.gitignore

 # Created by .gitignore support plugin (hsz.mobi)
 .idea/workspace.xml
-*.jar
-igv.sh
 /out/
+/build
+/build_java9
+/bin
+igv.log
+/.gradle
+.project
+.classpath
+/.idea/
+/.settings
\ No newline at end of file

.idea/.name

-IGV
\ No newline at end of file

.idea/compiler.xml

-<?xml version="1.0" encoding="UTF-8"?>
-<project version="4">
-  <component name="CompilerConfiguration">
-    <resourceExtensions />
-    <wildcardResourcePatterns>
-      <entry name="!?*.java" />
-      <entry name="!?*.form" />
-      <entry name="!?*.class" />
-      <entry name="!?*.groovy" />
-      <entry name="!?*.scala" />
-      <entry name="!?*.flex" />
-      <entry name="!?*.kt" />
-      <entry name="!?*.clj" />
-      <entry name="!?*.aj" />
-    </wildcardResourcePatterns>
-    <annotationProcessing>
-      <profile default="true" name="Default" enabled="false">
-        <processorPath useClasspath="true" />
-      </profile>
-    </annotationProcessing>
-  </component>
-</project>
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.idea/copyright/IGV.xml

-<component name="CopyrightManager">
-  <copyright>
-    <option name="notice" value=" The MIT License (MIT)&#10;&#10;Copyright (c) 2016 University of California San Diego&#10;&#10;Permission is hereby granted, free of charge, to any person obtaining a copy&#10;of this software and associated documentation files (the &quot;Software&quot;), to deal&#10;in the Software without restriction, including without limitation the rights&#10;to use, copy, modify, merge, publish, distribute, sublicense, and/or sell&#10;copies of the Software, and to permit persons to whom the Software is&#10;furnished to do so, subject to the following conditions:&#10;&#10;The above copyright notice and this permission notice shall be included in&#10;all copies or substantial portions of the Software.&#10; &#10;THE SOFTWARE IS PROVIDED &quot;AS IS&quot;, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR&#10;IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,&#10;FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE&#10;AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER&#10; LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,&#10;OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN&#10;THE SOFTWARE.&#10;&#10;" />
-    <option name="myName" value="IGV" />
-  </copyright>
-</component>
\ No newline at end of file

.idea/copyright/profiles_settings.xml

-<component name="CopyrightManager">
-  <settings default="" />
-</component>
\ No newline at end of file

.idea/encodings.xml

-<?xml version="1.0" encoding="UTF-8"?>
-<project version="4">
-  <component name="Encoding">
-    <file url="PROJECT" charset="UTF-8" />
-  </component>
-</project>
\ No newline at end of file

.idea/libraries/lib.xml

-<component name="libraryTable">
-  <library name="lib">
-    <CLASSES>
-      <root url="file://$PROJECT_DIR$/test/lib" />
-    </CLASSES>
-    <JAVADOC />
-    <SOURCES />
-    <jarDirectory url="file://$PROJECT_DIR$/test/lib" recursive="false" />
-  </library>
-</component>
\ No newline at end of file

.idea/libraries/lib1.xml

-<component name="libraryTable">
-  <library name="lib1">
-    <CLASSES>
-      <root url="file://$PROJECT_DIR$/lib" />
-    </CLASSES>
-    <JAVADOC />
-    <SOURCES>
-      <root url="file://$USER_HOME$/Google Drive/projects/htsjdk (1)/src/main/java" />
-      <root url="file://$USER_HOME$/Google Drive/projects/htsjdk/src/main/java" />
-    </SOURCES>
-    <jarDirectory url="file://$PROJECT_DIR$/lib" recursive="false" />
-  </library>
-</component>
\ No newline at end of file

.idea/libraries/ojdbc6.xml

-<component name="libraryTable">
-  <library name="ojdbc6">
-    <CLASSES>
-      <root url="jar://$PROJECT_DIR$/extras/ojdbc6.jar!/" />
-    </CLASSES>
-    <JAVADOC />
-    <SOURCES />
-  </library>
-</component>
\ No newline at end of file

.idea/misc.xml

-<?xml version="1.0" encoding="UTF-8"?>
-<project version="4">
-  <component name="EntryPointsManager">
-    <entry_points version="2.0" />
-  </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="ProjectRootManager" version="2" languageLevel="JDK_1_8" default="true" assert-keyword="true" jdk-15="true" project-jdk-name="1.8" project-jdk-type="JavaSDK">
-    <output url="file://$PROJECT_DIR$/out" />
-  </component>
-</project>
\ No newline at end of file

.idea/modules (HDBRF2XXX2A3201's conflicted copy 2016-10-31).xml

-<?xml version="1.0" encoding="UTF-8"?>
-<project version="4">
-  <component name="ProjectModuleManager">
-    <modules>
-      <module fileurl="file://$PROJECT_DIR$/IGV.iml" filepath="$PROJECT_DIR$/IGV.iml" />
-      <module fileurl="file://$PROJECT_DIR$/test/test.iml" filepath="$PROJECT_DIR$/test/test.iml" />
-    </modules>
-  </component>
-</project>
\ No newline at end of file

.idea/modules (HLBRFIIXX2A3201's conflicted copy 2016-09-26).xml

-<?xml version="1.0" encoding="UTF-8"?>
-<project version="4">
-  <component name="ProjectModuleManager">
-    <modules>
-      <module fileurl="file://$PROJECT_DIR$/IGV.iml" filepath="$PROJECT_DIR$/IGV.iml" />
-    </modules>
-  </component>
-</project>
\ No newline at end of file

.idea/modules.xml

-<?xml version="1.0" encoding="UTF-8"?>
-<project version="4">
-  <component name="ProjectModuleManager">
-    <modules>
-      <module fileurl="file://$PROJECT_DIR$/IGV.iml" filepath="$PROJECT_DIR$/IGV.iml" />
-    </modules>
-  </component>
-</project>
\ No newline at end of file

.idea/uiDesigner.xml

-<?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>
\ No newline at end of file

.idea/vcs.xml

-<?xml version="1.0" encoding="UTF-8"?>
-<project version="4">
-  <component name="VcsDirectoryMappings">
-    <mapping directory="$PROJECT_DIR$" vcs="Git" />
-  </component>
-</project>
\ No newline at end of file