From 29195cd3aab9a47118f71516ce55949b979d9967 Mon Sep 17 00:00:00 2001
From: Mauricio Carneiro <carneiro@broadinstitute.org>
Date: Thu, 27 Sep 2012 11:04:56 -0400
Subject: [PATCH] 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!)

---
 .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            |  12 --
 .idea/misc.xml                                |  32 -----
 .idea/modules.xml                             |   9 --
 .idea/scopes/scope_settings.xml               |   5 -
 .idea/uiDesigner.xml                          | 125 ------------------
 .idea/vcs.xml                                 |  10 --
 cmi-gatk.iml                                  |  31 -----
 16 files changed, 310 deletions(-)
 delete mode 100644 .idea/.name
 delete mode 100644 .idea/ant.xml
 delete mode 100644 .idea/codeStyleSettings.xml
 delete mode 100644 .idea/compiler.xml
 delete mode 100644 .idea/copyright/profiles_settings.xml
 delete mode 100644 .idea/encodings.xml
 delete mode 100644 .idea/highlighting.xml
 delete mode 100644 .idea/inspectionProfiles/Project_Default.xml
 delete mode 100644 .idea/inspectionProfiles/profiles_settings.xml
 delete mode 100644 .idea/libraries/GATK_libraries.xml
 delete mode 100644 .idea/misc.xml
 delete mode 100644 .idea/modules.xml
 delete mode 100644 .idea/scopes/scope_settings.xml
 delete mode 100644 .idea/uiDesigner.xml
 delete mode 100644 .idea/vcs.xml
 delete mode 100644 cmi-gatk.iml

diff --git a/.idea/.name b/.idea/.name
deleted file mode 100644
index 7014f65a5..000000000
--- a/.idea/.name
+++ /dev/null
@@ -1 +0,0 @@
-cmi-gatk
\ No newline at end of file
diff --git a/.idea/ant.xml b/.idea/ant.xml
deleted file mode 100644
index 4674eeac9..000000000
--- a/.idea/ant.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?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
deleted file mode 100644
index 9178b389f..000000000
--- a/.idea/codeStyleSettings.xml
+++ /dev/null
@@ -1,13 +0,0 @@
-<?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
deleted file mode 100644
index ded2e9a1d..000000000
--- a/.idea/compiler.xml
+++ /dev/null
@@ -1,21 +0,0 @@
-<?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
deleted file mode 100644
index 3572571ad..000000000
--- a/.idea/copyright/profiles_settings.xml
+++ /dev/null
@@ -1,5 +0,0 @@
-<component name="CopyrightManager">
-  <settings default="">
-    <module2copyright />
-  </settings>
-</component>
\ No newline at end of file
diff --git a/.idea/encodings.xml b/.idea/encodings.xml
deleted file mode 100644
index e206d70d8..000000000
--- a/.idea/encodings.xml
+++ /dev/null
@@ -1,5 +0,0 @@
-<?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
deleted file mode 100644
index f33b64d94..000000000
--- a/.idea/highlighting.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?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
deleted file mode 100644
index b8c243dbe..000000000
--- a/.idea/inspectionProfiles/Project_Default.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<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
deleted file mode 100644
index 3b312839b..000000000
--- a/.idea/inspectionProfiles/profiles_settings.xml
+++ /dev/null
@@ -1,7 +0,0 @@
-<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
deleted file mode 100644
index b363bbe6c..000000000
--- a/.idea/libraries/GATK_libraries.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<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>
\ No newline at end of file
diff --git a/.idea/misc.xml b/.idea/misc.xml
deleted file mode 100644
index a79280c52..000000000
--- a/.idea/misc.xml
+++ /dev/null
@@ -1,32 +0,0 @@
-<?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>
-
diff --git a/.idea/modules.xml b/.idea/modules.xml
deleted file mode 100644
index 09caa2933..000000000
--- a/.idea/modules.xml
+++ /dev/null
@@ -1,9 +0,0 @@
-<?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
deleted file mode 100644
index 922003b84..000000000
--- a/.idea/scopes/scope_settings.xml
+++ /dev/null
@@ -1,5 +0,0 @@
-<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
deleted file mode 100644
index 3b0002030..000000000
--- a/.idea/uiDesigner.xml
+++ /dev/null
@@ -1,125 +0,0 @@
-<?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$Separator" icon="/com/intellij/uiDesigner/icons/toolbarSeparator.png" removable="false" auto-create-binding="false" can-attach-label="false">
-        <default-constraints vsize-policy="0" hsize-policy="0" anchor="0" fill="1" />
-      </item>
-      <item class="javax.swing.JScrollBar" icon="/com/intellij/uiDesigner/icons/scrollbar.png" removable="false" auto-create-binding="true" can-attach-label="false">
-        <default-constraints vsize-policy="6" hsize-policy="0" anchor="0" fill="2" />
-      </item>
-    </group>
-  </component>
-</project>
-
diff --git a/.idea/vcs.xml b/.idea/vcs.xml
deleted file mode 100644
index cbc984988..000000000
--- a/.idea/vcs.xml
+++ /dev/null
@@ -1,10 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<project version="4">
-  <component name="ClearCaseSharedConfig">
-    <option name="myUseUcmModel" value="true" />
-  </component>
-  <component name="VcsDirectoryMappings">
-    <mapping directory="" vcs="Git" />
-  </component>
-</project>
-
diff --git a/cmi-gatk.iml b/cmi-gatk.iml
deleted file mode 100644
index 4dbee1336..000000000
--- a/cmi-gatk.iml
+++ /dev/null
@@ -1,31 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<module type="JAVA_MODULE" version="4">
-  <component name="FacetManager">
-    <facet type="scala" name="Scala">
-      <configuration>
-        <option name="compilerLibraryLevel" value="Project" />
-        <option name="compilerLibraryName" value="GATK libraries" />
-      </configuration>
-    </facet>
-  </component>
-  <component name="NewModuleRootManager" inherit-compiler-output="true">
-    <exclude-output />
-    <content url="file://$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>
-