2012-09-25 04:15:57 +08:00
<?xml version="1.0" encoding="UTF-8"?>
<project version= "4" >
<component name= "ChangeListManager" >
2012-09-25 22:51:53 +08:00
<list default= "true" id= "da24b138-3df4-4b46-abff-e428e3df7aee" name= "Default" comment= "Generic input file name recognition (still need to implement support to FastQ, but it now can at least accept it)" >
<change type= "MODIFICATION" beforePath= "$PROJECT_DIR$/.idea/libraries/GATK_libraries.xml" afterPath= "$PROJECT_DIR$/.idea/libraries/GATK_libraries.xml" />
<change type= "MODIFICATION" beforePath= "$PROJECT_DIR$/.idea/misc.xml" afterPath= "$PROJECT_DIR$/.idea/misc.xml" />
<change type= "MODIFICATION" beforePath= "$PROJECT_DIR$/.idea/workspace.xml" afterPath= "$PROJECT_DIR$/.idea/workspace.xml" />
<change type= "MODIFICATION" beforePath= "$PROJECT_DIR$/cmi-gatk.iml" afterPath= "$PROJECT_DIR$/cmi-gatk.iml" />
</list>
2012-09-25 04:15:57 +08:00
<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" >
2012-09-25 22:51:53 +08:00
<state line= "211" column= "39" selection-start= "9612" selection-end= "9612" vertical-scroll-proportion= "1.4740821" >
2012-09-25 04:15:57 +08:00
<folding />
</state>
</provider>
</entry>
</file>
2012-09-25 22:51:53 +08:00
<file leaf-file-name= "CompareBAMAlignments.java" pinned= "false" current= "false" current-in-tab= "false" >
<entry file= "file://$PROJECT_DIR$/private/java/src/org/broadinstitute/sting/tools/CompareBAMAlignments.java" >
2012-09-25 04:15:57 +08:00
<provider selected= "true" editor-type-id= "text-editor" >
2012-09-25 22:51:53 +08:00
<state line= "47" column= "81" selection-start= "1757" selection-end= "1757" vertical-scroll-proportion= "0.0" >
<folding >
<element signature= "imports" expanded= "true" />
</folding>
</state>
</provider>
</entry>
</file>
<file leaf-file-name= "ReduceReads.java" pinned= "false" current= "false" current-in-tab= "false" >
<entry file= "file://$PROJECT_DIR$/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReads.java" >
<provider selected= "true" editor-type-id= "text-editor" >
<state line= "331" column= "81" selection-start= "15985" selection-end= "15985" vertical-scroll-proportion= "0.0" >
2012-09-25 04:15:57 +08:00
<folding />
</state>
</provider>
</entry>
</file>
</leaf>
</component>
2012-09-25 22:51:53 +08:00
<component name= "FindManager" >
<FindUsagesManager >
<setting name= "OPEN_NEW_TAB" value= "false" />
</FindUsagesManager>
</component>
2012-09-25 04:15:57 +08:00
<component name= "Git.Settings" >
<option name= "RECENT_GIT_ROOT_PATH" value= "$PROJECT_DIR$" />
</component>
2012-09-25 22:51:53 +08:00
<component name= "IdeDocumentHistory" >
<option name= "changedFiles" >
<list >
<option value= "$PROJECT_DIR$/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala" />
</list>
</option>
</component>
2012-09-25 04:15:57 +08:00
<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" >
2012-09-25 22:51:53 +08:00
<navigator proportions= "" version= "1" splitterProportion= "0.5" >
2012-09-25 04:15:57 +08:00
<flattenPackages />
<showMembers />
<showModules />
<showLibraryContents />
<hideEmptyPackages />
<abbreviatePackageNames />
<autoscrollToSource />
<autoscrollFromSource />
<sortByType />
</navigator>
2012-09-25 22:51:53 +08:00
<panes />
2012-09-25 04:15:57 +08:00
</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" />
2012-09-25 22:51:53 +08:00
<property name= "project.structure.side.proportion" value= "0.2" />
2012-09-25 04:15:57 +08:00
<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= "<template>" type= "JUnit" default= "true" selected= "false" >
<option name= "MAIN_CLASS_NAME" />
<option name= "VM_PARAMETERS" value= "-ea" />
<option name= "PARAMETERS" />
<option name= "WORKING_DIRECTORY" value= "$PROJECT_DIR$" />
</configuration>
<configuration name= "<template>" 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= "$PROJECT_DIR$" />
</configuration>
<configuration name= "<template>" type= "#org.jetbrains.idea.devkit.run.PluginConfigurationType" default= "true" selected= "false" >
<option name= "VM_PARAMETERS" value= "-Xmx512m -Xms256m -XX:MaxPermSize=250m" />
</configuration>
<configuration name= "<template>" type= "WebApp" default= "true" selected= "false" >
<Host > localhost</Host>
<Port > 5050</Port>
</configuration>
</component>
<component name= "ShelveChangesManager" show_recycled= "false" />
<component name= "ToolWindowManager" >
<frame x= "-1200" y= "-870" width= "1200" height= "1562" extended-state= "0" />
2012-09-25 22:51:53 +08:00
<editor active= "false" />
2012-09-25 04:15:57 +08:00
<layout >
2012-09-25 22:51:53 +08:00
<window_info id= "Messages" active= "true" anchor= "bottom" auto_hide= "false" internal_type= "DOCKED" type= "DOCKED" visible= "true" weight= "0.3296322" sideWeight= "0.5" order= "7" side_tool= "false" content_ui= "tabs" />
2012-09-25 04:15:57 +08:00
<window_info id= "Changes" active= "false" anchor= "bottom" auto_hide= "false" internal_type= "DOCKED" type= "DOCKED" visible= "false" weight= "0.33" sideWeight= "0.5" order= "7" side_tool= "false" content_ui= "tabs" />
<window_info id= "Palette" active= "false" anchor= "right" auto_hide= "false" internal_type= "DOCKED" type= "DOCKED" visible= "false" weight= "0.33" sideWeight= "0.5" order= "3" side_tool= "false" content_ui= "tabs" />
<window_info id= "TODO" active= "false" anchor= "bottom" auto_hide= "false" internal_type= "DOCKED" type= "DOCKED" visible= "false" weight= "0.33" sideWeight= "0.5" order= "6" side_tool= "false" content_ui= "tabs" />
<window_info id= "Ant Build" active= "false" anchor= "right" auto_hide= "false" internal_type= "DOCKED" type= "DOCKED" visible= "false" weight= "0.25" sideWeight= "0.5" order= "1" side_tool= "false" content_ui= "tabs" />
<window_info id= "Structure" active= "false" anchor= "left" auto_hide= "false" internal_type= "DOCKED" type= "DOCKED" visible= "false" weight= "0.25" sideWeight= "0.5" order= "1" side_tool= "true" content_ui= "tabs" />
<window_info id= "Project" active= "false" anchor= "left" auto_hide= "false" internal_type= "DOCKED" type= "DOCKED" visible= "false" weight= "0.24956672" sideWeight= "0.6703678" order= "0" side_tool= "false" content_ui= "combo" />
<window_info id= "Debug" active= "false" anchor= "bottom" auto_hide= "false" internal_type= "DOCKED" type= "DOCKED" visible= "false" weight= "0.4" sideWeight= "0.5" order= "3" side_tool= "false" content_ui= "tabs" />
<window_info id= "Favorites" active= "false" anchor= "left" auto_hide= "false" internal_type= "DOCKED" type= "DOCKED" visible= "false" weight= "0.33" sideWeight= "0.5" order= "2" side_tool= "true" content_ui= "tabs" />
<window_info id= "Event Log" active= "false" anchor= "bottom" auto_hide= "false" internal_type= "DOCKED" type= "DOCKED" visible= "false" weight= "0.3296322" sideWeight= "0.5" order= "7" side_tool= "true" content_ui= "tabs" />
<window_info id= "Run" active= "false" anchor= "bottom" auto_hide= "false" internal_type= "DOCKED" type= "DOCKED" visible= "false" weight= "0.33" sideWeight= "0.5" order= "2" side_tool= "false" content_ui= "tabs" />
<window_info id= "Version Control" active= "false" anchor= "bottom" auto_hide= "false" internal_type= "DOCKED" type= "DOCKED" visible= "false" weight= "0.33" sideWeight= "0.5" order= "7" side_tool= "false" content_ui= "tabs" />
<window_info id= "Cvs" active= "false" anchor= "bottom" auto_hide= "false" internal_type= "DOCKED" type= "DOCKED" visible= "false" weight= "0.25" sideWeight= "0.5" order= "4" side_tool= "false" content_ui= "tabs" />
<window_info id= "Message" active= "false" anchor= "bottom" auto_hide= "false" internal_type= "DOCKED" type= "DOCKED" visible= "false" weight= "0.33" sideWeight= "0.5" order= "0" side_tool= "false" content_ui= "tabs" />
<window_info id= "Find" active= "false" anchor= "bottom" auto_hide= "false" internal_type= "DOCKED" type= "DOCKED" visible= "false" weight= "0.33" sideWeight= "0.5" order= "1" side_tool= "false" content_ui= "tabs" />
<window_info id= "Commander" active= "false" anchor= "right" auto_hide= "false" internal_type= "DOCKED" type= "DOCKED" visible= "false" weight= "0.4" sideWeight= "0.5" order= "0" side_tool= "false" content_ui= "tabs" />
<window_info id= "Hierarchy" active= "false" anchor= "right" auto_hide= "false" internal_type= "DOCKED" type= "DOCKED" visible= "false" weight= "0.25" sideWeight= "0.5" order= "2" side_tool= "false" content_ui= "combo" />
<window_info id= "Inspection" active= "false" anchor= "bottom" auto_hide= "false" internal_type= "DOCKED" type= "DOCKED" visible= "false" weight= "0.4" sideWeight= "0.5" order= "5" side_tool= "false" content_ui= "tabs" />
</layout>
</component>
<component name= "VcsContentAnnotationSettings" >
<option name= "myLimit" value= "2678400000" />
</component>
<component name= "VcsManagerConfiguration" >
<option name= "OFFER_MOVE_TO_ANOTHER_CHANGELIST_ON_PARTIAL_COMMIT" value= "true" />
<option name= "CHECK_CODE_SMELLS_BEFORE_PROJECT_COMMIT" value= "true" />
<option name= "CHECK_NEW_TODO" value= "true" />
<option name= "myTodoPanelSettings" >
<value >
<are-packages-shown value= "false" />
<are-modules-shown value= "false" />
<flatten-packages value= "false" />
<is-autoscroll-to-source value= "false" />
</value>
</option>
<option name= "PERFORM_UPDATE_IN_BACKGROUND" value= "true" />
<option name= "PERFORM_COMMIT_IN_BACKGROUND" value= "true" />
<option name= "PERFORM_EDIT_IN_BACKGROUND" value= "true" />
<option name= "PERFORM_CHECKOUT_IN_BACKGROUND" value= "true" />
<option name= "PERFORM_ADD_REMOVE_IN_BACKGROUND" value= "true" />
<option name= "PERFORM_ROLLBACK_IN_BACKGROUND" value= "false" />
<option name= "CHECK_LOCALLY_CHANGED_CONFLICTS_IN_BACKGROUND" value= "false" />
<option name= "ENABLE_BACKGROUND_PROCESSES" value= "false" />
<option name= "CHANGED_ON_SERVER_INTERVAL" value= "60" />
<option name= "SHOW_ONLY_CHANGED_IN_SELECTION_DIFF" value= "true" />
<option name= "CHECK_COMMIT_MESSAGE_SPELLING" value= "true" />
<option name= "DEFAULT_PATCH_EXTENSION" value= "patch" />
<option name= "SHORT_DIFF_HORISONTALLY" value= "true" />
<option name= "SHORT_DIFF_EXTRA_LINES" value= "2" />
<option name= "SOFT_WRAPS_IN_SHORT_DIFF" value= "true" />
<option name= "INCLUDE_TEXT_INTO_PATCH" value= "false" />
<option name= "INCLUDE_TEXT_INTO_SHELF" value= "false" />
<option name= "CREATE_PATCH_EXPAND_DETAILS_DEFAULT" value= "true" />
<option name= "SHOW_FILE_HISTORY_DETAILS" value= "true" />
<option name= "SHOW_VCS_ERROR_NOTIFICATIONS" value= "true" />
<option name= "FORCE_NON_EMPTY_COMMENT" value= "false" />
<option name= "CLEAR_INITIAL_COMMIT_MESSAGE" value= "false" />
2012-09-25 22:51:53 +08:00
<option name= "LAST_COMMIT_MESSAGE" value= "Updating working environment and adding scala to the project" />
2012-09-25 04:15:57 +08:00
<option name= "MAKE_NEW_CHANGELIST_ACTIVE" value= "false" />
<option name= "OPTIMIZE_IMPORTS_BEFORE_PROJECT_COMMIT" value= "false" />
<option name= "CHECK_FILES_UP_TO_DATE_BEFORE_COMMIT" value= "false" />
<option name= "REFORMAT_BEFORE_PROJECT_COMMIT" value= "false" />
<option name= "REFORMAT_BEFORE_FILE_COMMIT" value= "false" />
<option name= "FILE_HISTORY_DIALOG_COMMENTS_SPLITTER_PROPORTION" value= "0.8" />
<option name= "FILE_HISTORY_DIALOG_SPLITTER_PROPORTION" value= "0.5" />
<option name= "ACTIVE_VCS_NAME" />
<option name= "UPDATE_GROUP_BY_PACKAGES" value= "false" />
<option name= "UPDATE_GROUP_BY_CHANGELIST" value= "false" />
<option name= "SHOW_FILE_HISTORY_AS_TREE" value= "false" />
<option name= "FILE_HISTORY_SPLITTER_PROPORTION" value= "0.6" />
2012-09-25 22:51:53 +08:00
<MESSAGE value= "Generic input file name recognition (still need to implement support to FastQ, but it now can at least accept it)" />
<MESSAGE value= "Updating working environment and adding scala to the project" />
2012-09-25 04:15:57 +08:00
</component>
<component name= "XDebuggerManager" >
<breakpoint-manager />
</component>
2012-09-25 22:51:53 +08:00
<component name= "antWorkspaceConfiguration" >
<option name= "IS_AUTOSCROLL_TO_SOURCE" value= "false" />
<option name= "FILTER_TARGETS" value= "false" />
<buildFile url= "file://$PROJECT_DIR$/build.xml" >
<antCommandLine value= "" />
<runInBackground value= "true" />
<targetFilters >
<filter targetName= "queue" isVisible= "false" />
<filter targetName= "queuelite.binary.release.tests" isVisible= "false" />
<filter targetName= "test" isVisible= "false" />
<filter targetName= "generate.build.version" isVisible= "false" />
<filter targetName= "clean.gsalib" isVisible= "false" />
<filter targetName= "package" isVisible= "true" />
<filter targetName= "gatklite.binary.release.tests" isVisible= "false" />
<filter targetName= "javadoc" isVisible= "false" />
<filter targetName= "init.scaladoc" isVisible= "false" />
<filter targetName= "sting-utils.manifests" isVisible= "false" />
<filter targetName= "test.init.compile" isVisible= "false" />
<filter targetName= "queue.manifests" isVisible= "false" />
<filter targetName= "release.queue.full" isVisible= "false" />
<filter targetName= "init.scala.compile" isVisible= "true" />
<filter targetName= "extracthelp" isVisible= "true" />
<filter targetName= "R.public.tar" isVisible= "false" />
<filter targetName= "init.manifests" isVisible= "false" />
<filter targetName= "gsalib" isVisible= "false" />
<filter targetName= "init.buildqueuefull" isVisible= "false" />
<filter targetName= "test.init" isVisible= "false" />
<filter targetName= "package.queue.lite" isVisible= "false" />
<filter targetName= "test.java.internal.compile" isVisible= "false" />
<filter targetName= "integrationtest" isVisible= "true" />
<filter targetName= "queue.jar" isVisible= "false" />
<filter targetName= "scala.compile" isVisible= "false" />
<filter targetName= "clean.gatkdocs" isVisible= "false" />
<filter targetName= "scaladoc" isVisible= "false" />
<filter targetName= "init.publicprotectedonly" isVisible= "false" />
<filter targetName= "init" isVisible= "false" />
<filter targetName= "gatkfull.binary.release.tests" isVisible= "false" />
<filter targetName= "failed-pipeline" isVisible= "false" />
<filter targetName= "require.executable" isVisible= "false" />
<filter targetName= "tagged.build.version" isVisible= "false" />
<filter targetName= "init.publiconly" isVisible= "false" />
<filter targetName= "unittest" isVisible= "true" />
<filter targetName= "test.scala.compile" isVisible= "false" />
<filter targetName= "init.buildgatklite" isVisible= "false" />
<filter targetName= "release.gatk.lite" isVisible= "false" />
<filter targetName= "package.gatk.full" isVisible= "false" />
<filter targetName= "gatk" isVisible= "false" />
<filter targetName= "init.buildqueuelite" isVisible= "false" />
<filter targetName= "scala.jar" isVisible= "false" />
<filter targetName= "release" isVisible= "true" />
<filter targetName= "test.java.compile" isVisible= "false" />
<filter targetName= "init.testqueuejar" isVisible= "false" />
<filter targetName= "dist" isVisible= "false" />
<filter targetName= "failed-largescale" isVisible= "false" />
<filter targetName= "untagged.build.version" isVisible= "false" />
<filter targetName= "gatk.contracts" isVisible= "false" />
<filter targetName= "release.gatk.full" isVisible= "false" />
<filter targetName= "stage" isVisible= "true" />
<filter targetName= "scala" isVisible= "true" />
<filter targetName= "failed-integration" isVisible= "false" />
<filter targetName= "queuefull.binary.release.tests" isVisible= "false" />
<filter targetName= "test.java.external.compile" isVisible= "false" />
<filter targetName= "init.queue-extensions.generate" isVisible= "false" />
<filter targetName= "largescaletest" isVisible= "true" />
<filter targetName= "init.javaandscala" isVisible= "false" />
<filter targetName= "init.usecontracts" isVisible= "false" />
<filter targetName= "git.rev-parse" isVisible= "false" />
<filter targetName= "clean" isVisible= "true" />
<filter targetName= "sting.manifests" isVisible= "false" />
<filter targetName= "clean.javadoc" isVisible= "false" />
<filter targetName= "pipelinetest" isVisible= "true" />
<filter targetName= "init.javaonly" isVisible= "false" />
<filter targetName= "vcf.jar" isVisible= "false" />
<filter targetName= "gatk.compile.external.source" isVisible= "false" />
<filter targetName= "resolve" isVisible= "true" />
<filter targetName= "init.buildgatkfull" isVisible= "false" />
<filter targetName= "fasttest" isVisible= "false" />
<filter targetName= "sting-utils.jar" isVisible= "false" />
<filter targetName= "gatk.compile" isVisible= "false" />
<filter targetName= "gatkdocs" isVisible= "true" />
<filter targetName= "clean.scaladoc" isVisible= "false" />
<filter targetName= "init.extracthelp" isVisible= "false" />
<filter targetName= "gatk.jar" isVisible= "true" />
<filter targetName= "gatk.compile.internal.source" isVisible= "false" />
<filter targetName= "committests" isVisible= "false" />
<filter targetName= "git.describe" isVisible= "false" />
<filter targetName= "package.gatk.lite" isVisible= "false" />
<filter targetName= "init.testgatkjar" isVisible= "false" />
<filter targetName= "init.jar" isVisible= "false" />
<filter targetName= "queue-extensions.generate" isVisible= "true" />
<filter targetName= "test.compile" isVisible= "false" />
<filter targetName= "gatk.manifests" isVisible= "false" />
<filter targetName= "sting.jar" isVisible= "false" />
<filter targetName= "R.script.stage" isVisible= "false" />
<filter targetName= "init.resolve" isVisible= "false" />
<filter targetName= "release.queue.lite" isVisible= "false" />
<filter targetName= "gatk.compile.source" isVisible= "true" />
<filter targetName= "init.javadoc" isVisible= "false" />
<filter targetName= "build-picard-private" isVisible= "false" />
<filter targetName= "package.queue.full" isVisible= "false" />
<filter targetName= "failed-unit" isVisible= "false" />
<filter targetName= "pipelinetestrun" isVisible= "true" />
<filter targetName= "sting.compile" isVisible= "false" />
</targetFilters>
<treeView value= "true" />
<verbose value= "true" />
<viewClosedWhenNoErrors value= "false" />
<expanded value= "true" />
</buildFile>
</component>
2012-09-25 04:15:57 +08:00
<component name= "editorHistoryManager" >
<entry file= "file://$PROJECT_DIR$/public/scala/src/org/broadinstitute/sting/queue/util/QScriptUtils.scala" >
<provider selected= "true" editor-type-id= "text-editor" >
2012-09-25 22:51:53 +08:00
<state line= "46" column= "6" selection-start= "1607" selection-end= "1607" vertical-scroll-proportion= "0.21216407" >
<folding />
</state>
</provider>
</entry>
<entry file= "file://$PROJECT_DIR$/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReads.java" >
<provider selected= "true" editor-type-id= "text-editor" >
<state line= "331" column= "81" selection-start= "15985" selection-end= "15985" vertical-scroll-proportion= "0.0" >
2012-09-25 04:15:57 +08:00
<folding />
</state>
</provider>
</entry>
2012-09-25 22:51:53 +08:00
<entry file= "file://$PROJECT_DIR$/private/java/src/org/broadinstitute/sting/tools/CompareBAMAlignments.java" >
<provider selected= "true" editor-type-id= "text-editor" >
<state line= "47" column= "81" selection-start= "1757" selection-end= "1757" vertical-scroll-proportion= "0.0" >
<folding >
<element signature= "imports" expanded= "true" />
</folding>
</state>
</provider>
</entry>
2012-09-25 04:15:57 +08:00
<entry file= "file://$PROJECT_DIR$/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala" >
<provider selected= "true" editor-type-id= "text-editor" >
2012-09-25 22:51:53 +08:00
<state line= "211" column= "39" selection-start= "9612" selection-end= "9612" vertical-scroll-proportion= "1.4740821" >
2012-09-25 04:15:57 +08:00
<folding />
</state>
</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>
2012-09-25 22:51:53 +08:00
<state key= "FacetStructureConfigurable.UI" >
<settings >
<last-edited > Detection</last-edited>
<splitter-proportions >
<option name= "proportions" >
<list >
<option value= "0.2" />
</list>
</option>
</splitter-proportions>
</settings>
</state>
2012-09-25 04:15:57 +08:00
<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 >
2012-09-25 22:51:53 +08:00
<last-edited > 1.6</last-edited>
2012-09-25 04:15:57 +08:00
<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" />
</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>