From ca8458644371eb47596a22a385b92679924a9b33 Mon Sep 17 00:00:00 2001
From: Mauricio Carneiro <carneiro@broadinstitute.org>
Date: Mon, 24 Sep 2012 16:15:57 -0400
Subject: [PATCH] Adding default intellij configuration files

---
 .idea/.name                                   |   1 +
 .idea/ant.xml                                 |  15 +
 .idea/codeStyleSettings.xml                   |  13 +
 .idea/compiler.xml                            |  21 +
 .idea/copyright/profiles_settings.xml         |   5 +
 .idea/encodings.xml                           |   5 +
 .idea/highlighting.xml                        |   8 +
 .idea/inspectionProfiles/Project_Default.xml  |  11 +
 .../inspectionProfiles/profiles_settings.xml  |   7 +
 .idea/libraries/GATK_libraries.xml            |  13 +
 .idea/misc.xml                                |  32 ++
 .idea/modules.xml                             |   9 +
 .idea/scopes/scope_settings.xml               |   5 +
 .idea/uiDesigner.xml                          | 125 ++++++
 .idea/vcs.xml                                 |  10 +
 .idea/workspace.xml                           | 386 ++++++++++++++++++
 cmi-gatk.iml                                  |  23 ++
 17 files changed, 689 insertions(+)
 create mode 100644 .idea/.name
 create mode 100644 .idea/ant.xml
 create mode 100644 .idea/codeStyleSettings.xml
 create mode 100644 .idea/compiler.xml
 create mode 100644 .idea/copyright/profiles_settings.xml
 create mode 100644 .idea/encodings.xml
 create mode 100644 .idea/highlighting.xml
 create mode 100644 .idea/inspectionProfiles/Project_Default.xml
 create mode 100644 .idea/inspectionProfiles/profiles_settings.xml
 create mode 100644 .idea/libraries/GATK_libraries.xml
 create mode 100644 .idea/misc.xml
 create mode 100644 .idea/modules.xml
 create mode 100644 .idea/scopes/scope_settings.xml
 create mode 100644 .idea/uiDesigner.xml
 create mode 100644 .idea/vcs.xml
 create mode 100644 .idea/workspace.xml
 create mode 100644 cmi-gatk.iml

diff --git a/.idea/.name b/.idea/.name
new file mode 100644
index 000000000..7014f65a5
--- /dev/null
+++ b/.idea/.name
@@ -0,0 +1 @@
+cmi-gatk
\ No newline at end of file
diff --git a/.idea/ant.xml b/.idea/ant.xml
new file mode 100644
index 000000000..4674eeac9
--- /dev/null
+++ b/.idea/ant.xml
@@ -0,0 +1,15 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+  <component name="AntConfiguration">
+    <defaultAnt bundledAnt="true" />
+    <buildFile url="file://$PROJECT_DIR$/build.xml">
+      <additionalClassPath />
+      <antReference projectDefault="true" />
+      <customJdkName value="" />
+      <maximumHeapSize value="128" />
+      <maximumStackSize value="2" />
+      <properties />
+    </buildFile>
+  </component>
+</project>
+
diff --git a/.idea/codeStyleSettings.xml b/.idea/codeStyleSettings.xml
new file mode 100644
index 000000000..9178b389f
--- /dev/null
+++ b/.idea/codeStyleSettings.xml
@@ -0,0 +1,13 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+  <component name="ProjectCodeStyleSettingsManager">
+    <option name="PER_PROJECT_SETTINGS">
+      <value>
+        <XML>
+          <option name="XML_LEGACY_SETTINGS_IMPORTED" value="true" />
+        </XML>
+      </value>
+    </option>
+  </component>
+</project>
+
diff --git a/.idea/compiler.xml b/.idea/compiler.xml
new file mode 100644
index 000000000..ded2e9a1d
--- /dev/null
+++ b/.idea/compiler.xml
@@ -0,0 +1,21 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+  <component name="CompilerConfiguration">
+    <option name="DEFAULT_COMPILER" value="Javac" />
+    <resourceExtensions />
+    <wildcardResourcePatterns>
+      <entry name="?*.properties" />
+      <entry name="?*.xml" />
+      <entry name="?*.gif" />
+      <entry name="?*.png" />
+      <entry name="?*.jpeg" />
+      <entry name="?*.jpg" />
+      <entry name="?*.html" />
+      <entry name="?*.dtd" />
+      <entry name="?*.tld" />
+      <entry name="?*.ftl" />
+    </wildcardResourcePatterns>
+    <annotationProcessing enabled="true" useClasspath="true" />
+  </component>
+</project>
+
diff --git a/.idea/copyright/profiles_settings.xml b/.idea/copyright/profiles_settings.xml
new file mode 100644
index 000000000..3572571ad
--- /dev/null
+++ b/.idea/copyright/profiles_settings.xml
@@ -0,0 +1,5 @@
+<component name="CopyrightManager">
+  <settings default="">
+    <module2copyright />
+  </settings>
+</component>
\ No newline at end of file
diff --git a/.idea/encodings.xml b/.idea/encodings.xml
new file mode 100644
index 000000000..e206d70d8
--- /dev/null
+++ b/.idea/encodings.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+  <component name="Encoding" useUTFGuessing="true" native2AsciiForPropertiesFiles="false" />
+</project>
+
diff --git a/.idea/highlighting.xml b/.idea/highlighting.xml
new file mode 100644
index 000000000..f33b64d94
--- /dev/null
+++ b/.idea/highlighting.xml
@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+  <component name="HighlightingAdvisor">
+    <option name="SUGGEST_TYPE_AWARE_HIGHLIGHTING" value="false" />
+    <option name="TYPE_AWARE_HIGHLIGHTING_ENABLED" value="true" />
+  </component>
+</project>
+
diff --git a/.idea/inspectionProfiles/Project_Default.xml b/.idea/inspectionProfiles/Project_Default.xml
new file mode 100644
index 000000000..b8c243dbe
--- /dev/null
+++ b/.idea/inspectionProfiles/Project_Default.xml
@@ -0,0 +1,11 @@
+<component name="InspectionProjectProfileManager">
+  <profile version="1.0" is_locked="false">
+    <option name="myName" value="Project Default" />
+    <option name="myLocal" value="false" />
+    <inspection_tool class="SpellCheckingInspection" enabled="false" level="TYPO" enabled_by_default="false">
+      <option name="processCode" value="true" />
+      <option name="processLiterals" value="false" />
+      <option name="processComments" value="true" />
+    </inspection_tool>
+  </profile>
+</component>
\ No newline at end of file
diff --git a/.idea/inspectionProfiles/profiles_settings.xml b/.idea/inspectionProfiles/profiles_settings.xml
new file mode 100644
index 000000000..3b312839b
--- /dev/null
+++ b/.idea/inspectionProfiles/profiles_settings.xml
@@ -0,0 +1,7 @@
+<component name="InspectionProjectProfileManager">
+  <settings>
+    <option name="PROJECT_PROFILE" value="Project Default" />
+    <option name="USE_PROJECT_PROFILE" value="true" />
+    <version value="1.0" />
+  </settings>
+</component>
\ No newline at end of file
diff --git a/.idea/libraries/GATK_libraries.xml b/.idea/libraries/GATK_libraries.xml
new file mode 100644
index 000000000..970d0a3dc
--- /dev/null
+++ b/.idea/libraries/GATK_libraries.xml
@@ -0,0 +1,13 @@
+<component name="libraryTable">
+  <library name="GATK libraries">
+    <CLASSES>
+      <root url="file://$PROJECT_DIR$/lib" />
+    </CLASSES>
+    <JAVADOC />
+    <SOURCES>
+      <root url="file://$PROJECT_DIR$/../../picard/src/java" />
+      <root url="jar:///Library/Java/JavaVirtualMachines/1.6.0_31-b04-411.jdk/Contents/Home/src.jar!/src" />
+    </SOURCES>
+    <jarDirectory url="file://$PROJECT_DIR$/lib" recursive="false" />
+  </library>
+</component>
\ No newline at end of file
diff --git a/.idea/misc.xml b/.idea/misc.xml
new file mode 100644
index 000000000..afd7f3778
--- /dev/null
+++ b/.idea/misc.xml
@@ -0,0 +1,32 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+  <component name="EntryPointsManager">
+    <entry_points version="2.0" />
+  </component>
+  <component name="IdProvider" IDEtalkID="1AD151C138300C50536BAE046D66308C" />
+  <component name="JavadocGenerationManager">
+    <option name="OUTPUT_DIRECTORY" />
+    <option name="OPTION_SCOPE" value="protected" />
+    <option name="OPTION_HIERARCHY" value="true" />
+    <option name="OPTION_NAVIGATOR" value="true" />
+    <option name="OPTION_INDEX" value="true" />
+    <option name="OPTION_SEPARATE_INDEX" value="true" />
+    <option name="OPTION_DOCUMENT_TAG_USE" value="false" />
+    <option name="OPTION_DOCUMENT_TAG_AUTHOR" value="false" />
+    <option name="OPTION_DOCUMENT_TAG_VERSION" value="false" />
+    <option name="OPTION_DOCUMENT_TAG_DEPRECATED" value="true" />
+    <option name="OPTION_DEPRECATED_LIST" value="true" />
+    <option name="OTHER_OPTIONS" value="" />
+    <option name="HEAP_SIZE" />
+    <option name="LOCALE" />
+    <option name="OPEN_IN_BROWSER" value="true" />
+  </component>
+  <component name="ProjectResources">
+    <default-html-doctype>http://www.w3.org/1999/xhtml</default-html-doctype>
+  </component>
+  <component name="ProjectRootManager" version="2" languageLevel="JDK_1_6" assert-keyword="true" jdk-15="true">
+    <output url="file://$PROJECT_DIR$/out" />
+  </component>
+  <component name="WebServicesPlugin" addRequiredLibraries="true" />
+</project>
+
diff --git a/.idea/modules.xml b/.idea/modules.xml
new file mode 100644
index 000000000..09caa2933
--- /dev/null
+++ b/.idea/modules.xml
@@ -0,0 +1,9 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+  <component name="ProjectModuleManager">
+    <modules>
+      <module fileurl="file://$PROJECT_DIR$/cmi-gatk.iml" filepath="$PROJECT_DIR$/cmi-gatk.iml" />
+    </modules>
+  </component>
+</project>
+
diff --git a/.idea/scopes/scope_settings.xml b/.idea/scopes/scope_settings.xml
new file mode 100644
index 000000000..922003b84
--- /dev/null
+++ b/.idea/scopes/scope_settings.xml
@@ -0,0 +1,5 @@
+<component name="DependencyValidationManager">
+  <state>
+    <option name="SKIP_IMPORT_STATEMENTS" value="false" />
+  </state>
+</component>
\ No newline at end of file
diff --git a/.idea/uiDesigner.xml b/.idea/uiDesigner.xml
new file mode 100644
index 000000000..3b0002030
--- /dev/null
+++ b/.idea/uiDesigner.xml
@@ -0,0 +1,125 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+  <component name="Palette2">
+    <group name="Swing">
+      <item class="com.intellij.uiDesigner.HSpacer" tooltip-text="Horizontal Spacer" icon="/com/intellij/uiDesigner/icons/hspacer.png" removable="false" auto-create-binding="false" can-attach-label="false">
+        <default-constraints vsize-policy="1" hsize-policy="6" anchor="0" fill="1" />
+      </item>
+      <item class="com.intellij.uiDesigner.VSpacer" tooltip-text="Vertical Spacer" icon="/com/intellij/uiDesigner/icons/vspacer.png" removable="false" auto-create-binding="false" can-attach-label="false">
+        <default-constraints vsize-policy="6" hsize-policy="1" anchor="0" fill="2" />
+      </item>
+      <item class="javax.swing.JPanel" icon="/com/intellij/uiDesigner/icons/panel.png" removable="false" auto-create-binding="false" can-attach-label="false">
+        <default-constraints vsize-policy="3" hsize-policy="3" anchor="0" fill="3" />
+      </item>
+      <item class="javax.swing.JScrollPane" icon="/com/intellij/uiDesigner/icons/scrollPane.png" removable="false" auto-create-binding="false" can-attach-label="true">
+        <default-constraints vsize-policy="7" hsize-policy="7" anchor="0" fill="3" />
+      </item>
+      <item class="javax.swing.JButton" icon="/com/intellij/uiDesigner/icons/button.png" removable="false" auto-create-binding="true" can-attach-label="false">
+        <default-constraints vsize-policy="0" hsize-policy="3" anchor="0" fill="1" />
+        <initial-values>
+          <property name="text" value="Button" />
+        </initial-values>
+      </item>
+      <item class="javax.swing.JRadioButton" icon="/com/intellij/uiDesigner/icons/radioButton.png" removable="false" auto-create-binding="true" can-attach-label="false">
+        <default-constraints vsize-policy="0" hsize-policy="3" anchor="8" fill="0" />
+        <initial-values>
+          <property name="text" value="RadioButton" />
+        </initial-values>
+      </item>
+      <item class="javax.swing.JCheckBox" icon="/com/intellij/uiDesigner/icons/checkBox.png" removable="false" auto-create-binding="true" can-attach-label="false">
+        <default-constraints vsize-policy="0" hsize-policy="3" anchor="8" fill="0" />
+        <initial-values>
+          <property name="text" value="CheckBox" />
+        </initial-values>
+      </item>
+      <item class="javax.swing.JLabel" icon="/com/intellij/uiDesigner/icons/label.png" removable="false" auto-create-binding="false" can-attach-label="false">
+        <default-constraints vsize-policy="0" hsize-policy="0" anchor="8" fill="0" />
+        <initial-values>
+          <property name="text" value="Label" />
+        </initial-values>
+      </item>
+      <item class="javax.swing.JTextField" icon="/com/intellij/uiDesigner/icons/textField.png" removable="false" auto-create-binding="true" can-attach-label="true">
+        <default-constraints vsize-policy="0" hsize-policy="6" anchor="8" fill="1">
+          <preferred-size width="150" height="-1" />
+        </default-constraints>
+      </item>
+      <item class="javax.swing.JPasswordField" icon="/com/intellij/uiDesigner/icons/passwordField.png" removable="false" auto-create-binding="true" can-attach-label="true">
+        <default-constraints vsize-policy="0" hsize-policy="6" anchor="8" fill="1">
+          <preferred-size width="150" height="-1" />
+        </default-constraints>
+      </item>
+      <item class="javax.swing.JFormattedTextField" icon="/com/intellij/uiDesigner/icons/formattedTextField.png" removable="false" auto-create-binding="true" can-attach-label="true">
+        <default-constraints vsize-policy="0" hsize-policy="6" anchor="8" fill="1">
+          <preferred-size width="150" height="-1" />
+        </default-constraints>
+      </item>
+      <item class="javax.swing.JTextArea" icon="/com/intellij/uiDesigner/icons/textArea.png" removable="false" auto-create-binding="true" can-attach-label="true">
+        <default-constraints vsize-policy="6" hsize-policy="6" anchor="0" fill="3">
+          <preferred-size width="150" height="50" />
+        </default-constraints>
+      </item>
+      <item class="javax.swing.JTextPane" icon="/com/intellij/uiDesigner/icons/textPane.png" removable="false" auto-create-binding="true" can-attach-label="true">
+        <default-constraints vsize-policy="6" hsize-policy="6" anchor="0" fill="3">
+          <preferred-size width="150" height="50" />
+        </default-constraints>
+      </item>
+      <item class="javax.swing.JEditorPane" icon="/com/intellij/uiDesigner/icons/editorPane.png" removable="false" auto-create-binding="true" can-attach-label="true">
+        <default-constraints vsize-policy="6" hsize-policy="6" anchor="0" fill="3">
+          <preferred-size width="150" height="50" />
+        </default-constraints>
+      </item>
+      <item class="javax.swing.JComboBox" icon="/com/intellij/uiDesigner/icons/comboBox.png" removable="false" auto-create-binding="true" can-attach-label="true">
+        <default-constraints vsize-policy="0" hsize-policy="2" anchor="8" fill="1" />
+      </item>
+      <item class="javax.swing.JTable" icon="/com/intellij/uiDesigner/icons/table.png" removable="false" auto-create-binding="true" can-attach-label="false">
+        <default-constraints vsize-policy="6" hsize-policy="6" anchor="0" fill="3">
+          <preferred-size width="150" height="50" />
+        </default-constraints>
+      </item>
+      <item class="javax.swing.JList" icon="/com/intellij/uiDesigner/icons/list.png" removable="false" auto-create-binding="true" can-attach-label="false">
+        <default-constraints vsize-policy="6" hsize-policy="2" anchor="0" fill="3">
+          <preferred-size width="150" height="50" />
+        </default-constraints>
+      </item>
+      <item class="javax.swing.JTree" icon="/com/intellij/uiDesigner/icons/tree.png" removable="false" auto-create-binding="true" can-attach-label="false">
+        <default-constraints vsize-policy="6" hsize-policy="6" anchor="0" fill="3">
+          <preferred-size width="150" height="50" />
+        </default-constraints>
+      </item>
+      <item class="javax.swing.JTabbedPane" icon="/com/intellij/uiDesigner/icons/tabbedPane.png" removable="false" auto-create-binding="true" can-attach-label="false">
+        <default-constraints vsize-policy="3" hsize-policy="3" anchor="0" fill="3">
+          <preferred-size width="200" height="200" />
+        </default-constraints>
+      </item>
+      <item class="javax.swing.JSplitPane" icon="/com/intellij/uiDesigner/icons/splitPane.png" removable="false" auto-create-binding="false" can-attach-label="false">
+        <default-constraints vsize-policy="3" hsize-policy="3" anchor="0" fill="3">
+          <preferred-size width="200" height="200" />
+        </default-constraints>
+      </item>
+      <item class="javax.swing.JSpinner" icon="/com/intellij/uiDesigner/icons/spinner.png" removable="false" auto-create-binding="true" can-attach-label="true">
+        <default-constraints vsize-policy="0" hsize-policy="6" anchor="8" fill="1" />
+      </item>
+      <item class="javax.swing.JSlider" icon="/com/intellij/uiDesigner/icons/slider.png" removable="false" auto-create-binding="true" can-attach-label="false">
+        <default-constraints vsize-policy="0" hsize-policy="6" anchor="8" fill="1" />
+      </item>
+      <item class="javax.swing.JSeparator" icon="/com/intellij/uiDesigner/icons/separator.png" removable="false" auto-create-binding="false" can-attach-label="false">
+        <default-constraints vsize-policy="6" hsize-policy="6" anchor="0" fill="3" />
+      </item>
+      <item class="javax.swing.JProgressBar" icon="/com/intellij/uiDesigner/icons/progressbar.png" removable="false" auto-create-binding="true" can-attach-label="false">
+        <default-constraints vsize-policy="0" hsize-policy="6" anchor="0" fill="1" />
+      </item>
+      <item class="javax.swing.JToolBar" icon="/com/intellij/uiDesigner/icons/toolbar.png" removable="false" auto-create-binding="false" can-attach-label="false">
+        <default-constraints vsize-policy="0" hsize-policy="6" anchor="0" fill="1">
+          <preferred-size width="-1" height="20" />
+        </default-constraints>
+      </item>
+      <item class="javax.swing.JToolBar$Separator" icon="/com/intellij/uiDesigner/icons/toolbarSeparator.png" removable="false" auto-create-binding="false" can-attach-label="false">
+        <default-constraints vsize-policy="0" hsize-policy="0" anchor="0" fill="1" />
+      </item>
+      <item class="javax.swing.JScrollBar" icon="/com/intellij/uiDesigner/icons/scrollbar.png" removable="false" auto-create-binding="true" can-attach-label="false">
+        <default-constraints vsize-policy="6" hsize-policy="0" anchor="0" fill="2" />
+      </item>
+    </group>
+  </component>
+</project>
+
diff --git a/.idea/vcs.xml b/.idea/vcs.xml
new file mode 100644
index 000000000..cbc984988
--- /dev/null
+++ b/.idea/vcs.xml
@@ -0,0 +1,10 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+  <component name="ClearCaseSharedConfig">
+    <option name="myUseUcmModel" value="true" />
+  </component>
+  <component name="VcsDirectoryMappings">
+    <mapping directory="" vcs="Git" />
+  </component>
+</project>
+
diff --git a/.idea/workspace.xml b/.idea/workspace.xml
new file mode 100644
index 000000000..87ab79287
--- /dev/null
+++ b/.idea/workspace.xml
@@ -0,0 +1,386 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+  <component name="ChangeListManager">
+    <list default="true" id="da24b138-3df4-4b46-abff-e428e3df7aee" name="Default" comment="" />
+    <ignored path="gatk.unstable.iws" />
+    <ignored path=".idea/workspace.xml" />
+    <option name="TRACKING_ENABLED" value="true" />
+    <option name="SHOW_DIALOG" value="false" />
+    <option name="HIGHLIGHT_CONFLICTS" value="true" />
+    <option name="HIGHLIGHT_NON_ACTIVE_CHANGELIST" value="false" />
+    <option name="LAST_RESOLUTION" value="IGNORE" />
+  </component>
+  <component name="ChangesViewManager" flattened_view="true" show_ignored="false" />
+  <component name="CreatePatchCommitExecutor">
+    <option name="PATCH_PATH" value="" />
+  </component>
+  <component name="DaemonCodeAnalyzer">
+    <disable_hints />
+  </component>
+  <component name="DebuggerManager">
+    <breakpoint_any>
+      <breakpoint>
+        <option name="NOTIFY_CAUGHT" value="true" />
+        <option name="NOTIFY_UNCAUGHT" value="true" />
+        <option name="ENABLED" value="false" />
+        <option name="LOG_ENABLED" value="false" />
+        <option name="LOG_EXPRESSION_ENABLED" value="false" />
+        <option name="SUSPEND_POLICY" value="SuspendAll" />
+        <option name="COUNT_FILTER_ENABLED" value="false" />
+        <option name="COUNT_FILTER" value="0" />
+        <option name="CONDITION_ENABLED" value="false" />
+        <option name="CLASS_FILTERS_ENABLED" value="false" />
+        <option name="INSTANCE_FILTERS_ENABLED" value="false" />
+        <option name="CONDITION" value="" />
+        <option name="LOG_MESSAGE" value="" />
+      </breakpoint>
+      <breakpoint>
+        <option name="NOTIFY_CAUGHT" value="true" />
+        <option name="NOTIFY_UNCAUGHT" value="true" />
+        <option name="ENABLED" value="false" />
+        <option name="LOG_ENABLED" value="false" />
+        <option name="LOG_EXPRESSION_ENABLED" value="false" />
+        <option name="SUSPEND_POLICY" value="SuspendAll" />
+        <option name="COUNT_FILTER_ENABLED" value="false" />
+        <option name="COUNT_FILTER" value="0" />
+        <option name="CONDITION_ENABLED" value="false" />
+        <option name="CLASS_FILTERS_ENABLED" value="false" />
+        <option name="INSTANCE_FILTERS_ENABLED" value="false" />
+        <option name="CONDITION" value="" />
+        <option name="LOG_MESSAGE" value="" />
+      </breakpoint>
+    </breakpoint_any>
+    <breakpoint_rules />
+    <ui_properties />
+  </component>
+  <component name="FavoritesManager">
+    <favorites_list name="gatk.unstable" />
+  </component>
+  <component name="FileEditorManager">
+    <leaf>
+      <file leaf-file-name="DataProcessingPipeline.scala" pinned="false" current="true" current-in-tab="true">
+        <entry file="file://$PROJECT_DIR$/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala">
+          <provider selected="true" editor-type-id="text-editor">
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+      <abbreviatePackageNames />
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+      <option name="SHMEM_ADDRESS" value="javadebug" />
+      <option name="HOST" value="localhost" />
+      <option name="PORT" value="5005" />
+      <method>
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+        <option name="BuildArtifacts" enabled="false" />
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+    </configuration>
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+      <option name="HTML_FILE_NAME" />
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+      <option name="POLICY_FILE" value="$APPLICATION_HOME_DIR$/bin/appletviewer.policy" />
+      <option name="VM_PARAMETERS" />
+      <option name="ALTERNATIVE_JRE_PATH_ENABLED" value="false" />
+      <option name="ALTERNATIVE_JRE_PATH" />
+      <method>
+        <option name="AntTarget" enabled="false" />
+        <option name="BuildArtifacts" enabled="false" />
+        <option name="Make" enabled="true" />
+      </method>
+    </configuration>
+    <configuration default="true" type="Application" factoryName="Application">
+      <option name="MAIN_CLASS_NAME" />
+      <option name="VM_PARAMETERS" />
+      <option name="PROGRAM_PARAMETERS" />
+      <option name="WORKING_DIRECTORY" value="$PROJECT_DIR$" />
+      <option name="ALTERNATIVE_JRE_PATH_ENABLED" value="false" />
+      <option name="ALTERNATIVE_JRE_PATH" />
+      <option name="ENABLE_SWING_INSPECTOR" value="false" />
+      <option name="ENV_VARIABLES" />
+      <option name="PASS_PARENT_ENVS" value="true" />
+      <module name="" />
+      <envs />
+      <method>
+        <option name="AntTarget" enabled="false" />
+        <option name="BuildArtifacts" enabled="false" />
+        <option name="Make" enabled="true" />
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+    </configuration>
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+      <option name="MAIN_CLASS_NAME" />
+      <option name="VM_PARAMETERS" value="-ea" />
+      <option name="PARAMETERS" />
+      <option name="WORKING_DIRECTORY" value="$PROJECT_DIR$" />
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+    <configuration name="&lt;template&gt;" type="TestNG" default="true" selected="false">
+      <option name="MAIN_CLASS_NAME" />
+      <option name="VM_PARAMETERS" value="-ea" />
+      <option name="PARAMETERS" />
+      <option name="WORKING_DIRECTORY" value="$PROJECT_DIR$" />
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+      <option name="VM_PARAMETERS" value="-Xmx512m -Xms256m -XX:MaxPermSize=250m" />
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+    <configuration name="&lt;template&gt;" type="WebApp" default="true" selected="false">
+      <Host>localhost</Host>
+      <Port>5050</Port>
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+    <option name="PERFORM_ADD_REMOVE_IN_BACKGROUND" value="true" />
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+    <entry file="file://$PROJECT_DIR$/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala">
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+          <folding />
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+      </provider>
+    </entry>
+  </component>
+  <component name="masterDetails">
+    <states>
+      <state key="ArtifactsStructureConfigurable.UI">
+        <settings>
+          <artifact-editor />
+          <splitter-proportions>
+            <option name="proportions">
+              <list>
+                <option value="0.2" />
+              </list>
+            </option>
+          </splitter-proportions>
+        </settings>
+      </state>
+      <state key="GlobalLibrariesConfigurable.UI">
+        <settings>
+          <splitter-proportions>
+            <option name="proportions">
+              <list>
+                <option value="0.2" />
+              </list>
+            </option>
+          </splitter-proportions>
+        </settings>
+      </state>
+      <state key="JdkListConfigurable.UI">
+        <settings>
+          <splitter-proportions>
+            <option name="proportions">
+              <list>
+                <option value="0.2" />
+              </list>
+            </option>
+          </splitter-proportions>
+        </settings>
+      </state>
+      <state key="ModuleStructureConfigurable.UI">
+        <settings>
+          <last-edited>cmi-gatk</last-edited>
+          <splitter-proportions>
+            <option name="proportions">
+              <list>
+                <option value="0.2" />
+                <option value="0.5" />
+              </list>
+            </option>
+          </splitter-proportions>
+        </settings>
+      </state>
+      <state key="ProjectLibrariesConfigurable.UI">
+        <settings>
+          <last-edited>GATK libraries</last-edited>
+          <splitter-proportions>
+            <option name="proportions">
+              <list>
+                <option value="0.2" />
+              </list>
+            </option>
+          </splitter-proportions>
+        </settings>
+      </state>
+    </states>
+  </component>
+</project>
+
diff --git a/cmi-gatk.iml b/cmi-gatk.iml
new file mode 100644
index 000000000..e63aff535
--- /dev/null
+++ b/cmi-gatk.iml
@@ -0,0 +1,23 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<module type="JAVA_MODULE" version="4">
+  <component name="NewModuleRootManager" inherit-compiler-output="true">
+    <exclude-output />
+    <content url="file://$MODULE_DIR$">
+      <sourceFolder url="file://$MODULE_DIR$/public/java/src" isTestSource="false" />
+      <sourceFolder url="file://$MODULE_DIR$/private/java/src" isTestSource="false" />
+      <sourceFolder url="file://$MODULE_DIR$/private/java/test" isTestSource="true" />
+      <sourceFolder url="file://$MODULE_DIR$/public/java/test" isTestSource="true" />
+      <sourceFolder url="file://$MODULE_DIR$/private/scala/src" isTestSource="false" />
+      <sourceFolder url="file://$MODULE_DIR$/public/scala/src" isTestSource="false" />
+      <sourceFolder url="file://$MODULE_DIR$/private/scala/test" isTestSource="true" />
+      <sourceFolder url="file://$MODULE_DIR$/public/scala/test" isTestSource="true" />
+      <sourceFolder url="file://$MODULE_DIR$/build/queue-extensions/src" isTestSource="false" />
+      <sourceFolder url="file://$MODULE_DIR$/protected/java/src" isTestSource="false" />
+      <sourceFolder url="file://$MODULE_DIR$/protected/java/test" isTestSource="true" />
+    </content>
+    <orderEntry type="inheritedJdk" />
+    <orderEntry type="sourceFolder" forTests="false" />
+    <orderEntry type="library" name="lib" level="project" />
+  </component>
+</module>
+