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Adding default intellij configuration files

This commit is contained in:
Mauricio Carneiro 2012-09-24 16:15:57 -04:00
parent 7cf9911924
commit ca84586443
17 changed files with 689 additions and 0 deletions
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1
.idea/.name 100644
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cmi-gatk

15
.idea/ant.xml 100644
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<?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>

13
.idea/codeStyleSettings.xml 100644
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<?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>

21
.idea/compiler.xml 100644
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<?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>

5
.idea/copyright/profiles_settings.xml 100644
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<component name="CopyrightManager">
<settings default="">
<module2copyright />
</settings>
</component>

5
.idea/encodings.xml 100644
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<?xml version="1.0" encoding="UTF-8"?>
<project version="4">
<component name="Encoding" useUTFGuessing="true" native2AsciiForPropertiesFiles="false" />
</project>

8
.idea/highlighting.xml 100644
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<?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>

11
.idea/inspectionProfiles/Project_Default.xml 100644
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<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>

7
.idea/inspectionProfiles/profiles_settings.xml 100644
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<component name="InspectionProjectProfileManager">
<settings>
<option name="PROJECT_PROFILE" value="Project Default" />
<option name="USE_PROJECT_PROFILE" value="true" />
<version value="1.0" />
</settings>
</component>

13
.idea/libraries/GATK_libraries.xml 100644
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<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>

32
.idea/misc.xml 100644
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<?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>

9
.idea/modules.xml 100644
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<?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>

5
.idea/scopes/scope_settings.xml 100644
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<component name="DependencyValidationManager">
<state>
<option name="SKIP_IMPORT_STATEMENTS" value="false" />
</state>
</component>

125
.idea/uiDesigner.xml 100644
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<?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>

10
.idea/vcs.xml 100644
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<?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>

386
.idea/workspace.xml 100644
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<?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">
<state line="234" column="40" selection-start="10480" selection-end="10480" vertical-scroll-proportion="0.40685225">
<folding />
</state>
</provider>
</entry>
</file>
<file leaf-file-name="QScriptUtils.scala" pinned="false" current="false" current-in-tab="false">
<entry file="file://$PROJECT_DIR$/public/scala/src/org/broadinstitute/sting/queue/util/QScriptUtils.scala">
<provider selected="true" editor-type-id="text-editor">
<state line="46" column="6" selection-start="1607" selection-end="1607" vertical-scroll-proportion="0.0">
<folding />
</state>
</provider>
</entry>
</file>
</leaf>
</component>
<component name="Git.Settings">
<option name="RECENT_GIT_ROOT_PATH" value="$PROJECT_DIR$" />
</component>
<component name="ProjectFrameBounds">
<option name="x" value="-1200" />
<option name="y" value="-870" />
<option name="width" value="1200" />
<option name="height" value="1562" />
</component>
<component name="ProjectLevelVcsManager" settingsEditedManually="false">
<OptionsSetting value="true" id="Add" />
<OptionsSetting value="true" id="Remove" />
<OptionsSetting value="true" id="Checkout" />
<OptionsSetting value="true" id="Update" />
<OptionsSetting value="true" id="Status" />
<OptionsSetting value="true" id="Edit" />
<ConfirmationsSetting value="0" id="Add" />
<ConfirmationsSetting value="0" id="Remove" />
</component>
<component name="ProjectReloadState">
<option name="STATE" value="0" />
</component>
<component name="ProjectView">
<navigator currentView="ProjectPane" proportions="" version="1" splitterProportion="0.5">
<flattenPackages />
<showMembers />
<showModules />
<showLibraryContents />
<hideEmptyPackages />
<abbreviatePackageNames />
<autoscrollToSource />
<autoscrollFromSource />
<sortByType />
</navigator>
<panes>
<pane id="PackagesPane">
<subPane>
<PATH>
<PATH_ELEMENT>
<option name="myItemId" value="cmi-gatk" />
<option name="myItemType" value="com.intellij.ide.projectView.impl.nodes.PackageViewProjectNode" />
</PATH_ELEMENT>
<PATH_ELEMENT>
<option name="myItemId" value="cmi-gatk" />
<option name="myItemType" value="com.intellij.ide.projectView.impl.nodes.PackageViewModuleNode" />
</PATH_ELEMENT>
</PATH>
</subPane>
</pane>
<pane id="ProjectPane">
<subPane>
<PATH>
<PATH_ELEMENT>
<option name="myItemId" value="cmi-gatk" />
<option name="myItemType" value="com.intellij.ide.projectView.impl.nodes.ProjectViewProjectNode" />
</PATH_ELEMENT>
</PATH>
</subPane>
</pane>
<pane id="Scope" />
</panes>
</component>
<component name="PropertiesComponent">
<property name="GoToFile.includeJavaFiles" value="false" />
<property name="project.structure.last.edited" value="Modules" />
<property name="project.structure.proportion" value="0.15" />
<property name="options.splitter.main.proportions" value="0.3" />
<property name="MemberChooser.sorted" value="false" />
<property name="options.lastSelected" value="project.propVCSSupport.VCSs.Git" />
<property name="project.structure.side.proportion" value="0.0" />
<property name="GoToClass.includeJavaFiles" value="false" />
<property name="MemberChooser.copyJavadoc" value="false" />
<property name="GoToClass.toSaveIncludeLibraries" value="false" />
<property name="FullScreen" value="false" />
<property name="MemberChooser.showClasses" value="true" />
<property name="GoToClass.includeLibraries" value="false" />
<property name="options.searchVisible" value="true" />
<property name="options.splitter.details.proportions" value="0.2" />
</component>
<component name="RunManager">
<configuration default="true" type="Remote" factoryName="Remote">
<option name="USE_SOCKET_TRANSPORT" value="true" />
<option name="SERVER_MODE" value="false" />
<option name="SHMEM_ADDRESS" value="javadebug" />
<option name="HOST" value="localhost" />
<option name="PORT" value="5005" />
<method>
<option name="AntTarget" enabled="false" />
<option name="BuildArtifacts" enabled="false" />
</method>
</configuration>
<configuration default="true" type="Applet" factoryName="Applet">
<module name="" />
<option name="MAIN_CLASS_NAME" />
<option name="HTML_FILE_NAME" />
<option name="HTML_USED" value="false" />
<option name="WIDTH" value="400" />
<option name="HEIGHT" value="300" />
<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" />
</method>
</configuration>
<list size="0" />
<configuration name="&lt;template&gt;" type="JUnit" default="true" selected="false">
<option name="MAIN_CLASS_NAME" />
<option name="VM_PARAMETERS" value="-ea" />
<option name="PARAMETERS" />
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<last-edited>cmi-gatk</last-edited>
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23
cmi-gatk.iml 100644
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@ -0,0 +1,23 @@
<?xml version="1.0" encoding="UTF-8"?>
<module type="JAVA_MODULE" version="4">
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