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gatk-3.8
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Removed the intellij files from the root and made an example package for new users. This allows users to start at the same page and then change it as they see fit without interfering with the repo (thanks guillermo!)

This commit is contained in:
Mauricio Carneiro 2012-09-27 11:04:56 -04:00
parent b9dab068ee
commit 3e68fee764
17 changed files with 0 additions and 310 deletions
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1
.idea/.name
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cmi-gatk

15
.idea/ant.xml
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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
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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
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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
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<component name="CopyrightManager">
<settings default="">
<module2copyright />
</settings>
</component>

5
.idea/encodings.xml
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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
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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
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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
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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>

12
.idea/libraries/GATK_libraries.xml
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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" />
</SOURCES>
<jarDirectory url="file://$PROJECT_DIR$/lib" recursive="false" />
</library>
</component>

32
.idea/misc.xml
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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" project-jdk-name="1.6" project-jdk-type="JavaSDK">
<output url="file://$PROJECT_DIR$/out" />
</component>
<component name="WebServicesPlugin" addRequiredLibraries="true" />
</project>

9
.idea/modules.xml
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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
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<component name="DependencyValidationManager">
<state>
<option name="SKIP_IMPORT_STATEMENTS" value="false" />
</state>
</component>

125
.idea/uiDesigner.xml
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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
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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>

31
cmi-gatk.iml
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<?xml version="1.0" encoding="UTF-8"?>
<module type="JAVA_MODULE" version="4">
<component name="FacetManager">
<facet type="scala" name="Scala">
<configuration>
<option name="compilerLibraryLevel" value="Project" />
<option name="compilerLibraryName" value="GATK libraries" />
</configuration>
</facet>
</component>
<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="GATK libraries" level="project" />
</component>
</module>

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intellij_example.tar.bz2 100644
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