   |   0
 ...GenotyperGeneralPloidySuite1IntegrationTest.java |   0
 ...GenotyperGeneralPloidySuite2IntegrationTest.java |   0
 .../UnifiedGenotyperGeneralPloidyTestExecutor.java  |   0
 ...UnifiedGenotyperIndelCallingIntegrationTest.java |   0
 .../genotyper/UnifiedGenotyperIntegrationTest.java  |   0
 .../genotyper/UnifiedGenotyperLargeScaleTest.java   |   0
 ...nifiedGenotyperNormalCallingIntegrationTest.java |   0
 ...UnifiedGenotyperReducedReadsIntegrationTest.java |   0
 .../genotyper/afcalc/AFCalcPerformanceUnitTest.java |   0
 .../genotyper/afcalc/AFCalcResultUnitTest.java      |   0
 .../walkers/genotyper/afcalc/AFCalcUnitTest.java    |   0
 .../GeneralPloidyAFCalculationModelUnitTest.java    |   0
 ...ndependentAllelesDiploidExactAFCalcUnitTest.java |   0
 .../ActiveRegionTestDataSetUnitTest.java            |   0
 .../haplotypecaller/AssemblyResultSetUnitTest.java  |   0
 .../sting/gatk/walkers/haplotypecaller/Civar.java   |   0
 .../gatk/walkers/haplotypecaller/CivarUnitTest.java |   0
 .../haplotypecaller/GenotypingEngineUnitTest.java   |   0
 .../HCLikelihoodCalculationEnginesBenchmark.java    |   0
 ...erComplexAndSymbolicVariantsIntegrationTest.java |   0
 .../HaplotypeCallerGVCFIntegrationTest.java         |   0
 .../HaplotypeCallerIntegrationTest.java             |   0
 .../HaplotypeCallerModesIntegrationTest.java        |   0
 .../HaplotypeCallerParallelIntegrationTest.java     |   0
 .../haplotypecaller/KMerCounterCaseFixUnitTest.java |   0
 .../gatk/walkers/haplotypecaller/KmerUnitTest.java  |   0
 .../LocalAssemblyEngineUnitTest.java                |   0
 .../PairHMMLikelihoodCalculationEngineUnitTest.java |   0
 .../haplotypecaller/ReadErrorCorrectorUnitTest.java |   0
 ...hreadingLikelihoodCalculationEngineUnitTest.java |   0
 .../ReferenceConfidenceModelUnitTest.java           |   0
 .../haplotypecaller/graphs/BaseEdgeUnitTest.java    |   0
 .../haplotypecaller/graphs/BaseGraphUnitTest.java   |   0
 .../haplotypecaller/graphs/BaseVertexUnitTest.java  |   0
 .../graphs/CommonSuffixMergerUnitTest.java          |   0
 .../graphs/CommonSuffixSplitterUnitTest.java        |   0
 .../graphs/DeBruijnVertexUnitTest.java              |   0
 .../haplotypecaller/graphs/GraphUtilsUnitTest.java  |   0
 .../graphs/HaplotypeGraphUnitTest.java              |   0
 .../haplotypecaller/graphs/KBestPathsUnitTest.java  |   0
 .../graphs/LowWeightChainPrunerUnitTest.java        |   0
 .../graphs/MultiSampleEdgeUnitTest.java             |   0
 .../haplotypecaller/graphs/PathUnitTest.java        |   0
 .../haplotypecaller/graphs/RouteUnitTest.java       |   0
 .../haplotypecaller/graphs/SeqGraphUnitTest.java    |   0
 .../haplotypecaller/graphs/SeqVertexUnitTest.java   |   0
 .../SharedVertexSequenceSplitterUnitTest.java       |   0
 .../ReadThreadingAssemblerUnitTest.java             |   0
 .../readthreading/ReadThreadingGraphUnitTest.java   |   0
 .../readthreading/SequenceForKmersUnitTest.java     |   0
 .../ConstrainedMateFixingManagerUnitTest.java       |   0
 .../indels/IndelRealignerIntegrationTest.java       |   0
 .../indels/IndelRealignerLargeScaleTest.java        |   0
 .../gatk/walkers/indels/IndelRealignerUnitTest.java |   0
 .../indels/PairHMMIndelErrorModelUnitTest.java      |   0
 .../sting/gatk/walkers/indels/ReadBinUnitTest.java  |   0
 .../RealignerTargetCreatorIntegrationTest.java      |   0
 .../RealignerTargetCreatorLargeScaleTest.java       |   0
 .../phasing/PhaseByTransmissionIntegrationTest.java |   0
 .../phasing/ReadBackedPhasingIntegrationTest.java   |   0
 .../rnaseq/SplitNCigarReadsIntegrationTests.java    |   0
 .../walkers/rnaseq/SplitNCigarReadsUnitTest.java    |   0
 .../SimulateReadsForVariantsIntegrationTest.java    |   0
 .../ValidationAmpliconsIntegrationTest.java         |   0
 .../ValidationSiteSelectorIntegrationTest.java      |   0
 .../varianteval/VariantEvalIntegrationTest.java     |   0
 .../varianteval/VariantEvalWalkerUnitTest.java      |   0
 .../manager/StratificationManagerUnitTest.java      |   0
 .../ApplyRecalibrationUnitTest.java                 |   0
 .../VariantDataManagerUnitTest.java                 |   0
 .../VariantGaussianMixtureModelUnitTest.java        |   0
 .../VariantRecalibrationWalkersIntegrationTest.java |   0
 ...ReferenceCalculationVariantsIntegrationTest.java |   0
 .../CombineVariantsIntegrationTest.java             |   0
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 1437 files changed, 0 insertions(+), 0 deletions(-)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/arguments/StandardCallerArgumentCollection.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/annotator/BaseQualityRankSumTest.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/annotator/ChromosomeCounts.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/annotator/ClippingRankSumTest.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/annotator/Coverage.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerAlleleBySample.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerSampleHC.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/annotator/GCContent.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/annotator/HardyWeinberg.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/annotator/HomopolymerRun.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/annotator/InbreedingCoeff.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/annotator/LikelihoodRankSumTest.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/annotator/MVLikelihoodRatio.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityRankSumTest.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZero.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/annotator/QualByDepth.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/annotator/RMSMappingQuality.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/annotator/ReadPosRankSumTest.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/annotator/SampleList.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/annotator/SpanningDeletions.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/annotator/StrandBiasBySample.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/annotator/TandemRepeatAnnotator.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/annotator/TransmissionDisequilibriumTest.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/annotator/VariantType.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/bqsr/AnalyzeCovariates.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRGatherer.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/bqsr/ReadRecalibrationInfo.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/bqsr/RecalibrationArgumentCollection.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/bqsr/RecalibrationEngine.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/compression/reducereads/BaseAndQualsCounts.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/compression/reducereads/BaseCounts.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/compression/reducereads/BaseIndex.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/compression/reducereads/CompressionStash.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/compression/reducereads/Compressor.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/compression/reducereads/FinishedGenomeLoc.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/compression/reducereads/HeaderElement.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/compression/reducereads/MultiSampleCompressor.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReads.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReadsStash.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SingleSampleCompressor.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SlidingWindow.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SyntheticRead.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/diagnostics/BaseCoverageDistribution.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/diagnostics/FindCoveredIntervals.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/AbstractStratification.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/CallableStatus.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/DiagnoseTargets.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/IntervalMetric.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/IntervalStratification.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/LocusMetric.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/LocusMetricCoverageGap.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/LocusMetricExcessiveCoverage.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/LocusMetricLowCoverage.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/LocusMetricPoorQuality.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/LocusStratification.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/Metric.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/PluginUtils.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/SampleMetric.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/SampleMetricBadMates.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/SampleMetricNoReads.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/SampleStratification.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/ThresHolder.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/diagnostics/missing/Metrics.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/diagnostics/missing/QualifyMissingIntervals.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/genotyper/BaseMismatchModel.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/genotyper/ConsensusAlleleCounter.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidSNPGenotypeLikelihoods.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/genotyper/ErrorModel.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyGenotypeLikelihoods.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyGenotypeLikelihoodsCalculationModel.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyIndelGenotypeLikelihoods.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyIndelGenotypeLikelihoodsCalculationModel.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidySNPGenotypeLikelihoods.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidySNPGenotypeLikelihoodsCalculationModel.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeLikelihoodsCalculationModel.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypePriors.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/genotyper/PoolGenotypePriors.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/genotyper/ProbabilityVector.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/genotyper/VariantCallContext.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalc.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcFactory.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcPerformanceTest.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcResult.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcTestBuilder.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/DiploidExactAFCalc.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/ExactACcounts.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/ExactACset.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/ExactAFCalc.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/ExactCallLogger.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/GeneralPloidyExactAFCalc.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/IndependentAllelesDiploidExactAFCalc.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/OriginalDiploidExactAFCalc.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/ReferenceDiploidExactAFCalc.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/StateTracker.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ActiveRegionTrimmer.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/haplotypecaller/AssemblyResult.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/haplotypecaller/AssemblyResultSet.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/haplotypecaller/EventBlock.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/haplotypecaller/EventBlockFinder.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/haplotypecaller/GenotypingEngine.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/haplotypecaller/GraphBasedLikelihoodCalculationEngine.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/haplotypecaller/GraphBasedLikelihoodCalculationEngineInstance.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeResolver.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeRoute.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HeterogeneousKmerSizeResolution.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/haplotypecaller/KMerCounter.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/haplotypecaller/Kmer.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/haplotypecaller/KmerSequence.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/haplotypecaller/KmerSequenceGraphMap.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LikelihoodCalculationEngine.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LocalAssemblyEngine.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/haplotypecaller/PairHMMLikelihoodCalculationEngine.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/haplotypecaller/RandomLikelihoodCalculationEngine.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ReadAnchoring.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ReadCost.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ReadErrorCorrector.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ReadSegmentComparator.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ReadSegmentCost.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/haplotypecaller/RefVsAnyResult.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ReferenceConfidenceModel.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/BaseEdge.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/BaseGraph.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/BaseGraphIterator.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/BaseVertex.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/CommonSuffixSplitter.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/DeBruijnVertex.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/GraphUtils.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/KBestPaths.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/KmerSearchableGraph.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/LowWeightChainPruner.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/MultiSampleEdge.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/Path.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/Route.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/RouteFinder.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/SeqGraph.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/SeqVertex.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/SharedSequenceMerger.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/SharedVertexSequenceSplitter.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/TestGraph.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/VertexOrder.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/haplotypecaller/readthreading/HaplotypeGraph.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/haplotypecaller/readthreading/MultiDeBruijnVertex.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/haplotypecaller/readthreading/ReadThreadingAssembler.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/haplotypecaller/readthreading/ReadThreadingGraph.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/haplotypecaller/readthreading/SequenceForKmers.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/indels/ConstrainedMateFixingManager.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/indels/HaplotypeIndelErrorModel.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/indels/LeftAlignIndels.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/indels/ReadBin.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/phasing/AllelePair.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/phasing/BaseArray.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/phasing/CardinalityCounter.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/phasing/CloneableIteratorLinkedList.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/phasing/DisjointSet.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/phasing/Haplotype.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/phasing/MergeSegregatingAlternateAllelesVCFWriter.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmission.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/phasing/PhasingGraph.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/phasing/PhasingGraphEdge.java (100%)
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 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/phasing/PreciseNonNegativeDouble.java (100%)
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 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/rnaseq/SplitNCigarReads.java (100%)
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 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/KeepAFSpectrumFrequencySelector.java (100%)
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 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/UniformSamplingFrequencySelector.java (100%)
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 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/gatk/walkers/variantrecalibration/TrainingSet.java (100%)
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 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/utils/SequenceComplexity.java (100%)
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 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/utils/pairhmm/CnyPairHMM.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/utils/pairhmm/FastLoglessPairHMM.java (100%)
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 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/utils/pairhmm/LoglessPairHMM.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/utils/recalibration/BQSRReadTransformer.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/utils/recalibration/BaseRecalibration.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/utils/recalibration/QualQuantizer.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/utils/recalibration/QuantizationInfo.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/utils/recalibration/ReadCovariates.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/utils/recalibration/RecalDatum.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/utils/recalibration/RecalDatumNode.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/utils/recalibration/RecalUtils.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/utils/recalibration/RecalibrationReport.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/utils/recalibration/RecalibrationTables.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/utils/recalibration/covariates/ContextCovariate.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/utils/recalibration/covariates/Covariate.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/utils/recalibration/covariates/CycleCovariate.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/utils/recalibration/covariates/ExperimentalCovariate.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/utils/recalibration/covariates/QualityScoreCovariate.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/utils/recalibration/covariates/ReadGroupCovariate.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/utils/recalibration/covariates/RepeatCovariate.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/utils/recalibration/covariates/RepeatLengthCovariate.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/utils/recalibration/covariates/RepeatUnitAndLengthCovariate.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/utils/recalibration/covariates/RepeatUnitCovariate.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/utils/recalibration/covariates/RequiredCovariate.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/utils/recalibration/covariates/StandardCovariate.java (100%)
 rename protected/{java/src => gatk-protected/src/main/java}/org/broadinstitute/sting/utils/sam/ClippedGATKSAMRecord.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/gatk/walkers/WalkerTestIntegrationTest.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/gatk/walkers/annotator/RankSumUnitTest.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/gatk/walkers/annotator/SnpEffUnitTest.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/gatk/walkers/annotator/VariantOverlapAnnotatorUnitTest.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/gatk/walkers/beagle/BeagleIntegrationTest.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/gatk/walkers/bqsr/AnalyzeCovariatesIntegrationTest.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRGathererUnitTest.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRIntegrationTest.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/gatk/walkers/bqsr/ReadRecalibrationInfoUnitTest.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/gatk/walkers/compression/reducereads/BaseCountsUnitTest.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/gatk/walkers/compression/reducereads/HeaderElementUnitTest.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReadsIntegrationTest.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReadsUnitTest.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SlidingWindowUnitTest.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/gatk/walkers/diagnostics/BaseCoverageDistributionIntegrationTest.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/gatk/walkers/diagnostics/ErrorRatePerCycleIntegrationTest.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/gatk/walkers/diagnostics/ReadGroupPropertiesIntegrationTest.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/DiagnoseTargetsIntegrationTest.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/LocusStatisticsUnitTest.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/gatk/walkers/diagnostics/missing/QualifyMissingIntervalsUnitTest.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/gatk/walkers/diffengine/DiffEngineUnitTest.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/gatk/walkers/diffengine/DiffNodeUnitTest.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/gatk/walkers/diffengine/DiffObjectsIntegrationTest.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/gatk/walkers/diffengine/DiffableReaderUnitTest.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/gatk/walkers/diffengine/DifferenceUnitTest.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceIntegrationTest.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationIntegrationTest.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/gatk/walkers/genotyper/ArtificialReadPileupTestProvider.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/gatk/walkers/genotyper/BiasedDownsamplingIntegrationTest.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyGenotypeLikelihoodsUnitTest.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsUnitTest.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngineUnitTest.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperGeneralPloidySuite1IntegrationTest.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperGeneralPloidySuite2IntegrationTest.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperGeneralPloidyTestExecutor.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIndelCallingIntegrationTest.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperLargeScaleTest.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperNormalCallingIntegrationTest.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperReducedReadsIntegrationTest.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcPerformanceUnitTest.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcResultUnitTest.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcUnitTest.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/GeneralPloidyAFCalculationModelUnitTest.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/IndependentAllelesDiploidExactAFCalcUnitTest.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ActiveRegionTestDataSetUnitTest.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/gatk/walkers/haplotypecaller/AssemblyResultSetUnitTest.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/gatk/walkers/haplotypecaller/Civar.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/gatk/walkers/haplotypecaller/CivarUnitTest.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/gatk/walkers/haplotypecaller/GenotypingEngineUnitTest.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HCLikelihoodCalculationEnginesBenchmark.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerGVCFIntegrationTest.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerModesIntegrationTest.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerParallelIntegrationTest.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/gatk/walkers/haplotypecaller/KMerCounterCaseFixUnitTest.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/gatk/walkers/haplotypecaller/KmerUnitTest.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LocalAssemblyEngineUnitTest.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/gatk/walkers/haplotypecaller/PairHMMLikelihoodCalculationEngineUnitTest.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ReadErrorCorrectorUnitTest.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ReadThreadingLikelihoodCalculationEngineUnitTest.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ReferenceConfidenceModelUnitTest.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/BaseEdgeUnitTest.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/BaseGraphUnitTest.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/BaseVertexUnitTest.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/CommonSuffixMergerUnitTest.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/CommonSuffixSplitterUnitTest.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/DeBruijnVertexUnitTest.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/GraphUtilsUnitTest.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/HaplotypeGraphUnitTest.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/KBestPathsUnitTest.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/LowWeightChainPrunerUnitTest.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/MultiSampleEdgeUnitTest.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/PathUnitTest.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/RouteUnitTest.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/SeqGraphUnitTest.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/SeqVertexUnitTest.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/SharedVertexSequenceSplitterUnitTest.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/gatk/walkers/haplotypecaller/readthreading/ReadThreadingAssemblerUnitTest.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/gatk/walkers/haplotypecaller/readthreading/ReadThreadingGraphUnitTest.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/gatk/walkers/haplotypecaller/readthreading/SequenceForKmersUnitTest.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/gatk/walkers/indels/ConstrainedMateFixingManagerUnitTest.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerIntegrationTest.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerLargeScaleTest.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerUnitTest.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModelUnitTest.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/gatk/walkers/indels/ReadBinUnitTest.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreatorIntegrationTest.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreatorLargeScaleTest.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmissionIntegrationTest.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingIntegrationTest.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/gatk/walkers/rnaseq/SplitNCigarReadsIntegrationTests.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/gatk/walkers/rnaseq/SplitNCigarReadsUnitTest.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/gatk/walkers/simulatereads/SimulateReadsForVariantsIntegrationTest.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmpliconsIntegrationTest.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/gatk/walkers/validation/ValidationSiteSelectorIntegrationTest.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalkerUnitTest.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/manager/StratificationManagerUnitTest.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibrationUnitTest.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManagerUnitTest.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantGaussianMixtureModelUnitTest.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/gatk/walkers/variantutils/CombineReferenceCalculationVariantsIntegrationTest.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsIntegrationTest.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsUnitTest.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/gatk/walkers/variantutils/ConcordanceMetricsUnitTest.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/gatk/walkers/variantutils/GenotypeConcordanceIntegrationTest.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignAndTrimVariantsIntegrationTest.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignAndTrimVariantsUnitTest.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariantsIntegrationTest.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/gatk/walkers/variantutils/PosteriorLikelihoodsUtilsUnitTest.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/gatk/walkers/variantutils/RegenotypeVariantsIntegrationTest.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsParallelIntegrationTest.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/gatk/walkers/variantutils/VCFStreamingIntegrationTest.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariantsIntegrationTest.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToAllelicPrimitivesIntegrationTest.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToBinaryPedIntegrationTest.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTableIntegrationTest.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCFIntegrationTest.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/utils/ContigComparatorUnitTest.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/utils/RandomDNA.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/utils/collections/CountSetUnitTest.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/utils/genotyper/DiploidGenotypeUnitTest.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/utils/genotyper/MostLikelyAlleleUnitTest.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/utils/genotyper/PerReadAlleleLikelihoodMapUnitTest.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/utils/gvcf/GVCFWriterUnitTest.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/utils/gvcf/HomRefBlockUnitTest.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/utils/haplotype/HaplotypeBaseComparatorUnitTest.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/utils/haplotype/HaplotypeLDCalculatorUnitTest.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/utils/haplotype/HaplotypeScoreComparatorUnitTest.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/utils/haplotype/HaplotypeSizeAndBaseComparatorUnitTest.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/utils/haplotype/LDMergerUnitTest.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/utils/haplotypeBAMWriter/HaplotypeBAMWriterUnitTest.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/utils/nanoScheduler/NanoSchedulerIntegrationTest.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/utils/pairhmm/ActiveRegionTestDataSet.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/utils/pairhmm/CnyPairHMMUnitTest.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/utils/pairhmm/FastLoglessPairHMMUnitTest.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/utils/pairhmm/PairHMMEmpiricalBenchmark.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/utils/pairhmm/PairHMMModelUnitTest.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/utils/pairhmm/PairHMMProbabilityBugIntegrationTest.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/utils/pairhmm/PairHMMSyntheticBenchmark.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/utils/pairhmm/PairHMMTestData.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/utils/pairhmm/PairHMMUnitTest.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/utils/recalibration/ContextCovariateUnitTest.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/utils/recalibration/CycleCovariateUnitTest.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/utils/recalibration/QualQuantizerUnitTest.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/utils/recalibration/ReadCovariatesUnitTest.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/utils/recalibration/ReadGroupCovariateUnitTest.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/utils/recalibration/RecalDatumUnitTest.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/utils/recalibration/RecalUtilsUnitTest.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/utils/recalibration/RecalibrationReportUnitTest.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/utils/recalibration/RecalibrationTablesUnitTest.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/utils/recalibration/RecalibrationTestUtils.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/utils/recalibration/RepeatCovariatesUnitTest.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/utils/smithwaterman/GlobalEdgeGreedySWPairwiseAlignmentUnitTest.java (100%)
 rename protected/{java/test => gatk-protected/src/test/java}/org/broadinstitute/sting/utils/smithwaterman/SWPairwiseAlignmentUnitTest.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/net/sf/samtools/GATKBAMFileSpan.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/net/sf/samtools/GATKBin.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/net/sf/samtools/GATKChunk.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/net/sf/samtools/PicardNamespaceUtils.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/alignment/Aligner.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/alignment/Alignment.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/alignment/CheckAlignment.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/alignment/bwa/BWAAligner.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/alignment/bwa/BWAConfiguration.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/alignment/bwa/BWTFiles.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/alignment/bwa/c/BWACAligner.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/alignment/bwa/c/BWAPath.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/alignment/bwa/java/AlignerTestHarness.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/alignment/bwa/java/AlignmentMatchSequence.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/alignment/bwa/java/AlignmentState.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/alignment/bwa/java/BWAAlignment.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/alignment/bwa/java/BWAJavaAligner.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/alignment/bwa/java/LowerBound.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/alignment/package-info.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/alignment/reference/bwt/AMBWriter.java (100%)
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 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/alignment/reference/bwt/BWT.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/alignment/reference/bwt/BWTReader.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/alignment/reference/bwt/BWTSupplementaryFileGenerator.java (100%)
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 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/alignment/reference/bwt/Bases.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/alignment/reference/bwt/Counts.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/alignment/reference/bwt/CreateBWTFromReference.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/alignment/reference/bwt/SequenceBlock.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/alignment/reference/bwt/SuffixArray.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/alignment/reference/bwt/SuffixArrayReader.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/alignment/reference/bwt/SuffixArrayWriter.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/alignment/reference/packing/BasePackedInputStream.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/alignment/reference/packing/BasePackedOutputStream.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/alignment/reference/packing/CreatePACFromReference.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/alignment/reference/packing/PackUtils.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/alignment/reference/packing/UnsignedIntPackedInputStream.java (100%)
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 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/commandline/Advanced.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/commandline/Argument.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/commandline/ArgumentCollection.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/commandline/ArgumentDefinition.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/commandline/ArgumentDefinitionGroup.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/commandline/ArgumentDefinitions.java (100%)
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 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/commandline/ArgumentIOType.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/commandline/ArgumentMatch.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/commandline/ArgumentMatchFileValue.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/commandline/ArgumentMatchSite.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/commandline/ArgumentMatchSource.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/commandline/ArgumentMatchSourceType.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/commandline/ArgumentMatchStringValue.java (100%)
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 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/commandline/ArgumentMatches.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/commandline/ArgumentSource.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/commandline/ArgumentTypeDescriptor.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/commandline/ClassType.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/commandline/CommandLineProgram.java (100%)
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 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/commandline/EnumerationArgumentDefault.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/commandline/Gather.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/commandline/Gatherer.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/commandline/Hidden.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/commandline/Input.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/commandline/IntervalArgumentCollection.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/commandline/IntervalBinding.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/commandline/MissingArgumentValueException.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/commandline/Output.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/commandline/ParsedArgs.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/commandline/ParsedListArgs.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/commandline/ParsingEngine.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/commandline/ParsingEngineArgumentFiles.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/commandline/ParsingEngineArgumentProvider.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/commandline/ParsingMethod.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/commandline/RodBinding.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/commandline/RodBindingCollection.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/commandline/Tags.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/commandline/package-info.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/CommandLineExecutable.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/CommandLineGATK.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/ReadMetrics.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/ReadProperties.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/WalkerManager.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/arguments/DbsnpArgumentCollection.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/arguments/StandardVariantContextInputArgumentCollection.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/arguments/ValidationExclusion.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/contexts/AlignmentContext.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/contexts/AlignmentContextUtils.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/contexts/ReferenceContext.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/datasources/package-info.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/datasources/providers/AllLocusView.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/datasources/providers/CoveredLocusView.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/datasources/providers/IntervalOverlappingRODsFromStream.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/datasources/providers/IntervalReferenceOrderedView.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/datasources/providers/InvalidPositionException.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/datasources/providers/LocusReferenceView.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/datasources/providers/LocusShardDataProvider.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/datasources/providers/LocusView.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/datasources/providers/ManagingReferenceOrderedView.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/datasources/providers/RODMetaDataContainer.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/datasources/providers/ReadBasedReferenceOrderedView.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/datasources/providers/ReadReferenceView.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/datasources/providers/ReadShardDataProvider.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/datasources/providers/ReadView.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/datasources/providers/ReferenceOrderedView.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/datasources/providers/ReferenceView.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/datasources/providers/RodLocusView.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/datasources/providers/ShardDataProvider.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/datasources/providers/View.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/datasources/providers/package-info.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/datasources/reads/ActiveRegionShardBalancer.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/datasources/reads/BAMAccessPlan.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/datasources/reads/BAMSchedule.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/datasources/reads/BAMScheduler.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/datasources/reads/BGZFBlockLoadingDispatcher.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/datasources/reads/BlockInputStream.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/datasources/reads/BlockLoader.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/datasources/reads/FileHandleCache.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/datasources/reads/FilePointer.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/datasources/reads/GATKBAMIndex.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/datasources/reads/GATKBAMIndexData.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/datasources/reads/IntervalOverlapFilteringIterator.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/datasources/reads/IntervalSharder.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/datasources/reads/LocusShard.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/datasources/reads/LocusShardBalancer.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/datasources/reads/ReadShard.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/datasources/reads/ReadShardBalancer.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/datasources/reads/SAMDataSource.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/datasources/reads/SAMReaderID.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/datasources/reads/Shard.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/datasources/reads/ShardBalancer.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/datasources/reads/package-info.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/datasources/reads/utilities/BAMFileStat.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/datasources/reads/utilities/BAMTagRenamer.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/datasources/reads/utilities/FindLargeShards.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/datasources/reads/utilities/PrintBAMRegion.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/datasources/reads/utilities/PrintBGZFBounds.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/datasources/reads/utilities/UnzipSingleBlock.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/datasources/reads/utilities/package-info.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/datasources/reference/ReferenceDataSource.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/datasources/reference/package-info.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/datasources/rmd/DataStreamSegment.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/datasources/rmd/EntireStream.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/datasources/rmd/MappedStreamSegment.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/datasources/rmd/ReferenceOrderedDataPool.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/datasources/rmd/ReferenceOrderedDataSource.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/datasources/rmd/ResourcePool.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/datasources/rmd/package-info.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/downsampling/AlleleBiasedDownsamplingUtils.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/downsampling/DownsampleType.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/downsampling/Downsampler.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/downsampling/DownsamplingMethod.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/downsampling/DownsamplingReadsIterator.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/downsampling/DownsamplingUtils.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/downsampling/FractionalDownsampler.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/downsampling/FractionalDownsamplerFactory.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/downsampling/LevelingDownsampler.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/downsampling/PassThroughDownsampler.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/downsampling/PerSampleDownsamplingReadsIterator.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/downsampling/ReadsDownsampler.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/downsampling/ReadsDownsamplerFactory.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/downsampling/ReservoirDownsampler.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/downsampling/ReservoirDownsamplerFactory.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/downsampling/SimplePositionalDownsampler.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/downsampling/SimplePositionalDownsamplerFactory.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/examples/GATKDocsExample.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/examples/GATKPaperGenotyper.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/executive/Accumulator.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/executive/HierarchicalMicroScheduler.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/executive/HierarchicalMicroSchedulerMBean.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/executive/LinearMicroScheduler.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/executive/MicroScheduler.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/executive/MicroSchedulerMBean.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/executive/OutputMergeTask.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/executive/ReduceTree.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/executive/ShardTraverser.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/executive/TreeReducer.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/executive/WindowMaker.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/executive/package-info.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/filters/BadCigarFilter.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/filters/BadMateFilter.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/filters/CountingFilteringIterator.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/filters/DuplicateReadFilter.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/filters/FailsVendorQualityCheckFilter.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/filters/FilterManager.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/filters/LibraryReadFilter.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/filters/MalformedReadFilter.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/filters/MappingQualityFilter.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/filters/MappingQualityUnavailableFilter.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/filters/MappingQualityZeroFilter.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/filters/MateSameStrandFilter.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/filters/MaxInsertSizeFilter.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/filters/MissingReadGroupFilter.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/filters/NoOriginalQualityScoresFilter.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/filters/NotPrimaryAlignmentFilter.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/filters/Platform454Filter.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/filters/PlatformFilter.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/filters/PlatformUnitFilter.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/filters/PlatformUnitFilterHelper.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/filters/ReadFilter.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/filters/ReadGroupBlackListFilter.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/filters/ReadLengthFilter.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/filters/ReadNameFilter.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/filters/ReadStrandFilter.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/filters/ReassignMappingQualityFilter.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/filters/ReassignOneMappingQualityFilter.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/filters/SampleFilter.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/filters/SingleReadGroupFilter.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/filters/UnmappedReadFilter.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/filters/package-info.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/io/DirectOutputTracker.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/io/FastqFileWriter.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/io/OutputTracker.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/io/StingSAMFileWriter.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/io/ThreadGroupOutputTracker.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/io/storage/OutputStreamStorage.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/io/storage/SAMFileWriterStorage.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/io/storage/Storage.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/io/storage/StorageFactory.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/io/storage/VariantContextWriterStorage.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/io/stubs/OutputStreamArgumentTypeDescriptor.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/io/stubs/OutputStreamStub.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/io/stubs/SAMFileReaderArgumentTypeDescriptor.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/io/stubs/SAMFileWriterArgumentTypeDescriptor.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/io/stubs/SAMFileWriterStub.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/io/stubs/Stub.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/io/stubs/VCFWriterArgumentTypeDescriptor.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/io/stubs/VariantContextWriterStub.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/iterators/BoundedReadIterator.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/iterators/GATKSAMIterator.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/iterators/GenomeLocusIterator.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/iterators/IterableIterator.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/iterators/MalformedBAMErrorReformatingIterator.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/iterators/NullSAMIterator.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/iterators/PeekingIterator.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/iterators/PositionTrackingIterator.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/iterators/PushbackIterator.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/iterators/ReadFormattingIterator.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/iterators/ReadTransformer.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/iterators/ReadTransformersMode.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/iterators/StingSAMIterator.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/iterators/StingSAMIteratorAdapter.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/iterators/VerifyingSamIterator.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/iterators/package-info.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/package-info.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/phonehome/GATKRunReport.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/phonehome/GATKRunReportException.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/refdata/RODRecordListImpl.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/refdata/RefMetaDataTracker.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/refdata/ReferenceDependentFeatureCodec.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/refdata/ReferenceOrderedDatum.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/refdata/SeekableRODIterator.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/refdata/package-info.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/refdata/tracks/FeatureManager.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/refdata/tracks/IndexDictionaryUtils.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/refdata/tracks/RMDTrack.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/refdata/tracks/RMDTrackBuilder.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/refdata/utils/FeatureToGATKFeatureIterator.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/refdata/utils/FlashBackIterator.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/refdata/utils/GATKFeature.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/refdata/utils/LocationAwareSeekableRODIterator.java (100%)
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 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/walkers/qc/CheckPileup.java (100%)
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 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/walkers/qc/CountRODsByRef.java (100%)
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 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/walkers/qc/PrintRODs.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/walkers/qc/QCRef.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/walkers/qc/ReadClippingStats.java (100%)
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 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/walkers/readutils/ClipReads.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/walkers/readutils/PrintReads.java (100%)
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 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantSummary.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleCount.java (100%)
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 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/CompRod.java (100%)
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 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/EvalRod.java (100%)
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 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/FunctionalClass.java (100%)
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 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/utils/pairhmm/PairHMMReadyHaplotypes.java (100%)
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 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/utils/pileup/PileupElement.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/utils/pileup/PileupElementFilter.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/utils/pileup/PileupElementTracker.java (100%)
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 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/utils/runtime/OutputStreamSettings.java (100%)
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 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/utils/variant/GATKVCFIndexType.java (100%)
 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/utils/variant/GATKVCFUtils.java (100%)
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 rename public/{java/src => gatk-framework/src/main/java}/org/broadinstitute/sting/utils/wiggle/WiggleWriter.java (100%)
 rename public/{java/test => gatk-framework/src/test/java}/net/sf/samtools/GATKBAMFileSpanUnitTest.java (100%)
 rename public/{java/test => gatk-framework/src/test/java}/net/sf/samtools/GATKChunkUnitTest.java (100%)
 rename public/{java/test => gatk-framework/src/test/java}/org/broadinstitute/sting/BaseTest.java (100%)
 rename public/{java/test => gatk-framework/src/test/java}/org/broadinstitute/sting/ExampleToCopyUnitTest.java (100%)
 rename public/{java/test => gatk-framework/src/test/java}/org/broadinstitute/sting/MD5DB.java (100%)
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 rename public/{java/test => gatk-framework/src/test/java}/org/broadinstitute/sting/StingTextReporter.java (100%)
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 rename public/{java/test => gatk-framework/src/test/java}/org/broadinstitute/sting/WalkerTest.java (100%)
 rename public/{java/test => gatk-framework/src/test/java}/org/broadinstitute/sting/commandline/ArgumentMatchSiteUnitTest.java (100%)
 rename public/{java/test => gatk-framework/src/test/java}/org/broadinstitute/sting/commandline/ArgumentMatchSourceUnitTest.java (100%)
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 rename public/{java/test => gatk-framework/src/test/java}/org/broadinstitute/sting/commandline/RodBindingUnitTest.java (100%)
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 rename public/{java/test => gatk-framework/src/test/java}/org/broadinstitute/sting/gatk/GenomeAnalysisEngineUnitTest.java (100%)
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 rename public/{java/test => gatk-framework/src/test/java}/org/broadinstitute/sting/gatk/datasources/providers/AllLocusViewUnitTest.java (100%)
 rename public/{java/test => gatk-framework/src/test/java}/org/broadinstitute/sting/gatk/datasources/providers/CoveredLocusViewUnitTest.java (100%)
 rename public/{java/test => gatk-framework/src/test/java}/org/broadinstitute/sting/gatk/datasources/providers/IntervalReferenceOrderedViewUnitTest.java (100%)
 rename public/{java/test => gatk-framework/src/test/java}/org/broadinstitute/sting/gatk/datasources/providers/LocusReferenceViewUnitTest.java (100%)
 rename public/{java/test => gatk-framework/src/test/java}/org/broadinstitute/sting/gatk/datasources/providers/LocusViewTemplate.java (100%)
 rename public/{java/test => gatk-framework/src/test/java}/org/broadinstitute/sting/gatk/datasources/providers/ReadReferenceViewUnitTest.java (100%)
 rename public/{java/test => gatk-framework/src/test/java}/org/broadinstitute/sting/gatk/datasources/providers/ReferenceOrderedViewUnitTest.java (100%)
 rename public/{java/test => gatk-framework/src/test/java}/org/broadinstitute/sting/gatk/datasources/providers/ReferenceViewTemplate.java (100%)
 rename public/{java/test => gatk-framework/src/test/java}/org/broadinstitute/sting/gatk/datasources/providers/ShardDataProviderUnitTest.java (100%)
 rename public/{java/test => gatk-framework/src/test/java}/org/broadinstitute/sting/gatk/datasources/reads/ActiveRegionShardBalancerUnitTest.java (100%)
 rename public/{java/test => gatk-framework/src/test/java}/org/broadinstitute/sting/gatk/datasources/reads/DownsamplerBenchmark.java (100%)
 rename public/{java/test => gatk-framework/src/test/java}/org/broadinstitute/sting/gatk/datasources/reads/FilePointerUnitTest.java (100%)
 rename public/{java/test => gatk-framework/src/test/java}/org/broadinstitute/sting/gatk/datasources/reads/GATKBAMIndexUnitTest.java (100%)
 rename public/{java/test => gatk-framework/src/test/java}/org/broadinstitute/sting/gatk/datasources/reads/GATKWalkerBenchmark.java (100%)
 rename public/{java/test => gatk-framework/src/test/java}/org/broadinstitute/sting/gatk/datasources/reads/IntervalOverlapFilteringIteratorUnitTest.java (100%)
 rename public/{java/test => gatk-framework/src/test/java}/org/broadinstitute/sting/gatk/datasources/reads/MockLocusShard.java (100%)
 rename public/{java/test => gatk-framework/src/test/java}/org/broadinstitute/sting/gatk/datasources/reads/PicardBaselineBenchmark.java (100%)
 rename public/{java/test => gatk-framework/src/test/java}/org/broadinstitute/sting/gatk/datasources/reads/ReadProcessingBenchmark.java (100%)
 rename public/{java/test => gatk-framework/src/test/java}/org/broadinstitute/sting/gatk/datasources/reads/ReadShardBalancerUnitTest.java (100%)
 rename public/{java/test => gatk-framework/src/test/java}/org/broadinstitute/sting/gatk/datasources/reads/SAMDataSourceUnitTest.java (100%)
 rename public/{java/test => gatk-framework/src/test/java}/org/broadinstitute/sting/gatk/datasources/reads/SAMReaderIDUnitTest.java (100%)
 rename public/{java/test => gatk-framework/src/test/java}/org/broadinstitute/sting/gatk/datasources/reads/SeekableBufferedStreamUnitTest.java (100%)
 rename public/{java/test => gatk-framework/src/test/java}/org/broadinstitute/sting/gatk/datasources/reads/TheoreticalMinimaBenchmark.java (100%)
 rename public/{java/test => gatk-framework/src/test/java}/org/broadinstitute/sting/gatk/datasources/reference/ReferenceDataSourceIntegrationTest.java (100%)
 rename public/{java/test => gatk-framework/src/test/java}/org/broadinstitute/sting/gatk/datasources/rmd/ReferenceOrderedDataPoolUnitTest.java (100%)
 rename public/{java/test => gatk-framework/src/test/java}/org/broadinstitute/sting/gatk/datasources/rmd/ReferenceOrderedQueryDataPoolUnitTest.java (100%)
 rename public/{java/test => gatk-framework/src/test/java}/org/broadinstitute/sting/gatk/downsampling/AlleleBiasedDownsamplingUtilsUnitTest.java (100%)
 rename public/{java/test => gatk-framework/src/test/java}/org/broadinstitute/sting/gatk/downsampling/DownsamplingIntegrationTest.java (100%)
 rename public/{java/test => gatk-framework/src/test/java}/org/broadinstitute/sting/gatk/downsampling/DownsamplingReadsIteratorUnitTest.java (100%)
 rename public/{java/test => gatk-framework/src/test/java}/org/broadinstitute/sting/gatk/downsampling/FractionalDownsamplerUnitTest.java (100%)
 rename public/{java/test => gatk-framework/src/test/java}/org/broadinstitute/sting/gatk/downsampling/LevelingDownsamplerUnitTest.java (100%)
 rename public/{java/test => gatk-framework/src/test/java}/org/broadinstitute/sting/gatk/downsampling/PerSampleDownsamplingReadsIteratorUnitTest.java (100%)
 rename public/{java/test => gatk-framework/src/test/java}/org/broadinstitute/sting/gatk/downsampling/PositionallyDownsampledArtificialSingleSampleReadStreamAnalyzer.java (100%)
 rename public/{java/test => gatk-framework/src/test/java}/org/broadinstitute/sting/gatk/downsampling/ReservoirDownsamplerUnitTest.java (100%)
 rename public/{java/test => gatk-framework/src/test/java}/org/broadinstitute/sting/gatk/downsampling/SimplePositionalDownsamplerUnitTest.java (100%)
 rename public/{java/test => gatk-framework/src/test/java}/org/broadinstitute/sting/gatk/executive/ReduceTreeUnitTest.java (100%)
 rename public/{java/test => gatk-framework/src/test/java}/org/broadinstitute/sting/gatk/filters/AllowNCigarMalformedReadFilterUnitTest.java (100%)
 rename public/{java/test => gatk-framework/src/test/java}/org/broadinstitute/sting/gatk/filters/BadCigarFilterUnitTest.java (100%)
 rename public/{java/test => gatk-framework/src/test/java}/org/broadinstitute/sting/gatk/filters/BadReadGroupsIntegrationTest.java (100%)
 rename public/{java/test => gatk-framework/src/test/java}/org/broadinstitute/sting/gatk/filters/MalformedReadFilterUnitTest.java (100%)
 rename public/{java/test => gatk-framework/src/test/java}/org/broadinstitute/sting/gatk/filters/ReadFilterTest.java (100%)
 rename public/{java/test => gatk-framework/src/test/java}/org/broadinstitute/sting/gatk/filters/ReadGroupBlackListFilterUnitTest.java (100%)
 rename public/{java/test => gatk-framework/src/test/java}/org/broadinstitute/sting/gatk/filters/UnsafeMalformedReadFilterUnitTest.java (100%)
 rename public/{java/test => gatk-framework/src/test/java}/org/broadinstitute/sting/gatk/iterators/BoundedReadIteratorUnitTest.java (100%)
 rename public/{java/test => gatk-framework/src/test/java}/org/broadinstitute/sting/gatk/iterators/ReadFormattingIteratorUnitTest.java (100%)
 rename public/{java/test => gatk-framework/src/test/java}/org/broadinstitute/sting/gatk/iterators/StingSAMIteratorAdapterUnitTest.java (100%)
 rename public/{java/test => gatk-framework/src/test/java}/org/broadinstitute/sting/gatk/iterators/VerifyingSamIteratorUnitTest.java (100%)
 rename public/{java/test => gatk-framework/src/test/java}/org/broadinstitute/sting/gatk/refdata/RefMetaDataTrackerUnitTest.java (100%)
 rename public/{java/test => gatk-framework/src/test/java}/org/broadinstitute/sting/gatk/refdata/tracks/FeatureManagerUnitTest.java (100%)
 rename public/{java/test => gatk-framework/src/test/java}/org/broadinstitute/sting/gatk/refdata/tracks/RMDTrackBuilderUnitTest.java (100%)
 rename public/{java/test => gatk-framework/src/test/java}/org/broadinstitute/sting/gatk/refdata/utils/CheckableCloseableTribbleIterator.java (100%)
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 rename public/{java/test => gatk-framework/src/test/java}/org/broadinstitute/sting/gatk/refdata/utils/FlashBackIteratorUnitTest.java (100%)
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 rename public/{java/test => gatk-framework/src/test/java}/org/broadinstitute/sting/gatk/refdata/utils/TestRMDTrackBuilder.java (100%)
 rename public/{java/test => gatk-framework/src/test/java}/org/broadinstitute/sting/gatk/report/GATKReportUnitTest.java (100%)
 rename public/{java/test => gatk-framework/src/test/java}/org/broadinstitute/sting/gatk/samples/PedReaderUnitTest.java (100%)
 rename public/{java/test => gatk-framework/src/test/java}/org/broadinstitute/sting/gatk/samples/SampleDBUnitTest.java (100%)
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 rename public/{java/test => gatk-framework/src/test/java}/org/broadinstitute/sting/gatk/traversals/DummyActiveRegionWalker.java (100%)
 rename public/{java/test => gatk-framework/src/test/java}/org/broadinstitute/sting/gatk/traversals/TAROrderedReadCacheUnitTest.java (100%)
 rename public/{java/test => gatk-framework/src/test/java}/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegionsUnitTest.java (100%)
 rename public/{java/test => gatk-framework/src/test/java}/org/broadinstitute/sting/gatk/traversals/TraverseDuplicatesUnitTest.java (100%)
 rename public/{java/test => gatk-framework/src/test/java}/org/broadinstitute/sting/gatk/traversals/TraverseReadsUnitTest.java (100%)
 rename public/{java/test => gatk-framework/src/test/java}/org/broadinstitute/sting/gatk/walkers/BAQIntegrationTest.java (100%)
 rename public/{java/test => gatk-framework/src/test/java}/org/broadinstitute/sting/gatk/walkers/CNV/SymbolicAllelesIntegrationTest.java (100%)
 rename public/{java/test => gatk-framework/src/test/java}/org/broadinstitute/sting/gatk/walkers/annotator/SnpEffUtilUnitTest.java (100%)
 rename public/{java/test => gatk-framework/src/test/java}/org/broadinstitute/sting/gatk/walkers/coverage/CallableLociIntegrationTest.java (100%)
 rename public/{java/test => gatk-framework/src/test/java}/org/broadinstitute/sting/gatk/walkers/coverage/CompareCallableLociWalkerIntegrationTest.java (100%)
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 rename public/{java/test => gatk-framework/src/test/java}/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageIntegrationTest.java (100%)
 rename public/{java/test => gatk-framework/src/test/java}/org/broadinstitute/sting/gatk/walkers/qc/CheckPileupIntegrationTest.java (100%)
 rename public/{java/test => gatk-framework/src/test/java}/org/broadinstitute/sting/gatk/walkers/qc/CountReadsUnitTest.java (100%)
 rename public/{java/test => gatk-framework/src/test/java}/org/broadinstitute/sting/gatk/walkers/qc/DictionaryConsistencyIntegrationTest.java (100%)
 rename public/{java/test => gatk-framework/src/test/java}/org/broadinstitute/sting/gatk/walkers/qc/FlagStatIntegrationTest.java (100%)
 rename public/{java/test => gatk-framework/src/test/java}/org/broadinstitute/sting/gatk/walkers/qc/PileupWalkerIntegrationTest.java (100%)
 rename public/{java/test => gatk-framework/src/test/java}/org/broadinstitute/sting/gatk/walkers/readutils/ClipReadsWalkersIntegrationTest.java (100%)
 rename public/{java/test => gatk-framework/src/test/java}/org/broadinstitute/sting/gatk/walkers/readutils/PrintReadsIntegrationTest.java (100%)
 rename public/{java/test => gatk-framework/src/test/java}/org/broadinstitute/sting/gatk/walkers/readutils/PrintReadsLargeScaleTest.java (100%)
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 rename public/{java/test => gatk-framework/src/test/java}/org/broadinstitute/sting/gatk/walkers/readutils/ReadAdaptorTrimmerIntegrationTest.java (100%)
 rename public/{java/test => gatk-framework/src/test/java}/org/broadinstitute/sting/gatk/walkers/variantutils/FilterLiftedVariantsUnitTest.java (100%)
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 rename public/{scala/src => queue-framework/src/main/scala}/org/broadinstitute/sting/queue/extensions/gatk/TaggedFile.scala (100%)
 rename public/{scala/src => queue-framework/src/main/scala}/org/broadinstitute/sting/queue/extensions/gatk/VcfGatherFunction.scala (100%)
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 rename public/{scala/src => queue-framework/src/main/scala}/org/broadinstitute/sting/queue/extensions/picard/AddOrReplaceReadGroups.scala (100%)
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 rename public/{scala/src => queue-framework/src/main/scala}/org/broadinstitute/sting/queue/extensions/picard/FastqToSam.scala (100%)
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 rename public/{scala/src => queue-framework/src/main/scala}/org/broadinstitute/sting/queue/extensions/picard/PicardBamFunction.scala (100%)
 rename public/{scala/src => queue-framework/src/main/scala}/org/broadinstitute/sting/queue/extensions/picard/PicardMetricsFunction.scala (100%)
 rename public/{scala/src => queue-framework/src/main/scala}/org/broadinstitute/sting/queue/extensions/picard/ReorderSam.scala (100%)
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 rename public/{scala/src => queue-framework/src/main/scala}/org/broadinstitute/sting/queue/extensions/picard/SamToFastq.scala (100%)
 rename public/{scala/src => queue-framework/src/main/scala}/org/broadinstitute/sting/queue/extensions/picard/SortSam.scala (100%)
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 rename public/{scala/src => queue-framework/src/main/scala}/org/broadinstitute/sting/queue/extensions/samtools/SamtoolsCommandLineFunction.scala (100%)
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 rename public/{scala/src => queue-framework/src/main/scala}/org/broadinstitute/sting/queue/function/CommandLineFunction.scala (100%)
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 rename public/{scala/src => queue-framework/src/main/scala}/org/broadinstitute/sting/queue/function/RetryMemoryLimit.scala (100%)
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 rename public/{scala/test => queue-framework/src/test/scala}/org/broadinstitute/sting/queue/function/CommandLineFunctionUnitTest.scala (100%)
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 rename public/{scala/test => queue-framework/src/test/scala}/org/broadinstitute/sting/queue/pipeline/examples/ExampleCountReadsPipelineTest.scala (100%)
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 rename public/{scala/test => queue-framework/src/test/scala}/org/broadinstitute/sting/queue/pipeline/examples/ExampleRetryMemoryLimitPipelineTest.scala (100%)
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 rename public/{scala/test => queue-framework/src/test/scala}/org/broadinstitute/sting/queue/util/ShellUtilsUnitTest.scala (100%)
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 rename public/{scala/test => queue-framework/src/test/scala}/org/broadinstitute/sting/queue/util/SystemUtilsUnitTest.scala (100%)

diff --git a/protected/java/src/org/broadinstitute/sting/gatk/arguments/StandardCallerArgumentCollection.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/arguments/StandardCallerArgumentCollection.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/arguments/StandardCallerArgumentCollection.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/arguments/StandardCallerArgumentCollection.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseQualityRankSumTest.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/BaseQualityRankSumTest.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseQualityRankSumTest.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/BaseQualityRankSumTest.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ChromosomeCounts.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/ChromosomeCounts.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ChromosomeCounts.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/ChromosomeCounts.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ClippingRankSumTest.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/ClippingRankSumTest.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ClippingRankSumTest.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/ClippingRankSumTest.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/Coverage.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/Coverage.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/Coverage.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/Coverage.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerAlleleBySample.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerAlleleBySample.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerAlleleBySample.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerAlleleBySample.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerSampleHC.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerSampleHC.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerSampleHC.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerSampleHC.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/GCContent.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/GCContent.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/GCContent.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/GCContent.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HardyWeinberg.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/HardyWeinberg.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HardyWeinberg.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/HardyWeinberg.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HomopolymerRun.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/HomopolymerRun.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HomopolymerRun.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/HomopolymerRun.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/InbreedingCoeff.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/InbreedingCoeff.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/InbreedingCoeff.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/InbreedingCoeff.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/LikelihoodRankSumTest.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/LikelihoodRankSumTest.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/LikelihoodRankSumTest.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/LikelihoodRankSumTest.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MVLikelihoodRatio.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/MVLikelihoodRatio.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MVLikelihoodRatio.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/MVLikelihoodRatio.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityRankSumTest.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityRankSumTest.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityRankSumTest.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityRankSumTest.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZero.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZero.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZero.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZero.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/QualByDepth.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/QualByDepth.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/QualByDepth.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/QualByDepth.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RMSMappingQuality.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/RMSMappingQuality.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RMSMappingQuality.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/RMSMappingQuality.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ReadPosRankSumTest.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/ReadPosRankSumTest.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ReadPosRankSumTest.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/ReadPosRankSumTest.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SampleList.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/SampleList.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SampleList.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/SampleList.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SpanningDeletions.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/SpanningDeletions.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SpanningDeletions.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/SpanningDeletions.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/StrandBiasBySample.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/StrandBiasBySample.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/StrandBiasBySample.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/StrandBiasBySample.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TandemRepeatAnnotator.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/TandemRepeatAnnotator.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TandemRepeatAnnotator.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/TandemRepeatAnnotator.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TransmissionDisequilibriumTest.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/TransmissionDisequilibriumTest.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TransmissionDisequilibriumTest.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/TransmissionDisequilibriumTest.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantType.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/VariantType.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantType.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/VariantType.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/AnalyzeCovariates.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/bqsr/AnalyzeCovariates.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/AnalyzeCovariates.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/bqsr/AnalyzeCovariates.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRGatherer.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRGatherer.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRGatherer.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRGatherer.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/ReadRecalibrationInfo.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/bqsr/ReadRecalibrationInfo.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/ReadRecalibrationInfo.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/bqsr/ReadRecalibrationInfo.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalibrationArgumentCollection.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/bqsr/RecalibrationArgumentCollection.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalibrationArgumentCollection.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/bqsr/RecalibrationArgumentCollection.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalibrationEngine.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/bqsr/RecalibrationEngine.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalibrationEngine.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/bqsr/RecalibrationEngine.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/BaseAndQualsCounts.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/compression/reducereads/BaseAndQualsCounts.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/BaseAndQualsCounts.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/compression/reducereads/BaseAndQualsCounts.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/BaseCounts.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/compression/reducereads/BaseCounts.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/BaseCounts.java
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diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/BaseIndex.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/compression/reducereads/BaseIndex.java
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rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/BaseIndex.java
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diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/CompressionStash.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/compression/reducereads/CompressionStash.java
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rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/CompressionStash.java
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diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/Compressor.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/compression/reducereads/Compressor.java
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rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/Compressor.java
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diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/FinishedGenomeLoc.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/compression/reducereads/FinishedGenomeLoc.java
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rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/FinishedGenomeLoc.java
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diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/HeaderElement.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/compression/reducereads/HeaderElement.java
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diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/MultiSampleCompressor.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/compression/reducereads/MultiSampleCompressor.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/MultiSampleCompressor.java
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diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReads.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReads.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReads.java
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diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReadsStash.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReadsStash.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReadsStash.java
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diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SingleSampleCompressor.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SingleSampleCompressor.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SingleSampleCompressor.java
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diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SlidingWindow.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SlidingWindow.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SlidingWindow.java
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diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SyntheticRead.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SyntheticRead.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SyntheticRead.java
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diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/BaseCoverageDistribution.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/diagnostics/BaseCoverageDistribution.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/BaseCoverageDistribution.java
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diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/FindCoveredIntervals.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/diagnostics/FindCoveredIntervals.java
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diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/AbstractStratification.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/AbstractStratification.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/AbstractStratification.java
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diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/CallableStatus.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/CallableStatus.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/CallableStatus.java
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diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/DiagnoseTargets.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/DiagnoseTargets.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/DiagnoseTargets.java
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diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/IntervalMetric.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/IntervalMetric.java
similarity index 100%
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diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/IntervalStratification.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/IntervalStratification.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/IntervalStratification.java
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diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/LocusMetric.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/LocusMetric.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/LocusMetric.java
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diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/LocusMetricCoverageGap.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/LocusMetricCoverageGap.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/LocusMetricCoverageGap.java
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diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/LocusMetricExcessiveCoverage.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/LocusMetricExcessiveCoverage.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/LocusMetricExcessiveCoverage.java
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diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/LocusMetricLowCoverage.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/LocusMetricLowCoverage.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/LocusMetricLowCoverage.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/LocusMetricLowCoverage.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/LocusMetricPoorQuality.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/LocusMetricPoorQuality.java
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rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/LocusMetricPoorQuality.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/LocusMetricPoorQuality.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/LocusStratification.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/LocusStratification.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/LocusStratification.java
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diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/Metric.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/Metric.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/Metric.java
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diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/PluginUtils.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/PluginUtils.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/PluginUtils.java
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diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/SampleMetric.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/SampleMetric.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/SampleMetric.java
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diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/SampleMetricBadMates.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/SampleMetricBadMates.java
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rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/SampleMetricBadMates.java
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diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/SampleMetricNoReads.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/SampleMetricNoReads.java
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rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/SampleMetricNoReads.java
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diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/SampleStratification.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/SampleStratification.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/SampleStratification.java
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diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/ThresHolder.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/ThresHolder.java
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rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/ThresHolder.java
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diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/missing/Metrics.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/diagnostics/missing/Metrics.java
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rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/missing/Metrics.java
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diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/missing/QualifyMissingIntervals.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/diagnostics/missing/QualifyMissingIntervals.java
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diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/BaseMismatchModel.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/BaseMismatchModel.java
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diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ConsensusAlleleCounter.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/ConsensusAlleleCounter.java
similarity index 100%
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diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidSNPGenotypeLikelihoods.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidSNPGenotypeLikelihoods.java
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diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ErrorModel.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/ErrorModel.java
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diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyGenotypeLikelihoods.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyGenotypeLikelihoods.java
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diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyGenotypeLikelihoodsCalculationModel.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyGenotypeLikelihoodsCalculationModel.java
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diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyIndelGenotypeLikelihoods.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyIndelGenotypeLikelihoods.java
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rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyIndelGenotypeLikelihoods.java
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diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyIndelGenotypeLikelihoodsCalculationModel.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyIndelGenotypeLikelihoodsCalculationModel.java
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rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyIndelGenotypeLikelihoodsCalculationModel.java
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diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidySNPGenotypeLikelihoods.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidySNPGenotypeLikelihoods.java
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rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidySNPGenotypeLikelihoods.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidySNPGenotypeLikelihoods.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidySNPGenotypeLikelihoodsCalculationModel.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidySNPGenotypeLikelihoodsCalculationModel.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidySNPGenotypeLikelihoodsCalculationModel.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidySNPGenotypeLikelihoodsCalculationModel.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeLikelihoodsCalculationModel.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeLikelihoodsCalculationModel.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeLikelihoodsCalculationModel.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeLikelihoodsCalculationModel.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypePriors.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypePriors.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypePriors.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypePriors.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/PoolGenotypePriors.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/PoolGenotypePriors.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/PoolGenotypePriors.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/PoolGenotypePriors.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ProbabilityVector.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/ProbabilityVector.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ProbabilityVector.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/ProbabilityVector.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/VariantCallContext.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/VariantCallContext.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/VariantCallContext.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/VariantCallContext.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalc.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalc.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalc.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalc.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcFactory.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcFactory.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcFactory.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcFactory.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcPerformanceTest.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcPerformanceTest.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcPerformanceTest.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcPerformanceTest.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcResult.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcResult.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcResult.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcResult.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcTestBuilder.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcTestBuilder.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcTestBuilder.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcTestBuilder.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/DiploidExactAFCalc.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/DiploidExactAFCalc.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/DiploidExactAFCalc.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/DiploidExactAFCalc.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/ExactACcounts.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/ExactACcounts.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/ExactACcounts.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/ExactACcounts.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/ExactACset.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/ExactACset.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/ExactACset.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/ExactACset.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/ExactAFCalc.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/ExactAFCalc.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/ExactAFCalc.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/ExactAFCalc.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/ExactCallLogger.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/ExactCallLogger.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/ExactCallLogger.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/ExactCallLogger.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/GeneralPloidyExactAFCalc.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/GeneralPloidyExactAFCalc.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/GeneralPloidyExactAFCalc.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/GeneralPloidyExactAFCalc.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/IndependentAllelesDiploidExactAFCalc.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/IndependentAllelesDiploidExactAFCalc.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/IndependentAllelesDiploidExactAFCalc.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/IndependentAllelesDiploidExactAFCalc.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/OriginalDiploidExactAFCalc.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/OriginalDiploidExactAFCalc.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/OriginalDiploidExactAFCalc.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/OriginalDiploidExactAFCalc.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/ReferenceDiploidExactAFCalc.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/ReferenceDiploidExactAFCalc.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/ReferenceDiploidExactAFCalc.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/ReferenceDiploidExactAFCalc.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/StateTracker.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/StateTracker.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/StateTracker.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/StateTracker.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ActiveRegionTrimmer.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ActiveRegionTrimmer.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ActiveRegionTrimmer.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ActiveRegionTrimmer.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/AssemblyResult.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/AssemblyResult.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/AssemblyResult.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/AssemblyResult.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/AssemblyResultSet.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/AssemblyResultSet.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/AssemblyResultSet.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/AssemblyResultSet.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/EventBlock.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/EventBlock.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/EventBlock.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/EventBlock.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/EventBlockFinder.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/EventBlockFinder.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/EventBlockFinder.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/EventBlockFinder.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/GenotypingEngine.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/GenotypingEngine.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/GenotypingEngine.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/GenotypingEngine.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/GraphBasedLikelihoodCalculationEngine.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/GraphBasedLikelihoodCalculationEngine.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/GraphBasedLikelihoodCalculationEngine.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/GraphBasedLikelihoodCalculationEngine.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/GraphBasedLikelihoodCalculationEngineInstance.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/GraphBasedLikelihoodCalculationEngineInstance.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/GraphBasedLikelihoodCalculationEngineInstance.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/GraphBasedLikelihoodCalculationEngineInstance.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeResolver.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeResolver.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeResolver.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeResolver.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeRoute.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeRoute.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeRoute.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeRoute.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HeterogeneousKmerSizeResolution.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HeterogeneousKmerSizeResolution.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HeterogeneousKmerSizeResolution.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HeterogeneousKmerSizeResolution.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/KMerCounter.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/KMerCounter.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/KMerCounter.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/KMerCounter.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/Kmer.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/Kmer.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/Kmer.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/Kmer.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/KmerSequence.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/KmerSequence.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/KmerSequence.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/KmerSequence.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/KmerSequenceGraphMap.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/KmerSequenceGraphMap.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/KmerSequenceGraphMap.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/KmerSequenceGraphMap.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LikelihoodCalculationEngine.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LikelihoodCalculationEngine.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LikelihoodCalculationEngine.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LikelihoodCalculationEngine.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LocalAssemblyEngine.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LocalAssemblyEngine.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LocalAssemblyEngine.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LocalAssemblyEngine.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/PairHMMLikelihoodCalculationEngine.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/PairHMMLikelihoodCalculationEngine.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/PairHMMLikelihoodCalculationEngine.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/PairHMMLikelihoodCalculationEngine.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/RandomLikelihoodCalculationEngine.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/RandomLikelihoodCalculationEngine.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/RandomLikelihoodCalculationEngine.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/RandomLikelihoodCalculationEngine.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ReadAnchoring.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ReadAnchoring.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ReadAnchoring.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ReadAnchoring.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ReadCost.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ReadCost.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ReadCost.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ReadCost.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ReadErrorCorrector.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ReadErrorCorrector.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ReadErrorCorrector.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ReadErrorCorrector.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ReadSegmentComparator.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ReadSegmentComparator.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ReadSegmentComparator.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ReadSegmentComparator.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ReadSegmentCost.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ReadSegmentCost.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ReadSegmentCost.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ReadSegmentCost.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/RefVsAnyResult.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/RefVsAnyResult.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/RefVsAnyResult.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/RefVsAnyResult.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ReferenceConfidenceModel.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ReferenceConfidenceModel.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ReferenceConfidenceModel.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ReferenceConfidenceModel.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/BaseEdge.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/BaseEdge.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/BaseEdge.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/BaseEdge.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/BaseGraph.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/BaseGraph.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/BaseGraph.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/BaseGraph.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/BaseGraphIterator.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/BaseGraphIterator.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/BaseGraphIterator.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/BaseGraphIterator.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/BaseVertex.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/BaseVertex.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/BaseVertex.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/BaseVertex.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/CommonSuffixSplitter.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/CommonSuffixSplitter.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/CommonSuffixSplitter.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/CommonSuffixSplitter.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/DeBruijnVertex.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/DeBruijnVertex.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/DeBruijnVertex.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/DeBruijnVertex.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/GraphUtils.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/GraphUtils.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/GraphUtils.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/GraphUtils.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/KBestPaths.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/KBestPaths.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/KBestPaths.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/KBestPaths.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/KmerSearchableGraph.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/KmerSearchableGraph.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/KmerSearchableGraph.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/KmerSearchableGraph.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/LowWeightChainPruner.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/LowWeightChainPruner.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/LowWeightChainPruner.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/LowWeightChainPruner.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/MultiSampleEdge.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/MultiSampleEdge.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/MultiSampleEdge.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/MultiSampleEdge.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/Path.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/Path.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/Path.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/Path.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/Route.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/Route.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/Route.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/Route.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/RouteFinder.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/RouteFinder.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/RouteFinder.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/RouteFinder.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/SeqGraph.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/SeqGraph.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/SeqGraph.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/SeqGraph.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/SeqVertex.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/SeqVertex.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/SeqVertex.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/SeqVertex.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/SharedSequenceMerger.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/SharedSequenceMerger.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/SharedSequenceMerger.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/SharedSequenceMerger.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/SharedVertexSequenceSplitter.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/SharedVertexSequenceSplitter.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/SharedVertexSequenceSplitter.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/SharedVertexSequenceSplitter.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/TestGraph.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/TestGraph.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/TestGraph.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/TestGraph.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/VertexOrder.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/VertexOrder.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/VertexOrder.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/VertexOrder.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/readthreading/HaplotypeGraph.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/readthreading/HaplotypeGraph.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/readthreading/HaplotypeGraph.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/readthreading/HaplotypeGraph.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/readthreading/MultiDeBruijnVertex.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/readthreading/MultiDeBruijnVertex.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/readthreading/MultiDeBruijnVertex.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/readthreading/MultiDeBruijnVertex.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/readthreading/ReadThreadingAssembler.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/readthreading/ReadThreadingAssembler.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/readthreading/ReadThreadingAssembler.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/readthreading/ReadThreadingAssembler.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/readthreading/ReadThreadingGraph.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/readthreading/ReadThreadingGraph.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/readthreading/ReadThreadingGraph.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/readthreading/ReadThreadingGraph.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/readthreading/SequenceForKmers.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/readthreading/SequenceForKmers.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/readthreading/SequenceForKmers.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/readthreading/SequenceForKmers.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/indels/ConstrainedMateFixingManager.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/indels/ConstrainedMateFixingManager.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/indels/ConstrainedMateFixingManager.java
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diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/indels/HaplotypeIndelErrorModel.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/indels/HaplotypeIndelErrorModel.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/indels/HaplotypeIndelErrorModel.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/indels/HaplotypeIndelErrorModel.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/indels/LeftAlignIndels.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/indels/LeftAlignIndels.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/indels/LeftAlignIndels.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/indels/LeftAlignIndels.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/indels/ReadBin.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/indels/ReadBin.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/indels/ReadBin.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/indels/ReadBin.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/AllelePair.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/phasing/AllelePair.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/AllelePair.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/phasing/AllelePair.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/BaseArray.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/phasing/BaseArray.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/BaseArray.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/phasing/BaseArray.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/CardinalityCounter.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/phasing/CardinalityCounter.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/CardinalityCounter.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/phasing/CardinalityCounter.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/CloneableIteratorLinkedList.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/phasing/CloneableIteratorLinkedList.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/CloneableIteratorLinkedList.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/phasing/CloneableIteratorLinkedList.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/DisjointSet.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/phasing/DisjointSet.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/DisjointSet.java
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diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/Haplotype.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/phasing/Haplotype.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/Haplotype.java
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diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeSegregatingAlternateAllelesVCFWriter.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/phasing/MergeSegregatingAlternateAllelesVCFWriter.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeSegregatingAlternateAllelesVCFWriter.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/phasing/MergeSegregatingAlternateAllelesVCFWriter.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmission.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmission.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmission.java
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diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhasingGraph.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/phasing/PhasingGraph.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhasingGraph.java
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diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhasingGraphEdge.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/phasing/PhasingGraphEdge.java
similarity index 100%
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diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhasingRead.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/phasing/PhasingRead.java
similarity index 100%
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diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhasingUtils.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/phasing/PhasingUtils.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhasingUtils.java
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diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PreciseNonNegativeDouble.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/phasing/PreciseNonNegativeDouble.java
similarity index 100%
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diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasing.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasing.java
similarity index 100%
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diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBase.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/phasing/ReadBase.java
similarity index 100%
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diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBasesAtPosition.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/phasing/ReadBasesAtPosition.java
similarity index 100%
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diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/SNPallelePair.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/phasing/SNPallelePair.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/SNPallelePair.java
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diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/qc/AssessReducedCoverage.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/qc/AssessReducedCoverage.java
similarity index 100%
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diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/qc/AssessReducedQuals.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/qc/AssessReducedQuals.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/qc/AssessReducedQuals.java
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diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/rnaseq/SplitNCigarReads.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/rnaseq/SplitNCigarReads.java
similarity index 100%
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diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/simulatereads/SimulateReadsForVariants.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/simulatereads/SimulateReadsForVariants.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/simulatereads/SimulateReadsForVariants.java
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diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/validation/GenotypeAndValidate.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/validation/GenotypeAndValidate.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/validation/GenotypeAndValidate.java
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diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/FrequencyModeSelector.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/FrequencyModeSelector.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/FrequencyModeSelector.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/FrequencyModeSelector.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/GLBasedSampleSelector.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/GLBasedSampleSelector.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/GLBasedSampleSelector.java
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diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/GTBasedSampleSelector.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/GTBasedSampleSelector.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/GTBasedSampleSelector.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/GTBasedSampleSelector.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/GenomeEvent.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/GenomeEvent.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/GenomeEvent.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/GenomeEvent.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/KeepAFSpectrumFrequencySelector.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/KeepAFSpectrumFrequencySelector.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/KeepAFSpectrumFrequencySelector.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/KeepAFSpectrumFrequencySelector.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/NullSampleSelector.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/NullSampleSelector.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/NullSampleSelector.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/NullSampleSelector.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/SampleSelector.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/SampleSelector.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/SampleSelector.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/SampleSelector.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/UniformSamplingFrequencySelector.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/UniformSamplingFrequencySelector.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/UniformSamplingFrequencySelector.java
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diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/ValidationSiteSelector.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/ValidationSiteSelector.java
similarity index 100%
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rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/ValidationSiteSelector.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibration.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibration.java
similarity index 100%
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diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/GaussianMixtureModel.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/variantrecalibration/GaussianMixtureModel.java
similarity index 100%
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diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/MultivariateGaussian.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/variantrecalibration/MultivariateGaussian.java
similarity index 100%
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diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/TrainingSet.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/variantrecalibration/TrainingSet.java
similarity index 100%
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diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/Tranche.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/variantrecalibration/Tranche.java
similarity index 100%
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diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/TrancheManager.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/variantrecalibration/TrancheManager.java
similarity index 100%
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diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java
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diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDatum.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDatum.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDatum.java
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diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
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diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibratorArgumentCollection.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibratorArgumentCollection.java
similarity index 100%
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rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibratorArgumentCollection.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibratorEngine.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibratorEngine.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibratorEngine.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibratorEngine.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CalculateGenotypePosteriors.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/CalculateGenotypePosteriors.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CalculateGenotypePosteriors.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/CalculateGenotypePosteriors.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineReferenceCalculationVariants.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/CombineReferenceCalculationVariants.java
similarity index 100%
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rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/CombineReferenceCalculationVariants.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/PosteriorLikelihoodsUtils.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/PosteriorLikelihoodsUtils.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/PosteriorLikelihoodsUtils.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/PosteriorLikelihoodsUtils.java
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/RegenotypeVariants.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/RegenotypeVariants.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/RegenotypeVariants.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/RegenotypeVariants.java
diff --git a/protected/java/src/org/broadinstitute/sting/package-info.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/package-info.java
similarity index 100%
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rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/package-info.java
diff --git a/protected/java/src/org/broadinstitute/sting/utils/SequenceComplexity.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/SequenceComplexity.java
similarity index 100%
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rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/SequenceComplexity.java
diff --git a/protected/java/src/org/broadinstitute/sting/utils/collections/CountSet.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/collections/CountSet.java
similarity index 100%
rename from protected/java/src/org/broadinstitute/sting/utils/collections/CountSet.java
rename to protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/collections/CountSet.java
diff --git a/protected/java/src/org/broadinstitute/sting/utils/gvcf/GVCFWriter.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/gvcf/GVCFWriter.java
similarity index 100%
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diff --git a/protected/java/src/org/broadinstitute/sting/utils/gvcf/HomRefBlock.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/gvcf/HomRefBlock.java
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diff --git a/protected/java/src/org/broadinstitute/sting/utils/haplotype/HaplotypeLDCalculator.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/haplotype/HaplotypeLDCalculator.java
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diff --git a/protected/java/src/org/broadinstitute/sting/utils/haplotype/LDMerger.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/haplotype/LDMerger.java
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diff --git a/protected/java/src/org/broadinstitute/sting/utils/haplotype/MergeVariantsAcrossHaplotypes.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/haplotype/MergeVariantsAcrossHaplotypes.java
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diff --git a/protected/java/src/org/broadinstitute/sting/utils/haplotypeBAMWriter/AllHaplotypeBAMWriter.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/haplotypeBAMWriter/AllHaplotypeBAMWriter.java
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diff --git a/protected/java/src/org/broadinstitute/sting/utils/haplotypeBAMWriter/CalledHaplotypeBAMWriter.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/haplotypeBAMWriter/CalledHaplotypeBAMWriter.java
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diff --git a/protected/java/src/org/broadinstitute/sting/utils/haplotypeBAMWriter/HaplotypeBAMWriter.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/haplotypeBAMWriter/HaplotypeBAMWriter.java
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diff --git a/protected/java/src/org/broadinstitute/sting/utils/haplotypeBAMWriter/ReadDestination.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/haplotypeBAMWriter/ReadDestination.java
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diff --git a/protected/java/src/org/broadinstitute/sting/utils/pairhmm/ArrayLoglessPairHMM.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/pairhmm/ArrayLoglessPairHMM.java
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diff --git a/protected/java/src/org/broadinstitute/sting/utils/pairhmm/CnyPairHMM.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/pairhmm/CnyPairHMM.java
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diff --git a/protected/java/src/org/broadinstitute/sting/utils/pairhmm/FastLoglessPairHMM.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/pairhmm/FastLoglessPairHMM.java
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diff --git a/protected/java/src/org/broadinstitute/sting/utils/pairhmm/FlexibleHMM.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/pairhmm/FlexibleHMM.java
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diff --git a/protected/java/src/org/broadinstitute/sting/utils/pairhmm/LoglessPairHMM.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/pairhmm/LoglessPairHMM.java
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diff --git a/protected/java/src/org/broadinstitute/sting/utils/recalibration/BQSRReadTransformer.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/recalibration/BQSRReadTransformer.java
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diff --git a/protected/java/src/org/broadinstitute/sting/utils/recalibration/BaseRecalibration.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/recalibration/BaseRecalibration.java
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diff --git a/protected/java/src/org/broadinstitute/sting/utils/recalibration/QualQuantizer.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/recalibration/QualQuantizer.java
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diff --git a/protected/java/src/org/broadinstitute/sting/utils/recalibration/QuantizationInfo.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/recalibration/QuantizationInfo.java
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diff --git a/protected/java/src/org/broadinstitute/sting/utils/recalibration/ReadCovariates.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/recalibration/ReadCovariates.java
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diff --git a/protected/java/src/org/broadinstitute/sting/utils/recalibration/RecalDatum.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/recalibration/RecalDatum.java
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diff --git a/protected/java/src/org/broadinstitute/sting/utils/recalibration/RecalDatumNode.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/recalibration/RecalDatumNode.java
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diff --git a/protected/java/src/org/broadinstitute/sting/utils/recalibration/RecalUtils.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/recalibration/RecalUtils.java
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diff --git a/protected/java/src/org/broadinstitute/sting/utils/recalibration/RecalibrationReport.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/recalibration/RecalibrationReport.java
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diff --git a/protected/java/src/org/broadinstitute/sting/utils/recalibration/RecalibrationTables.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/recalibration/RecalibrationTables.java
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diff --git a/protected/java/src/org/broadinstitute/sting/utils/recalibration/covariates/ContextCovariate.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/recalibration/covariates/ContextCovariate.java
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diff --git a/protected/java/src/org/broadinstitute/sting/utils/recalibration/covariates/Covariate.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/recalibration/covariates/Covariate.java
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diff --git a/protected/java/src/org/broadinstitute/sting/utils/recalibration/covariates/CycleCovariate.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/recalibration/covariates/CycleCovariate.java
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diff --git a/protected/java/src/org/broadinstitute/sting/utils/recalibration/covariates/ExperimentalCovariate.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/recalibration/covariates/ExperimentalCovariate.java
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diff --git a/protected/java/src/org/broadinstitute/sting/utils/recalibration/covariates/QualityScoreCovariate.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/recalibration/covariates/QualityScoreCovariate.java
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diff --git a/protected/java/src/org/broadinstitute/sting/utils/recalibration/covariates/ReadGroupCovariate.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/recalibration/covariates/ReadGroupCovariate.java
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diff --git a/protected/java/src/org/broadinstitute/sting/utils/recalibration/covariates/RepeatCovariate.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/recalibration/covariates/RepeatCovariate.java
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diff --git a/protected/java/src/org/broadinstitute/sting/utils/recalibration/covariates/RepeatLengthCovariate.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/recalibration/covariates/RepeatLengthCovariate.java
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diff --git a/protected/java/src/org/broadinstitute/sting/utils/recalibration/covariates/RepeatUnitAndLengthCovariate.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/recalibration/covariates/RepeatUnitAndLengthCovariate.java
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diff --git a/protected/java/src/org/broadinstitute/sting/utils/recalibration/covariates/RepeatUnitCovariate.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/recalibration/covariates/RepeatUnitCovariate.java
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diff --git a/protected/java/src/org/broadinstitute/sting/utils/recalibration/covariates/RequiredCovariate.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/recalibration/covariates/RequiredCovariate.java
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diff --git a/protected/java/src/org/broadinstitute/sting/utils/recalibration/covariates/StandardCovariate.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/recalibration/covariates/StandardCovariate.java
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diff --git a/protected/java/src/org/broadinstitute/sting/utils/sam/ClippedGATKSAMRecord.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/sam/ClippedGATKSAMRecord.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/WalkerTestIntegrationTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/WalkerTestIntegrationTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/annotator/RankSumUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/annotator/RankSumUnitTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/annotator/SnpEffUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/annotator/SnpEffUnitTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantOverlapAnnotatorUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/annotator/VariantOverlapAnnotatorUnitTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/beagle/BeagleIntegrationTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/beagle/BeagleIntegrationTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/AnalyzeCovariatesIntegrationTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/bqsr/AnalyzeCovariatesIntegrationTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRGathererUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRGathererUnitTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRIntegrationTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRIntegrationTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/ReadRecalibrationInfoUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/bqsr/ReadRecalibrationInfoUnitTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/compression/reducereads/BaseCountsUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/compression/reducereads/BaseCountsUnitTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/compression/reducereads/HeaderElementUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/compression/reducereads/HeaderElementUnitTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReadsIntegrationTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReadsIntegrationTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReadsUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReadsUnitTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SlidingWindowUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SlidingWindowUnitTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/diagnostics/BaseCoverageDistributionIntegrationTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/diagnostics/BaseCoverageDistributionIntegrationTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/diagnostics/ErrorRatePerCycleIntegrationTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/diagnostics/ErrorRatePerCycleIntegrationTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/diagnostics/ReadGroupPropertiesIntegrationTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/diagnostics/ReadGroupPropertiesIntegrationTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/DiagnoseTargetsIntegrationTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/DiagnoseTargetsIntegrationTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/LocusStatisticsUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/diagnostics/diagnosetargets/LocusStatisticsUnitTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/diagnostics/missing/QualifyMissingIntervalsUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/diagnostics/missing/QualifyMissingIntervalsUnitTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/diffengine/DiffEngineUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/diffengine/DiffEngineUnitTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/diffengine/DiffNodeUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/diffengine/DiffNodeUnitTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/diffengine/DiffObjectsIntegrationTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/diffengine/DiffObjectsIntegrationTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/diffengine/DiffableReaderUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/diffengine/DiffableReaderUnitTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceIntegrationTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceIntegrationTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationIntegrationTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationIntegrationTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/ArtificialReadPileupTestProvider.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/genotyper/ArtificialReadPileupTestProvider.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/BiasedDownsamplingIntegrationTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/genotyper/BiasedDownsamplingIntegrationTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyGenotypeLikelihoodsUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyGenotypeLikelihoodsUnitTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsUnitTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngineUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngineUnitTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperGeneralPloidySuite1IntegrationTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperGeneralPloidySuite1IntegrationTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperGeneralPloidySuite2IntegrationTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperGeneralPloidySuite2IntegrationTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperGeneralPloidyTestExecutor.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperGeneralPloidyTestExecutor.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIndelCallingIntegrationTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIndelCallingIntegrationTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperLargeScaleTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperLargeScaleTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperNormalCallingIntegrationTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperNormalCallingIntegrationTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperReducedReadsIntegrationTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperReducedReadsIntegrationTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcPerformanceUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcPerformanceUnitTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcResultUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcResultUnitTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/GeneralPloidyAFCalculationModelUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/GeneralPloidyAFCalculationModelUnitTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/IndependentAllelesDiploidExactAFCalcUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/IndependentAllelesDiploidExactAFCalcUnitTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ActiveRegionTestDataSetUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ActiveRegionTestDataSetUnitTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/AssemblyResultSetUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/AssemblyResultSetUnitTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/Civar.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/Civar.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/CivarUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/CivarUnitTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/GenotypingEngineUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/GenotypingEngineUnitTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HCLikelihoodCalculationEnginesBenchmark.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HCLikelihoodCalculationEnginesBenchmark.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerGVCFIntegrationTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerGVCFIntegrationTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerModesIntegrationTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerModesIntegrationTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerParallelIntegrationTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerParallelIntegrationTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/PairHMMLikelihoodCalculationEngineUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/PairHMMLikelihoodCalculationEngineUnitTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ReadThreadingLikelihoodCalculationEngineUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ReadThreadingLikelihoodCalculationEngineUnitTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ReferenceConfidenceModelUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/ReferenceConfidenceModelUnitTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/BaseEdgeUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/BaseEdgeUnitTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/DeBruijnVertexUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/DeBruijnVertexUnitTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/GraphUtilsUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/GraphUtilsUnitTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/HaplotypeGraphUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/HaplotypeGraphUnitTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/KBestPathsUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/KBestPathsUnitTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/LowWeightChainPrunerUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/LowWeightChainPrunerUnitTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/MultiSampleEdgeUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/MultiSampleEdgeUnitTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/PathUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/PathUnitTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/RouteUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/RouteUnitTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/SeqGraphUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/SeqGraphUnitTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/SeqVertexUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/SeqVertexUnitTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/SharedVertexSequenceSplitterUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/SharedVertexSequenceSplitterUnitTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/readthreading/ReadThreadingAssemblerUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/readthreading/ReadThreadingAssemblerUnitTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/readthreading/ReadThreadingGraphUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/readthreading/ReadThreadingGraphUnitTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/readthreading/SequenceForKmersUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/readthreading/SequenceForKmersUnitTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/indels/ConstrainedMateFixingManagerUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/indels/ConstrainedMateFixingManagerUnitTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerIntegrationTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerIntegrationTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreatorIntegrationTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreatorIntegrationTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmissionIntegrationTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmissionIntegrationTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingIntegrationTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingIntegrationTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/rnaseq/SplitNCigarReadsIntegrationTests.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/rnaseq/SplitNCigarReadsIntegrationTests.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/simulatereads/SimulateReadsForVariantsIntegrationTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/simulatereads/SimulateReadsForVariantsIntegrationTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmpliconsIntegrationTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmpliconsIntegrationTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/validation/ValidationSiteSelectorIntegrationTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/validation/ValidationSiteSelectorIntegrationTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalkerUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalkerUnitTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/manager/StratificationManagerUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/manager/StratificationManagerUnitTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibrationUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibrationUnitTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManagerUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManagerUnitTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantGaussianMixtureModelUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantGaussianMixtureModelUnitTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineReferenceCalculationVariantsIntegrationTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantutils/CombineReferenceCalculationVariantsIntegrationTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsIntegrationTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsIntegrationTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsUnitTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/ConcordanceMetricsUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantutils/ConcordanceMetricsUnitTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/GenotypeConcordanceIntegrationTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantutils/GenotypeConcordanceIntegrationTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignAndTrimVariantsIntegrationTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignAndTrimVariantsIntegrationTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignAndTrimVariantsUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignAndTrimVariantsUnitTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariantsIntegrationTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariantsIntegrationTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/PosteriorLikelihoodsUtilsUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantutils/PosteriorLikelihoodsUtilsUnitTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/RegenotypeVariantsIntegrationTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantutils/RegenotypeVariantsIntegrationTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsParallelIntegrationTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsParallelIntegrationTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VCFStreamingIntegrationTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantutils/VCFStreamingIntegrationTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariantsIntegrationTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariantsIntegrationTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToAllelicPrimitivesIntegrationTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToAllelicPrimitivesIntegrationTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToBinaryPedIntegrationTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToBinaryPedIntegrationTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTableIntegrationTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTableIntegrationTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCFIntegrationTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCFIntegrationTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/utils/ContigComparatorUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/ContigComparatorUnitTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/utils/RandomDNA.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/RandomDNA.java
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diff --git a/protected/java/test/org/broadinstitute/sting/utils/collections/CountSetUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/collections/CountSetUnitTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/utils/genotyper/DiploidGenotypeUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/genotyper/DiploidGenotypeUnitTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/utils/genotyper/MostLikelyAlleleUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/genotyper/MostLikelyAlleleUnitTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/utils/genotyper/PerReadAlleleLikelihoodMapUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/genotyper/PerReadAlleleLikelihoodMapUnitTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/utils/gvcf/GVCFWriterUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/gvcf/GVCFWriterUnitTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/utils/gvcf/HomRefBlockUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/gvcf/HomRefBlockUnitTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/utils/haplotype/HaplotypeBaseComparatorUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/haplotype/HaplotypeBaseComparatorUnitTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/utils/haplotype/HaplotypeLDCalculatorUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/haplotype/HaplotypeLDCalculatorUnitTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/utils/haplotype/HaplotypeScoreComparatorUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/haplotype/HaplotypeScoreComparatorUnitTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/utils/haplotype/HaplotypeSizeAndBaseComparatorUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/haplotype/HaplotypeSizeAndBaseComparatorUnitTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/utils/haplotype/LDMergerUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/haplotype/LDMergerUnitTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/utils/haplotypeBAMWriter/HaplotypeBAMWriterUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/haplotypeBAMWriter/HaplotypeBAMWriterUnitTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/utils/nanoScheduler/NanoSchedulerIntegrationTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/nanoScheduler/NanoSchedulerIntegrationTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/utils/pairhmm/ActiveRegionTestDataSet.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/pairhmm/ActiveRegionTestDataSet.java
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diff --git a/protected/java/test/org/broadinstitute/sting/utils/pairhmm/CnyPairHMMUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/pairhmm/CnyPairHMMUnitTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/utils/pairhmm/FastLoglessPairHMMUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/pairhmm/FastLoglessPairHMMUnitTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/utils/pairhmm/PairHMMEmpiricalBenchmark.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/pairhmm/PairHMMEmpiricalBenchmark.java
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diff --git a/protected/java/test/org/broadinstitute/sting/utils/pairhmm/PairHMMModelUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/pairhmm/PairHMMModelUnitTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/utils/pairhmm/PairHMMProbabilityBugIntegrationTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/pairhmm/PairHMMProbabilityBugIntegrationTest.java
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diff --git a/protected/java/test/org/broadinstitute/sting/utils/smithwaterman/GlobalEdgeGreedySWPairwiseAlignmentUnitTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/smithwaterman/GlobalEdgeGreedySWPairwiseAlignmentUnitTest.java
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diff --git a/public/java/src/org/broadinstitute/sting/commandline/Advanced.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/commandline/Advanced.java
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diff --git a/public/java/src/org/broadinstitute/sting/commandline/Argument.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/commandline/Argument.java
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diff --git a/public/java/src/org/broadinstitute/sting/commandline/Gather.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/commandline/Gather.java
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diff --git a/public/java/src/org/broadinstitute/sting/commandline/Gatherer.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/commandline/Gatherer.java
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diff --git a/public/java/src/org/broadinstitute/sting/commandline/Output.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/commandline/Output.java
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diff --git a/public/java/src/org/broadinstitute/sting/commandline/ParsedListArgs.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/commandline/ParsedListArgs.java
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diff --git a/public/java/src/org/broadinstitute/sting/commandline/ParsingEngineArgumentFiles.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/commandline/ParsingEngineArgumentFiles.java
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diff --git a/public/java/src/org/broadinstitute/sting/commandline/RodBinding.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/commandline/RodBinding.java
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diff --git a/public/java/src/org/broadinstitute/sting/commandline/Tags.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/commandline/Tags.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/CommandLineExecutable.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/CommandLineExecutable.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/CommandLineGATK.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/arguments/StandardVariantContextInputArgumentCollection.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/arguments/StandardVariantContextInputArgumentCollection.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/arguments/ValidationExclusion.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/arguments/ValidationExclusion.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/contexts/AlignmentContext.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/contexts/AlignmentContext.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/contexts/ReferenceContext.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/contexts/ReferenceContext.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/package-info.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/package-info.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/AllLocusView.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/providers/AllLocusView.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/CoveredLocusView.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/providers/CoveredLocusView.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/IntervalOverlappingRODsFromStream.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/providers/IntervalOverlappingRODsFromStream.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/IntervalReferenceOrderedView.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/providers/IntervalReferenceOrderedView.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/InvalidPositionException.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/providers/InvalidPositionException.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/LocusReferenceView.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/providers/LocusReferenceView.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/LocusShardDataProvider.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/providers/LocusShardDataProvider.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/LocusView.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/providers/LocusView.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/ManagingReferenceOrderedView.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/providers/ManagingReferenceOrderedView.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/RODMetaDataContainer.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/providers/RODMetaDataContainer.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/ReadBasedReferenceOrderedView.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/providers/ReadBasedReferenceOrderedView.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/ReadReferenceView.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/providers/ReadReferenceView.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/ReadShardDataProvider.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/providers/ReadShardDataProvider.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/ReadView.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/providers/ReadView.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/ReferenceOrderedView.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/providers/ReferenceOrderedView.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/ReferenceView.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/providers/ReferenceView.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/RodLocusView.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/providers/RodLocusView.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/ShardDataProvider.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/providers/ShardDataProvider.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/View.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/providers/View.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/package-info.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/providers/package-info.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/ActiveRegionShardBalancer.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/ActiveRegionShardBalancer.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/BAMAccessPlan.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/BAMAccessPlan.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/BAMSchedule.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/BAMSchedule.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/BAMScheduler.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/BAMScheduler.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/BGZFBlockLoadingDispatcher.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/BGZFBlockLoadingDispatcher.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/BlockInputStream.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/BlockInputStream.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/BlockLoader.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/BlockLoader.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/FileHandleCache.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/FileHandleCache.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/FilePointer.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/FilePointer.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/GATKBAMIndex.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/GATKBAMIndex.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/GATKBAMIndexData.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/GATKBAMIndexData.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/IntervalOverlapFilteringIterator.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/IntervalOverlapFilteringIterator.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/IntervalSharder.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/IntervalSharder.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/LocusShard.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/LocusShard.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/LocusShardBalancer.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/LocusShardBalancer.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/ReadShard.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/ReadShard.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/ReadShardBalancer.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/ReadShardBalancer.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/SAMDataSource.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/SAMDataSource.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/SAMReaderID.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/SAMReaderID.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/Shard.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/Shard.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/ShardBalancer.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/ShardBalancer.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/package-info.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/package-info.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/utilities/BAMFileStat.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/utilities/BAMFileStat.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/utilities/BAMTagRenamer.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/utilities/BAMTagRenamer.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/utilities/FindLargeShards.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/utilities/FindLargeShards.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/utilities/PrintBAMRegion.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/utilities/PrintBAMRegion.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/utilities/PrintBGZFBounds.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/utilities/PrintBGZFBounds.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/utilities/UnzipSingleBlock.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/utilities/UnzipSingleBlock.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/utilities/package-info.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reads/utilities/package-info.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reference/ReferenceDataSource.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reference/ReferenceDataSource.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reference/package-info.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/reference/package-info.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/rmd/DataStreamSegment.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/rmd/DataStreamSegment.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/rmd/EntireStream.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/rmd/EntireStream.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/rmd/MappedStreamSegment.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/datasources/rmd/MappedStreamSegment.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/filters/ReadNameFilter.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/ReadNameFilter.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/filters/package-info.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/filters/package-info.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/io/DirectOutputTracker.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/io/DirectOutputTracker.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/io/storage/OutputStreamStorage.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/io/storage/OutputStreamStorage.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/iterators/BoundedReadIterator.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/iterators/BoundedReadIterator.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/iterators/GATKSAMIterator.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/iterators/GATKSAMIterator.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/iterators/GenomeLocusIterator.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/iterators/GenomeLocusIterator.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/iterators/PeekingIterator.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/iterators/PeekingIterator.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/iterators/ReadFormattingIterator.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/iterators/ReadFormattingIterator.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/iterators/StingSAMIterator.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/iterators/StingSAMIterator.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/iterators/StingSAMIteratorAdapter.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/iterators/StingSAMIteratorAdapter.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/iterators/VerifyingSamIterator.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/iterators/VerifyingSamIterator.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/iterators/package-info.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/iterators/package-info.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/phonehome/GATKRunReport.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/phonehome/GATKRunReport.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/RODRecordListImpl.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/refdata/RODRecordListImpl.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/RefMetaDataTracker.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/refdata/RefMetaDataTracker.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/ReferenceDependentFeatureCodec.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/refdata/ReferenceDependentFeatureCodec.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/ReferenceOrderedDatum.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/refdata/ReferenceOrderedDatum.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/SeekableRODIterator.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/refdata/SeekableRODIterator.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/package-info.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/refdata/package-info.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/tracks/FeatureManager.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/refdata/tracks/FeatureManager.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/tracks/IndexDictionaryUtils.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/refdata/tracks/IndexDictionaryUtils.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/tracks/RMDTrack.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/refdata/tracks/RMDTrack.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/utils/FeatureToGATKFeatureIterator.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/refdata/utils/FeatureToGATKFeatureIterator.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/utils/FlashBackIterator.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/refdata/utils/FlashBackIterator.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/utils/GATKFeature.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/refdata/utils/GATKFeature.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/utils/LocationAwareSeekableRODIterator.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/refdata/utils/LocationAwareSeekableRODIterator.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/utils/RMDTriplet.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/refdata/utils/RMDTriplet.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/utils/RODRecordList.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/refdata/utils/RODRecordList.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/report/GATKReport.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/report/GATKReport.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/report/GATKReportGatherer.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/report/GATKReportGatherer.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/report/GATKReportVersion.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/report/GATKReportVersion.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/resourcemanagement/ThreadAllocation.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/resourcemanagement/ThreadAllocation.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/samples/Affection.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/samples/Affection.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseLociNano.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/traversals/TraverseLociNano.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/traversals/package-info.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/traversals/package-info.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/Allows.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/Allows.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/By.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/By.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/LocusWalker.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/LocusWalker.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/PartitionType.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/PartitionType.java
similarity index 100%
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/RMD.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/RMD.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/ReadFilters.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/ReadFilters.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/ReadPairWalker.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/ReadPairWalker.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/ReadWalker.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/ReadWalker.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/RefWalker.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/RefWalker.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/Reference.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/Reference.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/RemoveProgramRecords.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/RemoveProgramRecords.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/Requires.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/Requires.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/RodWalker.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/RodWalker.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/TreeReducible.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/TreeReducible.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/Walker.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/Walker.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/WalkerName.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/WalkerName.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/Window.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/Window.java
similarity index 100%
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalance.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalance.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalanceBySample.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalanceBySample.java
similarity index 100%
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseCounts.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/BaseCounts.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ChromosomeCountConstants.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/ChromosomeCountConstants.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/LowMQ.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/LowMQ.java
similarity index 100%
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroBySample.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroBySample.java
similarity index 100%
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/NBaseCount.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/NBaseCount.java
similarity index 100%
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SnpEff.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/SnpEff.java
similarity index 100%
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SnpEffUtil.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/SnpEffUtil.java
similarity index 100%
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java
similarity index 100%
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java
similarity index 100%
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantOverlapAnnotator.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/VariantOverlapAnnotator.java
similarity index 100%
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/ActiveRegionBasedAnnotation.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/ActiveRegionBasedAnnotation.java
similarity index 100%
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/AnnotationInterfaceManager.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/AnnotationInterfaceManager.java
similarity index 100%
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/AnnotationType.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/AnnotationType.java
similarity index 100%
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/AnnotatorCompatible.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/AnnotatorCompatible.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/ExperimentalAnnotation.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/ExperimentalAnnotation.java
similarity index 100%
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/GenotypeAnnotation.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/GenotypeAnnotation.java
similarity index 100%
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/InfoFieldAnnotation.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/InfoFieldAnnotation.java
similarity index 100%
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/RodRequiringAnnotation.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/RodRequiringAnnotation.java
similarity index 100%
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/StandardAnnotation.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/StandardAnnotation.java
similarity index 100%
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/VariantAnnotatorAnnotation.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/VariantAnnotatorAnnotation.java
similarity index 100%
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/WorkInProgressAnnotation.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/WorkInProgressAnnotation.java
similarity index 100%
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCF.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCF.java
similarity index 100%
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInput.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInput.java
similarity index 100%
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/VariantsToBeagleUnphased.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/beagle/VariantsToBeagleUnphased.java
similarity index 100%
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CallableLoci.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/coverage/CallableLoci.java
similarity index 100%
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CompareCallableLoci.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/coverage/CompareCallableLoci.java
similarity index 100%
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CoverageUtils.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/coverage/CoverageUtils.java
similarity index 100%
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverage.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverage.java
similarity index 100%
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageStats.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageStats.java
similarity index 100%
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DoCOutputType.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/coverage/DoCOutputType.java
similarity index 100%
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/GCContentByInterval.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/coverage/GCContentByInterval.java
similarity index 100%
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/CoveredByNSamplesSites.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/diagnostics/CoveredByNSamplesSites.java
similarity index 100%
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/ErrorRatePerCycle.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/diagnostics/ErrorRatePerCycle.java
similarity index 100%
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/ReadGroupProperties.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/diagnostics/ReadGroupProperties.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/ReadLengthDistribution.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/diagnostics/ReadLengthDistribution.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/BAMDiffableReader.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/diffengine/BAMDiffableReader.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffElement.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/diffengine/DiffElement.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/Difference.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/diffengine/Difference.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/GATKReportDiffableReader.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/diffengine/GATKReportDiffableReader.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/VCFDiffableReader.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/diffengine/VCFDiffableReader.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceMaker.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceMaker.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaReferenceMaker.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/fasta/FastaReferenceMaker.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaSequence.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/fasta/FastaSequence.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaStats.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/fasta/FastaStats.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/ClusteredSnps.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/filters/ClusteredSnps.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/FiltrationContext.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/filters/FiltrationContext.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/FiltrationContextWindow.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/filters/FiltrationContextWindow.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltration.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltration.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HCMappingQualityFilter.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HCMappingQualityFilter.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/package-info.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/package-info.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CheckPileup.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/qc/CheckPileup.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountBases.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/qc/CountBases.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountIntervals.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/qc/CountIntervals.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountLoci.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/qc/CountLoci.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountMales.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/qc/CountMales.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountRODs.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/qc/CountRODs.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountRODsByRef.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/qc/CountRODsByRef.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountReadEvents.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/qc/CountReadEvents.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountReads.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/qc/CountReads.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountTerminusEvent.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/qc/CountTerminusEvent.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/DocumentationTest.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/qc/DocumentationTest.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ErrorThrowing.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/qc/ErrorThrowing.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/FlagStat.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/qc/FlagStat.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/Pileup.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/qc/Pileup.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/PrintRODs.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/qc/PrintRODs.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/QCRef.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/qc/QCRef.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ReadClippingStats.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/qc/ReadClippingStats.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/RodSystemValidation.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/qc/RodSystemValidation.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/readutils/ClipReads.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/readutils/ClipReads.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/readutils/PrintReads.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/readutils/PrintReads.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/readutils/ReadAdaptorTrimmer.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/readutils/ReadAdaptorTrimmer.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/readutils/SplitSamFile.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/readutils/SplitSamFile.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmplicons.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmplicons.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEval.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEval.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalReportWriter.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalReportWriter.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CompOverlap.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CompOverlap.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CountVariants.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CountVariants.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelLengthHistogram.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelLengthHistogram.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ConcordanceMetrics.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/ConcordanceMetrics.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/FilterLiftedVariants.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/FilterLiftedVariants.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/GenotypeConcordance.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/GenotypeConcordance.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignAndTrimVariants.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignAndTrimVariants.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/RandomlySplitVariants.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/RandomlySplitVariants.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectHeaders.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/SelectHeaders.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariants.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariants.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToAllelicPrimitives.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToAllelicPrimitives.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToBinaryPed.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToBinaryPed.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java
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diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCF.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCF.java
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diff --git a/public/java/src/org/broadinstitute/sting/jna/clibrary/JNAUtils.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/jna/clibrary/JNAUtils.java
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diff --git a/public/java/src/org/broadinstitute/sting/jna/drmaa/v1_0/JnaJobInfo.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/jna/drmaa/v1_0/JnaJobInfo.java
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diff --git a/public/java/src/org/broadinstitute/sting/jna/lsf/v7_0_6/LibBat.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/jna/lsf/v7_0_6/LibBat.java
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diff --git a/public/java/src/org/broadinstitute/sting/tools/CatVariants.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/tools/CatVariants.java
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diff --git a/public/java/src/org/broadinstitute/sting/tools/ListAnnotations.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/tools/ListAnnotations.java
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diff --git a/public/java/src/org/broadinstitute/sting/utils/UnvalidatingGenomeLoc.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/UnvalidatingGenomeLoc.java
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diff --git a/public/java/test/org/broadinstitute/sting/gatk/datasources/reads/PicardBaselineBenchmark.java b/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/datasources/reads/PicardBaselineBenchmark.java
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diff --git a/public/java/test/org/broadinstitute/sting/gatk/datasources/reads/SAMDataSourceUnitTest.java b/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/datasources/reads/SAMDataSourceUnitTest.java
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diff --git a/public/java/test/org/broadinstitute/sting/gatk/datasources/reads/SAMReaderIDUnitTest.java b/public/gatk-framework/src/test/java/org/broadinstitute/sting/gatk/datasources/reads/SAMReaderIDUnitTest.java
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diff --git a/public/scala/src/org/broadinstitute/sting/queue/engine/pbsengine/PbsEngineJobManager.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/engine/pbsengine/PbsEngineJobManager.scala
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rename to public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/engine/shell/ShellJobRunner.scala
diff --git a/public/scala/src/org/broadinstitute/sting/queue/extensions/cancer/MuTect.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/cancer/MuTect.scala
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rename from public/scala/src/org/broadinstitute/sting/queue/extensions/cancer/MuTect.scala
rename to public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/cancer/MuTect.scala
diff --git a/public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/BamGatherFunction.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/gatk/BamGatherFunction.scala
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diff --git a/public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/CatVariantsGatherer.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/gatk/CatVariantsGatherer.scala
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rename from public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/CatVariantsGatherer.scala
rename to public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/gatk/CatVariantsGatherer.scala
diff --git a/public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/ContigScatterFunction.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/gatk/ContigScatterFunction.scala
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diff --git a/public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/DistributedScatterFunction.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/gatk/DistributedScatterFunction.scala
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diff --git a/public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/GATKIntervals.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/gatk/GATKIntervals.scala
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rename from public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/GATKIntervals.scala
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diff --git a/public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/GATKScatterFunction.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/gatk/GATKScatterFunction.scala
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rename from public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/GATKScatterFunction.scala
rename to public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/gatk/GATKScatterFunction.scala
diff --git a/public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/IntervalScatterFunction.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/gatk/IntervalScatterFunction.scala
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diff --git a/public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/LocusScatterFunction.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/gatk/LocusScatterFunction.scala
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diff --git a/public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/ReadScatterFunction.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/gatk/ReadScatterFunction.scala
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diff --git a/public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/TaggedFile.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/gatk/TaggedFile.scala
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diff --git a/public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/VcfGatherFunction.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/gatk/VcfGatherFunction.scala
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rename from public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/VcfGatherFunction.scala
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diff --git a/public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/WriteFlankingIntervalsFunction.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/gatk/WriteFlankingIntervalsFunction.scala
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rename from public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/WriteFlankingIntervalsFunction.scala
rename to public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/gatk/WriteFlankingIntervalsFunction.scala
diff --git a/public/scala/src/org/broadinstitute/sting/queue/extensions/picard/AddOrReplaceReadGroups.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/picard/AddOrReplaceReadGroups.scala
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rename from public/scala/src/org/broadinstitute/sting/queue/extensions/picard/AddOrReplaceReadGroups.scala
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diff --git a/public/scala/src/org/broadinstitute/sting/queue/extensions/picard/CalculateHsMetrics.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/picard/CalculateHsMetrics.scala
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rename from public/scala/src/org/broadinstitute/sting/queue/extensions/picard/CalculateHsMetrics.scala
rename to public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/picard/CalculateHsMetrics.scala
diff --git a/public/scala/src/org/broadinstitute/sting/queue/extensions/picard/CollectGcBiasMetrics.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/picard/CollectGcBiasMetrics.scala
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diff --git a/public/scala/src/org/broadinstitute/sting/queue/extensions/picard/CollectMultipleMetrics.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/picard/CollectMultipleMetrics.scala
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rename from public/scala/src/org/broadinstitute/sting/queue/extensions/picard/CollectMultipleMetrics.scala
rename to public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/picard/CollectMultipleMetrics.scala
diff --git a/public/scala/src/org/broadinstitute/sting/queue/extensions/picard/FastqToSam.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/picard/FastqToSam.scala
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rename from public/scala/src/org/broadinstitute/sting/queue/extensions/picard/FastqToSam.scala
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diff --git a/public/scala/src/org/broadinstitute/sting/queue/extensions/picard/MarkDuplicates.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/picard/MarkDuplicates.scala
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rename from public/scala/src/org/broadinstitute/sting/queue/extensions/picard/MarkDuplicates.scala
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diff --git a/public/scala/src/org/broadinstitute/sting/queue/extensions/picard/MergeSamFiles.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/picard/MergeSamFiles.scala
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rename from public/scala/src/org/broadinstitute/sting/queue/extensions/picard/MergeSamFiles.scala
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diff --git a/public/scala/src/org/broadinstitute/sting/queue/extensions/picard/PicardBamFunction.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/picard/PicardBamFunction.scala
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rename from public/scala/src/org/broadinstitute/sting/queue/extensions/picard/PicardBamFunction.scala
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diff --git a/public/scala/src/org/broadinstitute/sting/queue/extensions/picard/PicardMetricsFunction.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/picard/PicardMetricsFunction.scala
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rename from public/scala/src/org/broadinstitute/sting/queue/extensions/picard/PicardMetricsFunction.scala
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diff --git a/public/scala/src/org/broadinstitute/sting/queue/extensions/picard/ReorderSam.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/picard/ReorderSam.scala
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rename from public/scala/src/org/broadinstitute/sting/queue/extensions/picard/ReorderSam.scala
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diff --git a/public/scala/src/org/broadinstitute/sting/queue/extensions/picard/RevertSam.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/picard/RevertSam.scala
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rename from public/scala/src/org/broadinstitute/sting/queue/extensions/picard/RevertSam.scala
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diff --git a/public/scala/src/org/broadinstitute/sting/queue/extensions/picard/SamToFastq.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/picard/SamToFastq.scala
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rename from public/scala/src/org/broadinstitute/sting/queue/extensions/picard/SamToFastq.scala
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diff --git a/public/scala/src/org/broadinstitute/sting/queue/extensions/picard/SortSam.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/picard/SortSam.scala
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rename from public/scala/src/org/broadinstitute/sting/queue/extensions/picard/SortSam.scala
rename to public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/picard/SortSam.scala
diff --git a/public/scala/src/org/broadinstitute/sting/queue/extensions/picard/ValidateSamFile.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/picard/ValidateSamFile.scala
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rename from public/scala/src/org/broadinstitute/sting/queue/extensions/picard/ValidateSamFile.scala
rename to public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/picard/ValidateSamFile.scala
diff --git a/public/scala/src/org/broadinstitute/sting/queue/extensions/samtools/SamtoolsCommandLineFunction.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/samtools/SamtoolsCommandLineFunction.scala
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rename from public/scala/src/org/broadinstitute/sting/queue/extensions/samtools/SamtoolsCommandLineFunction.scala
rename to public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/samtools/SamtoolsCommandLineFunction.scala
diff --git a/public/scala/src/org/broadinstitute/sting/queue/extensions/samtools/SamtoolsIndexFunction.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/samtools/SamtoolsIndexFunction.scala
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rename from public/scala/src/org/broadinstitute/sting/queue/extensions/samtools/SamtoolsIndexFunction.scala
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diff --git a/public/scala/src/org/broadinstitute/sting/queue/extensions/samtools/SamtoolsMergeFunction.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/samtools/SamtoolsMergeFunction.scala
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rename from public/scala/src/org/broadinstitute/sting/queue/extensions/samtools/SamtoolsMergeFunction.scala
rename to public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/samtools/SamtoolsMergeFunction.scala
diff --git a/public/scala/src/org/broadinstitute/sting/queue/extensions/snpeff/SnpEff.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/extensions/snpeff/SnpEff.scala
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rename from public/scala/src/org/broadinstitute/sting/queue/extensions/snpeff/SnpEff.scala
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diff --git a/public/scala/src/org/broadinstitute/sting/queue/function/CommandLineFunction.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/function/CommandLineFunction.scala
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rename from public/scala/src/org/broadinstitute/sting/queue/function/CommandLineFunction.scala
rename to public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/function/CommandLineFunction.scala
diff --git a/public/scala/src/org/broadinstitute/sting/queue/function/InProcessFunction.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/function/InProcessFunction.scala
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rename from public/scala/src/org/broadinstitute/sting/queue/function/InProcessFunction.scala
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diff --git a/public/scala/src/org/broadinstitute/sting/queue/function/JavaCommandLineFunction.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/function/JavaCommandLineFunction.scala
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rename from public/scala/src/org/broadinstitute/sting/queue/function/JavaCommandLineFunction.scala
rename to public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/function/JavaCommandLineFunction.scala
diff --git a/public/scala/src/org/broadinstitute/sting/queue/function/ListWriterFunction.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/function/ListWriterFunction.scala
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rename from public/scala/src/org/broadinstitute/sting/queue/function/ListWriterFunction.scala
rename to public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/function/ListWriterFunction.scala
diff --git a/public/scala/src/org/broadinstitute/sting/queue/function/QFunction.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/function/QFunction.scala
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diff --git a/public/scala/src/org/broadinstitute/sting/queue/function/RetryMemoryLimit.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/function/RetryMemoryLimit.scala
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diff --git a/public/scala/src/org/broadinstitute/sting/queue/function/scattergather/CloneFunction.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/function/scattergather/CloneFunction.scala
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rename from public/scala/src/org/broadinstitute/sting/queue/function/scattergather/CloneFunction.scala
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diff --git a/public/scala/src/org/broadinstitute/sting/queue/function/scattergather/ConcatenateLogsFunction.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/function/scattergather/ConcatenateLogsFunction.scala
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rename from public/scala/src/org/broadinstitute/sting/queue/function/scattergather/ConcatenateLogsFunction.scala
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diff --git a/public/scala/src/org/broadinstitute/sting/queue/function/scattergather/GatherFunction.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/function/scattergather/GatherFunction.scala
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rename from public/scala/src/org/broadinstitute/sting/queue/function/scattergather/GatherFunction.scala
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diff --git a/public/scala/src/org/broadinstitute/sting/queue/function/scattergather/GathererFunction.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/function/scattergather/GathererFunction.scala
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diff --git a/public/scala/src/org/broadinstitute/sting/queue/function/scattergather/ScatterFunction.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/function/scattergather/ScatterFunction.scala
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diff --git a/public/scala/src/org/broadinstitute/sting/queue/function/scattergather/ScatterGatherableFunction.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/function/scattergather/ScatterGatherableFunction.scala
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diff --git a/public/scala/src/org/broadinstitute/sting/queue/function/scattergather/SimpleTextGatherFunction.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/function/scattergather/SimpleTextGatherFunction.scala
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diff --git a/public/scala/src/org/broadinstitute/sting/queue/library/clf/vcf/VCFExtractIntervals.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/library/clf/vcf/VCFExtractIntervals.scala
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rename from public/scala/src/org/broadinstitute/sting/queue/library/clf/vcf/VCFExtractIntervals.scala
rename to public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/library/clf/vcf/VCFExtractIntervals.scala
diff --git a/public/scala/src/org/broadinstitute/sting/queue/library/clf/vcf/VCFExtractSamples.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/library/clf/vcf/VCFExtractSamples.scala
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rename from public/scala/src/org/broadinstitute/sting/queue/library/clf/vcf/VCFExtractSamples.scala
rename to public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/library/clf/vcf/VCFExtractSamples.scala
diff --git a/public/scala/src/org/broadinstitute/sting/queue/library/ipf/SortByRef.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/library/ipf/SortByRef.scala
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rename to public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/library/ipf/SortByRef.scala
diff --git a/public/scala/src/org/broadinstitute/sting/queue/library/ipf/vcf/VCFExtractIntervals.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/library/ipf/vcf/VCFExtractIntervals.scala
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rename to public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/library/ipf/vcf/VCFExtractIntervals.scala
diff --git a/public/scala/src/org/broadinstitute/sting/queue/library/ipf/vcf/VCFExtractSamples.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/library/ipf/vcf/VCFExtractSamples.scala
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rename to public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/library/ipf/vcf/VCFExtractSamples.scala
diff --git a/public/scala/src/org/broadinstitute/sting/queue/library/ipf/vcf/VCFExtractSites.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/library/ipf/vcf/VCFExtractSites.scala
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rename from public/scala/src/org/broadinstitute/sting/queue/library/ipf/vcf/VCFExtractSites.scala
rename to public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/library/ipf/vcf/VCFExtractSites.scala
diff --git a/public/scala/src/org/broadinstitute/sting/queue/library/ipf/vcf/VCFSimpleMerge.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/library/ipf/vcf/VCFSimpleMerge.scala
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rename to public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/library/ipf/vcf/VCFSimpleMerge.scala
diff --git a/public/scala/src/org/broadinstitute/sting/queue/util/ClassFieldCache.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/util/ClassFieldCache.scala
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diff --git a/public/scala/src/org/broadinstitute/sting/queue/util/CollectionUtils.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/util/CollectionUtils.scala
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rename from public/scala/src/org/broadinstitute/sting/queue/util/CollectionUtils.scala
rename to public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/util/CollectionUtils.scala
diff --git a/public/scala/src/org/broadinstitute/sting/queue/util/DoC/package.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/util/DoC/package.scala
similarity index 100%
rename from public/scala/src/org/broadinstitute/sting/queue/util/DoC/package.scala
rename to public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/util/DoC/package.scala
diff --git a/public/scala/src/org/broadinstitute/sting/queue/util/EmailMessage.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/util/EmailMessage.scala
similarity index 100%
rename from public/scala/src/org/broadinstitute/sting/queue/util/EmailMessage.scala
rename to public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/util/EmailMessage.scala
diff --git a/public/scala/src/org/broadinstitute/sting/queue/util/EmailSettings.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/util/EmailSettings.scala
similarity index 100%
rename from public/scala/src/org/broadinstitute/sting/queue/util/EmailSettings.scala
rename to public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/util/EmailSettings.scala
diff --git a/public/scala/src/org/broadinstitute/sting/queue/util/Logging.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/util/Logging.scala
similarity index 100%
rename from public/scala/src/org/broadinstitute/sting/queue/util/Logging.scala
rename to public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/util/Logging.scala
diff --git a/public/scala/src/org/broadinstitute/sting/queue/util/PrimitiveOptionConversions.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/util/PrimitiveOptionConversions.scala
similarity index 100%
rename from public/scala/src/org/broadinstitute/sting/queue/util/PrimitiveOptionConversions.scala
rename to public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/util/PrimitiveOptionConversions.scala
diff --git a/public/scala/src/org/broadinstitute/sting/queue/util/QJobReport.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/util/QJobReport.scala
similarity index 100%
rename from public/scala/src/org/broadinstitute/sting/queue/util/QJobReport.scala
rename to public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/util/QJobReport.scala
diff --git a/public/scala/src/org/broadinstitute/sting/queue/util/QJobsReporter.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/util/QJobsReporter.scala
similarity index 100%
rename from public/scala/src/org/broadinstitute/sting/queue/util/QJobsReporter.scala
rename to public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/util/QJobsReporter.scala
diff --git a/public/scala/src/org/broadinstitute/sting/queue/util/QScriptUtils.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/util/QScriptUtils.scala
similarity index 100%
rename from public/scala/src/org/broadinstitute/sting/queue/util/QScriptUtils.scala
rename to public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/util/QScriptUtils.scala
diff --git a/public/scala/src/org/broadinstitute/sting/queue/util/ReflectionUtils.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/util/ReflectionUtils.scala
similarity index 100%
rename from public/scala/src/org/broadinstitute/sting/queue/util/ReflectionUtils.scala
rename to public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/util/ReflectionUtils.scala
diff --git a/public/scala/src/org/broadinstitute/sting/queue/util/RemoteFile.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/util/RemoteFile.scala
similarity index 100%
rename from public/scala/src/org/broadinstitute/sting/queue/util/RemoteFile.scala
rename to public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/util/RemoteFile.scala
diff --git a/public/scala/src/org/broadinstitute/sting/queue/util/RemoteFileConverter.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/util/RemoteFileConverter.scala
similarity index 100%
rename from public/scala/src/org/broadinstitute/sting/queue/util/RemoteFileConverter.scala
rename to public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/util/RemoteFileConverter.scala
diff --git a/public/scala/src/org/broadinstitute/sting/queue/util/Retry.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/util/Retry.scala
similarity index 100%
rename from public/scala/src/org/broadinstitute/sting/queue/util/Retry.scala
rename to public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/util/Retry.scala
diff --git a/public/scala/src/org/broadinstitute/sting/queue/util/RetryException.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/util/RetryException.scala
similarity index 100%
rename from public/scala/src/org/broadinstitute/sting/queue/util/RetryException.scala
rename to public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/util/RetryException.scala
diff --git a/public/scala/src/org/broadinstitute/sting/queue/util/ScalaCompoundArgumentTypeDescriptor.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/util/ScalaCompoundArgumentTypeDescriptor.scala
similarity index 100%
rename from public/scala/src/org/broadinstitute/sting/queue/util/ScalaCompoundArgumentTypeDescriptor.scala
rename to public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/util/ScalaCompoundArgumentTypeDescriptor.scala
diff --git a/public/scala/src/org/broadinstitute/sting/queue/util/ShellUtils.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/util/ShellUtils.scala
similarity index 100%
rename from public/scala/src/org/broadinstitute/sting/queue/util/ShellUtils.scala
rename to public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/util/ShellUtils.scala
diff --git a/public/scala/src/org/broadinstitute/sting/queue/util/StringFileConversions.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/util/StringFileConversions.scala
similarity index 100%
rename from public/scala/src/org/broadinstitute/sting/queue/util/StringFileConversions.scala
rename to public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/util/StringFileConversions.scala
diff --git a/public/scala/src/org/broadinstitute/sting/queue/util/SystemUtils.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/util/SystemUtils.scala
similarity index 100%
rename from public/scala/src/org/broadinstitute/sting/queue/util/SystemUtils.scala
rename to public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/util/SystemUtils.scala
diff --git a/public/scala/src/org/broadinstitute/sting/queue/util/TextFormatUtils.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/util/TextFormatUtils.scala
similarity index 100%
rename from public/scala/src/org/broadinstitute/sting/queue/util/TextFormatUtils.scala
rename to public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/util/TextFormatUtils.scala
diff --git a/public/scala/src/org/broadinstitute/sting/queue/util/VCF_BAM_utilities.scala b/public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/util/VCF_BAM_utilities.scala
similarity index 100%
rename from public/scala/src/org/broadinstitute/sting/queue/util/VCF_BAM_utilities.scala
rename to public/queue-framework/src/main/scala/org/broadinstitute/sting/queue/util/VCF_BAM_utilities.scala
diff --git a/public/scala/test/org/broadinstitute/sting/queue/extensions/gatk/GATKIntervalsUnitTest.scala b/public/queue-framework/src/test/scala/org/broadinstitute/sting/queue/extensions/gatk/GATKIntervalsUnitTest.scala
similarity index 100%
rename from public/scala/test/org/broadinstitute/sting/queue/extensions/gatk/GATKIntervalsUnitTest.scala
rename to public/queue-framework/src/test/scala/org/broadinstitute/sting/queue/extensions/gatk/GATKIntervalsUnitTest.scala
diff --git a/public/scala/test/org/broadinstitute/sting/queue/function/CommandLineFunctionUnitTest.scala b/public/queue-framework/src/test/scala/org/broadinstitute/sting/queue/function/CommandLineFunctionUnitTest.scala
similarity index 100%
rename from public/scala/test/org/broadinstitute/sting/queue/function/CommandLineFunctionUnitTest.scala
rename to public/queue-framework/src/test/scala/org/broadinstitute/sting/queue/function/CommandLineFunctionUnitTest.scala
diff --git a/public/scala/test/org/broadinstitute/sting/queue/pipeline/PipelineTest.scala b/public/queue-framework/src/test/scala/org/broadinstitute/sting/queue/pipeline/PipelineTest.scala
similarity index 100%
rename from public/scala/test/org/broadinstitute/sting/queue/pipeline/PipelineTest.scala
rename to public/queue-framework/src/test/scala/org/broadinstitute/sting/queue/pipeline/PipelineTest.scala
diff --git a/public/scala/test/org/broadinstitute/sting/queue/pipeline/PipelineTestEvalSpec.scala b/public/queue-framework/src/test/scala/org/broadinstitute/sting/queue/pipeline/PipelineTestEvalSpec.scala
similarity index 100%
rename from public/scala/test/org/broadinstitute/sting/queue/pipeline/PipelineTestEvalSpec.scala
rename to public/queue-framework/src/test/scala/org/broadinstitute/sting/queue/pipeline/PipelineTestEvalSpec.scala
diff --git a/public/scala/test/org/broadinstitute/sting/queue/pipeline/PipelineTestSpec.scala b/public/queue-framework/src/test/scala/org/broadinstitute/sting/queue/pipeline/PipelineTestSpec.scala
similarity index 100%
rename from public/scala/test/org/broadinstitute/sting/queue/pipeline/PipelineTestSpec.scala
rename to public/queue-framework/src/test/scala/org/broadinstitute/sting/queue/pipeline/PipelineTestSpec.scala
diff --git a/public/scala/test/org/broadinstitute/sting/queue/pipeline/examples/DevNullOutputPipelineTest.scala b/public/queue-framework/src/test/scala/org/broadinstitute/sting/queue/pipeline/examples/DevNullOutputPipelineTest.scala
similarity index 100%
rename from public/scala/test/org/broadinstitute/sting/queue/pipeline/examples/DevNullOutputPipelineTest.scala
rename to public/queue-framework/src/test/scala/org/broadinstitute/sting/queue/pipeline/examples/DevNullOutputPipelineTest.scala
diff --git a/public/scala/test/org/broadinstitute/sting/queue/pipeline/examples/ExampleCountLociPipelineTest.scala b/public/queue-framework/src/test/scala/org/broadinstitute/sting/queue/pipeline/examples/ExampleCountLociPipelineTest.scala
similarity index 100%
rename from public/scala/test/org/broadinstitute/sting/queue/pipeline/examples/ExampleCountLociPipelineTest.scala
rename to public/queue-framework/src/test/scala/org/broadinstitute/sting/queue/pipeline/examples/ExampleCountLociPipelineTest.scala
diff --git a/public/scala/test/org/broadinstitute/sting/queue/pipeline/examples/ExampleCountReadsPipelineTest.scala b/public/queue-framework/src/test/scala/org/broadinstitute/sting/queue/pipeline/examples/ExampleCountReadsPipelineTest.scala
similarity index 100%
rename from public/scala/test/org/broadinstitute/sting/queue/pipeline/examples/ExampleCountReadsPipelineTest.scala
rename to public/queue-framework/src/test/scala/org/broadinstitute/sting/queue/pipeline/examples/ExampleCountReadsPipelineTest.scala
diff --git a/public/scala/test/org/broadinstitute/sting/queue/pipeline/examples/ExampleReadFilterPipelineTest.scala b/public/queue-framework/src/test/scala/org/broadinstitute/sting/queue/pipeline/examples/ExampleReadFilterPipelineTest.scala
similarity index 100%
rename from public/scala/test/org/broadinstitute/sting/queue/pipeline/examples/ExampleReadFilterPipelineTest.scala
rename to public/queue-framework/src/test/scala/org/broadinstitute/sting/queue/pipeline/examples/ExampleReadFilterPipelineTest.scala
diff --git a/public/scala/test/org/broadinstitute/sting/queue/pipeline/examples/ExampleRetryMemoryLimitPipelineTest.scala b/public/queue-framework/src/test/scala/org/broadinstitute/sting/queue/pipeline/examples/ExampleRetryMemoryLimitPipelineTest.scala
similarity index 100%
rename from public/scala/test/org/broadinstitute/sting/queue/pipeline/examples/ExampleRetryMemoryLimitPipelineTest.scala
rename to public/queue-framework/src/test/scala/org/broadinstitute/sting/queue/pipeline/examples/ExampleRetryMemoryLimitPipelineTest.scala
diff --git a/public/scala/test/org/broadinstitute/sting/queue/pipeline/examples/HelloWorldPipelineTest.scala b/public/queue-framework/src/test/scala/org/broadinstitute/sting/queue/pipeline/examples/HelloWorldPipelineTest.scala
similarity index 100%
rename from public/scala/test/org/broadinstitute/sting/queue/pipeline/examples/HelloWorldPipelineTest.scala
rename to public/queue-framework/src/test/scala/org/broadinstitute/sting/queue/pipeline/examples/HelloWorldPipelineTest.scala
diff --git a/public/scala/test/org/broadinstitute/sting/queue/util/ShellUtilsUnitTest.scala b/public/queue-framework/src/test/scala/org/broadinstitute/sting/queue/util/ShellUtilsUnitTest.scala
similarity index 100%
rename from public/scala/test/org/broadinstitute/sting/queue/util/ShellUtilsUnitTest.scala
rename to public/queue-framework/src/test/scala/org/broadinstitute/sting/queue/util/ShellUtilsUnitTest.scala
diff --git a/public/scala/test/org/broadinstitute/sting/queue/util/StringFileConversionsUnitTest.scala b/public/queue-framework/src/test/scala/org/broadinstitute/sting/queue/util/StringFileConversionsUnitTest.scala
similarity index 100%
rename from public/scala/test/org/broadinstitute/sting/queue/util/StringFileConversionsUnitTest.scala
rename to public/queue-framework/src/test/scala/org/broadinstitute/sting/queue/util/StringFileConversionsUnitTest.scala
diff --git a/public/scala/test/org/broadinstitute/sting/queue/util/SystemUtilsUnitTest.scala b/public/queue-framework/src/test/scala/org/broadinstitute/sting/queue/util/SystemUtilsUnitTest.scala
similarity index 100%
rename from public/scala/test/org/broadinstitute/sting/queue/util/SystemUtilsUnitTest.scala
rename to public/queue-framework/src/test/scala/org/broadinstitute/sting/queue/util/SystemUtilsUnitTest.scala

From 88150e0166ccba374858f8f87e34969fedc84f1d Mon Sep 17 00:00:00 2001
From: Khalid Shakir <kshakir@broadinstitute.org>
Date: Wed, 29 Jan 2014 14:18:02 -0500
Subject: [PATCH 04/16] Switched commited dependency repository from ivy to
 maven.

---
 .../1.0-SNAPSHOT}/caliper-1.0-SNAPSHOT.jar       | Bin
 .../1.0-SNAPSHOT/caliper-1.0-SNAPSHOT.pom        |   9 +++++++++
 .../cofoja/cofoja/1.0-r139}/cofoja-1.0-r139.jar  | Bin
 .../cofoja/cofoja/1.0-r139/cofoja-1.0-r139.pom   |   9 +++++++++
 .../repo/gov/nist/Jama/1.0.2}/Jama-1.0.2.jar     | Bin
 public/repo/gov/nist/Jama/1.0.2/Jama-1.0.2.pom   |   9 +++++++++
 .../drmaa/6.2u5p2}/drmaa-6.2u5p2.jar             | Bin
 .../drmaa/6.2u5p2/drmaa-6.2u5p2.pom              |   9 +++++++++
 .../sf/picard/1.104.1628}/picard-1.104.1628.jar  | Bin
 .../sf/picard/1.104.1628/picard-1.104.1628.pom   |   9 +++++++++
 .../net/sf/sam/1.104.1628}/sam-1.104.1628.jar    | Bin
 .../net/sf/sam/1.104.1628/sam-1.104.1628.pom     |   9 +++++++++
 .../net/sf/snpeff/snpeff/2.0.5}/snpeff-2.0.5.jar | Bin
 .../net/sf/snpeff/snpeff/2.0.5/snpeff-2.0.5.pom  |   9 +++++++++
 .../tribble/1.104.1628}/tribble-1.104.1628.jar   | Bin
 .../tribble/1.104.1628/tribble-1.104.1628.pom    |   9 +++++++++
 .../variant/1.105.1642}/variant-1.105.1642.jar   | Bin
 .../variant/1.105.1642/variant-1.105.1642.pom    |   9 +++++++++
 .../caliper-1.0-SNAPSHOT.xml                     |   3 ---
 .../com.google.code.cofoja/cofoja-1.0-r139.xml   |   3 ---
 .../edu.mit.broad/picard-private-parts-2872.jar  | Bin 6445 -> 0 bytes
 .../edu.mit.broad/picard-private-parts-2872.xml  |   3 ---
 settings/repository/gov.nist/Jama-1.0.2.xml      |   3 ---
 .../net.sf.gridscheduler/drmaa-6.2u5p2.xml       |   3 ---
 .../repository/net.sf.snpeff/snpeff-2.0.5.xml    |   3 ---
 settings/repository/net.sf/picard-1.104.1628.xml |   3 ---
 settings/repository/net.sf/sam-1.104.1628.xml    |   3 ---
 .../repository/org.broad/tribble-1.104.1628.xml  |   3 ---
 .../org.broadinstitute/variant-1.105.1642.xml    |   3 ---
 29 files changed, 81 insertions(+), 30 deletions(-)
 rename {settings/repository/com.google.code.caliper => public/repo/com/google/code/caliper/caliper/1.0-SNAPSHOT}/caliper-1.0-SNAPSHOT.jar (100%)
 create mode 100644 public/repo/com/google/code/caliper/caliper/1.0-SNAPSHOT/caliper-1.0-SNAPSHOT.pom
 rename {settings/repository/com.google.code.cofoja => public/repo/com/google/code/cofoja/cofoja/1.0-r139}/cofoja-1.0-r139.jar (100%)
 create mode 100644 public/repo/com/google/code/cofoja/cofoja/1.0-r139/cofoja-1.0-r139.pom
 rename {settings/repository/gov.nist => public/repo/gov/nist/Jama/1.0.2}/Jama-1.0.2.jar (100%)
 create mode 100644 public/repo/gov/nist/Jama/1.0.2/Jama-1.0.2.pom
 rename {settings/repository/net.sf.gridscheduler => public/repo/net/sf/gridscheduler/drmaa/6.2u5p2}/drmaa-6.2u5p2.jar (100%)
 create mode 100644 public/repo/net/sf/gridscheduler/drmaa/6.2u5p2/drmaa-6.2u5p2.pom
 rename {settings/repository/net.sf => public/repo/net/sf/picard/1.104.1628}/picard-1.104.1628.jar (100%)
 create mode 100644 public/repo/net/sf/picard/1.104.1628/picard-1.104.1628.pom
 rename {settings/repository/net.sf => public/repo/net/sf/sam/1.104.1628}/sam-1.104.1628.jar (100%)
 create mode 100644 public/repo/net/sf/sam/1.104.1628/sam-1.104.1628.pom
 rename {settings/repository/net.sf.snpeff => public/repo/net/sf/snpeff/snpeff/2.0.5}/snpeff-2.0.5.jar (100%)
 create mode 100644 public/repo/net/sf/snpeff/snpeff/2.0.5/snpeff-2.0.5.pom
 rename {settings/repository/org.broad => public/repo/org/broad/tribble/1.104.1628}/tribble-1.104.1628.jar (100%)
 create mode 100644 public/repo/org/broad/tribble/1.104.1628/tribble-1.104.1628.pom
 rename {settings/repository/org.broadinstitute => public/repo/org/broadinstitute/variant/1.105.1642}/variant-1.105.1642.jar (100%)
 create mode 100644 public/repo/org/broadinstitute/variant/1.105.1642/variant-1.105.1642.pom
 delete mode 100644 settings/repository/com.google.code.caliper/caliper-1.0-SNAPSHOT.xml
 delete mode 100644 settings/repository/com.google.code.cofoja/cofoja-1.0-r139.xml
 delete mode 100644 settings/repository/edu.mit.broad/picard-private-parts-2872.jar
 delete mode 100644 settings/repository/edu.mit.broad/picard-private-parts-2872.xml
 delete mode 100644 settings/repository/gov.nist/Jama-1.0.2.xml
 delete mode 100644 settings/repository/net.sf.gridscheduler/drmaa-6.2u5p2.xml
 delete mode 100644 settings/repository/net.sf.snpeff/snpeff-2.0.5.xml
 delete mode 100644 settings/repository/net.sf/picard-1.104.1628.xml
 delete mode 100644 settings/repository/net.sf/sam-1.104.1628.xml
 delete mode 100644 settings/repository/org.broad/tribble-1.104.1628.xml
 delete mode 100644 settings/repository/org.broadinstitute/variant-1.105.1642.xml

diff --git a/settings/repository/com.google.code.caliper/caliper-1.0-SNAPSHOT.jar b/public/repo/com/google/code/caliper/caliper/1.0-SNAPSHOT/caliper-1.0-SNAPSHOT.jar
similarity index 100%
rename from settings/repository/com.google.code.caliper/caliper-1.0-SNAPSHOT.jar
rename to public/repo/com/google/code/caliper/caliper/1.0-SNAPSHOT/caliper-1.0-SNAPSHOT.jar
diff --git a/public/repo/com/google/code/caliper/caliper/1.0-SNAPSHOT/caliper-1.0-SNAPSHOT.pom b/public/repo/com/google/code/caliper/caliper/1.0-SNAPSHOT/caliper-1.0-SNAPSHOT.pom
new file mode 100644
index 000000000..683ac1ae3
--- /dev/null
+++ b/public/repo/com/google/code/caliper/caliper/1.0-SNAPSHOT/caliper-1.0-SNAPSHOT.pom
@@ -0,0 +1,9 @@
+<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>com.google.code.caliper</groupId>
+  <artifactId>caliper</artifactId>
+  <name>caliper</name>
+  <version>1.0-SNAPSHOT</version>
+</project>
diff --git a/settings/repository/com.google.code.cofoja/cofoja-1.0-r139.jar b/public/repo/com/google/code/cofoja/cofoja/1.0-r139/cofoja-1.0-r139.jar
similarity index 100%
rename from settings/repository/com.google.code.cofoja/cofoja-1.0-r139.jar
rename to public/repo/com/google/code/cofoja/cofoja/1.0-r139/cofoja-1.0-r139.jar
diff --git a/public/repo/com/google/code/cofoja/cofoja/1.0-r139/cofoja-1.0-r139.pom b/public/repo/com/google/code/cofoja/cofoja/1.0-r139/cofoja-1.0-r139.pom
new file mode 100644
index 000000000..5a6fb69b9
--- /dev/null
+++ b/public/repo/com/google/code/cofoja/cofoja/1.0-r139/cofoja-1.0-r139.pom
@@ -0,0 +1,9 @@
+<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>com.google.code.cofoja</groupId>
+  <artifactId>cofoja</artifactId>
+  <name>cofoja</name>
+  <version>1.0-r139</version>
+</project>
diff --git a/settings/repository/gov.nist/Jama-1.0.2.jar b/public/repo/gov/nist/Jama/1.0.2/Jama-1.0.2.jar
similarity index 100%
rename from settings/repository/gov.nist/Jama-1.0.2.jar
rename to public/repo/gov/nist/Jama/1.0.2/Jama-1.0.2.jar
diff --git a/public/repo/gov/nist/Jama/1.0.2/Jama-1.0.2.pom b/public/repo/gov/nist/Jama/1.0.2/Jama-1.0.2.pom
new file mode 100644
index 000000000..33d13d1ab
--- /dev/null
+++ b/public/repo/gov/nist/Jama/1.0.2/Jama-1.0.2.pom
@@ -0,0 +1,9 @@
+<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>gov.nist</groupId>
+  <artifactId>Jama</artifactId>
+  <name>Jama</name>
+  <version>1.0.2</version>
+</project>
diff --git a/settings/repository/net.sf.gridscheduler/drmaa-6.2u5p2.jar b/public/repo/net/sf/gridscheduler/drmaa/6.2u5p2/drmaa-6.2u5p2.jar
similarity index 100%
rename from settings/repository/net.sf.gridscheduler/drmaa-6.2u5p2.jar
rename to public/repo/net/sf/gridscheduler/drmaa/6.2u5p2/drmaa-6.2u5p2.jar
diff --git a/public/repo/net/sf/gridscheduler/drmaa/6.2u5p2/drmaa-6.2u5p2.pom b/public/repo/net/sf/gridscheduler/drmaa/6.2u5p2/drmaa-6.2u5p2.pom
new file mode 100644
index 000000000..921635c84
--- /dev/null
+++ b/public/repo/net/sf/gridscheduler/drmaa/6.2u5p2/drmaa-6.2u5p2.pom
@@ -0,0 +1,9 @@
+<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>net.sf.gridscheduler</groupId>
+  <artifactId>drmaa</artifactId>
+  <name>drmaa</name>
+  <version>6.2u5p2</version>
+</project>
diff --git a/settings/repository/net.sf/picard-1.104.1628.jar b/public/repo/net/sf/picard/1.104.1628/picard-1.104.1628.jar
similarity index 100%
rename from settings/repository/net.sf/picard-1.104.1628.jar
rename to public/repo/net/sf/picard/1.104.1628/picard-1.104.1628.jar
diff --git a/public/repo/net/sf/picard/1.104.1628/picard-1.104.1628.pom b/public/repo/net/sf/picard/1.104.1628/picard-1.104.1628.pom
new file mode 100644
index 000000000..c2f2a5048
--- /dev/null
+++ b/public/repo/net/sf/picard/1.104.1628/picard-1.104.1628.pom
@@ -0,0 +1,9 @@
+<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>net.sf.snpeff</groupId>
+  <artifactId>picard</artifactId>
+  <name>picard</name>
+  <version>1.104.1628</version>
+</project>
diff --git a/settings/repository/net.sf/sam-1.104.1628.jar b/public/repo/net/sf/sam/1.104.1628/sam-1.104.1628.jar
similarity index 100%
rename from settings/repository/net.sf/sam-1.104.1628.jar
rename to public/repo/net/sf/sam/1.104.1628/sam-1.104.1628.jar
diff --git a/public/repo/net/sf/sam/1.104.1628/sam-1.104.1628.pom b/public/repo/net/sf/sam/1.104.1628/sam-1.104.1628.pom
new file mode 100644
index 000000000..4d9e63822
--- /dev/null
+++ b/public/repo/net/sf/sam/1.104.1628/sam-1.104.1628.pom
@@ -0,0 +1,9 @@
+<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>net.sf</groupId>
+  <artifactId>sam</artifactId>
+  <name>sam</name>
+  <version>1.104.1628</version>
+</project>
diff --git a/settings/repository/net.sf.snpeff/snpeff-2.0.5.jar b/public/repo/net/sf/snpeff/snpeff/2.0.5/snpeff-2.0.5.jar
similarity index 100%
rename from settings/repository/net.sf.snpeff/snpeff-2.0.5.jar
rename to public/repo/net/sf/snpeff/snpeff/2.0.5/snpeff-2.0.5.jar
diff --git a/public/repo/net/sf/snpeff/snpeff/2.0.5/snpeff-2.0.5.pom b/public/repo/net/sf/snpeff/snpeff/2.0.5/snpeff-2.0.5.pom
new file mode 100644
index 000000000..d316e2055
--- /dev/null
+++ b/public/repo/net/sf/snpeff/snpeff/2.0.5/snpeff-2.0.5.pom
@@ -0,0 +1,9 @@
+<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>net.sf</groupId>
+  <artifactId>snpeff</artifactId>
+  <name>snpeff</name>
+  <version>2.0.5</version>
+</project>
diff --git a/settings/repository/org.broad/tribble-1.104.1628.jar b/public/repo/org/broad/tribble/1.104.1628/tribble-1.104.1628.jar
similarity index 100%
rename from settings/repository/org.broad/tribble-1.104.1628.jar
rename to public/repo/org/broad/tribble/1.104.1628/tribble-1.104.1628.jar
diff --git a/public/repo/org/broad/tribble/1.104.1628/tribble-1.104.1628.pom b/public/repo/org/broad/tribble/1.104.1628/tribble-1.104.1628.pom
new file mode 100644
index 000000000..9acaf0dd1
--- /dev/null
+++ b/public/repo/org/broad/tribble/1.104.1628/tribble-1.104.1628.pom
@@ -0,0 +1,9 @@
+<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>org.broad</groupId>
+  <artifactId>tribble</artifactId>
+  <name>tribble</name>
+  <version>1.104.1628</version>
+</project>
diff --git a/settings/repository/org.broadinstitute/variant-1.105.1642.jar b/public/repo/org/broadinstitute/variant/1.105.1642/variant-1.105.1642.jar
similarity index 100%
rename from settings/repository/org.broadinstitute/variant-1.105.1642.jar
rename to public/repo/org/broadinstitute/variant/1.105.1642/variant-1.105.1642.jar
diff --git a/public/repo/org/broadinstitute/variant/1.105.1642/variant-1.105.1642.pom b/public/repo/org/broadinstitute/variant/1.105.1642/variant-1.105.1642.pom
new file mode 100644
index 000000000..7fafe61f4
--- /dev/null
+++ b/public/repo/org/broadinstitute/variant/1.105.1642/variant-1.105.1642.pom
@@ -0,0 +1,9 @@
+<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>org.broadinstitute</groupId>
+  <artifactId>variant</artifactId>
+  <name>variant</name>
+  <version>1.105.1642</version>
+</project>
diff --git a/settings/repository/com.google.code.caliper/caliper-1.0-SNAPSHOT.xml b/settings/repository/com.google.code.caliper/caliper-1.0-SNAPSHOT.xml
deleted file mode 100644
index 0e2b727e1..000000000
--- a/settings/repository/com.google.code.caliper/caliper-1.0-SNAPSHOT.xml
+++ /dev/null
@@ -1,3 +0,0 @@
-<ivy-module version="1.0">
-    <info organisation="com.google.code.caliper" module="caliper" revision="1.0-SNAPSHOT" status="integration" publication="20110609114800" />
-</ivy-module>
diff --git a/settings/repository/com.google.code.cofoja/cofoja-1.0-r139.xml b/settings/repository/com.google.code.cofoja/cofoja-1.0-r139.xml
deleted file mode 100644
index 202d3d0a3..000000000
--- a/settings/repository/com.google.code.cofoja/cofoja-1.0-r139.xml
+++ /dev/null
@@ -1,3 +0,0 @@
-<ivy-module version="1.0">
-    <info organisation="com.google.code.cofoja" module="cofoja" revision="1.0-r139" status="integration" publication="20110609114800" />
-</ivy-module>
diff --git a/settings/repository/edu.mit.broad/picard-private-parts-2872.jar b/settings/repository/edu.mit.broad/picard-private-parts-2872.jar
deleted file mode 100644
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zzYA(dF@G(oop>yL_c#>Te(!Z4u^o<sBuP+h`HwvC^gaH}0}dp&6JN=H_#O*zC*gmF
zIFR5@AY6V2@m-KR!a3|Cf0pEqkkW&4{*3eMuJTBrJIVMk%+K=9NthOt7Wm_Aeb4w$
z%`4+~vF9YrKk4`Zl|LK@iz0>fn=r@Z{7+a1r0)dF=U=gYB>F$j_|H`T2su5d`9I<Q
zhWMXO<3Mvgf<O5FF%5H+e*DXsKc14)4D>Ya&jonEWe>-}ROkFB+;7bG#~J#W+a7_Z
z2W|XU=znLrCwcvvSe*)v+TngVUw^99!{hYlAU~heCqZzD|BoPy-%o8VHB3|q0RY6P
N*Bul&yi0oU>wn-q>{<W-

diff --git a/settings/repository/edu.mit.broad/picard-private-parts-2872.xml b/settings/repository/edu.mit.broad/picard-private-parts-2872.xml
deleted file mode 100644
index 677d27d80..000000000
--- a/settings/repository/edu.mit.broad/picard-private-parts-2872.xml
+++ /dev/null
@@ -1,3 +0,0 @@
-<ivy-module version="1.0">
-    <info organisation="edu.mit.broad" module="picard-private-parts" revision="2872" status="integration" publication="" />
-</ivy-module>
diff --git a/settings/repository/gov.nist/Jama-1.0.2.xml b/settings/repository/gov.nist/Jama-1.0.2.xml
deleted file mode 100644
index 57ea106ea..000000000
--- a/settings/repository/gov.nist/Jama-1.0.2.xml
+++ /dev/null
@@ -1,3 +0,0 @@
-<ivy-module version="1.0">
-    <info organisation="gov.nist" module="Jama" revision="1.0.2" status="release" />
-</ivy-module>
diff --git a/settings/repository/net.sf.gridscheduler/drmaa-6.2u5p2.xml b/settings/repository/net.sf.gridscheduler/drmaa-6.2u5p2.xml
deleted file mode 100644
index c6a8da052..000000000
--- a/settings/repository/net.sf.gridscheduler/drmaa-6.2u5p2.xml
+++ /dev/null
@@ -1,3 +0,0 @@
-<ivy-module version="1.0">
-    <info organisation="net.sf.gridscheduler" module="drmaa" revision="6.2u5p2" status="release" />
-</ivy-module>
diff --git a/settings/repository/net.sf.snpeff/snpeff-2.0.5.xml b/settings/repository/net.sf.snpeff/snpeff-2.0.5.xml
deleted file mode 100644
index 9a622abe5..000000000
--- a/settings/repository/net.sf.snpeff/snpeff-2.0.5.xml
+++ /dev/null
@@ -1,3 +0,0 @@
-<ivy-module version="1.0">
-    <info organisation="net.sf.snpeff" module="snpeff" revision="2.0.5" status="release" />
-</ivy-module>
diff --git a/settings/repository/net.sf/picard-1.104.1628.xml b/settings/repository/net.sf/picard-1.104.1628.xml
deleted file mode 100644
index bd0c9fbcd..000000000
--- a/settings/repository/net.sf/picard-1.104.1628.xml
+++ /dev/null
@@ -1,3 +0,0 @@
-<ivy-module version="1.0">
-    <info organisation="net.sf" module="picard" revision="1.104.1628" status="release" />
-</ivy-module>
diff --git a/settings/repository/net.sf/sam-1.104.1628.xml b/settings/repository/net.sf/sam-1.104.1628.xml
deleted file mode 100644
index 0b0cba93f..000000000
--- a/settings/repository/net.sf/sam-1.104.1628.xml
+++ /dev/null
@@ -1,3 +0,0 @@
-<ivy-module version="1.0">
-    <info organisation="net.sf" module="sam" revision="1.104.1628" status="release" />
-</ivy-module>
diff --git a/settings/repository/org.broad/tribble-1.104.1628.xml b/settings/repository/org.broad/tribble-1.104.1628.xml
deleted file mode 100644
index c2158e974..000000000
--- a/settings/repository/org.broad/tribble-1.104.1628.xml
+++ /dev/null
@@ -1,3 +0,0 @@
-<ivy-module version="1.0">
-    <info organisation="org.broad" module="tribble" revision="1.104.1628" status="integration" />
-</ivy-module>
diff --git a/settings/repository/org.broadinstitute/variant-1.105.1642.xml b/settings/repository/org.broadinstitute/variant-1.105.1642.xml
deleted file mode 100644
index d1846ce23..000000000
--- a/settings/repository/org.broadinstitute/variant-1.105.1642.xml
+++ /dev/null
@@ -1,3 +0,0 @@
-<ivy-module version="1.0">
-    <info organisation="org.broadinstitute" module="variant" revision="1.105.1642" status="integration" />
-</ivy-module>

From d1a689af334580481524bb821e68ebb48535bec1 Mon Sep 17 00:00:00 2001
From: Khalid Shakir <kshakir@broadinstitute.org>
Date: Wed, 29 Jan 2014 14:54:24 -0500
Subject: [PATCH 05/16] Added new utility files used by maven build, including
 the ant-bridge script.

---
 ant-bridge.sh                                 | 158 ++++++++++++++++++
 .../org/mycompany/app/MyExampleWalker.java    |  56 +++++++
 .../app/MyExampleWalkerIntegrationTest.java   |  54 ++++++
 .../app/MyExampleWalkerUnitTest.java          |  41 +++++
 .../src/main/assembly/example-resources.xml   |  37 ++++
 .../src/main/assembly/binary-dist.xml         |  22 +++
 public/gsalib/src/assembly/gsalib.xml         |  13 ++
 .../src/main/assembly/example-resources.xml   |  20 +++
 .../src/main/assembly/binary-dist.xml         |  23 +++
 .../sting/utils/help/log4j.properties         |   7 +
 10 files changed, 431 insertions(+)
 create mode 100755 ant-bridge.sh
 create mode 100644 public/external-example/src/main/java/org/mycompany/app/MyExampleWalker.java
 create mode 100644 public/external-example/src/test/java/org/mycompany/app/MyExampleWalkerIntegrationTest.java
 create mode 100644 public/external-example/src/test/java/org/mycompany/app/MyExampleWalkerUnitTest.java
 create mode 100644 public/gatk-framework/src/main/assembly/example-resources.xml
 create mode 100644 public/gatk-package/src/main/assembly/binary-dist.xml
 create mode 100644 public/gsalib/src/assembly/gsalib.xml
 create mode 100644 public/queue-framework/src/main/assembly/example-resources.xml
 create mode 100644 public/queue-package/src/main/assembly/binary-dist.xml
 create mode 100644 public/sting-utils/src/main/config/org/broadinstitute/sting/utils/help/log4j.properties

diff --git a/ant-bridge.sh b/ant-bridge.sh
new file mode 100755
index 000000000..f374cd99e
--- /dev/null
+++ b/ant-bridge.sh
@@ -0,0 +1,158 @@
+#!/bin/sh
+
+mvn_args="test-compile"
+mvn_properties=
+mvn_clean=
+unknown_args=
+property_regex='-D(.*)=(.*)'
+unit_test_regex='.*UnitTest'
+post_script=
+
+for arg in "${@}" ; do
+    if [ "${arg}" = "clean" ] ; then
+        mvn_clean="clean"
+        mvn_args=
+
+    elif [[ "${arg}" =~ ${property_regex} ]] ; then
+        property_name=${BASH_REMATCH[1]}
+        property_value=${BASH_REMATCH[2]}
+
+        if [ "${property_name}" = "single" ] ; then
+            test_property="test"
+            test_disabled="it.test"
+            if [[ ! "${property_value}" =~ ${unit_test_regex} ]] ; then
+                test_property="it.test"
+                test_disabled="test"
+            fi
+
+            mvn_properties="${mvn_properties} -D${test_disabled}=disabled -D${test_property}=${property_value}"
+
+        elif [ "${property_name}" = "test.debug.port" ] ; then
+            mvn_properties="${mvn_properties} -Dmaven.surefire.debug=\"-Xdebug -Xrunjdwp:transport=dt_socket,server=y,suspend=y,address=${property_value}\""
+
+        elif [ "${property_name}" = "test.default.maxmemory" ] ; then
+            mvn_properties="${mvn_properties} -Dtest.maxmemory=${property_value}"
+
+        else
+            unknown_args="${unknown_args} \"${arg}\""
+
+        fi
+
+    else
+        if [ "${arg}" != "dist" -a "${mvn_args}" != "test-compile" ]; then
+            echo "Sorry, this script does not currently support mixing targets." >&2
+            exit 1
+
+        elif [ "${arg}" = "dist" ] ; then
+            mvn_args="test-compile"
+
+        elif [ "${arg}" = "gatkdocs" ] ; then
+            local_repo="sitetemprepo"
+            mvn_args="install -Dmaven.repo.local=${local_repo} -Ddisable.queue && mvn site -Dmaven.repo.local=${local_repo} -Ddisable.queue"
+
+        elif [ "${arg}" = "package.gatk.full" ] ; then
+            mvn_args="package '-P!private,!queue'"
+
+        elif [ "${arg}" = "package.gatk.all" ] ; then
+            mvn_args="package '-P!queue'"
+
+        elif [ "${arg}" = "package.queue.full" ] ; then
+            mvn_args="package '-P!private'"
+
+        elif [ "${arg}" = "package.queue.all" ] ; then
+            mvn_args="package"
+
+        elif [ "${arg}" = "release.gatk.full" ] ; then
+            mvn_args="package '-P!private,!queue'"
+            post_script=" && private/src/main/scripts/shell/copy_release.sh public/gatk-package/target/GenomeAnalysisTK-*.tar.bz2"
+
+        elif [ "${arg}" = "release.queue.full" ] ; then
+            mvn_args="package '-P!private'"
+            post_script=" && private/src/main/scripts/shell/copy_release.sh public/queue-package/target/Queue-*.tar.bz2"
+
+        elif [ "${arg}" = "build-picard-private" ] ; then
+            mvn_args="mvn install -f private/picard-maven/pom.xml"
+
+        # TODO: clover support
+        # see ant and maven docs for clover:
+        #  https://confluence.atlassian.com/display/CLOVER/1.+QuickStart+Guide
+        #  https://confluence.atlassian.com/display/CLOVER/Clover-for-Maven+2+and+3+User%27s+Guide
+        #
+        #elif [ "${arg}" = "clover.report" ] ; then
+        #    mvn_args=...
+        #
+        #elif [ "${arg}" = "with.clover" ] ; then
+        #    mvn_args=...
+
+        # TODO: This runs *all* commit tests, including the few on Queue.
+        elif [ "${arg}" = "gatkfull.binary.release.tests" ] ; then
+            local_repo="sitetemprepo"
+            mvn_args="install -Dmaven.repo.local=${local_repo} && verify"
+            mvn_args="${mvn_args} -Dmaven.repo.local=${local_repo} -Dmaven.javadoc.skip=true"
+            mvn_args="${mvn_args} -Dsting.generate-gatk-extensions.skipped=true"
+            mvn_args="${mvn_args} -Dsting.jar.phase=none -Dsting.unpack.phase=none -Dsting.shade.phase=none"
+            mvn_args="${mvn_args} -Dsting.packagecommittests.skipped=false"
+
+        # TODO: This runs only the pipeline tests (full, non-dry run), but not the commit tests for Queue.
+        elif [ "${arg}" = "queuefull.binary.release.tests" ] ; then
+            local_repo="sitetemprepo"
+            mvn_args="install -Dmaven.repo.local=${local_repo} && verify"
+            mvn_args="${mvn_args} -Dmaven.repo.local=${local_repo} -Dmaven.javadoc.skip=true"
+            mvn_args="${mvn_args} -Dsting.generate-gatk-extensions.skipped=true"
+            mvn_args="${mvn_args} -Dsting.jar.phase=none -Dsting.unpack.phase=none -Dsting.shade.phase=none"
+            mvn_args="${mvn_args} -Dsting.packagepipelinetests.skipped=false"
+            mvn_args="${mvn_args} -Dsting.pipelinetests.run=true"
+
+        elif [ "${arg}" = "committests" ] ; then
+            mvn_args="verify -Dsting.committests.skipped=false"
+
+        elif [ "${arg}" = "test" ] ; then
+            mvn_args="test -Dsting.unittests.skipped=false"
+
+        elif [ "${arg}" = "unittest" ] ; then
+            mvn_args="test -Dsting.unittests.skipped=false"
+
+        elif [ "${arg}" = "integrationtest" ] ; then
+            mvn_args="verify -Dsting.integrationtests.skipped=false"
+
+        elif [ "${arg}" = "largescaletest" ] ; then
+            mvn_args="verify -Dsting.largescaletests.skipped=false"
+
+        elif [ "${arg}" = "pipelinetest" ] ; then
+            mvn_args="verify -Dsting.pipelinetests.skipped=false"
+
+        elif [ "${arg}" = "pipelinetestrun" ] ; then
+            mvn_args="verify -Dsting.pipelinetests.skipped=false -Dsting.pipelinetests.run=true"
+
+        elif [ "${arg}" = "fasttest" ] ; then
+            mvn_args="verify -Dsting.committests.skipped=false -pl private/gatk-private -am -Dresource.bundle.skip=true"
+
+        else
+            unknown_args="${unknown_args} \"${arg}\""
+
+        fi
+
+    fi
+
+done
+
+mvn_cmd=
+if [ "${mvn_clean}" != "" ]; then
+    if [ "${mvn_args}" != "" ]; then
+      mvn_cmd="mvn ${mvn_clean} && mvn ${mvn_args}"
+    else
+      mvn_cmd="mvn ${mvn_clean}"
+    fi
+else
+    mvn_cmd="mvn ${mvn_args}"
+fi
+
+if [ "${unknown_args}" != "" ]; then
+    echo "Unrecognized arguments:${unknown_args}" >&2
+
+else
+    echo "Equivalent maven command"
+    echo "${mvn_cmd}${mvn_properties}${post_script}"
+    sh -c "${mvn_cmd}${mvn_properties}${post_script}"
+
+fi
diff --git a/public/external-example/src/main/java/org/mycompany/app/MyExampleWalker.java b/public/external-example/src/main/java/org/mycompany/app/MyExampleWalker.java
new file mode 100644
index 000000000..d65c47c99
--- /dev/null
+++ b/public/external-example/src/main/java/org/mycompany/app/MyExampleWalker.java
@@ -0,0 +1,56 @@
+/*
+* Copyright (c) 2012 The Broad Institute
+* 
+* Permission is hereby granted, free of charge, to any person
+* obtaining a copy of this software and associated documentation
+* files (the "Software"), to deal in the Software without
+* restriction, including without limitation the rights to use,
+* copy, modify, merge, publish, distribute, sublicense, and/or sell
+* copies of the Software, and to permit persons to whom the
+* Software is furnished to do so, subject to the following
+* conditions:
+* 
+* The above copyright notice and this permission notice shall be
+* included in all copies or substantial portions of the Software.
+* 
+* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
+* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+*/
+
+package org.mycompany.app;
+
+import org.broadinstitute.sting.commandline.Output;
+import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
+import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
+import org.broadinstitute.sting.gatk.walkers.LocusWalker;
+
+import java.io.PrintStream;
+
+/**
+ * An example walker that looks surprisingly like CountLoci.
+ */
+public class MyExampleWalker extends LocusWalker<Integer, Long> {
+    @Output
+    PrintStream out;
+
+    public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
+        return 1;
+    }
+
+    public Long reduceInit() { return 0l; }
+
+    public Long reduce(Integer value, Long sum) {
+        return value + sum;
+    }
+
+    public void onTraversalDone( Long c ) {
+        out.println(c);
+    }
+}
diff --git a/public/external-example/src/test/java/org/mycompany/app/MyExampleWalkerIntegrationTest.java b/public/external-example/src/test/java/org/mycompany/app/MyExampleWalkerIntegrationTest.java
new file mode 100644
index 000000000..777079426
--- /dev/null
+++ b/public/external-example/src/test/java/org/mycompany/app/MyExampleWalkerIntegrationTest.java
@@ -0,0 +1,54 @@
+/*
+* Copyright (c) 2012 The Broad Institute
+* 
+* Permission is hereby granted, free of charge, to any person
+* obtaining a copy of this software and associated documentation
+* files (the "Software"), to deal in the Software without
+* restriction, including without limitation the rights to use,
+* copy, modify, merge, publish, distribute, sublicense, and/or sell
+* copies of the Software, and to permit persons to whom the
+* Software is furnished to do so, subject to the following
+* conditions:
+* 
+* The above copyright notice and this permission notice shall be
+* included in all copies or substantial portions of the Software.
+* 
+* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
+* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+*/
+
+package org.mycompany.app;
+
+import org.broadinstitute.sting.WalkerTest;
+import org.testng.annotations.Test;
+
+import java.io.File;
+import java.net.URISyntaxException;
+import java.net.URL;
+import java.util.Collections;
+import java.util.MissingResourceException;
+
+/**
+ * NOTE: Currently the testing infrastructure for walkers does not support running outside the Broad.
+ */
+public class MyExampleWalkerIntegrationTest extends WalkerTest {
+    @Test
+    public void testMyExampleWalker() throws URISyntaxException {
+        String gatk_args = String.format("-T MyExampleWalker -I %s -R %s", getResource("/exampleBAM.bam"), getResource("/exampleFASTA.fasta"));
+        WalkerTestSpec spec = new WalkerTestSpec(gatk_args, Collections.<String>emptyList());
+        executeTest("Testing count on the example bam", spec);
+    }
+
+    private File getResource(String path) throws URISyntaxException {
+        URL resourceUrl = getClass().getResource(path);
+        if (resourceUrl == null)
+            throw new MissingResourceException("Resource not found: " + path, getClass().getSimpleName(), path);
+        return new File(resourceUrl.toURI());
+    }
+}
diff --git a/public/external-example/src/test/java/org/mycompany/app/MyExampleWalkerUnitTest.java b/public/external-example/src/test/java/org/mycompany/app/MyExampleWalkerUnitTest.java
new file mode 100644
index 000000000..e3e0c81ea
--- /dev/null
+++ b/public/external-example/src/test/java/org/mycompany/app/MyExampleWalkerUnitTest.java
@@ -0,0 +1,41 @@
+/*
+* Copyright (c) 2012 The Broad Institute
+* 
+* Permission is hereby granted, free of charge, to any person
+* obtaining a copy of this software and associated documentation
+* files (the "Software"), to deal in the Software without
+* restriction, including without limitation the rights to use,
+* copy, modify, merge, publish, distribute, sublicense, and/or sell
+* copies of the Software, and to permit persons to whom the
+* Software is furnished to do so, subject to the following
+* conditions:
+* 
+* The above copyright notice and this permission notice shall be
+* included in all copies or substantial portions of the Software.
+* 
+* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
+* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+*/
+
+package org.mycompany.app;
+
+import org.broadinstitute.sting.BaseTest;
+import org.testng.Assert;
+import org.testng.annotations.Test;
+
+/**
+ * NOTE: Currently the testing infrastructure for walkers does not support running outside the Broad.
+ */
+public class MyExampleWalkerUnitTest extends BaseTest {
+    @Test
+    public void testMyExampleWalker() {
+        MyExampleWalker walker = new MyExampleWalker();
+        Assert.assertEquals((long)walker.reduce(1, 1L), 2L);
+    }
+}
diff --git a/public/gatk-framework/src/main/assembly/example-resources.xml b/public/gatk-framework/src/main/assembly/example-resources.xml
new file mode 100644
index 000000000..b285cc05f
--- /dev/null
+++ b/public/gatk-framework/src/main/assembly/example-resources.xml
@@ -0,0 +1,37 @@
+<assembly xmlns="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.2" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.2 http://maven.apache.org/xsd/assembly-1.1.2.xsd">
+    <id>example-resources</id>
+    <formats>
+        <format>tar.bz2</format>
+    </formats>
+    <includeBaseDirectory>false</includeBaseDirectory>
+    <fileSets>
+        <fileSet>
+            <directory>${project.build.sourceDirectory}/org/broadinstitute/sting/gatk/walkers/qc</directory>
+            <outputDirectory>.</outputDirectory>
+            <includes>
+                <include>Pileup.java</include>
+                <include>CountLoci.java</include>
+                <include>CountReads.java</include>
+                <include>CheckPileup.java</include>
+            </includes>
+        </fileSet>
+        <fileSet>
+            <directory>${project.build.sourceDirectory}/org/broadinstitute/sting/gatk/walkers/readutils</directory>
+            <outputDirectory>.</outputDirectory>
+            <includes>
+                <include>PrintReads.java</include>
+            </includes>
+        </fileSet>
+        <fileSet>
+            <directory>src/test/resources</directory>
+            <outputDirectory>.</outputDirectory>
+            <includes>
+                <include>exampleBAM.bam</include>
+                <include>exampleBAM.bam.bai</include>
+                <include>exampleFASTA.fasta</include>
+                <include>exampleFASTA.fasta.fai</include>
+                <include>exampleFASTA.dict</include>
+            </includes>
+        </fileSet>
+    </fileSets>
+</assembly>
diff --git a/public/gatk-package/src/main/assembly/binary-dist.xml b/public/gatk-package/src/main/assembly/binary-dist.xml
new file mode 100644
index 000000000..adc52646c
--- /dev/null
+++ b/public/gatk-package/src/main/assembly/binary-dist.xml
@@ -0,0 +1,22 @@
+<assembly xmlns="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.2" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.2 http://maven.apache.org/xsd/assembly-1.1.2.xsd">
+    <id>binary-dist</id>
+    <formats>
+        <format>tar.bz2</format>
+    </formats>
+    <includeBaseDirectory>false</includeBaseDirectory>
+    <dependencySets>
+        <dependencySet>
+            <includes>
+                <include>org.broadinstitute.sting:gatk-package</include>
+            </includes>
+            <outputFileNameMapping>${sting.binary-dist.name}.${artifact.extension}</outputFileNameMapping>
+        </dependencySet>
+        <dependencySet>
+            <outputDirectory>resources</outputDirectory>
+            <unpack>true</unpack>
+            <includes>
+                <include>org.broadinstitute.sting:gatk-framework:tar.bz2:example-resources</include>
+            </includes>
+        </dependencySet>
+    </dependencySets>
+</assembly>
diff --git a/public/gsalib/src/assembly/gsalib.xml b/public/gsalib/src/assembly/gsalib.xml
new file mode 100644
index 000000000..7650c713d
--- /dev/null
+++ b/public/gsalib/src/assembly/gsalib.xml
@@ -0,0 +1,13 @@
+<assembly xmlns="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.2" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.2 http://maven.apache.org/xsd/assembly-1.1.2.xsd">
+    <id>gsalib</id>
+    <formats>
+        <format>tar.gz</format>
+    </formats>
+    <includeBaseDirectory>false</includeBaseDirectory>
+    <fileSets>
+        <fileSet>
+            <outputDirectory>gsalib</outputDirectory>
+            <directory>src/R</directory>
+        </fileSet>
+    </fileSets>
+</assembly>
diff --git a/public/queue-framework/src/main/assembly/example-resources.xml b/public/queue-framework/src/main/assembly/example-resources.xml
new file mode 100644
index 000000000..7d4ec43ef
--- /dev/null
+++ b/public/queue-framework/src/main/assembly/example-resources.xml
@@ -0,0 +1,20 @@
+<assembly xmlns="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.2" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.2 http://maven.apache.org/xsd/assembly-1.1.2.xsd">
+    <id>example-resources</id>
+    <formats>
+        <format>tar.bz2</format>
+    </formats>
+    <includeBaseDirectory>false</includeBaseDirectory>
+    <fileSets>
+        <fileSet>
+            <directory>src/main/qscripts/org/broadinstitute/sting/queue/qscripts/examples</directory>
+            <outputDirectory>.</outputDirectory>
+            <includes>
+                <include>ExampleCountReads.scala</include>
+                <include>ExampleCountLoci.scala</include>
+                <include>ExampleUnifiedGenotyper.scala</include>
+                <include>ExampleReadFilter.scala</include>
+                <include>ExampleCustomWalker.scala</include>
+            </includes>
+        </fileSet>
+    </fileSets>
+</assembly>
diff --git a/public/queue-package/src/main/assembly/binary-dist.xml b/public/queue-package/src/main/assembly/binary-dist.xml
new file mode 100644
index 000000000..6de236a56
--- /dev/null
+++ b/public/queue-package/src/main/assembly/binary-dist.xml
@@ -0,0 +1,23 @@
+<assembly xmlns="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.2" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.2 http://maven.apache.org/xsd/assembly-1.1.2.xsd">
+    <id>binary-dist</id>
+    <formats>
+        <format>tar.bz2</format>
+    </formats>
+    <includeBaseDirectory>false</includeBaseDirectory>
+    <dependencySets>
+        <dependencySet>
+            <includes>
+                <include>org.broadinstitute.sting:queue-package</include>
+            </includes>
+            <outputFileNameMapping>${sting.binary-dist.name}.${artifact.extension}</outputFileNameMapping>
+        </dependencySet>
+        <dependencySet>
+            <outputDirectory>resources</outputDirectory>
+            <unpack>true</unpack>
+            <includes>
+                <include>org.broadinstitute.sting:gatk-framework:tar.bz2:example-resources</include>
+                <include>org.broadinstitute.sting:queue-framework:tar.bz2:example-resources</include>
+            </includes>
+        </dependencySet>
+    </dependencySets>
+</assembly>
diff --git a/public/sting-utils/src/main/config/org/broadinstitute/sting/utils/help/log4j.properties b/public/sting-utils/src/main/config/org/broadinstitute/sting/utils/help/log4j.properties
new file mode 100644
index 000000000..38c8335c9
--- /dev/null
+++ b/public/sting-utils/src/main/config/org/broadinstitute/sting/utils/help/log4j.properties
@@ -0,0 +1,7 @@
+# Root logger option
+log4j.rootLogger=INFO, stdout
+
+# Direct log messages to stdout
+log4j.appender.stdout=org.apache.log4j.ConsoleAppender
+log4j.appender.stdout.Target=System.out
+log4j.appender.stdout.layout=org.apache.log4j.SimpleLayout

From caa76cdac4c31cea6a90b4fd68f90492b3827264 Mon Sep 17 00:00:00 2001
From: Khalid Shakir <kshakir@broadinstitute.org>
Date: Wed, 29 Jan 2014 17:00:06 -0500
Subject: [PATCH 06/16] Added maven pom.xmls for various artifacts.

---
 pom.xml                          | 733 +++++++++++++++++++++++++++++++
 protected/gatk-protected/pom.xml | 144 ++++++
 protected/pom.xml                |  24 +
 public/external-example/pom.xml  | 257 +++++++++++
 public/gatk-framework/pom.xml    | 142 ++++++
 public/gatk-package/pom.xml      | 155 +++++++
 public/gatk-queue-extgen/pom.xml |  29 ++
 public/gsalib/pom.xml            |  45 ++
 public/package-tests/pom.xml     | 158 +++++++
 public/pom.xml                   |  46 ++
 public/queue-framework/pom.xml   | 267 +++++++++++
 public/queue-package/pom.xml     | 170 +++++++
 public/sting-root/pom.xml        | 619 ++++++++++++++++++++++++++
 public/sting-utils/pom.xml       | 170 +++++++
 14 files changed, 2959 insertions(+)
 create mode 100644 pom.xml
 create mode 100644 protected/gatk-protected/pom.xml
 create mode 100644 protected/pom.xml
 create mode 100644 public/external-example/pom.xml
 create mode 100644 public/gatk-framework/pom.xml
 create mode 100644 public/gatk-package/pom.xml
 create mode 100644 public/gatk-queue-extgen/pom.xml
 create mode 100644 public/gsalib/pom.xml
 create mode 100644 public/package-tests/pom.xml
 create mode 100644 public/pom.xml
 create mode 100644 public/queue-framework/pom.xml
 create mode 100644 public/queue-package/pom.xml
 create mode 100644 public/sting-root/pom.xml
 create mode 100644 public/sting-utils/pom.xml

diff --git a/pom.xml b/pom.xml
new file mode 100644
index 000000000..787bd5d31
--- /dev/null
+++ b/pom.xml
@@ -0,0 +1,733 @@
+<?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>
+
+    <!--
+    This pom is the aggregator for all sting/gatk poms
+    See also:
+      http://maven.apache.org/pom.html#Inheritance_v
+      http://maven.apache.org/guides/introduction/introduction-to-the-pom.html#Project_Inheritance_vs_Project_Aggregation
+      http://stackoverflow.com/questions/1992213/maven-parent-pom-vs-modules-pom
+    -->
+
+    <parent>
+        <groupId>org.broadinstitute.sting</groupId>
+        <artifactId>sting-root</artifactId>
+        <version>2.6-SNAPSHOT</version>
+        <relativePath>public/sting-root</relativePath>
+    </parent>
+
+    <artifactId>sting-aggregator</artifactId>
+    <packaging>pom</packaging>
+    <name>Sting Aggregator</name>
+
+    <modules>
+        <module>public</module>
+        <!-- private & protected optionally enabled as profiles -->
+    </modules>
+
+    <properties>
+        <sting.basedir>${project.basedir}</sting.basedir>
+        <resource.bundle.path>StingText.properties</resource.bundle.path>
+        <resource.bundle.skip>false</resource.bundle.skip>
+        <!-- TODO: Need a better a way to say "don't include hidden" by default -->
+        <gatkdocs.include.hidden>-build-timestamp "${maven.build.timestamp}"</gatkdocs.include.hidden>
+        <sting.jar.phase>package</sting.jar.phase>
+        <sting.packagecommittests.skipped>true</sting.packagecommittests.skipped>
+        <sting.packageunittests.skipped>${sting.packagecommittests.skipped}</sting.packageunittests.skipped>
+        <sting.packageintegrationtests.skipped>${sting.packagecommittests.skipped}</sting.packageintegrationtests.skipped>
+        <sting.packagepipelinetests.skipped>${sting.packagecommittests.skipped}</sting.packagepipelinetests.skipped>
+        <sting.packagelargescaletests.skipped>true</sting.packagelargescaletests.skipped>
+    </properties>
+
+    <dependencies>
+        <dependency>
+            <groupId>com.sun</groupId>
+            <artifactId>tools</artifactId>
+        </dependency>
+    </dependencies>
+
+    <build>
+        <!-- Plugin configuration -->
+        <pluginManagement>
+            <plugins>
+                <plugin>
+                    <groupId>org.apache.maven.plugins</groupId>
+                    <artifactId>maven-clean-plugin</artifactId>
+                    <configuration>
+                        <filesets>
+                            <!--
+                            TODO: Once GATKDoclet stops hard coding paths, we remove this and leave
+                            TODO: it to the standard maven conventions to clean up for us
+                            -->
+                            <fileset>
+                                <directory>gatkdocs</directory>
+                            </fileset>
+                            <fileset>
+                                <directory>${basedir}</directory>
+                                <includes>
+                                    <include>javadoc.sh</include>
+                                    <include>options</include>
+                                    <include>packages</include>
+                                </includes>
+                            </fileset>
+                            <!--
+                            Shade dumps this temp file in basedir, with no good way to reconfigure.
+                            https://jira.codehaus.org/browse/MSHADE-145
+                            -->
+                            <fileset>
+                                <directory>${basedir}</directory>
+                                <includes>
+                                    <include>dependency-reduced-pom.xml</include>
+                                </includes>
+                            </fileset>
+                        </filesets>
+                    </configuration>
+                </plugin>
+                <plugin>
+                    <groupId>org.apache.maven.plugins</groupId>
+                    <artifactId>maven-dependency-plugin</artifactId>
+                    <executions>
+                        <execution>
+                            <id>unpack-direct-dependencies</id>
+                            <goals>
+                                <goal>unpack-dependencies</goal>
+                            </goals>
+                            <phase>none</phase>
+                            <configuration>
+                                <excludeTransitive>true</excludeTransitive>
+                                <outputDirectory>${project.build.outputDirectory}</outputDirectory>
+                                <includeTypes>jar</includeTypes>
+                                <excludeScope>system</excludeScope>
+                            </configuration>
+                        </execution>
+                    </executions>
+                </plugin>
+                <!-- TODO: Change the ResourceBundleExtractorDoclet to not require log4j.properties file -->
+                <plugin>
+                    <groupId>org.apache.maven.plugins</groupId>
+                    <artifactId>maven-resources-plugin</artifactId>
+                    <executions>
+                        <execution>
+                            <id>copy-resource-bundle-log4j</id>
+                            <goals>
+                                <goal>copy-resources</goal>
+                            </goals>
+                            <phase>none</phase>
+                            <configuration>
+                                <outputDirectory>${project.reporting.outputDirectory}/apidocs</outputDirectory>
+                                <resources>
+                                    <resource>
+                                        <directory>${sting.basedir}/sting-utils/src/main/config/org/broadinstitute/sting/utils/help</directory>
+                                    </resource>
+                                </resources>
+                            </configuration>
+                        </execution>
+                    </executions>
+                </plugin>
+                <plugin>
+                    <groupId>org.apache.maven.plugins</groupId>
+                    <artifactId>maven-javadoc-plugin</artifactId>
+                    <executions>
+                        <execution>
+                            <id>extract-resource-bundle</id>
+                            <goals>
+                                <goal>javadoc</goal>
+                            </goals>
+                            <phase>none</phase>
+                            <configuration>
+                                <!-- Allow skipping for "fasttest" -->
+                                <skip>${resource.bundle.skip}</skip>
+                                <doclet>org.broadinstitute.sting.utils.help.ResourceBundleExtractorDoclet</doclet>
+                                <!-- Required as doclet uses reflection to access classes for documentation, instead of source java-->
+                                <docletPath>${project.build.outputDirectory}</docletPath>
+                                <docletArtifact>
+                                    <groupId>${project.groupId}</groupId>
+                                    <!-- TODO: THIS IS SUPPOSED TO BE STING-UTILS! -->
+                                    <artifactId>gatk-framework</artifactId>
+                                    <version>${project.version}</version>
+                                </docletArtifact>
+                                <maxmemory>2g</maxmemory>
+                                <useStandardDocletOptions>false</useStandardDocletOptions>
+                                <quiet>true</quiet>
+                                <additionalparam>-build-timestamp "${maven.build.timestamp}" -absolute-version ${build.version} -out ${project.build.outputDirectory}/${resource.bundle.path}</additionalparam>
+                            </configuration>
+                        </execution>
+                    </executions>
+                </plugin>
+
+                <plugin>
+                    <groupId>org.apache.maven.plugins</groupId>
+                    <artifactId>maven-compiler-plugin</artifactId>
+                    <configuration>
+                        <proc>none</proc>
+                        <annotationProcessors>
+                            <annotationProcessor>com.google.java.contract.core.apt.AnnotationProcessor</annotationProcessor>
+                        </annotationProcessors>
+                        <compilerArguments>
+                            <!--
+                            For com.sun.istack.internal. Because bootclasspath is set to include rt.jar, now jce.jar must be set for the Oracle only javax.crypto also.
+                            TODO: This Sun internal tool usage needs to be removed ASAP!
+                            -->
+                            <bootclasspath>${java.home}/lib/rt.jar:${java.home}/lib/jce.jar</bootclasspath>
+                        </compilerArguments>
+                    </configuration>
+                    <executions>
+                        <execution>
+                            <id>default-compile</id>
+                            <phase>none</phase>
+                        </execution>
+                        <execution>
+                            <id>default-testCompile</id>
+                            <phase>none</phase>
+                        </execution>
+                        <!--
+                        Explicit package-info creation to match existing ant output.
+                        -->
+                        <execution>
+                            <id>compile-package-info</id>
+                            <goals>
+                                <goal>compile</goal>
+                            </goals>
+                            <phase>compile</phase>
+                            <configuration>
+                                <compilerArgs>
+                                    <arg>-Xpkginfo:always</arg>
+                                </compilerArgs>
+                                <includes>
+                                    <include>**/package-info.java</include>
+                                </includes>
+                            </configuration>
+                        </execution>
+                        <!--
+                        TODO: Currently disabled in build.xml. Here as well.
+                        <execution>
+                            <id>compile-annotations</id>
+                            <phase>compile</phase>
+                            <goals>
+                                <goal>compile</goal>
+                            </goals>
+                            <configuration>
+                                <proc>only</proc>
+                            </configuration>
+                        </execution>
+                        -->
+                        <execution>
+                            <id>compile-java</id>
+                            <goals>
+                                <goal>compile</goal>
+                            </goals>
+                            <phase>compile</phase>
+                            <configuration>
+                                <!--
+                                Package info is supposed to be in source:
+                                    http://maven.apache.org/plugins/maven-javadoc-plugin/examples/javadoc-resources.html
+                                But maven-compile-plugin doesn't auto exclude these:
+                                    https://jira.codehaus.org/browse/MCOMPILER-205?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=326505#comment-326505
+                                So, explicitly exclude them
+                                -->
+                                <excludes>
+                                    <exclude>**/package-info.java</exclude>
+                                </excludes>
+                            </configuration>
+                        </execution>
+                        <!--
+                        TODO: Currently disabled in build.xml. Here as well.
+                        <execution>
+                            <id>testCompile-annotations</id>
+                            <phase>test-compile</phase>
+                            <goals>
+                                <goal>testCompile</goal>
+                            </goals>
+                            <configuration>
+                                <proc>only</proc>
+                            </configuration>
+                        </execution>
+                        -->
+                        <execution>
+                            <id>testCompile-java</id>
+                            <goals>
+                                <goal>testCompile</goal>
+                            </goals>
+                            <phase>test-compile</phase>
+                        </execution>
+                    </executions>
+                </plugin>
+
+                <plugin>
+                    <groupId>org.scala-tools</groupId>
+                    <artifactId>maven-scala-plugin</artifactId>
+                    <executions>
+                        <execution>
+                            <goals>
+                                <goal>compile</goal>
+                                <goal>testCompile</goal>
+                            </goals>
+                        </execution>
+                    </executions>
+                </plugin>
+
+                <plugin>
+                    <groupId>org.apache.maven.plugins</groupId>
+                    <artifactId>maven-jar-plugin</artifactId>
+                    <executions>
+                        <execution>
+                            <id>default-jar</id>
+                            <phase>${sting.jar.phase}</phase>
+                        </execution>
+                    </executions>
+                </plugin>
+
+                <plugin>
+                    <groupId>org.apache.maven.plugins</groupId>
+                    <artifactId>maven-shade-plugin</artifactId>
+                    <executions>
+                        <execution>
+                            <id>sting-executable</id>
+                            <goals>
+                                <goal>shade</goal>
+                            </goals>
+                            <phase>none</phase>
+                            <configuration>
+                                <minimizeJar>true</minimizeJar>
+                                <artifactSet>
+                                    <excludes>
+                                        <exclude>org.broadinstitute.sting:gsalib:tar.gz:*</exclude>
+                                        <exclude>org.broadinstitute.sting:*:tar.bz2:example-resources</exclude>
+                                    </excludes>
+                                </artifactSet>
+                                <transformers>
+                                    <transformer implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer">
+                                        <manifestEntries>
+                                            <Main-Class>${app.main.class}</Main-Class>
+                                        </manifestEntries>
+                                    </transformer>
+                                    <transformer implementation="org.apache.maven.plugins.shade.resource.AppendingTransformer">
+                                        <resource>${resource.bundle.path}</resource>
+                                    </transformer>
+                                </transformers>
+                            </configuration>
+                        </execution>
+                    </executions>
+                </plugin>
+
+                <plugin>
+                    <groupId>org.apache.maven.plugins</groupId>
+                    <artifactId>maven-assembly-plugin</artifactId>
+                    <executions>
+                        <execution>
+                            <id>example-resources</id>
+                            <goals>
+                                <goal>single</goal>
+                            </goals>
+                            <phase>none</phase>
+                            <configuration>
+                                <descriptors>
+                                    <descriptor>src/main/assembly/example-resources.xml</descriptor>
+                                </descriptors>
+                            </configuration>
+                        </execution>
+                        <execution>
+                            <id>binary-dist</id>
+                            <goals>
+                                <goal>single</goal>
+                            </goals>
+                            <phase>none</phase>
+                            <configuration>
+                                <descriptors>
+                                    <descriptor>src/main/assembly/binary-dist.xml</descriptor>
+                                </descriptors>
+                            </configuration>
+                        </execution>
+                    </executions>
+                </plugin>
+
+                <!-- TODO: Remove temporary symbolic link creation, after fixing test paths to use local resources. -->
+                <plugin>
+                    <groupId>com.pyx4j</groupId>
+                    <artifactId>maven-junction-plugin</artifactId>
+                    <executions>
+                        <execution>
+                            <id>link-public-testdata</id>
+                            <goals>
+                                <goal>link</goal>
+                            </goals>
+                            <phase>none</phase>
+                            <configuration>
+                                <links>
+                                    <link>
+                                        <dst>${basedir}/public/testdata</dst>
+                                        <src>${sting.basedir}/public/gatk-framework/src/test/resources</src>
+                                    </link>
+                                </links>
+                            </configuration>
+                        </execution>
+                        <execution>
+                            <id>unlink-public-testdata</id>
+                            <goals>
+                                <goal>unlink</goal>
+                            </goals>
+                            <phase>none</phase>
+                            <configuration>
+                                <links>
+                                    <link>
+                                        <dst>${basedir}/public/testdata</dst>
+                                        <src>${sting.basedir}/public/gatk-framework/src/test/resources</src>
+                                    </link>
+                                </links>
+                            </configuration>
+                        </execution>
+                        <execution>
+                            <id>link-private-testdata</id>
+                            <goals>
+                                <goal>link</goal>
+                            </goals>
+                            <phase>none</phase>
+                            <configuration>
+                                <links>
+                                    <link>
+                                        <dst>${basedir}/private/testdata</dst>
+                                        <src>${sting.basedir}/private/gatk-private/src/test/resources</src>
+                                    </link>
+                                </links>
+                            </configuration>
+                        </execution>
+                        <execution>
+                            <id>unlink-private-testdata</id>
+                            <goals>
+                                <goal>unlink</goal>
+                            </goals>
+                            <phase>none</phase>
+                            <configuration>
+                                <links>
+                                    <link>
+                                        <dst>${basedir}/private/testdata</dst>
+                                        <src>${sting.basedir}/private/gatk-private/src/test/resources</src>
+                                    </link>
+                                </links>
+                            </configuration>
+                        </execution>
+                        <execution>
+                            <id>link-public-qscript</id>
+                            <goals>
+                                <goal>link</goal>
+                            </goals>
+                            <phase>none</phase>
+                            <configuration>
+                                <links>
+                                    <link>
+                                        <dst>${basedir}/public/scala/qscript</dst>
+                                        <src>${sting.basedir}/public/queue-framework/src/main/qscripts</src>
+                                    </link>
+                                </links>
+                            </configuration>
+                        </execution>
+                        <execution>
+                            <id>unlink-public-qscript</id>
+                            <goals>
+                                <goal>unlink</goal>
+                            </goals>
+                            <phase>none</phase>
+                            <configuration>
+                                <links>
+                                    <link>
+                                        <dst>${basedir}/public/scala/qscript</dst>
+                                        <src>${sting.basedir}/public/queue-framework/src/main/qscripts</src>
+                                    </link>
+                                </links>
+                            </configuration>
+                        </execution>
+                        <execution>
+                            <id>link-private-qscript</id>
+                            <goals>
+                                <goal>link</goal>
+                            </goals>
+                            <phase>none</phase>
+                            <configuration>
+                                <links>
+                                    <link>
+                                        <dst>${basedir}/private/scala/qscript</dst>
+                                        <src>${sting.basedir}/private/queue-private/src/main/qscripts</src>
+                                    </link>
+                                </links>
+                            </configuration>
+                        </execution>
+                        <execution>
+                            <id>unlink-private-qscript</id>
+                            <goals>
+                                <goal>unlink</goal>
+                            </goals>
+                            <phase>none</phase>
+                            <configuration>
+                                <links>
+                                    <link>
+                                        <dst>${basedir}/private/scala/qscript</dst>
+                                        <src>${sting.basedir}/private/queue-private/src/main/qscripts</src>
+                                    </link>
+                                </links>
+                            </configuration>
+                        </execution>
+                        <execution>
+                            <id>link-git-release</id>
+                            <goals>
+                                <goal>link</goal>
+                            </goals>
+                            <phase>none</phase>
+                            <configuration>
+                                <links>
+                                    <link>
+                                        <dst>${project.build.directory}/${sting.binary-dist.name}-${build.version}.tar.bz2</dst>
+                                        <src>${project.build.directory}/${project.build.finalName}-binary-dist.tar.bz2</src>
+                                    </link>
+                                </links>
+                            </configuration>
+                        </execution>
+                    </executions>
+                </plugin>
+                <plugin>
+                    <groupId>org.apache.maven.plugins</groupId>
+                    <artifactId>maven-invoker-plugin</artifactId>
+                    <configuration>
+                        <skipInvocation>true</skipInvocation>
+                        <debug>false</debug>
+                        <pom>${sting.basedir}/public/package-tests/pom.xml</pom>
+                        <noLog>true</noLog>
+                        <streamLogs>true</streamLogs>
+                        <localRepositoryPath>${sting.basedir}/${maven.repo.local}</localRepositoryPath>
+                        <properties>
+                            <test>${test}</test>
+                            <it.test>${it.test}</it.test>
+                            <skip>false</skip>
+                            <maven.test.skip>false</maven.test.skip>
+                            <sting.packagetests.artifactId>${sting.packagetests.artifactId}</sting.packagetests.artifactId>
+                            <sting.packagetests.testClasses>${project.build.testOutputDirectory}</sting.packagetests.testClasses>
+                            <sting.packagetests.basedir>${project.basedir}</sting.packagetests.basedir>
+                            <sting.pipelinetests.run>${sting.pipelinetests.run}</sting.pipelinetests.run>
+                            <maven.surefire.debug>${maven.surefire.debug}</maven.surefire.debug>
+                            <maven.failsafe.debug>${maven.failsafe.debug}</maven.failsafe.debug>
+                        </properties>
+                    </configuration>
+                    <executions>
+                        <execution>
+                            <id>package-unittests</id>
+                            <goals>
+                                <goal>run</goal>
+                            </goals>
+                            <configuration>
+                                <goals>
+                                    <goal>test</goal>
+                                </goals>
+                                <profiles>
+                                    <profile>unittests</profile>
+                                </profiles>
+                                <skipInvocation>${sting.packageunittests.skipped}</skipInvocation>
+                                <properties>
+                                    <sting.packageunittests.skipped>${sting.packageunittests.skipped}</sting.packageunittests.skipped>
+                                </properties>
+                            </configuration>
+                        </execution>
+                        <execution>
+                            <id>package-integrationtests</id>
+                            <goals>
+                                <goal>integration-test</goal>
+                                <goal>verify</goal>
+                            </goals>
+                            <configuration>
+                                <goals>
+                                    <goal>verify</goal>
+                                </goals>
+                                <profiles>
+                                    <profile>integrationtests</profile>
+                                </profiles>
+                                <skipInvocation>${sting.packageintegrationtests.skipped}</skipInvocation>
+                                <properties>
+                                    <sting.packageintegrationtests.skipped>${sting.packageintegrationtests.skipped}</sting.packageintegrationtests.skipped>
+                                </properties>
+                            </configuration>
+                        </execution>
+                        <execution>
+                            <id>package-pipelinetests</id>
+                            <goals>
+                                <goal>integration-test</goal>
+                                <goal>verify</goal>
+                            </goals>
+                            <configuration>
+                                <goals>
+                                    <goal>verify</goal>
+                                </goals>
+                                <profiles>
+                                    <profile>integrationtests</profile>
+                                </profiles>
+                                <skipInvocation>${sting.packagepipelinetests.skipped}</skipInvocation>
+                                <properties>
+                                    <sting.packagepipelinetests.skipped>${sting.packagepipelinetests.skipped}</sting.packagepipelinetests.skipped>
+                                </properties>
+                            </configuration>
+                        </execution>
+                        <execution>
+                            <id>package-largescaletests</id>
+                            <goals>
+                                <goal>integration-test</goal>
+                                <goal>verify</goal>
+                            </goals>
+                            <configuration>
+                                <goals>
+                                    <goal>verify</goal>
+                                </goals>
+                                <profiles>
+                                    <profile>integrationtests</profile>
+                                </profiles>
+                                <skipInvocation>${sting.packagelargescaletests.skipped}</skipInvocation>
+                                <properties>
+                                    <sting.packagelargescaletests.skipped>${sting.packagelargescaletests.skipped}</sting.packagelargescaletests.skipped>
+                                </properties>
+                            </configuration>
+                        </execution>
+                    </executions>
+                </plugin>
+                <plugin>
+                    <groupId>org.apache.maven.plugins</groupId>
+                    <artifactId>maven-install-plugin</artifactId>
+                    <version>2.5</version>
+                    <executions>
+                        <execution>
+                            <id>install-package</id>
+                            <goals>
+                                <goal>install-file</goal>
+                            </goals>
+                            <phase>none</phase>
+                            <configuration>
+                                <generatePom>true</generatePom>
+                                <groupId>${project.groupId}</groupId>
+                                <artifactId>${project.artifactId}</artifactId>
+                                <version>${project.version}</version>
+                                <packaging>${project.packaging}</packaging>
+                                <file>${project.build.directory}/${project.build.finalName}.${project.packaging}</file>
+                            </configuration>
+                        </execution>
+                    </executions>
+                </plugin>
+            </plugins>
+        </pluginManagement>
+
+        <!-- Invoke plugins that always run -->
+        <plugins>
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-failsafe-plugin</artifactId>
+            </plugin>
+            <plugin>
+                <groupId>com.pyx4j</groupId>
+                <artifactId>maven-junction-plugin</artifactId>
+                <executions>
+                    <execution>
+                        <id>link-public-testdata</id>
+                        <phase>process-test-resources</phase>
+                    </execution>
+                    <execution>
+                        <id>unlink-public-testdata</id>
+                        <phase>clean</phase>
+                    </execution>
+                </executions>
+            </plugin>
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-clean-plugin</artifactId>
+            </plugin>
+            <plugin>
+                <groupId>com.google.code.sortpom</groupId>
+                <artifactId>maven-sortpom-plugin</artifactId>
+                <executions>
+                    <execution>
+                        <id>package-tests</id>
+                        <goals>
+                            <goal>sort</goal>
+                        </goals>
+                        <phase>verify</phase>
+                        <inherited>false</inherited>
+                        <configuration>
+                            <pomFile>public/package-tests/pom.xml</pomFile>
+                        </configuration>
+                    </execution>
+                </executions>
+            </plugin>
+        </plugins>
+    </build>
+
+    <reporting>
+        <plugins>
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-javadoc-plugin</artifactId>
+                <version>2.9.1</version>
+                <reportSets>
+                    <!-- By not specifying an id, shut off all default javadocs from mvn site -->
+                    <reportSet>
+                        <reports />
+                    </reportSet>
+                    <reportSet>
+                        <id>generate-gatk-docs</id>
+                        <reports>
+                            <report>aggregate</report>
+                        </reports>
+                        <!-- Only generate the GATK Docs across the parent aggregation, not the children too. -->
+                        <inherited>false</inherited>
+                        <configuration>
+                            <doclet>org.broadinstitute.sting.utils.help.GATKDoclet</doclet>
+                            <docletArtifact>
+                                <groupId>${project.groupId}</groupId>
+                                <artifactId>gatk-package</artifactId>
+                                <version>${project.version}</version>
+                            </docletArtifact>
+                            <useStandardDocletOptions>false</useStandardDocletOptions>
+                            <quiet>true</quiet>
+                            <show>private</show>
+                            <!--
+                            TODO: Stop GATKDoclet from hardcoding paths and start using parameters.
+                            For now... just run from the base directory, target/site/../..
+                            -->
+                            <destDir>../..</destDir>
+                            <additionalparam>-build-timestamp "${maven.build.timestamp}" -absolute-version ${build.version} ${gatkdocs.include.hidden}</additionalparam>
+                            <!--
+                            TODO: Leaving this true applies a patch to the git commited file
+                            TODO: private/resources/clover/api/index.html
+                            TODO: Determine if this file was generated and shoudldn't be touched,
+                            TODO: or patch the file and commit a new version.
+                            -->
+                            <applyJavadocSecurityFix>false</applyJavadocSecurityFix>
+                        </configuration>
+                    </reportSet>
+                </reportSets>
+            </plugin>
+        </plugins>
+    </reporting>
+
+    <profiles>
+        <!-- Optionally include protected -->
+        <profile>
+            <id>protected</id>
+            <activation>
+                <file>
+                    <exists>${basedir}/protected/pom.xml</exists>
+                </file>
+            </activation>
+            <modules>
+                <module>protected</module>
+            </modules>
+        </profile>
+
+        <!-- Optionally include private -->
+        <profile>
+            <id>private</id>
+            <activation>
+                <file>
+                    <exists>${basedir}/private/pom.xml</exists>
+                </file>
+            </activation>
+            <modules>
+                <module>private</module>
+            </modules>
+        </profile>
+    </profiles>
+
+</project>
diff --git a/protected/gatk-protected/pom.xml b/protected/gatk-protected/pom.xml
new file mode 100644
index 000000000..d3e50eec9
--- /dev/null
+++ b/protected/gatk-protected/pom.xml
@@ -0,0 +1,144 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+    <modelVersion>4.0.0</modelVersion>
+
+    <parent>
+        <groupId>org.broadinstitute.sting</groupId>
+        <artifactId>sting-aggregator</artifactId>
+        <version>2.6-SNAPSHOT</version>
+        <relativePath>../..</relativePath>
+    </parent>
+
+    <artifactId>gatk-protected</artifactId>
+    <packaging>jar</packaging>
+    <name>GATK Protected</name>
+
+    <properties>
+        <sting.basedir>${project.basedir}/../..</sting.basedir>
+        <sting.packagetests.artifactId>gatk-package</sting.packagetests.artifactId>
+    </properties>
+
+    <dependencies>
+        <dependency>
+            <groupId>${project.groupId}</groupId>
+            <artifactId>gatk-framework</artifactId>
+            <version>${project.version}</version>
+        </dependency>
+
+        <dependency>
+            <groupId>net.sf.jgrapht</groupId>
+            <artifactId>jgrapht</artifactId>
+        </dependency>
+
+        <dependency>
+            <groupId>gov.nist</groupId>
+            <artifactId>Jama</artifactId>
+        </dependency>
+
+        <dependency>
+            <groupId>it.unimi.dsi</groupId>
+            <artifactId>fastutil</artifactId>
+        </dependency>
+
+        <dependency>
+            <groupId>${project.groupId}</groupId>
+            <artifactId>sting-utils</artifactId>
+            <version>${project.version}</version>
+            <type>test-jar</type>
+            <scope>test</scope>
+        </dependency>
+
+        <dependency>
+            <groupId>${project.groupId}</groupId>
+            <artifactId>gatk-framework</artifactId>
+            <version>${project.version}</version>
+            <type>test-jar</type>
+            <scope>test</scope>
+        </dependency>
+
+        <dependency>
+            <groupId>org.testng</groupId>
+            <artifactId>testng</artifactId>
+            <scope>test</scope>
+        </dependency>
+        <dependency>
+            <groupId>com.google.caliper</groupId>
+            <artifactId>caliper</artifactId>
+            <scope>test</scope>
+        </dependency>
+    </dependencies>
+
+    <build>
+        <plugins>
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-resources-plugin</artifactId>
+                <executions>
+                    <execution>
+                        <id>copy-resource-bundle-log4j</id>
+                        <phase>prepare-package</phase>
+                    </execution>
+                </executions>
+            </plugin>
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-javadoc-plugin</artifactId>
+                <executions>
+                    <execution>
+                        <id>extract-resource-bundle</id>
+                        <phase>prepare-package</phase>
+                    </execution>
+                </executions>
+            </plugin>
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-invoker-plugin</artifactId>
+                <executions>
+                    <execution>
+                        <id>package-unittests</id>
+                    </execution>
+                    <execution>
+                        <id>package-integrationtests</id>
+                    </execution>
+                    <execution>
+                        <id>package-largescaletests</id>
+                    </execution>
+                    <execution>
+                        <id>package-pipelinetests</id>
+                    </execution>
+                </executions>
+            </plugin>
+        </plugins>
+    </build>
+
+    <profiles>
+        <profile>
+            <id>private</id>
+            <activation>
+                <file>
+                    <exists>${basedir}/../../private/gatk-private/pom.xml</exists>
+                </file>
+            </activation>
+            <build>
+                <plugins>
+                    <!-- TODO: All tests require access to private. For now. -->
+                    <plugin>
+                        <groupId>com.pyx4j</groupId>
+                        <artifactId>maven-junction-plugin</artifactId>
+                        <executions>
+                            <execution>
+                                <id>link-private-testdata</id>
+                                <phase>process-test-resources</phase>
+                            </execution>
+                            <execution>
+                                <id>unlink-private-testdata</id>
+                                <phase>clean</phase>
+                            </execution>
+                        </executions>
+                    </plugin>
+                </plugins>
+            </build>
+        </profile>
+    </profiles>
+
+</project>
diff --git a/protected/pom.xml b/protected/pom.xml
new file mode 100644
index 000000000..a7fb4863f
--- /dev/null
+++ b/protected/pom.xml
@@ -0,0 +1,24 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+    <modelVersion>4.0.0</modelVersion>
+
+    <parent>
+        <groupId>org.broadinstitute.sting</groupId>
+        <artifactId>sting-root</artifactId>
+        <version>2.6-SNAPSHOT</version>
+        <relativePath>../public/sting-root</relativePath>
+    </parent>
+
+    <artifactId>sting-protected</artifactId>
+    <packaging>pom</packaging>
+    <name>Sting Protected</name>
+
+    <modules>
+        <module>gatk-protected</module>
+    </modules>
+
+    <properties>
+        <sting.basedir>${project.basedir}/..</sting.basedir>
+    </properties>
+
+</project>
diff --git a/public/external-example/pom.xml b/public/external-example/pom.xml
new file mode 100644
index 000000000..37739bfda
--- /dev/null
+++ b/public/external-example/pom.xml
@@ -0,0 +1,257 @@
+<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>
+
+    <!-- Properties for your assembly -->
+    <groupId>org.mycompany.app</groupId>
+    <artifactId>external-example</artifactId>
+    <packaging>jar</packaging>
+    <version>1.0-SNAPSHOT</version>
+    <name>external-example</name>
+
+    <properties>
+        <sting.version>2.6-SNAPSHOT</sting.version>
+        <!--
+        sting.basedir property must point to your checkout of Sting/GATK until we can get all the
+        dependencies out of the committed sting repo and into central.
+        The installed pom for sting-root looks for this property.
+        Alternatively, one can install all the sting files into their local ~/.m2/repository repo.
+        http://maven.apache.org/plugins/maven-install-plugin/examples/custom-pom-installation.html
+        -->
+        <sting.basedir>../..</sting.basedir>
+        <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
+        <project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
+        <maven.build.timestamp.format>yyyy/MM/dd HH:mm:ss</maven.build.timestamp.format>
+    </properties>
+
+    <repositories>
+        <repository>
+            <id>sting.public.repo.local</id>
+            <name>Sting Public Local Repository</name>
+            <url>file:${sting.basedir}/public/repo</url>
+        </repository>
+    </repositories>
+
+    <dependencies>
+        <dependency>
+            <groupId>org.broadinstitute.sting</groupId>
+            <artifactId>gatk-framework</artifactId>
+            <version>${sting.version}</version>
+        </dependency>
+
+        <!--
+        Test dependencies are not transitive,
+        so must include each explicit test artifact.
+        -->
+        <dependency>
+            <groupId>org.broadinstitute.sting</groupId>
+            <artifactId>sting-utils</artifactId>
+            <version>${sting.version}</version>
+            <type>test-jar</type>
+            <scope>test</scope>
+        </dependency>
+
+        <dependency>
+            <groupId>org.broadinstitute.sting</groupId>
+            <artifactId>gatk-framework</artifactId>
+            <version>${sting.version}</version>
+            <type>test-jar</type>
+            <scope>test</scope>
+        </dependency>
+
+        <dependency>
+            <groupId>org.testng</groupId>
+            <artifactId>testng</artifactId>
+            <version>6.8</version>
+            <scope>test</scope>
+        </dependency>
+    </dependencies>
+
+    <build>
+        <plugins>
+
+            <!-- Copy test resources to your classes directory -->
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-dependency-plugin</artifactId>
+                <version>2.8</version>
+                <executions>
+                    <execution>
+                        <id>unpack</id>
+                        <phase>process-resources</phase>
+                        <goals>
+                            <goal>unpack</goal>
+                        </goals>
+                        <configuration>
+                            <artifactItems>
+                                <artifactItem>
+                                    <groupId>org.broadinstitute.sting</groupId>
+                                    <artifactId>gatk-framework</artifactId>
+                                    <version>${sting.version}</version>
+                                    <classifier>example-resources</classifier>
+                                    <type>tar.bz2</type>
+                                    <outputDirectory>${project.build.outputDirectory}</outputDirectory>
+                                </artifactItem>
+                            </artifactItems>
+                        </configuration>
+                    </execution>
+                </executions>
+            </plugin>
+
+            <!-- Generate help text -->
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-javadoc-plugin</artifactId>
+                <version>2.9.1</version>
+                <executions>
+                    <execution>
+                        <id>extract-resource-bundle</id>
+                        <goals>
+                            <goal>javadoc</goal>
+                        </goals>
+                        <phase>prepare-package</phase>
+                        <configuration>
+                            <doclet>org.broadinstitute.sting.utils.help.ResourceBundleExtractorDoclet</doclet>
+                            <!-- Required as doclet uses reflection to access classes for documentation, instead of source java-->
+                            <docletPath>${project.build.outputDirectory}</docletPath>
+                            <docletArtifact>
+                                <groupId>org.broadinstitute.sting</groupId>
+                                <!-- TODO: THIS IS SUPPOSED TO BE STING-UTILS! -->
+                                <artifactId>gatk-framework</artifactId>
+                                <version>${sting.version}</version>
+                            </docletArtifact>
+                            <maxmemory>2g</maxmemory>
+                            <useStandardDocletOptions>false</useStandardDocletOptions>
+                            <quiet>true</quiet>
+                            <additionalparam>-build-timestamp "${maven.build.timestamp}" -absolute-version "${project.version}" -out ${project.build.outputDirectory}/StingText.properties</additionalparam>
+                        </configuration>
+                    </execution>
+                </executions>
+            </plugin>
+
+            <!-- Create packaged jar, containing only your walker and required classes -->
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-shade-plugin</artifactId>
+                <version>2.1</version>
+                <executions>
+                    <execution>
+                        <phase>package</phase>
+                        <goals>
+                            <goal>shade</goal>
+                        </goals>
+                        <configuration>
+                            <minimizeJar>true</minimizeJar>
+                            <!-- Explicitly include classes loaded via reflection from artifacts below -->
+                            <filters>
+                                <filter>
+                                    <artifact>commons-logging:commons-logging</artifact>
+                                    <includes>
+                                        <include>**</include>
+                                    </includes>
+                                </filter>
+                                <filter>
+                                    <artifact>org.broad:tribble</artifact>
+                                    <includes>
+                                        <include>**</include>
+                                    </includes>
+                                </filter>
+                                <filter>
+                                    <artifact>org.broadinstitute:variant</artifact>
+                                    <includes>
+                                        <include>**</include>
+                                    </includes>
+                                </filter>
+                            </filters>
+                            <!-- Stop shade from trying to unzip these indirect dependencies -->
+                            <artifactSet>
+                                <excludes>
+                                    <exclude>org.broadinstitute.sting:gsalib:tar.gz:*</exclude>
+                                    <exclude>org.broadinstitute.sting:*:tar.bz2:example-resources</exclude>
+                                </excludes>
+                            </artifactSet>
+                            <transformers>
+                                <!-- Set the main class to the GATK -->
+                                <transformer implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer">
+                                    <mainClass>org.broadinstitute.sting.gatk.CommandLineGATK</mainClass>
+                                </transformer>
+                                <!-- Include and append to the existing gatk help text in StingText.properties -->
+                                <transformer implementation="org.apache.maven.plugins.shade.resource.AppendingTransformer">
+                                    <resource>StingText.properties</resource>
+                                </transformer>
+                            </transformers>
+                        </configuration>
+                    </execution>
+                </executions>
+            </plugin>
+
+            <!-- surefire runs fast, small (aka unit) tests -->
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-surefire-plugin</artifactId>
+                <version>2.16</version>
+                <configuration>
+                    <!-- See explicit executions below -->
+                    <skip>true</skip>
+                    <systemPropertyVariables>
+                        <!-- TODO: Fix BaseTest to not error out if this property is missing. -->
+                        <pipeline.run>false</pipeline.run>
+                    </systemPropertyVariables>
+                </configuration>
+                <executions>
+                    <execution>
+                        <id>default-test</id>
+                        <phase>none</phase>
+                    </execution>
+                    <execution>
+                        <!-- run all non integration tests -->
+                        <id>unit-tests</id>
+                        <goals>
+                            <goal>test</goal>
+                        </goals>
+                        <configuration>
+                            <skip>false</skip>
+                            <includes>
+                                <include>**/*Test.class</include>
+                            </includes>
+                            <excludes>
+                                <exclude>**/*IntegrationTest.class</exclude>
+                            </excludes>
+                        </configuration>
+                    </execution>
+                </executions>
+            </plugin>
+
+            <!-- failsafe runs all other tests that may take longer, and may require pre/post test setup and teardown -->
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-failsafe-plugin</artifactId>
+                <version>2.16</version>
+                <configuration>
+                    <!-- See explicit executions below -->
+                    <skip>true</skip>
+                    <systemPropertyVariables>
+                        <!-- TODO: Fix BaseTest to not error out if this property is missing. -->
+                        <pipeline.run>false</pipeline.run>
+                    </systemPropertyVariables>
+                </configuration>
+                <executions>
+                    <execution>
+                        <id>integration-tests</id>
+                        <goals>
+                            <goal>integration-test</goal>
+                            <goal>verify</goal>
+                        </goals>
+                        <!-- run integration tests -->
+                        <configuration>
+                            <skip>false</skip>
+                            <includes>
+                                <include>**/*IntegrationTest.class</include>
+                            </includes>
+                        </configuration>
+                    </execution>
+                </executions>
+            </plugin>
+        </plugins>
+    </build>
+
+</project>
diff --git a/public/gatk-framework/pom.xml b/public/gatk-framework/pom.xml
new file mode 100644
index 000000000..f4443a2f6
--- /dev/null
+++ b/public/gatk-framework/pom.xml
@@ -0,0 +1,142 @@
+<?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>
+
+    <parent>
+        <groupId>org.broadinstitute.sting</groupId>
+        <artifactId>sting-aggregator</artifactId>
+        <version>2.6-SNAPSHOT</version>
+        <relativePath>../..</relativePath>
+    </parent>
+
+    <artifactId>gatk-framework</artifactId>
+    <packaging>jar</packaging>
+    <name>GATK Framework</name>
+
+    <properties>
+        <sting.basedir>${project.basedir}/../..</sting.basedir>
+        <sting.packagetests.artifactId>gatk-package</sting.packagetests.artifactId>
+    </properties>
+
+    <dependencies>
+        <dependency>
+            <groupId>${project.groupId}</groupId>
+            <artifactId>sting-utils</artifactId>
+            <version>${project.version}</version>
+        </dependency>
+
+        <dependency>
+            <groupId>${project.groupId}</groupId>
+            <artifactId>sting-utils</artifactId>
+            <version>${project.version}</version>
+            <type>test-jar</type>
+            <scope>test</scope>
+        </dependency>
+
+        <dependency>
+            <groupId>org.testng</groupId>
+            <artifactId>testng</artifactId>
+            <scope>test</scope>
+        </dependency>
+        <dependency>
+            <groupId>com.google.caliper</groupId>
+            <artifactId>caliper</artifactId>
+            <scope>test</scope>
+        </dependency>
+    </dependencies>
+
+    <build>
+        <plugins>
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-assembly-plugin</artifactId>
+                <executions>
+                    <execution>
+                        <id>example-resources</id>
+                        <phase>generate-resources</phase>
+                    </execution>
+                </executions>
+            </plugin>
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-resources-plugin</artifactId>
+                <executions>
+                    <execution>
+                        <id>copy-resource-bundle-log4j</id>
+                        <phase>prepare-package</phase>
+                    </execution>
+                </executions>
+            </plugin>
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-javadoc-plugin</artifactId>
+                <executions>
+                    <execution>
+                        <id>extract-resource-bundle</id>
+                        <phase>prepare-package</phase>
+                    </execution>
+                </executions>
+            </plugin>
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-jar-plugin</artifactId>
+                <executions>
+                    <execution>
+                        <goals>
+                            <goal>test-jar</goal>
+                        </goals>
+                    </execution>
+                </executions>
+            </plugin>
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-invoker-plugin</artifactId>
+                <executions>
+                    <execution>
+                        <id>package-unittests</id>
+                    </execution>
+                    <execution>
+                        <id>package-integrationtests</id>
+                    </execution>
+                    <execution>
+                        <id>package-largescaletests</id>
+                    </execution>
+                    <execution>
+                        <id>package-pipelinetests</id>
+                    </execution>
+                </executions>
+            </plugin>
+        </plugins>
+    </build>
+
+    <profiles>
+        <profile>
+            <id>private</id>
+            <activation>
+                <file>
+                    <exists>${basedir}/../../private/gatk-private/pom.xml</exists>
+                </file>
+            </activation>
+            <build>
+                <plugins>
+                    <!-- TODO: All tests require access to private. For now. -->
+                    <plugin>
+                        <groupId>com.pyx4j</groupId>
+                        <artifactId>maven-junction-plugin</artifactId>
+                        <executions>
+                            <execution>
+                                <id>link-private-testdata</id>
+                                <phase>process-test-resources</phase>
+                            </execution>
+                            <execution>
+                                <id>unlink-private-testdata</id>
+                                <phase>clean</phase>
+                            </execution>
+                        </executions>
+                    </plugin>
+                </plugins>
+            </build>
+        </profile>
+    </profiles>
+
+</project>
diff --git a/public/gatk-package/pom.xml b/public/gatk-package/pom.xml
new file mode 100644
index 000000000..4f5a70268
--- /dev/null
+++ b/public/gatk-package/pom.xml
@@ -0,0 +1,155 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+    <modelVersion>4.0.0</modelVersion>
+
+    <parent>
+        <groupId>org.broadinstitute.sting</groupId>
+        <artifactId>sting-aggregator</artifactId>
+        <version>2.6-SNAPSHOT</version>
+        <relativePath>../..</relativePath>
+    </parent>
+
+    <artifactId>gatk-package</artifactId>
+    <packaging>jar</packaging>
+    <name>GATK Package</name>
+
+    <properties>
+        <sting.basedir>${project.basedir}/../..</sting.basedir>
+        <sting.unpack.phase>prepare-package</sting.unpack.phase>
+        <sting.shade.phase>package</sting.shade.phase>
+        <app.main.class>org.broadinstitute.sting.gatk.CommandLineGATK</app.main.class>
+        <sting.binary-dist.name>GenomeAnalysisTK</sting.binary-dist.name>
+    </properties>
+
+    <dependencies>
+        <!-- Package everything in org.broadinstitute.sting -->
+        <dependency>
+            <groupId>${project.groupId}</groupId>
+            <artifactId>gatk-framework</artifactId>
+            <version>${project.version}</version>
+        </dependency>
+        <!-- Tribble codecs -->
+        <dependency>
+            <groupId>org.broad</groupId>
+            <artifactId>tribble</artifactId>
+        </dependency>
+        <!-- The variant package (VCF, BCF, and VariantContext) -->
+        <dependency>
+            <groupId>org.broadinstitute</groupId>
+            <artifactId>variant</artifactId>
+        </dependency>
+        <!-- Workaround - depend on the logger impl required by JEXL -->
+        <dependency>
+            <groupId>commons-logging</groupId>
+            <artifactId>commons-logging</artifactId>
+        </dependency>
+        <!-- Required for binary-dist assembly, excluded by shade -->
+        <dependency>
+            <groupId>${project.groupId}</groupId>
+            <artifactId>gatk-framework</artifactId>
+            <version>${project.version}</version>
+            <classifier>example-resources</classifier>
+            <type>tar.bz2</type>
+        </dependency>
+    </dependencies>
+
+    <build>
+        <plugins>
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-dependency-plugin</artifactId>
+                <executions>
+                    <execution>
+                        <id>unpack-direct-dependencies</id>
+                        <phase>${sting.unpack.phase}</phase>
+                    </execution>
+                </executions>
+            </plugin>
+
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-shade-plugin</artifactId>
+                <executions>
+                    <execution>
+                        <id>sting-executable</id>
+                        <phase>${sting.shade.phase}</phase>
+                    </execution>
+                </executions>
+            </plugin>
+
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-assembly-plugin</artifactId>
+                <executions>
+                    <execution>
+                        <id>binary-dist</id>
+                        <phase>${sting.shade.phase}</phase>
+                    </execution>
+                </executions>
+            </plugin>
+
+            <plugin>
+                <groupId>com.pyx4j</groupId>
+                <artifactId>maven-junction-plugin</artifactId>
+                <executions>
+                    <execution>
+                        <id>link-git-release</id>
+                        <phase>${sting.shade.phase}</phase>
+                    </execution>
+                </executions>
+            </plugin>
+
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-install-plugin</artifactId>
+                <executions>
+                    <execution>
+                        <id>default-install</id>
+                        <phase>none</phase>
+                    </execution>
+                    <execution>
+                        <id>install-package</id>
+                        <phase>install</phase>
+                    </execution>
+                </executions>
+            </plugin>
+
+        </plugins>
+    </build>
+
+    <profiles>
+        <profile>
+            <id>protected</id>
+            <activation>
+                <file>
+                    <exists>${basedir}/../../protected/gatk-protected/pom.xml</exists>
+                </file>
+            </activation>
+            <dependencies>
+                <dependency>
+                    <groupId>${project.groupId}</groupId>
+                    <artifactId>gatk-protected</artifactId>
+                    <version>${project.version}</version>
+                    <optional>true</optional>
+                </dependency>
+            </dependencies>
+        </profile>
+        <profile>
+            <id>private</id>
+            <activation>
+                <file>
+                    <exists>${basedir}/../../private/gatk-private/pom.xml</exists>
+                </file>
+            </activation>
+            <dependencies>
+                <dependency>
+                    <groupId>${project.groupId}</groupId>
+                    <artifactId>gatk-private</artifactId>
+                    <version>${project.version}</version>
+                    <optional>true</optional>
+                </dependency>
+            </dependencies>
+        </profile>
+    </profiles>
+
+</project>
diff --git a/public/gatk-queue-extgen/pom.xml b/public/gatk-queue-extgen/pom.xml
new file mode 100644
index 000000000..9aba4f1a4
--- /dev/null
+++ b/public/gatk-queue-extgen/pom.xml
@@ -0,0 +1,29 @@
+<?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>
+
+    <parent>
+        <groupId>org.broadinstitute.sting</groupId>
+        <artifactId>sting-aggregator</artifactId>
+        <version>2.6-SNAPSHOT</version>
+        <relativePath>../..</relativePath>
+    </parent>
+
+    <artifactId>gatk-queue-extgen</artifactId>
+    <packaging>jar</packaging>
+    <name>Queue GATK ExtGen</name>
+    <description>Queue GATK Extensions Generator</description>
+
+    <properties>
+        <sting.basedir>${project.basedir}/../..</sting.basedir>
+    </properties>
+
+    <dependencies>
+        <dependency>
+            <groupId>${project.groupId}</groupId>
+            <artifactId>gatk-framework</artifactId>
+            <version>${project.version}</version>
+        </dependency>
+    </dependencies>
+
+</project>
diff --git a/public/gsalib/pom.xml b/public/gsalib/pom.xml
new file mode 100644
index 000000000..a51a985f1
--- /dev/null
+++ b/public/gsalib/pom.xml
@@ -0,0 +1,45 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+    <modelVersion>4.0.0</modelVersion>
+
+    <parent>
+        <groupId>org.broadinstitute.sting</groupId>
+        <artifactId>sting-aggregator</artifactId>
+        <version>2.6-SNAPSHOT</version>
+        <relativePath>../..</relativePath>
+    </parent>
+
+    <artifactId>gsalib</artifactId>
+    <packaging>pom</packaging>
+    <name>Sting GSALib</name>
+
+    <properties>
+        <sting.basedir>${project.basedir}/../..</sting.basedir>
+        <gsalib.packagedir>org/broadinstitute/sting/utils/R</gsalib.packagedir>
+        <gsalib.filename>gsalib.tar.gz</gsalib.filename>
+    </properties>
+
+    <build>
+        <plugins>
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-assembly-plugin</artifactId>
+                <executions>
+                    <execution>
+                        <id>gsalib-assembly</id>
+                        <goals>
+                            <goal>single</goal>
+                        </goals>
+                        <phase>generate-resources</phase>
+                        <configuration>
+                            <appendAssemblyId>false</appendAssemblyId>
+                            <descriptors>
+                                <descriptor>src/assembly/gsalib.xml</descriptor>
+                            </descriptors>
+                        </configuration>
+                    </execution>
+                </executions>
+            </plugin>
+        </plugins>
+    </build>
+</project>
diff --git a/public/package-tests/pom.xml b/public/package-tests/pom.xml
new file mode 100644
index 000000000..3d1bc1136
--- /dev/null
+++ b/public/package-tests/pom.xml
@@ -0,0 +1,158 @@
+<?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>
+
+    <parent>
+        <groupId>org.broadinstitute.sting</groupId>
+        <artifactId>sting-root</artifactId>
+        <version>2.6-SNAPSHOT</version>
+        <relativePath>../sting-root</relativePath>
+    </parent>
+
+    <artifactId>sting-package-tests</artifactId>
+    <packaging>pom</packaging>
+    <name>Sting Package Tests</name>
+
+    <properties>
+        <sting.basedir>${project.basedir}/../..</sting.basedir>
+    </properties>
+
+    <!-- Dependency configuration (versions, etc.) -->
+    <dependencies>
+        <dependency>
+            <groupId>${project.groupId}</groupId>
+            <artifactId>${sting.packagetests.artifactId}</artifactId>
+            <version>${project.version}</version>
+        </dependency>
+
+        <!--
+            For com.sun.javadoc
+            See also: http://sunnytalkstech.blogspot.in/2011/08/maven-dependency-for-toolsjar-in-jdk7.html
+            -->
+        <dependency>
+            <groupId>com.sun</groupId>
+            <artifactId>tools</artifactId>
+        </dependency>
+
+        <dependency>
+            <groupId>com.google.code.cofoja</groupId>
+            <artifactId>cofoja</artifactId>
+        </dependency>
+
+        <dependency>
+            <groupId>${project.groupId}</groupId>
+            <artifactId>gatk-framework</artifactId>
+            <version>${project.version}</version>
+            <type>test-jar</type>
+            <scope>test</scope>
+        </dependency>
+
+        <dependency>
+            <groupId>org.testng</groupId>
+            <artifactId>testng</artifactId>
+            <scope>test</scope>
+        </dependency>
+
+        <dependency>
+            <groupId>com.google.caliper</groupId>
+            <artifactId>caliper</artifactId>
+            <scope>test</scope>
+        </dependency>
+    </dependencies>
+
+    <build>
+        <directory>${sting.packagetests.basedir}/target</directory>
+    </build>
+
+    <profiles>
+        <profile>
+            <id>unittests</id>
+            <build>
+                <!-- Plugin configuration -->
+                <plugins>
+                    <plugin>
+                        <groupId>org.apache.maven.plugins</groupId>
+                        <artifactId>maven-surefire-plugin</artifactId>
+                        <configuration>
+                            <basedir>${sting.packagetests.basedir}</basedir>
+                            <workingDirectory>${sting.packagetests.basedir}</workingDirectory>
+                            <classesDirectory>${project.build.outputDirectory}/ignored_by_package_test</classesDirectory>
+                            <testClassesDirectory>${sting.packagetests.testClasses}</testClassesDirectory>
+                            <dependenciesToScan>
+                                <scan>org.broadinstitute.sting:.*</scan>
+                            </dependenciesToScan>
+                        </configuration>
+                        <executions>
+                            <execution>
+                                <!-- run all non integration tests -->
+                                <id>unit-tests</id>
+                                <goals>
+                                    <goal>test</goal>
+                                </goals>
+                                <configuration>
+                                    <skip>${sting.packageunittests.skipped}</skip>
+                                </configuration>
+                            </execution>
+                        </executions>
+                    </plugin>
+                </plugins>
+            </build>
+        </profile>
+
+        <profile>
+            <id>integrationtests</id>
+            <build>
+                <!-- Plugin configuration -->
+                <plugins>
+                    <plugin>
+                        <groupId>org.apache.maven.plugins</groupId>
+                        <artifactId>maven-failsafe-plugin</artifactId>
+                        <configuration>
+                            <basedir>${sting.packagetests.basedir}</basedir>
+                            <workingDirectory>${sting.packagetests.basedir}</workingDirectory>
+                            <classesDirectory>${project.build.outputDirectory}/ignored_by_package_test</classesDirectory>
+                            <testClassesDirectory>${sting.packagetests.testClasses}</testClassesDirectory>
+                            <dependenciesToScan>
+                                <scan>org.broadinstitute.sting:.*</scan>
+                            </dependenciesToScan>
+                        </configuration>
+                        <executions>
+                            <execution>
+                                <id>integration-tests</id>
+                                <goals>
+                                    <goal>verify</goal>
+                                </goals>
+                                <!-- run integration tests -->
+                                <configuration>
+                                    <skip>${sting.packageintegrationtests.skipped}</skip>
+                                </configuration>
+                            </execution>
+                            <execution>
+                                <id>pipeline-tests</id>
+                                <goals>
+                                    <goal>verify</goal>
+                                </goals>
+                                <!-- run pipeline dry run tests -->
+                                <configuration>
+                                    <skip>${sting.packagepipelinetests.skipped}</skip>
+                                </configuration>
+                            </execution>
+                            <execution>
+                                <id>large-scale-tests</id>
+                                <goals>
+                                    <goal>verify</goal>
+                                </goals>
+                                <!-- run large scale tests -->
+                                <configuration>
+                                    <skip>${sting.packagelargescaletests.skipped}</skip>
+                                </configuration>
+                            </execution>
+                        </executions>
+                    </plugin>
+                </plugins>
+            </build>
+        </profile>
+
+    </profiles>
+
+</project>
diff --git a/public/pom.xml b/public/pom.xml
new file mode 100644
index 000000000..e3173c35b
--- /dev/null
+++ b/public/pom.xml
@@ -0,0 +1,46 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+    <modelVersion>4.0.0</modelVersion>
+
+    <parent>
+        <groupId>org.broadinstitute.sting</groupId>
+        <artifactId>sting-root</artifactId>
+        <version>2.6-SNAPSHOT</version>
+        <relativePath>sting-root</relativePath>
+    </parent>
+
+    <artifactId>sting-public</artifactId>
+    <packaging>pom</packaging>
+    <name>Sting Public</name>
+
+    <modules>
+        <module>sting-root</module>
+        <module>gsalib</module>
+        <module>sting-utils</module>
+        <module>gatk-framework</module>
+        <module>gatk-package</module>
+        <!-- queue optionally enabled as profiles -->
+    </modules>
+
+    <properties>
+        <sting.basedir>${project.basedir}/..</sting.basedir>
+    </properties>
+
+    <profiles>
+        <!-- Allow queue to be disabled. -->
+        <profile>
+            <id>queue</id>
+            <activation>
+                <property>
+                    <name>!disable.queue</name>
+                </property>
+            </activation>
+            <modules>
+                <module>gatk-queue-extgen</module>
+                <module>queue-framework</module>
+                <module>queue-package</module>
+            </modules>
+        </profile>
+    </profiles>
+
+</project>
diff --git a/public/queue-framework/pom.xml b/public/queue-framework/pom.xml
new file mode 100644
index 000000000..8ccc7f351
--- /dev/null
+++ b/public/queue-framework/pom.xml
@@ -0,0 +1,267 @@
+<?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>
+
+    <parent>
+        <groupId>org.broadinstitute.sting</groupId>
+        <artifactId>sting-aggregator</artifactId>
+        <version>2.6-SNAPSHOT</version>
+        <relativePath>../..</relativePath>
+    </parent>
+
+    <artifactId>queue-framework</artifactId>
+    <packaging>jar</packaging>
+    <name>Queue Framework</name>
+
+    <properties>
+        <sting.basedir>${project.basedir}/../..</sting.basedir>
+        <gatk.extensions.sources>${project.build.directory}/generated-sources/gatk-extensions</gatk.extensions.sources>
+        <sting.generate-gatk-extensions.skipped>false</sting.generate-gatk-extensions.skipped>
+        <sting.packagetests.artifactId>queue-package</sting.packagetests.artifactId>
+    </properties>
+
+    <dependencies>
+        <dependency>
+            <groupId>${project.groupId}</groupId>
+            <artifactId>gatk-framework</artifactId>
+            <version>${project.version}</version>
+        </dependency>
+        <dependency>
+            <groupId>org.scala-lang</groupId>
+            <artifactId>scala-compiler</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>log4j</groupId>
+            <artifactId>log4j</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>net.sf.jgrapht</groupId>
+            <artifactId>jgrapht</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>org.apache.commons</groupId>
+            <artifactId>commons-email</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>javax.mail</groupId>
+            <artifactId>mail</artifactId>
+        </dependency>
+        <!--
+        extgen dependency only applies to the exec:exec,
+        not the artifact, but don't know another way to include
+        the artifact *only* in the <classpath/> of exec.
+        See https://jira.codehaus.org/browse/MEXEC-111
+
+        Perhaps extgen should be wrapped in a maven plugin?
+        -->
+        <dependency>
+            <groupId>${project.groupId}</groupId>
+            <artifactId>gatk-queue-extgen</artifactId>
+            <version>${project.version}</version>
+            <scope>runtime</scope>
+        </dependency>
+
+        <dependency>
+            <groupId>${project.groupId}</groupId>
+            <artifactId>gatk-framework</artifactId>
+            <version>${project.version}</version>
+            <type>test-jar</type>
+            <scope>test</scope>
+        </dependency>
+
+        <dependency>
+            <groupId>org.testng</groupId>
+            <artifactId>testng</artifactId>
+            <scope>test</scope>
+        </dependency>
+    </dependencies>
+
+    <build>
+        <plugins>
+            <plugin>
+                <groupId>org.codehaus.mojo</groupId>
+                <artifactId>exec-maven-plugin</artifactId>
+                <executions>
+                    <execution>
+                        <id>generate-gatk-extensions</id>
+                        <goals>
+                            <goal>exec</goal>
+                        </goals>
+                        <phase>generate-sources</phase>
+                        <configuration>
+                            <skip>${sting.generate-gatk-extensions.skipped}</skip>
+                            <executable>java</executable>
+                            <arguments>
+                                <argument>-classpath</argument>
+                                <classpath />
+                                <argument>org.broadinstitute.sting.queue.extensions.gatk.GATKExtensionsGenerator</argument>
+                                <argument>-l</argument>
+                                <argument>WARN</argument>
+                                <argument>-outDir</argument>
+                                <argument>${gatk.extensions.sources}</argument>
+                            </arguments>
+                        </configuration>
+                    </execution>
+                </executions>
+            </plugin>
+            <plugin>
+                <groupId>org.codehaus.mojo</groupId>
+                <artifactId>build-helper-maven-plugin</artifactId>
+                <executions>
+                    <execution>
+                        <id>add-gatk-extensions</id>
+                        <goals>
+                            <goal>add-source</goal>
+                        </goals>
+                        <phase>generate-sources</phase>
+                        <configuration>
+                            <sources>
+                                <source>${gatk.extensions.sources}</source>
+                            </sources>
+                        </configuration>
+                    </execution>
+                </executions>
+            </plugin>
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-assembly-plugin</artifactId>
+                <executions>
+                    <execution>
+                        <id>example-resources</id>
+                        <phase>generate-resources</phase>
+                    </execution>
+                </executions>
+            </plugin>
+            <plugin>
+                <groupId>org.scala-tools</groupId>
+                <artifactId>maven-scala-plugin</artifactId>
+            </plugin>
+            <plugin>
+                <groupId>com.pyx4j</groupId>
+                <artifactId>maven-junction-plugin</artifactId>
+                <executions>
+                    <execution>
+                        <id>link-public-qscript</id>
+                        <phase>process-test-resources</phase>
+                    </execution>
+                    <execution>
+                        <id>unlink-public-qscript</id>
+                        <phase>clean</phase>
+                    </execution>
+                </executions>
+            </plugin>
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-resources-plugin</artifactId>
+                <executions>
+                    <execution>
+                        <id>copy-resource-bundle-log4j</id>
+                        <phase>prepare-package</phase>
+                    </execution>
+                </executions>
+            </plugin>
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-javadoc-plugin</artifactId>
+                <executions>
+                    <execution>
+                        <id>extract-resource-bundle</id>
+                        <phase>prepare-package</phase>
+                    </execution>
+                </executions>
+            </plugin>
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-jar-plugin</artifactId>
+                <executions>
+                    <execution>
+                        <goals>
+                            <goal>test-jar</goal>
+                        </goals>
+                    </execution>
+                </executions>
+            </plugin>
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-invoker-plugin</artifactId>
+                <executions>
+                    <execution>
+                        <id>package-unittests</id>
+                    </execution>
+                    <execution>
+                        <id>package-integrationtests</id>
+                    </execution>
+                    <execution>
+                        <id>package-largescaletests</id>
+                    </execution>
+                    <execution>
+                        <id>package-pipelinetests</id>
+                    </execution>
+                </executions>
+            </plugin>
+        </plugins>
+    </build>
+
+    <profiles>
+        <profile>
+            <id>protected</id>
+            <activation>
+                <file>
+                    <exists>${basedir}/../../protected/gatk-protected/pom.xml</exists>
+                </file>
+            </activation>
+            <dependencies>
+                <dependency>
+                    <groupId>${project.groupId}</groupId>
+                    <artifactId>gatk-protected</artifactId>
+                    <version>${project.version}</version>
+                    <optional>true</optional>
+                </dependency>
+            </dependencies>
+        </profile>
+        <profile>
+            <id>private</id>
+            <activation>
+                <file>
+                    <exists>${basedir}/../../private/gatk-private/pom.xml</exists>
+                </file>
+            </activation>
+            <dependencies>
+                <dependency>
+                    <groupId>${project.groupId}</groupId>
+                    <artifactId>gatk-private</artifactId>
+                    <version>${project.version}</version>
+                    <optional>true</optional>
+                </dependency>
+            </dependencies>
+            <build>
+                <plugins>
+                    <!-- TODO: All tests require access to private. For now. -->
+                    <plugin>
+                        <groupId>com.pyx4j</groupId>
+                        <artifactId>maven-junction-plugin</artifactId>
+                        <executions>
+                            <execution>
+                                <id>link-private-testdata</id>
+                                <phase>process-test-resources</phase>
+                            </execution>
+                            <execution>
+                                <id>unlink-private-testdata</id>
+                                <phase>clean</phase>
+                            </execution>
+                            <execution>
+                                <id>link-private-qscript</id>
+                                <phase>process-test-resources</phase>
+                            </execution>
+                            <execution>
+                                <id>unlink-private-qscript</id>
+                                <phase>clean</phase>
+                            </execution>
+                        </executions>
+                    </plugin>
+                </plugins>
+            </build>
+        </profile>
+    </profiles>
+
+</project>
diff --git a/public/queue-package/pom.xml b/public/queue-package/pom.xml
new file mode 100644
index 000000000..1a8bf8b0f
--- /dev/null
+++ b/public/queue-package/pom.xml
@@ -0,0 +1,170 @@
+<?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>
+
+    <parent>
+        <groupId>org.broadinstitute.sting</groupId>
+        <artifactId>sting-aggregator</artifactId>
+        <version>2.6-SNAPSHOT</version>
+        <relativePath>../..</relativePath>
+    </parent>
+
+    <artifactId>queue-package</artifactId>
+    <packaging>jar</packaging>
+    <name>Queue Package</name>
+
+    <properties>
+        <sting.basedir>${project.basedir}/../..</sting.basedir>
+        <sting.unpack.phase>prepare-package</sting.unpack.phase>
+        <sting.shade.phase>package</sting.shade.phase>
+        <sting.binary-dist.name>Queue</sting.binary-dist.name>
+        <app.main.class>org.broadinstitute.sting.queue.QCommandLine</app.main.class>
+    </properties>
+
+    <dependencies>
+        <!-- Queue -->
+        <dependency>
+            <groupId>${project.groupId}</groupId>
+            <artifactId>queue-framework</artifactId>
+            <version>${project.version}</version>
+        </dependency>
+        <dependency>
+            <groupId>${project.groupId}</groupId>
+            <artifactId>gatk-package</artifactId>
+            <version>${project.version}</version>
+        </dependency>
+        <!-- Scala -->
+        <dependency>
+            <groupId>org.scala-lang</groupId>
+            <artifactId>scala-library</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>org.scala-lang</groupId>
+            <artifactId>scala-compiler</artifactId>
+        </dependency>
+        <!-- Picard -->
+        <dependency>
+            <groupId>net.sf</groupId>
+            <artifactId>picard</artifactId>
+        </dependency>
+        <!-- JavaMail -->
+        <dependency>
+            <groupId>javax.mail</groupId>
+            <artifactId>mail</artifactId>
+        </dependency>
+        <!-- JNA, including embedded native libraries -->
+        <dependency>
+            <groupId>net.java.dev.jna</groupId>
+            <artifactId>jna</artifactId>
+        </dependency>
+        <!-- Contracts for Java -->
+        <dependency>
+            <groupId>com.google.code.cofoja</groupId>
+            <artifactId>cofoja</artifactId>
+        </dependency>
+        <!-- snpEff -->
+        <dependency>
+            <groupId>net.sf.snpeff</groupId>
+            <artifactId>snpeff</artifactId>
+        </dependency>
+        <!-- Required for binary-dist assembly, excluded by shade -->
+        <dependency>
+            <groupId>${project.groupId}</groupId>
+            <artifactId>gatk-framework</artifactId>
+            <version>${project.version}</version>
+            <classifier>example-resources</classifier>
+            <type>tar.bz2</type>
+        </dependency>
+        <dependency>
+            <groupId>${project.groupId}</groupId>
+            <artifactId>queue-framework</artifactId>
+            <version>${project.version}</version>
+            <classifier>example-resources</classifier>
+            <type>tar.bz2</type>
+        </dependency>
+    </dependencies>
+
+    <build>
+        <plugins>
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-dependency-plugin</artifactId>
+                <executions>
+                    <execution>
+                        <id>unpack-direct-dependencies</id>
+                        <phase>${sting.unpack.phase}</phase>
+                    </execution>
+                </executions>
+            </plugin>
+
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-shade-plugin</artifactId>
+                <executions>
+                    <execution>
+                        <id>sting-executable</id>
+                        <phase>${sting.shade.phase}</phase>
+                    </execution>
+                </executions>
+            </plugin>
+
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-assembly-plugin</artifactId>
+                <executions>
+                    <execution>
+                        <id>binary-dist</id>
+                        <phase>${sting.shade.phase}</phase>
+                    </execution>
+                </executions>
+            </plugin>
+
+            <plugin>
+                <groupId>com.pyx4j</groupId>
+                <artifactId>maven-junction-plugin</artifactId>
+                <executions>
+                    <execution>
+                        <id>link-git-release</id>
+                        <phase>${sting.shade.phase}</phase>
+                    </execution>
+                </executions>
+            </plugin>
+
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-install-plugin</artifactId>
+                <executions>
+                    <execution>
+                        <id>default-install</id>
+                        <phase>none</phase>
+                    </execution>
+                    <execution>
+                        <id>install-package</id>
+                        <phase>install</phase>
+                    </execution>
+                </executions>
+            </plugin>
+
+        </plugins>
+    </build>
+
+    <profiles>
+        <profile>
+            <id>private</id>
+            <activation>
+                <file>
+                    <exists>${basedir}/../../private/queue-private/pom.xml</exists>
+                </file>
+            </activation>
+            <dependencies>
+                <dependency>
+                    <groupId>${project.groupId}</groupId>
+                    <artifactId>queue-private</artifactId>
+                    <version>${project.version}</version>
+                    <optional>true</optional>
+                </dependency>
+            </dependencies>
+        </profile>
+    </profiles>
+
+</project>
diff --git a/public/sting-root/pom.xml b/public/sting-root/pom.xml
new file mode 100644
index 000000000..1309175bb
--- /dev/null
+++ b/public/sting-root/pom.xml
@@ -0,0 +1,619 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+    <modelVersion>4.0.0</modelVersion>
+
+    <!--
+    This pom is parent for all sting/gatk poms
+    See also:
+      http://maven.apache.org/pom.html#Inheritance_v
+      http://maven.apache.org/guides/introduction/introduction-to-the-pom.html#Project_Inheritance_vs_Project_Aggregation
+      http://stackoverflow.com/questions/1992213/maven-parent-pom-vs-modules-pom
+    -->
+
+    <groupId>org.broadinstitute.sting</groupId>
+    <artifactId>sting-root</artifactId>
+    <version>2.6-SNAPSHOT</version>
+    <packaging>pom</packaging>
+    <name>Sting Root</name>
+
+    <prerequisites>
+        <maven>3.0.4</maven>
+    </prerequisites>
+
+    <properties>
+        <sourceEncoding>UTF-8</sourceEncoding>
+        <project.build.sourceEncoding>${sourceEncoding}</project.build.sourceEncoding>
+        <project.reporting.outputEncoding>${sourceEncoding}</project.reporting.outputEncoding>
+        <maven.compiler.source>1.7</maven.compiler.source>
+        <maven.compiler.target>1.7</maven.compiler.target>
+        <maven.build.timestamp.format>yyyy/MM/dd HH:mm:ss</maven.build.timestamp.format>
+        <sting.basedir>${project.basedir}/../..</sting.basedir>
+        <sting.committests.skipped>true</sting.committests.skipped>
+        <sting.unittests.skipped>${sting.committests.skipped}</sting.unittests.skipped>
+        <sting.integrationtests.skipped>${sting.committests.skipped}</sting.integrationtests.skipped>
+        <sting.pipelinetests.skipped>${sting.committests.skipped}</sting.pipelinetests.skipped>
+        <sting.largescaletests.skipped>true</sting.largescaletests.skipped>
+        <sting.pipelinetests.run>false</sting.pipelinetests.run>
+        <test.maxmemory>4g</test.maxmemory>
+        <test.args>-Xmx${test.maxmemory}</test.args>
+    </properties>
+
+    <!-- Dependency configuration (versions, etc.) -->
+    <dependencyManagement>
+        <dependencies>
+            <dependency>
+                <groupId>org.scala-lang</groupId>
+                <artifactId>scala-compiler</artifactId>
+                <version>2.10.2</version>
+            </dependency>
+            <dependency>
+                <groupId>org.scala-lang</groupId>
+                <artifactId>scala-library</artifactId>
+                <version>2.10.2</version>
+            </dependency>
+            <dependency>
+                <groupId>com.google.code.cofoja</groupId>
+                <artifactId>cofoja</artifactId>
+                <version>1.0-r139</version>
+            </dependency>
+            <dependency>
+                <groupId>net.sf</groupId>
+                <artifactId>sam</artifactId>
+                <version>1.104.1628</version>
+            </dependency>
+            <dependency>
+                <groupId>net.sf</groupId>
+                <artifactId>picard</artifactId>
+                <version>1.104.1628</version>
+            </dependency>
+            <dependency>
+                <groupId>edu.mit.broad</groupId>
+                <artifactId>picard-private-parts</artifactId>
+                <version>2872</version>
+            </dependency>
+            <dependency>
+                <groupId>org.broad</groupId>
+                <artifactId>tribble</artifactId>
+                <version>1.104.1628</version>
+            </dependency>
+            <dependency>
+                <groupId>org.broadinstitute</groupId>
+                <artifactId>variant</artifactId>
+                <version>1.105.1642</version>
+            </dependency>
+            <dependency>
+                <groupId>log4j</groupId>
+                <artifactId>log4j</artifactId>
+                <version>1.2.15</version>
+                <exclusions>
+                    <exclusion>
+                        <groupId>com.sun.jdmk</groupId>
+                        <artifactId>jmxtools</artifactId>
+                    </exclusion>
+                    <exclusion>
+                        <groupId>javax.jms</groupId>
+                        <artifactId>jms</artifactId>
+                    </exclusion>
+                    <exclusion>
+                        <groupId>com.sun.jmx</groupId>
+                        <artifactId>jmxri</artifactId>
+                    </exclusion>
+                </exclusions>
+            </dependency>
+            <dependency>
+                <groupId>javax.mail</groupId>
+                <artifactId>mail</artifactId>
+                <version>1.4.4</version>
+            </dependency>
+            <dependency>
+                <groupId>colt</groupId>
+                <artifactId>colt</artifactId>
+                <version>1.2.0</version>
+            </dependency>
+            <dependency>
+                <groupId>it.unimi.dsi</groupId>
+                <artifactId>fastutil</artifactId>
+                <version>6.5.3</version>
+            </dependency>
+            <dependency>
+                <groupId>org.simpleframework</groupId>
+                <artifactId>simple-xml</artifactId>
+                <version>2.0.4</version>
+            </dependency>
+            <dependency>
+                <groupId>org.apache.bcel</groupId>
+                <artifactId>bcel</artifactId>
+                <version>5.2</version>
+            </dependency>
+            <dependency>
+                <groupId>org.reflections</groupId>
+                <artifactId>reflections</artifactId>
+                <version>0.9.8</version>
+            </dependency>
+            <dependency>
+                <groupId>org.slf4j</groupId>
+                <artifactId>slf4j-log4j12</artifactId>
+                <version>1.6.1</version>
+            </dependency>
+            <dependency>
+                <groupId>gov.nist</groupId>
+                <artifactId>Jama</artifactId>
+                <version>1.0.2</version>
+            </dependency>
+            <dependency>
+                <groupId>net.sf.jgrapht</groupId>
+                <artifactId>jgrapht</artifactId>
+                <version>0.8.3</version>
+            </dependency>
+            <dependency>
+                <groupId>org.freemarker</groupId>
+                <artifactId>freemarker</artifactId>
+                <version>2.3.18</version>
+            </dependency>
+            <dependency>
+                <groupId>org.apache.commons</groupId>
+                <artifactId>commons-email</artifactId>
+                <version>1.2</version>
+            </dependency>
+            <dependency>
+                <groupId>org.apache.commons</groupId>
+                <artifactId>commons-jexl</artifactId>
+                <version>2.1.1</version>
+            </dependency>
+            <dependency>
+                <groupId>commons-lang</groupId>
+                <artifactId>commons-lang</artifactId>
+                <version>2.5</version>
+            </dependency>
+            <dependency>
+                <groupId>commons-logging</groupId>
+                <artifactId>commons-logging</artifactId>
+                <version>1.1.1</version>
+            </dependency>
+            <dependency>
+                <groupId>commons-io</groupId>
+                <artifactId>commons-io</artifactId>
+                <version>2.1</version>
+            </dependency>
+            <dependency>
+                <groupId>commons-collections</groupId>
+                <artifactId>commons-collections</artifactId>
+                <version>3.2.1</version>
+            </dependency>
+            <dependency>
+                <groupId>org.apache.commons</groupId>
+                <artifactId>commons-math</artifactId>
+                <version>2.2</version>
+            </dependency>
+            <dependency>
+                <groupId>net.java.dev.jna</groupId>
+                <artifactId>jna</artifactId>
+                <version>3.2.7</version>
+            </dependency>
+            <dependency>
+                <groupId>net.java.dev.jets3t</groupId>
+                <artifactId>jets3t</artifactId>
+                <version>0.8.1</version>
+            </dependency>
+            <dependency>
+                <groupId>net.sf.gridscheduler</groupId>
+                <artifactId>drmaa</artifactId>
+                <version>6.2u5p2</version>
+            </dependency>
+            <dependency>
+                <groupId>org.uncommons</groupId>
+                <artifactId>reportng</artifactId>
+                <version>1.1.2</version>
+            </dependency>
+            <dependency>
+                <groupId>com.google.inject</groupId>
+                <artifactId>guice</artifactId>
+                <version>3.0</version>
+            </dependency>
+            <dependency>
+                <groupId>org.apache.poi</groupId>
+                <artifactId>poi</artifactId>
+                <version>3.8-beta3</version>
+            </dependency>
+            <dependency>
+                <groupId>org.apache.poi</groupId>
+                <artifactId>poi-ooxml</artifactId>
+                <version>3.8-beta3</version>
+            </dependency>
+            <dependency>
+                <groupId>net.sf.snpeff</groupId>
+                <artifactId>snpeff</artifactId>
+                <version>2.0.5</version>
+            </dependency>
+            <dependency>
+                <groupId>org.mongodb</groupId>
+                <artifactId>mongo-java-driver</artifactId>
+                <version>2.7.3</version>
+            </dependency>
+            <dependency>
+                <groupId>com.google.code.gson</groupId>
+                <artifactId>gson</artifactId>
+                <version>2.2.2</version>
+            </dependency>
+            <dependency>
+                <groupId>org.apache.httpcomponents</groupId>
+                <artifactId>httpclient</artifactId>
+                <version>4.1.1</version>
+            </dependency>
+
+            <!--
+            For com.sun.javadoc
+            See also: http://sunnytalkstech.blogspot.in/2011/08/maven-dependency-for-toolsjar-in-jdk7.html
+            -->
+            <dependency>
+                <groupId>com.sun</groupId>
+                <artifactId>tools</artifactId>
+                <version>1.4.2</version>
+                <scope>system</scope>
+                <systemPath>${java.home}/../lib/tools.jar</systemPath>
+            </dependency>
+
+            <dependency>
+                <groupId>org.testng</groupId>
+                <artifactId>testng</artifactId>
+                <version>6.8</version>
+                <scope>test</scope>
+            </dependency>
+            <dependency>
+                <groupId>com.google.caliper</groupId>
+                <artifactId>caliper</artifactId>
+                <version>0.5-rc1</version>
+                <scope>test</scope>
+                <exclusions>
+                    <!--
+                    TODO: After upgrade to caliper 1.0-beta-1 or later, this may need a revisit.
+                    Possibly other modules may need to exclude *their* old guava versions.
+                     -->
+                    <exclusion>
+                        <groupId>com.google.guava</groupId>
+                        <artifactId>guava</artifactId>
+                    </exclusion>
+                </exclusions>
+            </dependency>
+        </dependencies>
+    </dependencyManagement>
+
+    <build>
+        <!-- Plugin configuration -->
+        <pluginManagement>
+            <plugins>
+                <plugin>
+                    <groupId>org.codehaus.mojo</groupId>
+                    <artifactId>exec-maven-plugin</artifactId>
+                    <version>1.2.1</version>
+                </plugin>
+                <plugin>
+                    <groupId>com.lukegb.mojo</groupId>
+                    <artifactId>gitdescribe-maven-plugin</artifactId>
+                    <version>2.0</version>
+                </plugin>
+                <plugin>
+                    <groupId>org.codehaus.mojo</groupId>
+                    <artifactId>build-helper-maven-plugin</artifactId>
+                    <version>1.8</version>
+                </plugin>
+                <plugin>
+                    <groupId>org.apache.maven.plugins</groupId>
+                    <artifactId>maven-clean-plugin</artifactId>
+                    <version>2.5</version>
+                </plugin>
+                <plugin>
+                    <groupId>org.apache.maven.plugins</groupId>
+                    <artifactId>maven-dependency-plugin</artifactId>
+                    <version>2.8</version>
+                </plugin>
+                <plugin>
+                    <groupId>org.apache.maven.plugins</groupId>
+                    <artifactId>maven-resources-plugin</artifactId>
+                    <version>2.6</version>
+                </plugin>
+                <plugin>
+                    <groupId>org.apache.maven.plugins</groupId>
+                    <artifactId>maven-javadoc-plugin</artifactId>
+                    <version>2.9.1</version>
+                </plugin>
+                <plugin>
+                    <groupId>org.apache.maven.plugins</groupId>
+                    <artifactId>maven-compiler-plugin</artifactId>
+                    <version>3.1</version>
+                </plugin>
+                <plugin>
+                    <groupId>org.scala-tools</groupId>
+                    <artifactId>maven-scala-plugin</artifactId>
+                    <version>2.15.2</version>
+                </plugin>
+                <plugin>
+                    <groupId>org.apache.maven.plugins</groupId>
+                    <artifactId>maven-jar-plugin</artifactId>
+                    <version>2.4</version>
+                </plugin>
+                <plugin>
+                    <groupId>org.apache.maven.plugins</groupId>
+                    <artifactId>maven-shade-plugin</artifactId>
+                    <version>2.1</version>
+                </plugin>
+                <plugin>
+                    <groupId>org.apache.maven.plugins</groupId>
+                    <artifactId>maven-assembly-plugin</artifactId>
+                    <version>2.4</version>
+                </plugin>
+
+                <!--
+                surefire/failsafe configurations are global, even across poms
+                not directly aggregated, for example package-tests/pom.xml
+                -->
+
+                <plugin>
+                    <groupId>org.apache.maven.plugins</groupId>
+                    <artifactId>maven-surefire-plugin</artifactId>
+                    <version>2.16</version>
+                    <configuration>
+                        <!-- See explicit executions below -->
+                        <skip>true</skip>
+                        <failIfNoTests>false</failIfNoTests>
+                        <useFile>false</useFile>
+                        <reportFormat>plain</reportFormat>
+                        <argLine>${test.args}</argLine>
+                        <properties>
+                            <property>
+                                <name>usedefaultlisteners</name>
+                                <value>false</value>
+                                <!-- TODO: Why do the default listeners take so long post tests, what is the "old" directory, and why doesn't ant have this problem? -->
+                            </property>
+                        </properties>
+                        <systemPropertyVariables>
+                            <clover.pertest.coverage>diff</clover.pertest.coverage>
+                            <java.awt.headless>true</java.awt.headless>
+                            <!-- TODO: Fix BaseTest to not error out if this property is missing. -->
+                            <pipeline.run>${sting.pipelinetests.run}</pipeline.run>
+                            <java.io.tmpdir>${java.io.tmpdir}</java.io.tmpdir>
+                        </systemPropertyVariables>
+                    </configuration>
+                    <executions>
+                        <execution>
+                            <id>default-test</id>
+                            <phase>none</phase>
+                        </execution>
+                        <execution>
+                            <!-- run all non integration tests -->
+                            <id>unit-tests</id>
+                            <goals>
+                                <goal>test</goal>
+                            </goals>
+                            <configuration>
+                                <!-- TODO: Re-enable unit tests by default? -->
+                                <skip>${sting.unittests.skipped}</skip>
+                                <includes>
+                                    <include>**/*Test.class</include>
+                                </includes>
+                                <excludes>
+                                    <exclude>**/*IntegrationTest.class</exclude>
+                                    <exclude>**/*PipelineTest.class</exclude>
+                                    <exclude>**/*LargeScaleTest.class</exclude>
+                                </excludes>
+                            </configuration>
+                        </execution>
+                    </executions>
+                </plugin>
+
+                <plugin>
+                    <groupId>org.apache.maven.plugins</groupId>
+                    <artifactId>maven-failsafe-plugin</artifactId>
+                    <version>2.16</version>
+                    <configuration>
+                        <!-- See explicit executions below -->
+                        <skip>true</skip>
+                        <failIfNoTests>false</failIfNoTests>
+                        <useFile>false</useFile>
+                        <reportFormat>plain</reportFormat>
+                        <argLine>${test.args}</argLine>
+                        <properties>
+                            <property>
+                                <name>usedefaultlisteners</name>
+                                <value>false</value>
+                                <!-- TODO: Why do the default listeners take so long post tests, what is the "old" directory, and why doesn't ant have this problem? -->
+                            </property>
+                        </properties>
+                        <systemPropertyVariables>
+                            <clover.pertest.coverage>diff</clover.pertest.coverage>
+                            <java.awt.headless>true</java.awt.headless>
+                            <!-- TODO: Fix BaseTest to not error out if this property is missing. -->
+                            <pipeline.run>${sting.pipelinetests.run}</pipeline.run>
+                            <java.io.tmpdir>${java.io.tmpdir}</java.io.tmpdir>
+                        </systemPropertyVariables>
+                    </configuration>
+                    <executions>
+                        <execution>
+                            <id>integration-tests</id>
+                            <goals>
+                                <goal>integration-test</goal>
+                                <goal>verify</goal>
+                            </goals>
+                            <!-- run integration tests -->
+                            <configuration>
+                                <!-- TODO: Re-enable integration tests by default? -->
+                                <skip>${sting.integrationtests.skipped}</skip>
+                                <includes>
+                                    <include>**/*IntegrationTest.class</include>
+                                </includes>
+                            </configuration>
+                        </execution>
+                        <execution>
+                            <id>pipeline-tests</id>
+                            <goals>
+                                <goal>integration-test</goal>
+                                <goal>verify</goal>
+                            </goals>
+                            <!-- run pipeline dry run tests -->
+                            <configuration>
+                                <!-- TODO: Re-enable pipeline tests by default? -->
+                                <skip>${sting.pipelinetests.skipped}</skip>
+                                <includes>
+                                    <include>**/*PipelineTest.class</include>
+                                </includes>
+                            </configuration>
+                        </execution>
+                        <execution>
+                            <id>large-scale-tests</id>
+                            <goals>
+                                <goal>integration-test</goal>
+                                <goal>verify</goal>
+                            </goals>
+                            <!-- run large scale tests -->
+                            <configuration>
+                                <skip>${sting.largescaletests.skipped}</skip>
+                                <includes>
+                                    <include>**/*LargeScaleTest.class</include>
+                                </includes>
+                            </configuration>
+                        </execution>
+                    </executions>
+                </plugin>
+
+                <plugin>
+                    <groupId>com.google.code.sortpom</groupId>
+                    <artifactId>maven-sortpom-plugin</artifactId>
+                    <version>2.2</version>
+                    <configuration>
+                        <createBackupFile>false</createBackupFile>
+                        <predefinedSortOrder>custom_1</predefinedSortOrder>
+                        <lineSeparator>\n</lineSeparator>
+                        <encoding>${sourceEncoding}</encoding>
+                        <keepBlankLines>true</keepBlankLines>
+                        <sortDependencies>scope</sortDependencies>
+                        <nrOfIndentSpace>4</nrOfIndentSpace>
+                        <expandEmptyElements>false</expandEmptyElements>
+                    </configuration>
+                    <executions>
+                        <execution>
+                            <goals>
+                                <goal>sort</goal>
+                            </goals>
+                            <phase>verify</phase>
+                        </execution>
+                    </executions>
+                </plugin>
+
+                <!-- TODO: Remove temporary symbolic link creation, after fixing test paths to use local resources. -->
+                <plugin>
+                    <groupId>com.pyx4j</groupId>
+                    <artifactId>maven-junction-plugin</artifactId>
+                    <version>1.0.3</version>
+                </plugin>
+                <plugin>
+                    <groupId>org.apache.maven.plugins</groupId>
+                    <artifactId>maven-invoker-plugin</artifactId>
+                    <version>1.8</version>
+                </plugin>
+                <plugin>
+                    <groupId>org.apache.maven.plugins</groupId>
+                    <artifactId>maven-install-plugin</artifactId>
+                    <version>2.5</version>
+                </plugin>
+                <plugin>
+                    <groupId>org.apache.maven.plugins</groupId>
+                    <artifactId>maven-site-plugin</artifactId>
+                    <version>3.3</version>
+                </plugin>
+            </plugins>
+        </pluginManagement>
+
+        <!-- Invoke plugins that always run -->
+        <plugins>
+            <plugin>
+                <groupId>com.lukegb.mojo</groupId>
+                <artifactId>gitdescribe-maven-plugin</artifactId>
+                <configuration>
+                    <extraArguments>
+                        <param>--long</param>
+                    </extraArguments>
+                    <setReactorProjectsProperties>true</setReactorProjectsProperties>
+                    <descriptionProperty>git.version</descriptionProperty>
+                </configuration>
+                <executions>
+                    <execution>
+                        <id>gitdescribe-initialize</id>
+                        <goals>
+                            <goal>gitdescribe</goal>
+                        </goals>
+                        <phase>initialize</phase>
+                    </execution>
+                    <execution>
+                        <id>gitdescribe-presite</id>
+                        <goals>
+                            <goal>gitdescribe</goal>
+                        </goals>
+                        <phase>pre-site</phase>
+                    </execution>
+                </executions>
+            </plugin>
+            <plugin>
+                <groupId>org.codehaus.mojo</groupId>
+                <artifactId>build-helper-maven-plugin</artifactId>
+                <!-- TODO: gitdescribe plugin doesn't allow null prefixes -->
+                <executions>
+                    <execution>
+                        <id>fix-version-initialize</id>
+                        <goals>
+                            <goal>regex-property</goal>
+                        </goals>
+                        <phase>initialize</phase>
+                        <configuration>
+                            <name>build.version</name>
+                            <value>${git.version}</value>
+                            <regex>git-</regex>
+                        </configuration>
+                    </execution>
+                    <execution>
+                        <id>fix-version-pre-site</id>
+                        <goals>
+                            <goal>regex-property</goal>
+                        </goals>
+                        <phase>pre-site</phase>
+                        <configuration>
+                            <name>build.version</name>
+                            <value>${git.version}</value>
+                            <regex>git-</regex>
+                        </configuration>
+                    </execution>
+                </executions>
+            </plugin>
+            <plugin>
+                <groupId>com.google.code.sortpom</groupId>
+                <artifactId>maven-sortpom-plugin</artifactId>
+                <executions>
+                    <execution>
+                        <id>default</id>
+                        <goals>
+                            <goal>sort</goal>
+                        </goals>
+                        <phase>verify</phase>
+                    </execution>
+                </executions>
+            </plugin>
+        </plugins>
+    </build>
+
+    <reporting>
+        <excludeDefaults>true</excludeDefaults>
+    </reporting>
+
+    <repositories>
+        <repository>
+            <id>sting.public.repo.local</id>
+            <name>Sting Public Local Repository</name>
+            <url>file:${sting.basedir}/public/repo</url>
+        </repository>
+        <repository>
+            <id>sting.private.repo.local</id>
+            <name>Sting Private Local Repository</name>
+            <url>file:${sting.basedir}/private/repo</url>
+        </repository>
+    </repositories>
+
+</project>
diff --git a/public/sting-utils/pom.xml b/public/sting-utils/pom.xml
new file mode 100644
index 000000000..7e68cf740
--- /dev/null
+++ b/public/sting-utils/pom.xml
@@ -0,0 +1,170 @@
+<?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>
+
+    <parent>
+        <groupId>org.broadinstitute.sting</groupId>
+        <artifactId>sting-aggregator</artifactId>
+        <version>2.6-SNAPSHOT</version>
+        <relativePath>../..</relativePath>
+    </parent>
+
+    <artifactId>sting-utils</artifactId>
+    <packaging>jar</packaging>
+    <name>Sting Utils</name>
+
+    <properties>
+        <sting.basedir>${project.basedir}/../..</sting.basedir>
+        <gsalib.packagedir>org/broadinstitute/sting/utils/R</gsalib.packagedir>
+        <gsalib.filename>gsalib.tar.gz</gsalib.filename>
+    </properties>
+
+    <dependencies>
+        <dependency>
+            <groupId>net.sf</groupId>
+            <artifactId>sam</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>net.sf</groupId>
+            <artifactId>picard</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>org.broad</groupId>
+            <artifactId>tribble</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>org.broadinstitute</groupId>
+            <artifactId>variant</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>log4j</groupId>
+            <artifactId>log4j</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>colt</groupId>
+            <artifactId>colt</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>it.unimi.dsi</groupId>
+            <artifactId>fastutil</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>org.simpleframework</groupId>
+            <artifactId>simple-xml</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>org.reflections</groupId>
+            <artifactId>reflections</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>org.slf4j</groupId>
+            <artifactId>slf4j-log4j12</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>org.freemarker</groupId>
+            <artifactId>freemarker</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>org.apache.commons</groupId>
+            <artifactId>commons-jexl</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>commons-lang</groupId>
+            <artifactId>commons-lang</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>commons-io</groupId>
+            <artifactId>commons-io</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>commons-collections</groupId>
+            <artifactId>commons-collections</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>org.apache.commons</groupId>
+            <artifactId>commons-math</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>net.java.dev.jna</groupId>
+            <artifactId>jna</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>net.java.dev.jets3t</groupId>
+            <artifactId>jets3t</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>net.sf.gridscheduler</groupId>
+            <artifactId>drmaa</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>com.google.code.gson</groupId>
+            <artifactId>gson</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>org.apache.httpcomponents</groupId>
+            <artifactId>httpclient</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>com.google.code.cofoja</groupId>
+            <artifactId>cofoja</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>${project.groupId}</groupId>
+            <artifactId>gsalib</artifactId>
+            <version>${project.version}</version>
+            <type>tar.gz</type>
+        </dependency>
+
+        <dependency>
+            <groupId>org.testng</groupId>
+            <artifactId>testng</artifactId>
+            <scope>test</scope>
+        </dependency>
+        <dependency>
+            <groupId>com.google.caliper</groupId>
+            <artifactId>caliper</artifactId>
+            <scope>test</scope>
+        </dependency>
+    </dependencies>
+
+    <build>
+        <plugins>
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-dependency-plugin</artifactId>
+                <executions>
+                    <execution>
+                        <id>copy-gsalib</id>
+                        <goals>
+                            <goal>copy</goal>
+                        </goals>
+                        <phase>process-resources</phase>
+                        <configuration>
+                            <artifactItems>
+                                <artifactItem>
+                                    <groupId>${project.groupId}</groupId>
+                                    <artifactId>gsalib</artifactId>
+                                    <version>${project.version}</version>
+                                    <type>tar.gz</type>
+                                    <outputDirectory>${project.build.outputDirectory}/${gsalib.packagedir}</outputDirectory>
+                                    <destFileName>${gsalib.filename}</destFileName>
+                                </artifactItem>
+                            </artifactItems>
+                        </configuration>
+                    </execution>
+                </executions>
+            </plugin>
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-jar-plugin</artifactId>
+                <executions>
+                    <execution>
+                        <goals>
+                            <goal>test-jar</goal>
+                        </goals>
+                    </execution>
+                </executions>
+            </plugin>
+        </plugins>
+    </build>
+</project>

From 25aee7164e9d460028ac5b22098628404f841e42 Mon Sep 17 00:00:00 2001
From: Khalid Shakir <kshakir@broadinstitute.org>
Date: Thu, 30 Jan 2014 17:47:54 +0800
Subject: [PATCH 07/16] Fixed missing "mvn" command execution in ant-bridge.
 Added pom.xml workarounds for duplicate classpath error, due to
 gatk-framework dependency containing required BaseTest, and jarred
 *UnitTest/*IntegrationTest classes that also exist as files under
 target/test-classes.

---
 ant-bridge.sh                   |  6 ++--
 pom.xml                         | 23 +++++++--------
 public/external-example/pom.xml |  5 +---
 public/gatk-framework/pom.xml   | 34 ++++++++++++++++++++++
 public/package-tests/pom.xml    | 51 +++++++++++++++++++++++++++------
 public/sting-root/pom.xml       |  7 +----
 6 files changed, 93 insertions(+), 33 deletions(-)

diff --git a/ant-bridge.sh b/ant-bridge.sh
index f374cd99e..e9af3e749 100755
--- a/ant-bridge.sh
+++ b/ant-bridge.sh
@@ -87,7 +87,7 @@ for arg in "${@}" ; do
         # TODO: This runs *all* commit tests, including the few on Queue.
         elif [ "${arg}" = "gatkfull.binary.release.tests" ] ; then
             local_repo="sitetemprepo"
-            mvn_args="install -Dmaven.repo.local=${local_repo} && verify"
+            mvn_args="install -Dmaven.repo.local=${local_repo} && mvn verify"
             mvn_args="${mvn_args} -Dmaven.repo.local=${local_repo} -Dmaven.javadoc.skip=true"
             mvn_args="${mvn_args} -Dsting.generate-gatk-extensions.skipped=true"
             mvn_args="${mvn_args} -Dsting.jar.phase=none -Dsting.unpack.phase=none -Dsting.shade.phase=none"
@@ -96,7 +96,7 @@ for arg in "${@}" ; do
         # TODO: This runs only the pipeline tests (full, non-dry run), but not the commit tests for Queue.
         elif [ "${arg}" = "queuefull.binary.release.tests" ] ; then
             local_repo="sitetemprepo"
-            mvn_args="install -Dmaven.repo.local=${local_repo} && verify"
+            mvn_args="install -Dmaven.repo.local=${local_repo} && mvn verify"
             mvn_args="${mvn_args} -Dmaven.repo.local=${local_repo} -Dmaven.javadoc.skip=true"
             mvn_args="${mvn_args} -Dsting.generate-gatk-extensions.skipped=true"
             mvn_args="${mvn_args} -Dsting.jar.phase=none -Dsting.unpack.phase=none -Dsting.shade.phase=none"
@@ -153,6 +153,6 @@ if [ "${unknown_args}" != "" ]; then
 else
     echo "Equivalent maven command"
     echo "${mvn_cmd}${mvn_properties}${post_script}"
-    sh -c "${mvn_cmd}${mvn_properties}${post_script}"
+#    sh -c "${mvn_cmd}${mvn_properties}${post_script}"
 
 fi
diff --git a/pom.xml b/pom.xml
index 787bd5d31..2100556ed 100644
--- a/pom.xml
+++ b/pom.xml
@@ -508,6 +508,9 @@
                         </properties>
                     </configuration>
                     <executions>
+                        <!--
+                        TODO: see description of disable.gatk-framework.test.dependency in gatk-framework/pom.xml
+                        -->
                         <execution>
                             <id>package-unittests</id>
                             <goals>
@@ -517,11 +520,10 @@
                                 <goals>
                                     <goal>test</goal>
                                 </goals>
-                                <profiles>
-                                    <profile>unittests</profile>
-                                </profiles>
                                 <skipInvocation>${sting.packageunittests.skipped}</skipInvocation>
                                 <properties>
+                                    <unittests.profile.enabled>true</unittests.profile.enabled>
+                                    <disable.gatk-framework.test.dependency>false</disable.gatk-framework.test.dependency>
                                     <sting.packageunittests.skipped>${sting.packageunittests.skipped}</sting.packageunittests.skipped>
                                 </properties>
                             </configuration>
@@ -536,11 +538,10 @@
                                 <goals>
                                     <goal>verify</goal>
                                 </goals>
-                                <profiles>
-                                    <profile>integrationtests</profile>
-                                </profiles>
                                 <skipInvocation>${sting.packageintegrationtests.skipped}</skipInvocation>
                                 <properties>
+                                    <integrationtests.profile.enabled>true</integrationtests.profile.enabled>
+                                    <disable.gatk-framework.test.dependency>false</disable.gatk-framework.test.dependency>
                                     <sting.packageintegrationtests.skipped>${sting.packageintegrationtests.skipped}</sting.packageintegrationtests.skipped>
                                 </properties>
                             </configuration>
@@ -555,11 +556,10 @@
                                 <goals>
                                     <goal>verify</goal>
                                 </goals>
-                                <profiles>
-                                    <profile>integrationtests</profile>
-                                </profiles>
                                 <skipInvocation>${sting.packagepipelinetests.skipped}</skipInvocation>
                                 <properties>
+                                    <integrationtests.profile.enabled>true</integrationtests.profile.enabled>
+                                    <disable.gatk-framework.test.dependency>false</disable.gatk-framework.test.dependency>
                                     <sting.packagepipelinetests.skipped>${sting.packagepipelinetests.skipped}</sting.packagepipelinetests.skipped>
                                 </properties>
                             </configuration>
@@ -574,11 +574,10 @@
                                 <goals>
                                     <goal>verify</goal>
                                 </goals>
-                                <profiles>
-                                    <profile>integrationtests</profile>
-                                </profiles>
                                 <skipInvocation>${sting.packagelargescaletests.skipped}</skipInvocation>
                                 <properties>
+                                    <integrationtests.profile.enabled>true</integrationtests.profile.enabled>
+                                    <disable.gatk-framework.test.dependency>false</disable.gatk-framework.test.dependency>
                                     <sting.packagelargescaletests.skipped>${sting.packagelargescaletests.skipped}</sting.packagelargescaletests.skipped>
                                 </properties>
                             </configuration>
diff --git a/public/external-example/pom.xml b/public/external-example/pom.xml
index 37739bfda..5aba7ab26 100644
--- a/public/external-example/pom.xml
+++ b/public/external-example/pom.xml
@@ -211,11 +211,8 @@
                         <configuration>
                             <skip>false</skip>
                             <includes>
-                                <include>**/*Test.class</include>
+                                <include>**/*UnitTest.class</include>
                             </includes>
-                            <excludes>
-                                <exclude>**/*IntegrationTest.class</exclude>
-                            </excludes>
                         </configuration>
                     </execution>
                 </executions>
diff --git a/public/gatk-framework/pom.xml b/public/gatk-framework/pom.xml
index f4443a2f6..1443c7037 100644
--- a/public/gatk-framework/pom.xml
+++ b/public/gatk-framework/pom.xml
@@ -88,21 +88,55 @@
                     </execution>
                 </executions>
             </plugin>
+            <!--
+            TODO: disable.gatk-framework.test.dependency is required because the the same test classes
+            TODO: cannot be in both the gatk-framework test artifact AND the test classes directory.
+
+            TODO: Otherwise maven throws an [ERROR] java.lang.RuntimeException: Duplicate test set
+
+            TODO: This is due to AbstractSurefireMojo.scanForTestClasses() adding both scanDirectories() and scanDependencies().
+            TODO: Pain to debug as exception is three maven invoker levels deep, outer maven, maven-inovker-plugin, then forked tests!
+
+            TODO: Move BaseTest and other non UnitTests into the sting-utils test jar/artifact.
+
+            TODO: Then that dependency won't have test classes that will also run from the gatk-framework
+            TODO: test classes directory during the invoked package test.
+            -->
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-invoker-plugin</artifactId>
                 <executions>
                     <execution>
                         <id>package-unittests</id>
+                        <configuration>
+                            <properties>
+                                <disable.gatk-framework.test.dependency>true</disable.gatk-framework.test.dependency>
+                            </properties>
+                        </configuration>
                     </execution>
                     <execution>
                         <id>package-integrationtests</id>
+                        <configuration>
+                            <properties>
+                                <disable.gatk-framework.test.dependency>true</disable.gatk-framework.test.dependency>
+                            </properties>
+                        </configuration>
                     </execution>
                     <execution>
                         <id>package-largescaletests</id>
+                        <configuration>
+                            <properties>
+                                <disable.gatk-framework.test.dependency>true</disable.gatk-framework.test.dependency>
+                            </properties>
+                        </configuration>
                     </execution>
                     <execution>
                         <id>package-pipelinetests</id>
+                        <configuration>
+                            <properties>
+                                <disable.gatk-framework.test.dependency>true</disable.gatk-framework.test.dependency>
+                            </properties>
+                        </configuration>
                     </execution>
                 </executions>
             </plugin>
diff --git a/public/package-tests/pom.xml b/public/package-tests/pom.xml
index 3d1bc1136..3483f4da3 100644
--- a/public/package-tests/pom.xml
+++ b/public/package-tests/pom.xml
@@ -2,6 +2,10 @@
 <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>
 
+    <!--
+    Run during package testing by the maven invoker plugin in the sting-aggregator /pom.xml
+    -->
+
     <parent>
         <groupId>org.broadinstitute.sting</groupId>
         <artifactId>sting-root</artifactId>
@@ -15,6 +19,10 @@
 
     <properties>
         <sting.basedir>${project.basedir}/../..</sting.basedir>
+        <sting.packageunittests.skipped>true</sting.packageunittests.skipped>
+        <sting.packageintegrationtests.skipped>true</sting.packageintegrationtests.skipped>
+        <sting.packagepipelinetests.skipped>true</sting.packagepipelinetests.skipped>
+        <sting.packagelargescaletests.skipped>true</sting.packagelargescaletests.skipped>
     </properties>
 
     <!-- Dependency configuration (versions, etc.) -->
@@ -39,14 +47,6 @@
             <artifactId>cofoja</artifactId>
         </dependency>
 
-        <dependency>
-            <groupId>${project.groupId}</groupId>
-            <artifactId>gatk-framework</artifactId>
-            <version>${project.version}</version>
-            <type>test-jar</type>
-            <scope>test</scope>
-        </dependency>
-
         <dependency>
             <groupId>org.testng</groupId>
             <artifactId>testng</artifactId>
@@ -65,8 +65,36 @@
     </build>
 
     <profiles>
+        <!--
+        TODO: see description of disable.gatk-framework.test.dependency in gatk-framework/pom.xml
+        -->
+        <profile>
+            <id>include-gatk-framework-tests</id>
+            <activation>
+                <property>
+                    <name>disable.gatk-framework.test.dependency</name>
+                    <value>false</value>
+                </property>
+            </activation>
+            <dependencies>
+                <dependency>
+                    <groupId>${project.groupId}</groupId>
+                    <artifactId>gatk-framework</artifactId>
+                    <version>${project.version}</version>
+                    <type>test-jar</type>
+                    <scope>test</scope>
+                </dependency>
+            </dependencies>
+        </profile>
         <profile>
             <id>unittests</id>
+            <activation>
+                <activeByDefault>false</activeByDefault>
+                <property>
+                    <name>unittests.profile.enabled</name>
+                    <value>true</value>
+                </property>
+            </activation>
             <build>
                 <!-- Plugin configuration -->
                 <plugins>
@@ -101,6 +129,13 @@
 
         <profile>
             <id>integrationtests</id>
+            <activation>
+                <activeByDefault>false</activeByDefault>
+                <property>
+                    <name>integrationtests.profile.enabled</name>
+                    <value>true</value>
+                </property>
+            </activation>
             <build>
                 <!-- Plugin configuration -->
                 <plugins>
diff --git a/public/sting-root/pom.xml b/public/sting-root/pom.xml
index 1309175bb..83e9b21aa 100644
--- a/public/sting-root/pom.xml
+++ b/public/sting-root/pom.xml
@@ -389,13 +389,8 @@
                                 <!-- TODO: Re-enable unit tests by default? -->
                                 <skip>${sting.unittests.skipped}</skip>
                                 <includes>
-                                    <include>**/*Test.class</include>
+                                    <include>**/*UnitTest.class</include>
                                 </includes>
-                                <excludes>
-                                    <exclude>**/*IntegrationTest.class</exclude>
-                                    <exclude>**/*PipelineTest.class</exclude>
-                                    <exclude>**/*LargeScaleTest.class</exclude>
-                                </excludes>
                             </configuration>
                         </execution>
                     </executions>

From de13f41fc3a78b9b21432b2cb914e047db01bf37 Mon Sep 17 00:00:00 2001
From: Khalid Shakir <kshakir@broadinstitute.org>
Date: Fri, 31 Jan 2014 20:25:58 +0800
Subject: [PATCH 08/16] One step closer to a proper test-utils artifact. Using
 the maven-jar-plugin to create a test classifer, excluding actual tests,
 until we can properly separate the classes into separate artifacts/modules.

---
 ant-bridge.sh                    |  2 +-
 pom.xml                          | 43 ++++++++++++++++++++++++++-----
 protected/gatk-protected/pom.xml |  4 +--
 public/external-example/pom.xml  |  7 +++--
 public/gatk-framework/pom.xml    | 44 +++-----------------------------
 public/package-tests/pom.xml     | 29 ++++++---------------
 public/queue-framework/pom.xml   | 14 ++--------
 public/sting-utils/pom.xml       | 12 +--------
 8 files changed, 59 insertions(+), 96 deletions(-)

diff --git a/ant-bridge.sh b/ant-bridge.sh
index e9af3e749..07498c8f3 100755
--- a/ant-bridge.sh
+++ b/ant-bridge.sh
@@ -153,6 +153,6 @@ if [ "${unknown_args}" != "" ]; then
 else
     echo "Equivalent maven command"
     echo "${mvn_cmd}${mvn_properties}${post_script}"
-#    sh -c "${mvn_cmd}${mvn_properties}${post_script}"
+    sh -c "${mvn_cmd}${mvn_properties}${post_script}"
 
 fi
diff --git a/pom.xml b/pom.xml
index 2100556ed..5474b5dfc 100644
--- a/pom.xml
+++ b/pom.xml
@@ -33,6 +33,7 @@
         <!-- TODO: Need a better a way to say "don't include hidden" by default -->
         <gatkdocs.include.hidden>-build-timestamp "${maven.build.timestamp}"</gatkdocs.include.hidden>
         <sting.jar.phase>package</sting.jar.phase>
+        <sting.test-utils.jar.phase>none</sting.test-utils.jar.phase>
         <sting.packagecommittests.skipped>true</sting.packagecommittests.skipped>
         <sting.packageunittests.skipped>${sting.packagecommittests.skipped}</sting.packageunittests.skipped>
         <sting.packageintegrationtests.skipped>${sting.packagecommittests.skipped}</sting.packageintegrationtests.skipped>
@@ -275,6 +276,41 @@
                             <id>default-jar</id>
                             <phase>${sting.jar.phase}</phase>
                         </execution>
+                        <execution>
+                            <id>test-utils</id>
+                            <goals>
+                                <goal>jar</goal>
+                            </goals>
+                            <phase>${sting.test-utils-jar.phase}</phase>
+                            <configuration>
+                                <classesDirectory>${project.build.testOutputDirectory}</classesDirectory>
+                                <classifier>test-utils</classifier>
+                                <!--
+                                TODO: Excluding actual tests from tests-utils jar is required because the same test classes
+                                TODO: cannot be in both the test artifact AND the test classes directory.
+
+                                TODO: Otherwise maven throws an [ERROR] java.lang.RuntimeException: Duplicate test set
+
+                                TODO: This is due to AbstractSurefireMojo.scanForTestClasses() adding both scanDirectories() and scanDependencies().
+                                TODO: Pain to debug as exception is three maven invoker levels deep, outer maven, maven-inovker-plugin, then forked tests!
+
+                                TODO: See also: http://maven.apache.org/plugins/maven-jar-plugin/usage.html#The_preferred_way
+
+                                TODO: Then that dependency won't have test classes that will also run from the
+                                TODO: test classes directory during the invoked package test.
+                                -->
+                                <excludes>
+                                    <exclude>**/*UnitTest.class</exclude>
+                                    <exclude>**/*UnitTest$*.class</exclude>
+                                    <exclude>**/*IntegrationTest.class</exclude>
+                                    <exclude>**/*IntegrationTest$*.class</exclude>
+                                    <exclude>**/*PipelineTest.class</exclude>
+                                    <exclude>**/*PipelineTest$*.class</exclude>
+                                    <exclude>**/*LargeScaleTest.class</exclude>
+                                    <exclude>**/*LargeScaleTest.class</exclude>
+                                </excludes>
+                            </configuration>
+                        </execution>
                     </executions>
                 </plugin>
 
@@ -508,9 +544,6 @@
                         </properties>
                     </configuration>
                     <executions>
-                        <!--
-                        TODO: see description of disable.gatk-framework.test.dependency in gatk-framework/pom.xml
-                        -->
                         <execution>
                             <id>package-unittests</id>
                             <goals>
@@ -523,7 +556,6 @@
                                 <skipInvocation>${sting.packageunittests.skipped}</skipInvocation>
                                 <properties>
                                     <unittests.profile.enabled>true</unittests.profile.enabled>
-                                    <disable.gatk-framework.test.dependency>false</disable.gatk-framework.test.dependency>
                                     <sting.packageunittests.skipped>${sting.packageunittests.skipped}</sting.packageunittests.skipped>
                                 </properties>
                             </configuration>
@@ -541,7 +573,6 @@
                                 <skipInvocation>${sting.packageintegrationtests.skipped}</skipInvocation>
                                 <properties>
                                     <integrationtests.profile.enabled>true</integrationtests.profile.enabled>
-                                    <disable.gatk-framework.test.dependency>false</disable.gatk-framework.test.dependency>
                                     <sting.packageintegrationtests.skipped>${sting.packageintegrationtests.skipped}</sting.packageintegrationtests.skipped>
                                 </properties>
                             </configuration>
@@ -559,7 +590,6 @@
                                 <skipInvocation>${sting.packagepipelinetests.skipped}</skipInvocation>
                                 <properties>
                                     <integrationtests.profile.enabled>true</integrationtests.profile.enabled>
-                                    <disable.gatk-framework.test.dependency>false</disable.gatk-framework.test.dependency>
                                     <sting.packagepipelinetests.skipped>${sting.packagepipelinetests.skipped}</sting.packagepipelinetests.skipped>
                                 </properties>
                             </configuration>
@@ -577,7 +607,6 @@
                                 <skipInvocation>${sting.packagelargescaletests.skipped}</skipInvocation>
                                 <properties>
                                     <integrationtests.profile.enabled>true</integrationtests.profile.enabled>
-                                    <disable.gatk-framework.test.dependency>false</disable.gatk-framework.test.dependency>
                                     <sting.packagelargescaletests.skipped>${sting.packagelargescaletests.skipped}</sting.packagelargescaletests.skipped>
                                 </properties>
                             </configuration>
diff --git a/protected/gatk-protected/pom.xml b/protected/gatk-protected/pom.xml
index d3e50eec9..14774def7 100644
--- a/protected/gatk-protected/pom.xml
+++ b/protected/gatk-protected/pom.xml
@@ -44,7 +44,7 @@
             <groupId>${project.groupId}</groupId>
             <artifactId>sting-utils</artifactId>
             <version>${project.version}</version>
-            <type>test-jar</type>
+            <classifier>test-utils</classifier>
             <scope>test</scope>
         </dependency>
 
@@ -52,7 +52,7 @@
             <groupId>${project.groupId}</groupId>
             <artifactId>gatk-framework</artifactId>
             <version>${project.version}</version>
-            <type>test-jar</type>
+            <classifier>test-utils</classifier>
             <scope>test</scope>
         </dependency>
 
diff --git a/public/external-example/pom.xml b/public/external-example/pom.xml
index 5aba7ab26..d51e5a6f5 100644
--- a/public/external-example/pom.xml
+++ b/public/external-example/pom.xml
@@ -41,12 +41,15 @@
         <!--
         Test dependencies are not transitive,
         so must include each explicit test artifact.
+
+        TODO: switch from test-utils classifier to a tests-utils artifact
+        TODO: see also http://maven.apache.org/plugins/maven-jar-plugin/usage.html#The_preferred_way
         -->
         <dependency>
             <groupId>org.broadinstitute.sting</groupId>
             <artifactId>sting-utils</artifactId>
             <version>${sting.version}</version>
-            <type>test-jar</type>
+            <classifier>test-utils</classifier>
             <scope>test</scope>
         </dependency>
 
@@ -54,7 +57,7 @@
             <groupId>org.broadinstitute.sting</groupId>
             <artifactId>gatk-framework</artifactId>
             <version>${sting.version}</version>
-            <type>test-jar</type>
+            <classifier>test-utils</classifier>
             <scope>test</scope>
         </dependency>
 
diff --git a/public/gatk-framework/pom.xml b/public/gatk-framework/pom.xml
index 1443c7037..e8b2f7c71 100644
--- a/public/gatk-framework/pom.xml
+++ b/public/gatk-framework/pom.xml
@@ -16,6 +16,7 @@
     <properties>
         <sting.basedir>${project.basedir}/../..</sting.basedir>
         <sting.packagetests.artifactId>gatk-package</sting.packagetests.artifactId>
+        <sting.test-utils-jar.phase>${sting.jar.phase}</sting.test-utils-jar.phase>
     </properties>
 
     <dependencies>
@@ -29,7 +30,7 @@
             <groupId>${project.groupId}</groupId>
             <artifactId>sting-utils</artifactId>
             <version>${project.version}</version>
-            <type>test-jar</type>
+            <classifier>test-utils</classifier>
             <scope>test</scope>
         </dependency>
 
@@ -77,66 +78,29 @@
                     </execution>
                 </executions>
             </plugin>
+            <!--
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-jar-plugin</artifactId>
                 <executions>
-                    <execution>
-                        <goals>
-                            <goal>test-jar</goal>
-                        </goals>
-                    </execution>
                 </executions>
             </plugin>
-            <!--
-            TODO: disable.gatk-framework.test.dependency is required because the the same test classes
-            TODO: cannot be in both the gatk-framework test artifact AND the test classes directory.
-
-            TODO: Otherwise maven throws an [ERROR] java.lang.RuntimeException: Duplicate test set
-
-            TODO: This is due to AbstractSurefireMojo.scanForTestClasses() adding both scanDirectories() and scanDependencies().
-            TODO: Pain to debug as exception is three maven invoker levels deep, outer maven, maven-inovker-plugin, then forked tests!
-
-            TODO: Move BaseTest and other non UnitTests into the sting-utils test jar/artifact.
-
-            TODO: Then that dependency won't have test classes that will also run from the gatk-framework
-            TODO: test classes directory during the invoked package test.
-            -->
+-->
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-invoker-plugin</artifactId>
                 <executions>
                     <execution>
                         <id>package-unittests</id>
-                        <configuration>
-                            <properties>
-                                <disable.gatk-framework.test.dependency>true</disable.gatk-framework.test.dependency>
-                            </properties>
-                        </configuration>
                     </execution>
                     <execution>
                         <id>package-integrationtests</id>
-                        <configuration>
-                            <properties>
-                                <disable.gatk-framework.test.dependency>true</disable.gatk-framework.test.dependency>
-                            </properties>
-                        </configuration>
                     </execution>
                     <execution>
                         <id>package-largescaletests</id>
-                        <configuration>
-                            <properties>
-                                <disable.gatk-framework.test.dependency>true</disable.gatk-framework.test.dependency>
-                            </properties>
-                        </configuration>
                     </execution>
                     <execution>
                         <id>package-pipelinetests</id>
-                        <configuration>
-                            <properties>
-                                <disable.gatk-framework.test.dependency>true</disable.gatk-framework.test.dependency>
-                            </properties>
-                        </configuration>
                     </execution>
                 </executions>
             </plugin>
diff --git a/public/package-tests/pom.xml b/public/package-tests/pom.xml
index 3483f4da3..f10518d7d 100644
--- a/public/package-tests/pom.xml
+++ b/public/package-tests/pom.xml
@@ -47,6 +47,14 @@
             <artifactId>cofoja</artifactId>
         </dependency>
 
+        <dependency>
+            <groupId>${project.groupId}</groupId>
+            <artifactId>gatk-framework</artifactId>
+            <version>${project.version}</version>
+            <classifier>test-utils</classifier>
+            <scope>test</scope>
+        </dependency>
+
         <dependency>
             <groupId>org.testng</groupId>
             <artifactId>testng</artifactId>
@@ -65,27 +73,6 @@
     </build>
 
     <profiles>
-        <!--
-        TODO: see description of disable.gatk-framework.test.dependency in gatk-framework/pom.xml
-        -->
-        <profile>
-            <id>include-gatk-framework-tests</id>
-            <activation>
-                <property>
-                    <name>disable.gatk-framework.test.dependency</name>
-                    <value>false</value>
-                </property>
-            </activation>
-            <dependencies>
-                <dependency>
-                    <groupId>${project.groupId}</groupId>
-                    <artifactId>gatk-framework</artifactId>
-                    <version>${project.version}</version>
-                    <type>test-jar</type>
-                    <scope>test</scope>
-                </dependency>
-            </dependencies>
-        </profile>
         <profile>
             <id>unittests</id>
             <activation>
diff --git a/public/queue-framework/pom.xml b/public/queue-framework/pom.xml
index 8ccc7f351..4dd3c188e 100644
--- a/public/queue-framework/pom.xml
+++ b/public/queue-framework/pom.xml
@@ -18,6 +18,7 @@
         <gatk.extensions.sources>${project.build.directory}/generated-sources/gatk-extensions</gatk.extensions.sources>
         <sting.generate-gatk-extensions.skipped>false</sting.generate-gatk-extensions.skipped>
         <sting.packagetests.artifactId>queue-package</sting.packagetests.artifactId>
+        <sting.test-utils-jar.phase>${sting.jar.phase}</sting.test-utils-jar.phase>
     </properties>
 
     <dependencies>
@@ -65,7 +66,7 @@
             <groupId>${project.groupId}</groupId>
             <artifactId>gatk-framework</artifactId>
             <version>${project.version}</version>
-            <type>test-jar</type>
+            <classifier>test-utils</classifier>
             <scope>test</scope>
         </dependency>
 
@@ -170,17 +171,6 @@
                     </execution>
                 </executions>
             </plugin>
-            <plugin>
-                <groupId>org.apache.maven.plugins</groupId>
-                <artifactId>maven-jar-plugin</artifactId>
-                <executions>
-                    <execution>
-                        <goals>
-                            <goal>test-jar</goal>
-                        </goals>
-                    </execution>
-                </executions>
-            </plugin>
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-invoker-plugin</artifactId>
diff --git a/public/sting-utils/pom.xml b/public/sting-utils/pom.xml
index 7e68cf740..54734efac 100644
--- a/public/sting-utils/pom.xml
+++ b/public/sting-utils/pom.xml
@@ -17,6 +17,7 @@
         <sting.basedir>${project.basedir}/../..</sting.basedir>
         <gsalib.packagedir>org/broadinstitute/sting/utils/R</gsalib.packagedir>
         <gsalib.filename>gsalib.tar.gz</gsalib.filename>
+        <sting.test-utils-jar.phase>${sting.jar.phase}</sting.test-utils-jar.phase>
     </properties>
 
     <dependencies>
@@ -154,17 +155,6 @@
                     </execution>
                 </executions>
             </plugin>
-            <plugin>
-                <groupId>org.apache.maven.plugins</groupId>
-                <artifactId>maven-jar-plugin</artifactId>
-                <executions>
-                    <execution>
-                        <goals>
-                            <goal>test-jar</goal>
-                        </goals>
-                    </execution>
-                </executions>
-            </plugin>
         </plugins>
     </build>
 </project>

From f968b8a58bd75139d8f8af0c4c709269f23de83f Mon Sep 17 00:00:00 2001
From: Khalid Shakir <kshakir@broadinstitute.org>
Date: Sat, 1 Feb 2014 02:25:07 +0800
Subject: [PATCH 09/16] Crash when integration tests fail by running install
 and verify at the same time, instead of trying to do them separately.

---
 pom.xml | 9 +++------
 1 file changed, 3 insertions(+), 6 deletions(-)

diff --git a/pom.xml b/pom.xml
index 5474b5dfc..469ff4a18 100644
--- a/pom.xml
+++ b/pom.xml
@@ -563,8 +563,7 @@
                         <execution>
                             <id>package-integrationtests</id>
                             <goals>
-                                <goal>integration-test</goal>
-                                <goal>verify</goal>
+                                <goal>run</goal>
                             </goals>
                             <configuration>
                                 <goals>
@@ -580,8 +579,7 @@
                         <execution>
                             <id>package-pipelinetests</id>
                             <goals>
-                                <goal>integration-test</goal>
-                                <goal>verify</goal>
+                                <goal>run</goal>
                             </goals>
                             <configuration>
                                 <goals>
@@ -597,8 +595,7 @@
                         <execution>
                             <id>package-largescaletests</id>
                             <goals>
-                                <goal>integration-test</goal>
-                                <goal>verify</goal>
+                                <goal>run</goal>
                             </goals>
                             <configuration>
                                 <goals>

From 9ca3004fc31148bc8ea40a667b5f1ebc54d913af Mon Sep 17 00:00:00 2001
From: Khalid Shakir <kshakir@broadinstitute.org>
Date: Sat, 1 Feb 2014 04:02:46 +0800
Subject: [PATCH 10/16] Setting the test-utils' type to test-jar, such that the
 multi-module build uses testClasses instead of classes as a directory
 dependency.

---
 protected/gatk-protected/pom.xml | 2 ++
 public/external-example/pom.xml  | 2 ++
 public/gatk-framework/pom.xml    | 1 +
 public/package-tests/pom.xml     | 1 +
 public/queue-framework/pom.xml   | 1 +
 5 files changed, 7 insertions(+)

diff --git a/protected/gatk-protected/pom.xml b/protected/gatk-protected/pom.xml
index 14774def7..2cce6a809 100644
--- a/protected/gatk-protected/pom.xml
+++ b/protected/gatk-protected/pom.xml
@@ -45,6 +45,7 @@
             <artifactId>sting-utils</artifactId>
             <version>${project.version}</version>
             <classifier>test-utils</classifier>
+            <type>test-jar</type>
             <scope>test</scope>
         </dependency>
 
@@ -53,6 +54,7 @@
             <artifactId>gatk-framework</artifactId>
             <version>${project.version}</version>
             <classifier>test-utils</classifier>
+            <type>test-jar</type>
             <scope>test</scope>
         </dependency>
 
diff --git a/public/external-example/pom.xml b/public/external-example/pom.xml
index d51e5a6f5..16d7f6d6f 100644
--- a/public/external-example/pom.xml
+++ b/public/external-example/pom.xml
@@ -50,6 +50,7 @@
             <artifactId>sting-utils</artifactId>
             <version>${sting.version}</version>
             <classifier>test-utils</classifier>
+            <type>test-jar</type>
             <scope>test</scope>
         </dependency>
 
@@ -58,6 +59,7 @@
             <artifactId>gatk-framework</artifactId>
             <version>${sting.version}</version>
             <classifier>test-utils</classifier>
+            <type>test-jar</type>
             <scope>test</scope>
         </dependency>
 
diff --git a/public/gatk-framework/pom.xml b/public/gatk-framework/pom.xml
index e8b2f7c71..5d0f3de5a 100644
--- a/public/gatk-framework/pom.xml
+++ b/public/gatk-framework/pom.xml
@@ -31,6 +31,7 @@
             <artifactId>sting-utils</artifactId>
             <version>${project.version}</version>
             <classifier>test-utils</classifier>
+            <type>test-jar</type>
             <scope>test</scope>
         </dependency>
 
diff --git a/public/package-tests/pom.xml b/public/package-tests/pom.xml
index f10518d7d..56804dbd1 100644
--- a/public/package-tests/pom.xml
+++ b/public/package-tests/pom.xml
@@ -52,6 +52,7 @@
             <artifactId>gatk-framework</artifactId>
             <version>${project.version}</version>
             <classifier>test-utils</classifier>
+            <type>test-jar</type>
             <scope>test</scope>
         </dependency>
 
diff --git a/public/queue-framework/pom.xml b/public/queue-framework/pom.xml
index 4dd3c188e..b65359c30 100644
--- a/public/queue-framework/pom.xml
+++ b/public/queue-framework/pom.xml
@@ -67,6 +67,7 @@
             <artifactId>gatk-framework</artifactId>
             <version>${project.version}</version>
             <classifier>test-utils</classifier>
+            <type>test-jar</type>
             <scope>test</scope>
         </dependency>
 

From 20b471ef7b9f28f780475d5e37a54ae9d26a286c Mon Sep 17 00:00:00 2001
From: Khalid Shakir <kshakir@broadinstitute.org>
Date: Sat, 1 Feb 2014 05:02:08 +0800
Subject: [PATCH 11/16] ant-bridge dist -> verify, test.compile -> test-compile
 Added a utility script for running a single test, usually in parallel.

---
 ant-bridge.sh | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/ant-bridge.sh b/ant-bridge.sh
index 07498c8f3..239ddb519 100755
--- a/ant-bridge.sh
+++ b/ant-bridge.sh
@@ -1,6 +1,6 @@
 #!/bin/sh
 
-mvn_args="test-compile"
+mvn_args="verify"
 mvn_properties=
 mvn_clean=
 unknown_args=
@@ -39,11 +39,14 @@ for arg in "${@}" ; do
         fi
 
     else
-        if [ "${arg}" != "dist" -a "${mvn_args}" != "test-compile" ]; then
+        if [ "${arg}" != "dist" -a "${mvn_args}" != "" ]; then
             echo "Sorry, this script does not currently support mixing targets." >&2
             exit 1
 
         elif [ "${arg}" = "dist" ] ; then
+            mvn_args="verify"
+
+        elif [ "${arg}" = "test.compile" ] ; then
             mvn_args="test-compile"
 
         elif [ "${arg}" = "gatkdocs" ] ; then

From 857e6e0d6f2c593e0fa0f7f2993a27908df3eeb0 Mon Sep 17 00:00:00 2001
From: Khalid Shakir <kshakir@broadinstitute.org>
Date: Sat, 1 Feb 2014 06:49:25 +0800
Subject: [PATCH 12/16] Bumped version to 2.8-SNAPSHOT, using new
 update_pom_versions.sh script.

---
 pom.xml                          | 2 +-
 protected/gatk-protected/pom.xml | 2 +-
 protected/pom.xml                | 2 +-
 public/external-example/pom.xml  | 2 +-
 public/gatk-framework/pom.xml    | 2 +-
 public/gatk-package/pom.xml      | 2 +-
 public/gatk-queue-extgen/pom.xml | 2 +-
 public/gsalib/pom.xml            | 2 +-
 public/package-tests/pom.xml     | 2 +-
 public/pom.xml                   | 2 +-
 public/queue-framework/pom.xml   | 2 +-
 public/queue-package/pom.xml     | 2 +-
 public/sting-root/pom.xml        | 2 +-
 public/sting-utils/pom.xml       | 2 +-
 14 files changed, 14 insertions(+), 14 deletions(-)

diff --git a/pom.xml b/pom.xml
index 469ff4a18..0e1720c41 100644
--- a/pom.xml
+++ b/pom.xml
@@ -13,7 +13,7 @@
     <parent>
         <groupId>org.broadinstitute.sting</groupId>
         <artifactId>sting-root</artifactId>
-        <version>2.6-SNAPSHOT</version>
+        <version>2.8-SNAPSHOT</version>
         <relativePath>public/sting-root</relativePath>
     </parent>
 
diff --git a/protected/gatk-protected/pom.xml b/protected/gatk-protected/pom.xml
index 2cce6a809..c0074b8bc 100644
--- a/protected/gatk-protected/pom.xml
+++ b/protected/gatk-protected/pom.xml
@@ -5,7 +5,7 @@
     <parent>
         <groupId>org.broadinstitute.sting</groupId>
         <artifactId>sting-aggregator</artifactId>
-        <version>2.6-SNAPSHOT</version>
+        <version>2.8-SNAPSHOT</version>
         <relativePath>../..</relativePath>
     </parent>
 
diff --git a/protected/pom.xml b/protected/pom.xml
index a7fb4863f..4b165d477 100644
--- a/protected/pom.xml
+++ b/protected/pom.xml
@@ -5,7 +5,7 @@
     <parent>
         <groupId>org.broadinstitute.sting</groupId>
         <artifactId>sting-root</artifactId>
-        <version>2.6-SNAPSHOT</version>
+        <version>2.8-SNAPSHOT</version>
         <relativePath>../public/sting-root</relativePath>
     </parent>
 
diff --git a/public/external-example/pom.xml b/public/external-example/pom.xml
index 16d7f6d6f..0f5e3934e 100644
--- a/public/external-example/pom.xml
+++ b/public/external-example/pom.xml
@@ -9,7 +9,7 @@
     <name>external-example</name>
 
     <properties>
-        <sting.version>2.6-SNAPSHOT</sting.version>
+        <sting.version>2.8-SNAPSHOT</sting.version>
         <!--
         sting.basedir property must point to your checkout of Sting/GATK until we can get all the
         dependencies out of the committed sting repo and into central.
diff --git a/public/gatk-framework/pom.xml b/public/gatk-framework/pom.xml
index 5d0f3de5a..bf46e8951 100644
--- a/public/gatk-framework/pom.xml
+++ b/public/gatk-framework/pom.xml
@@ -5,7 +5,7 @@
     <parent>
         <groupId>org.broadinstitute.sting</groupId>
         <artifactId>sting-aggregator</artifactId>
-        <version>2.6-SNAPSHOT</version>
+        <version>2.8-SNAPSHOT</version>
         <relativePath>../..</relativePath>
     </parent>
 
diff --git a/public/gatk-package/pom.xml b/public/gatk-package/pom.xml
index 4f5a70268..48c6168d3 100644
--- a/public/gatk-package/pom.xml
+++ b/public/gatk-package/pom.xml
@@ -5,7 +5,7 @@
     <parent>
         <groupId>org.broadinstitute.sting</groupId>
         <artifactId>sting-aggregator</artifactId>
-        <version>2.6-SNAPSHOT</version>
+        <version>2.8-SNAPSHOT</version>
         <relativePath>../..</relativePath>
     </parent>
 
diff --git a/public/gatk-queue-extgen/pom.xml b/public/gatk-queue-extgen/pom.xml
index 9aba4f1a4..532515ff8 100644
--- a/public/gatk-queue-extgen/pom.xml
+++ b/public/gatk-queue-extgen/pom.xml
@@ -5,7 +5,7 @@
     <parent>
         <groupId>org.broadinstitute.sting</groupId>
         <artifactId>sting-aggregator</artifactId>
-        <version>2.6-SNAPSHOT</version>
+        <version>2.8-SNAPSHOT</version>
         <relativePath>../..</relativePath>
     </parent>
 
diff --git a/public/gsalib/pom.xml b/public/gsalib/pom.xml
index a51a985f1..c751bc0f0 100644
--- a/public/gsalib/pom.xml
+++ b/public/gsalib/pom.xml
@@ -5,7 +5,7 @@
     <parent>
         <groupId>org.broadinstitute.sting</groupId>
         <artifactId>sting-aggregator</artifactId>
-        <version>2.6-SNAPSHOT</version>
+        <version>2.8-SNAPSHOT</version>
         <relativePath>../..</relativePath>
     </parent>
 
diff --git a/public/package-tests/pom.xml b/public/package-tests/pom.xml
index 56804dbd1..5e3269d0f 100644
--- a/public/package-tests/pom.xml
+++ b/public/package-tests/pom.xml
@@ -9,7 +9,7 @@
     <parent>
         <groupId>org.broadinstitute.sting</groupId>
         <artifactId>sting-root</artifactId>
-        <version>2.6-SNAPSHOT</version>
+        <version>2.8-SNAPSHOT</version>
         <relativePath>../sting-root</relativePath>
     </parent>
 
diff --git a/public/pom.xml b/public/pom.xml
index e3173c35b..5e3ae00a6 100644
--- a/public/pom.xml
+++ b/public/pom.xml
@@ -5,7 +5,7 @@
     <parent>
         <groupId>org.broadinstitute.sting</groupId>
         <artifactId>sting-root</artifactId>
-        <version>2.6-SNAPSHOT</version>
+        <version>2.8-SNAPSHOT</version>
         <relativePath>sting-root</relativePath>
     </parent>
 
diff --git a/public/queue-framework/pom.xml b/public/queue-framework/pom.xml
index b65359c30..7146e9694 100644
--- a/public/queue-framework/pom.xml
+++ b/public/queue-framework/pom.xml
@@ -5,7 +5,7 @@
     <parent>
         <groupId>org.broadinstitute.sting</groupId>
         <artifactId>sting-aggregator</artifactId>
-        <version>2.6-SNAPSHOT</version>
+        <version>2.8-SNAPSHOT</version>
         <relativePath>../..</relativePath>
     </parent>
 
diff --git a/public/queue-package/pom.xml b/public/queue-package/pom.xml
index 1a8bf8b0f..3bd9f262e 100644
--- a/public/queue-package/pom.xml
+++ b/public/queue-package/pom.xml
@@ -5,7 +5,7 @@
     <parent>
         <groupId>org.broadinstitute.sting</groupId>
         <artifactId>sting-aggregator</artifactId>
-        <version>2.6-SNAPSHOT</version>
+        <version>2.8-SNAPSHOT</version>
         <relativePath>../..</relativePath>
     </parent>
 
diff --git a/public/sting-root/pom.xml b/public/sting-root/pom.xml
index 83e9b21aa..080ed05c4 100644
--- a/public/sting-root/pom.xml
+++ b/public/sting-root/pom.xml
@@ -12,7 +12,7 @@
 
     <groupId>org.broadinstitute.sting</groupId>
     <artifactId>sting-root</artifactId>
-    <version>2.6-SNAPSHOT</version>
+    <version>2.8-SNAPSHOT</version>
     <packaging>pom</packaging>
     <name>Sting Root</name>
 
diff --git a/public/sting-utils/pom.xml b/public/sting-utils/pom.xml
index 54734efac..043be645f 100644
--- a/public/sting-utils/pom.xml
+++ b/public/sting-utils/pom.xml
@@ -5,7 +5,7 @@
     <parent>
         <groupId>org.broadinstitute.sting</groupId>
         <artifactId>sting-aggregator</artifactId>
-        <version>2.6-SNAPSHOT</version>
+        <version>2.8-SNAPSHOT</version>
         <relativePath>../..</relativePath>
     </parent>
 

From b10b42c10a51988d0515824a68496aa87aa8dba8 Mon Sep 17 00:00:00 2001
From: Khalid Shakir <kshakir@broadinstitute.org>
Date: Sat, 1 Feb 2014 11:27:25 +0800
Subject: [PATCH 13/16] Added a "dry" argument to ant-bridge.sh, that just
 prints the command that would run.

---
 ant-bridge.sh | 69 ++++++++++++++++++++++++++++-----------------------
 1 file changed, 38 insertions(+), 31 deletions(-)

diff --git a/ant-bridge.sh b/ant-bridge.sh
index 239ddb519..b37cc1822 100755
--- a/ant-bridge.sh
+++ b/ant-bridge.sh
@@ -7,9 +7,13 @@ unknown_args=
 property_regex='-D(.*)=(.*)'
 unit_test_regex='.*UnitTest'
 post_script=
+run_type="run"
 
 for arg in "${@}" ; do
-    if [ "${arg}" = "clean" ] ; then
+    if [[ "${arg}" == "dry" ]] ; then
+        run_type="dry"
+
+    elif [[ "${arg}" == "clean" ]] ; then
         mvn_clean="clean"
         mvn_args=
 
@@ -17,7 +21,7 @@ for arg in "${@}" ; do
         property_name=${BASH_REMATCH[1]}
         property_value=${BASH_REMATCH[2]}
 
-        if [ "${property_name}" = "single" ] ; then
+        if [[ "${property_name}" == "single" ]] ; then
             test_property="test"
             test_disabled="it.test"
             if [[ ! "${property_value}" =~ ${unit_test_regex} ]] ; then
@@ -27,10 +31,10 @@ for arg in "${@}" ; do
 
             mvn_properties="${mvn_properties} -D${test_disabled}=disabled -D${test_property}=${property_value}"
 
-        elif [ "${property_name}" = "test.debug.port" ] ; then
+        elif [[ "${property_name}" == "test.debug.port" ]] ; then
             mvn_properties="${mvn_properties} -Dmaven.surefire.debug=\"-Xdebug -Xrunjdwp:transport=dt_socket,server=y,suspend=y,address=${property_value}\""
 
-        elif [ "${property_name}" = "test.default.maxmemory" ] ; then
+        elif [[ "${property_name}" == "test.default.maxmemory" ]] ; then
             mvn_properties="${mvn_properties} -Dtest.maxmemory=${property_value}"
 
         else
@@ -39,41 +43,41 @@ for arg in "${@}" ; do
         fi
 
     else
-        if [ "${arg}" != "dist" -a "${mvn_args}" != "" ]; then
+        if [[ "${arg}" != "dist" && "${mvn_args}" != "" && "${mvn_args}" != "verify" ]] ; then
             echo "Sorry, this script does not currently support mixing targets." >&2
             exit 1
 
-        elif [ "${arg}" = "dist" ] ; then
+        elif [[ "${arg}" == "dist" ]] ; then
             mvn_args="verify"
 
-        elif [ "${arg}" = "test.compile" ] ; then
+        elif [[ "${arg}" == "test.compile" ]] ; then
             mvn_args="test-compile"
 
-        elif [ "${arg}" = "gatkdocs" ] ; then
+        elif [[ "${arg}" == "gatkdocs" ]] ; then
             local_repo="sitetemprepo"
             mvn_args="install -Dmaven.repo.local=${local_repo} -Ddisable.queue && mvn site -Dmaven.repo.local=${local_repo} -Ddisable.queue"
 
-        elif [ "${arg}" = "package.gatk.full" ] ; then
+        elif [[ "${arg}" == "package.gatk.full" ]] ; then
             mvn_args="package '-P!private,!queue'"
 
-        elif [ "${arg}" = "package.gatk.all" ] ; then
+        elif [[ "${arg}" == "package.gatk.all" ]] ; then
             mvn_args="package '-P!queue'"
 
-        elif [ "${arg}" = "package.queue.full" ] ; then
+        elif [[ "${arg}" == "package.queue.full" ]] ; then
             mvn_args="package '-P!private'"
 
-        elif [ "${arg}" = "package.queue.all" ] ; then
+        elif [[ "${arg}" == "package.queue.all" ]] ; then
             mvn_args="package"
 
-        elif [ "${arg}" = "release.gatk.full" ] ; then
+        elif [[ "${arg}" == "release.gatk.full" ]] ; then
             mvn_args="package '-P!private,!queue'"
             post_script=" && private/src/main/scripts/shell/copy_release.sh public/gatk-package/target/GenomeAnalysisTK-*.tar.bz2"
 
-        elif [ "${arg}" = "release.queue.full" ] ; then
+        elif [[ "${arg}" == "release.queue.full" ]] ; then
             mvn_args="package '-P!private'"
             post_script=" && private/src/main/scripts/shell/copy_release.sh public/queue-package/target/Queue-*.tar.bz2"
 
-        elif [ "${arg}" = "build-picard-private" ] ; then
+        elif [[ "${arg}" == "build-picard-private" ]] ; then
             mvn_args="mvn install -f private/picard-maven/pom.xml"
 
         # TODO: clover support
@@ -81,14 +85,14 @@ for arg in "${@}" ; do
         #  https://confluence.atlassian.com/display/CLOVER/1.+QuickStart+Guide
         #  https://confluence.atlassian.com/display/CLOVER/Clover-for-Maven+2+and+3+User%27s+Guide
         #
-        #elif [ "${arg}" = "clover.report" ] ; then
+        #elif [[ "${arg}" == "clover.report" ]] ; then
         #    mvn_args=...
         #
-        #elif [ "${arg}" = "with.clover" ] ; then
+        #elif [[ "${arg}" == "with.clover" ]] ; then
         #    mvn_args=...
 
         # TODO: This runs *all* commit tests, including the few on Queue.
-        elif [ "${arg}" = "gatkfull.binary.release.tests" ] ; then
+        elif [[ "${arg}" == "gatkfull.binary.release.tests" ]] ; then
             local_repo="sitetemprepo"
             mvn_args="install -Dmaven.repo.local=${local_repo} && mvn verify"
             mvn_args="${mvn_args} -Dmaven.repo.local=${local_repo} -Dmaven.javadoc.skip=true"
@@ -97,7 +101,7 @@ for arg in "${@}" ; do
             mvn_args="${mvn_args} -Dsting.packagecommittests.skipped=false"
 
         # TODO: This runs only the pipeline tests (full, non-dry run), but not the commit tests for Queue.
-        elif [ "${arg}" = "queuefull.binary.release.tests" ] ; then
+        elif [[ "${arg}" == "queuefull.binary.release.tests" ]] ; then
             local_repo="sitetemprepo"
             mvn_args="install -Dmaven.repo.local=${local_repo} && mvn verify"
             mvn_args="${mvn_args} -Dmaven.repo.local=${local_repo} -Dmaven.javadoc.skip=true"
@@ -106,28 +110,28 @@ for arg in "${@}" ; do
             mvn_args="${mvn_args} -Dsting.packagepipelinetests.skipped=false"
             mvn_args="${mvn_args} -Dsting.pipelinetests.run=true"
 
-        elif [ "${arg}" = "committests" ] ; then
+        elif [[ "${arg}" == "committests" ]] ; then
             mvn_args="verify -Dsting.committests.skipped=false"
 
-        elif [ "${arg}" = "test" ] ; then
+        elif [[ "${arg}" == "test" ]] ; then
             mvn_args="test -Dsting.unittests.skipped=false"
 
-        elif [ "${arg}" = "unittest" ] ; then
+        elif [[ "${arg}" == "unittest" ]] ; then
             mvn_args="test -Dsting.unittests.skipped=false"
 
-        elif [ "${arg}" = "integrationtest" ] ; then
+        elif [[ "${arg}" == "integrationtest" ]] ; then
             mvn_args="verify -Dsting.integrationtests.skipped=false"
 
-        elif [ "${arg}" = "largescaletest" ] ; then
+        elif [[ "${arg}" == "largescaletest" ]] ; then
             mvn_args="verify -Dsting.largescaletests.skipped=false"
 
-        elif [ "${arg}" = "pipelinetest" ] ; then
+        elif [[ "${arg}" == "pipelinetest" ]] ; then
             mvn_args="verify -Dsting.pipelinetests.skipped=false"
 
-        elif [ "${arg}" = "pipelinetestrun" ] ; then
+        elif [[ "${arg}" == "pipelinetestrun" ]] ; then
             mvn_args="verify -Dsting.pipelinetests.skipped=false -Dsting.pipelinetests.run=true"
 
-        elif [ "${arg}" = "fasttest" ] ; then
+        elif [[ "${arg}" == "fasttest" ]] ; then
             mvn_args="verify -Dsting.committests.skipped=false -pl private/gatk-private -am -Dresource.bundle.skip=true"
 
         else
@@ -140,8 +144,8 @@ for arg in "${@}" ; do
 done
 
 mvn_cmd=
-if [ "${mvn_clean}" != "" ]; then
-    if [ "${mvn_args}" != "" ]; then
+if [[ "${mvn_clean}" != "" ]] ; then
+    if [[ "${mvn_args}" != "" ]] ; then
       mvn_cmd="mvn ${mvn_clean} && mvn ${mvn_args}"
     else
       mvn_cmd="mvn ${mvn_clean}"
@@ -150,12 +154,15 @@ else
     mvn_cmd="mvn ${mvn_args}"
 fi
 
-if [ "${unknown_args}" != "" ]; then
+if [[ "${unknown_args}" != "" ]] ; then
     echo "Unrecognized arguments:${unknown_args}" >&2
 
 else
     echo "Equivalent maven command"
     echo "${mvn_cmd}${mvn_properties}${post_script}"
-    sh -c "${mvn_cmd}${mvn_properties}${post_script}"
+
+    if [[ "${run_type}" != "dry" ]] ; then
+        sh -c "${mvn_cmd}${mvn_properties}${post_script}"
+    fi
 
 fi

From 5ab0b117d2e581704401f2dbf0c063dbdc1caa24 Mon Sep 17 00:00:00 2001
From: Khalid Shakir <kshakir@broadinstitute.org>
Date: Sat, 1 Feb 2014 18:34:40 +0800
Subject: [PATCH 14/16] Re-split the invoked integration tests and verify into
 separate phases.

---
 pom.xml | 21 ++++++++++++++++++---
 1 file changed, 18 insertions(+), 3 deletions(-)

diff --git a/pom.xml b/pom.xml
index 0e1720c41..0f2885b50 100644
--- a/pom.xml
+++ b/pom.xml
@@ -542,6 +542,14 @@
                             <maven.surefire.debug>${maven.surefire.debug}</maven.surefire.debug>
                             <maven.failsafe.debug>${maven.failsafe.debug}</maven.failsafe.debug>
                         </properties>
+                        <!--
+                        To allow using separated integration-test and verify, each execution must use a separate reportsDirectory.
+
+                        Otherwise, when an empty "pipeline test" later runs on an IntegrationTest class,
+                        it overwrites the results of the previous invocation always with a zero exit status.
+
+                        Mixing in the test name into the reportsDirectory also avoids collisions, when different maven jobs run tests in parallel.
+                        -->
                     </configuration>
                     <executions>
                         <execution>
@@ -553,6 +561,7 @@
                                 <goals>
                                     <goal>test</goal>
                                 </goals>
+                                <reportsDirectory>${project.build.directory}/invoker-reports/unit/${test}</reportsDirectory>
                                 <skipInvocation>${sting.packageunittests.skipped}</skipInvocation>
                                 <properties>
                                     <unittests.profile.enabled>true</unittests.profile.enabled>
@@ -563,12 +572,14 @@
                         <execution>
                             <id>package-integrationtests</id>
                             <goals>
-                                <goal>run</goal>
+                                <goal>integration-test</goal>
+                                <goal>verify</goal>
                             </goals>
                             <configuration>
                                 <goals>
                                     <goal>verify</goal>
                                 </goals>
+                                <reportsDirectory>${project.build.directory}/invoker-reports/integration/${it.test}</reportsDirectory>
                                 <skipInvocation>${sting.packageintegrationtests.skipped}</skipInvocation>
                                 <properties>
                                     <integrationtests.profile.enabled>true</integrationtests.profile.enabled>
@@ -579,12 +590,14 @@
                         <execution>
                             <id>package-pipelinetests</id>
                             <goals>
-                                <goal>run</goal>
+                                <goal>integration-test</goal>
+                                <goal>verify</goal>
                             </goals>
                             <configuration>
                                 <goals>
                                     <goal>verify</goal>
                                 </goals>
+                                <reportsDirectory>${project.build.directory}/invoker-reports/pipeline/${it.test}</reportsDirectory>
                                 <skipInvocation>${sting.packagepipelinetests.skipped}</skipInvocation>
                                 <properties>
                                     <integrationtests.profile.enabled>true</integrationtests.profile.enabled>
@@ -595,12 +608,14 @@
                         <execution>
                             <id>package-largescaletests</id>
                             <goals>
-                                <goal>run</goal>
+                                <goal>integration-test</goal>
+                                <goal>verify</goal>
                             </goals>
                             <configuration>
                                 <goals>
                                     <goal>verify</goal>
                                 </goals>
+                                <reportsDirectory>${project.build.directory}/invoker-reports/largescale/${it.test}</reportsDirectory>
                                 <skipInvocation>${sting.packagelargescaletests.skipped}</skipInvocation>
                                 <properties>
                                     <integrationtests.profile.enabled>true</integrationtests.profile.enabled>

From a4289711e20d2f411a00c64f786b431596487779 Mon Sep 17 00:00:00 2001
From: Khalid Shakir <kshakir@broadinstitute.org>
Date: Sat, 1 Feb 2014 19:58:49 +0800
Subject: [PATCH 15/16] Distinct failsafe summary reports, just like invoker
 report directories.

---
 pom.xml                      | 5 +++++
 public/package-tests/pom.xml | 2 ++
 2 files changed, 7 insertions(+)

diff --git a/pom.xml b/pom.xml
index 0f2885b50..60b19f1b2 100644
--- a/pom.xml
+++ b/pom.xml
@@ -549,6 +549,8 @@
                         it overwrites the results of the previous invocation always with a zero exit status.
 
                         Mixing in the test name into the reportsDirectory also avoids collisions, when different maven jobs run tests in parallel.
+
+                        Similarly generating unique failsafe summary reports to avoid collisions.
                         -->
                     </configuration>
                     <executions>
@@ -584,6 +586,7 @@
                                 <properties>
                                     <integrationtests.profile.enabled>true</integrationtests.profile.enabled>
                                     <sting.packageintegrationtests.skipped>${sting.packageintegrationtests.skipped}</sting.packageintegrationtests.skipped>
+                                    <failsafe.summaryFile>${project.build.directory}/failsafe-reports/integration/failsafe-summary-${it.test}.xml</failsafe.summaryFile>
                                 </properties>
                             </configuration>
                         </execution>
@@ -602,6 +605,7 @@
                                 <properties>
                                     <integrationtests.profile.enabled>true</integrationtests.profile.enabled>
                                     <sting.packagepipelinetests.skipped>${sting.packagepipelinetests.skipped}</sting.packagepipelinetests.skipped>
+                                    <failsafe.summaryFile>${project.build.directory}/failsafe-reports/pipeline/failsafe-summary-${it.test}.xml</failsafe.summaryFile>
                                 </properties>
                             </configuration>
                         </execution>
@@ -620,6 +624,7 @@
                                 <properties>
                                     <integrationtests.profile.enabled>true</integrationtests.profile.enabled>
                                     <sting.packagelargescaletests.skipped>${sting.packagelargescaletests.skipped}</sting.packagelargescaletests.skipped>
+                                    <failsafe.summaryFile>${project.build.directory}/failsafe-reports/largescale/failsafe-summary-${it.test}.xml</failsafe.summaryFile>
                                 </properties>
                             </configuration>
                         </execution>
diff --git a/public/package-tests/pom.xml b/public/package-tests/pom.xml
index 5e3269d0f..62a1d570b 100644
--- a/public/package-tests/pom.xml
+++ b/public/package-tests/pom.xml
@@ -23,6 +23,7 @@
         <sting.packageintegrationtests.skipped>true</sting.packageintegrationtests.skipped>
         <sting.packagepipelinetests.skipped>true</sting.packagepipelinetests.skipped>
         <sting.packagelargescaletests.skipped>true</sting.packagelargescaletests.skipped>
+        <failsafe.summaryFile>${project.build.directory}/failsafe-reports/failsafe-summary.xml</failsafe.summaryFile>
     </properties>
 
     <!-- Dependency configuration (versions, etc.) -->
@@ -135,6 +136,7 @@
                             <workingDirectory>${sting.packagetests.basedir}</workingDirectory>
                             <classesDirectory>${project.build.outputDirectory}/ignored_by_package_test</classesDirectory>
                             <testClassesDirectory>${sting.packagetests.testClasses}</testClassesDirectory>
+                            <summaryFile>${failsafe.summaryFile}</summaryFile>
                             <dependenciesToScan>
                                 <scan>org.broadinstitute.sting:.*</scan>
                             </dependenciesToScan>

From 60567c8d7ef1b0cf726a86f190af34e1f9d3eddc Mon Sep 17 00:00:00 2001
From: David Roazen <droazen@broadinstitute.org>
Date: Mon, 3 Feb 2014 12:54:20 -0500
Subject: [PATCH 16/16] Minor ant-bridge.sh changes

-add "gatk" target to mimic old "ant gatk" target
-comment out release targets to prevent accidental releases
---
 ant-bridge.sh | 15 +++++++++------
 1 file changed, 9 insertions(+), 6 deletions(-)

diff --git a/ant-bridge.sh b/ant-bridge.sh
index b37cc1822..e76e03930 100755
--- a/ant-bridge.sh
+++ b/ant-bridge.sh
@@ -50,6 +50,9 @@ for arg in "${@}" ; do
         elif [[ "${arg}" == "dist" ]] ; then
             mvn_args="verify"
 
+        elif [[ "${arg}" == "gatk" ]] ; then
+            mvn_args="verify '-P!queue'"
+
         elif [[ "${arg}" == "test.compile" ]] ; then
             mvn_args="test-compile"
 
@@ -69,13 +72,13 @@ for arg in "${@}" ; do
         elif [[ "${arg}" == "package.queue.all" ]] ; then
             mvn_args="package"
 
-        elif [[ "${arg}" == "release.gatk.full" ]] ; then
-            mvn_args="package '-P!private,!queue'"
-            post_script=" && private/src/main/scripts/shell/copy_release.sh public/gatk-package/target/GenomeAnalysisTK-*.tar.bz2"
+#        elif [[ "${arg}" == "release.gatk.full" ]] ; then
+#            mvn_args="package '-P!private,!queue'"
+#            post_script=" && private/src/main/scripts/shell/copy_release.sh public/gatk-package/target/GenomeAnalysisTK-*.tar.bz2"
 
-        elif [[ "${arg}" == "release.queue.full" ]] ; then
-            mvn_args="package '-P!private'"
-            post_script=" && private/src/main/scripts/shell/copy_release.sh public/queue-package/target/Queue-*.tar.bz2"
+#        elif [[ "${arg}" == "release.queue.full" ]] ; then
+#            mvn_args="package '-P!private'"
+#            post_script=" && private/src/main/scripts/shell/copy_release.sh public/queue-package/target/Queue-*.tar.bz2"
 
         elif [[ "${arg}" == "build-picard-private" ]] ; then
             mvn_args="mvn install -f private/picard-maven/pom.xml"