Updating Intellij enviroment and adding Scala
This commit is contained in:
Mauricio Carneiro
parent
4aad135f8c
commit
4324bd72fd
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@ -6,7 +6,6 @@
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|||
<JAVADOC />
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<SOURCES>
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<root url="file://$PROJECT_DIR$/../../picard/src/java" />
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<root url="jar:///Library/Java/JavaVirtualMachines/1.6.0_31-b04-411.jdk/Contents/Home/src.jar!/src" />
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</SOURCES>
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<jarDirectory url="file://$PROJECT_DIR$/lib" recursive="false" />
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</library>
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|
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|||
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@ -24,7 +24,7 @@
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<component name="ProjectResources">
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<default-html-doctype>http://www.w3.org/1999/xhtml</default-html-doctype>
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</component>
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||||
<component name="ProjectRootManager" version="2" languageLevel="JDK_1_6" assert-keyword="true" jdk-15="true">
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<component name="ProjectRootManager" version="2" languageLevel="JDK_1_6" assert-keyword="true" jdk-15="true" project-jdk-name="1.6" project-jdk-type="JavaSDK">
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<output url="file://$PROJECT_DIR$/out" />
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</component>
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<component name="WebServicesPlugin" addRequiredLibraries="true" />
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@ -1,7 +1,12 @@
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<?xml version="1.0" encoding="UTF-8"?>
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<project version="4">
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<component name="ChangeListManager">
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<list default="true" id="da24b138-3df4-4b46-abff-e428e3df7aee" name="Default" comment="" />
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<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)">
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<change type="MODIFICATION" beforePath="$PROJECT_DIR$/.idea/libraries/GATK_libraries.xml" afterPath="$PROJECT_DIR$/.idea/libraries/GATK_libraries.xml" />
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<change type="MODIFICATION" beforePath="$PROJECT_DIR$/.idea/misc.xml" afterPath="$PROJECT_DIR$/.idea/misc.xml" />
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<change type="MODIFICATION" beforePath="$PROJECT_DIR$/.idea/workspace.xml" afterPath="$PROJECT_DIR$/.idea/workspace.xml" />
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<change type="MODIFICATION" beforePath="$PROJECT_DIR$/cmi-gatk.iml" afterPath="$PROJECT_DIR$/cmi-gatk.iml" />
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</list>
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<ignored path="gatk.unstable.iws" />
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<ignored path=".idea/workspace.xml" />
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<option name="TRACKING_ENABLED" value="true" />
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@ -61,16 +66,27 @@
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<file leaf-file-name="DataProcessingPipeline.scala" pinned="false" current="true" current-in-tab="true">
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<entry file="file://$PROJECT_DIR$/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala">
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<provider selected="true" editor-type-id="text-editor">
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<state line="234" column="40" selection-start="10480" selection-end="10480" vertical-scroll-proportion="0.40685225">
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<state line="211" column="39" selection-start="9612" selection-end="9612" vertical-scroll-proportion="1.4740821">
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<folding />
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</state>
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</provider>
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</entry>
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</file>
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<file leaf-file-name="QScriptUtils.scala" pinned="false" current="false" current-in-tab="false">
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<entry file="file://$PROJECT_DIR$/public/scala/src/org/broadinstitute/sting/queue/util/QScriptUtils.scala">
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<file leaf-file-name="CompareBAMAlignments.java" pinned="false" current="false" current-in-tab="false">
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<entry file="file://$PROJECT_DIR$/private/java/src/org/broadinstitute/sting/tools/CompareBAMAlignments.java">
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<provider selected="true" editor-type-id="text-editor">
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<state line="46" column="6" selection-start="1607" selection-end="1607" vertical-scroll-proportion="0.0">
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<state line="47" column="81" selection-start="1757" selection-end="1757" vertical-scroll-proportion="0.0">
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<folding>
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<element signature="imports" expanded="true" />
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</folding>
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</state>
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</provider>
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</entry>
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</file>
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<file leaf-file-name="ReduceReads.java" pinned="false" current="false" current-in-tab="false">
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<entry file="file://$PROJECT_DIR$/protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReads.java">
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<provider selected="true" editor-type-id="text-editor">
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<state line="331" column="81" selection-start="15985" selection-end="15985" vertical-scroll-proportion="0.0">
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<folding />
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</state>
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</provider>
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@ -78,9 +94,21 @@
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</file>
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</leaf>
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</component>
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<component name="FindManager">
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<FindUsagesManager>
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<setting name="OPEN_NEW_TAB" value="false" />
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</FindUsagesManager>
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</component>
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<component name="Git.Settings">
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<option name="RECENT_GIT_ROOT_PATH" value="$PROJECT_DIR$" />
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</component>
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<component name="IdeDocumentHistory">
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<option name="changedFiles">
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<list>
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<option value="$PROJECT_DIR$/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala" />
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</list>
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</option>
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</component>
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<component name="ProjectFrameBounds">
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<option name="x" value="-1200" />
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<option name="y" value="-870" />
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@ -101,7 +129,7 @@
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<option name="STATE" value="0" />
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</component>
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<component name="ProjectView">
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<navigator currentView="ProjectPane" proportions="" version="1" splitterProportion="0.5">
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<navigator proportions="" version="1" splitterProportion="0.5">
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<flattenPackages />
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<showMembers />
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<showModules />
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@ -112,33 +140,7 @@
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<autoscrollFromSource />
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<sortByType />
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</navigator>
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<panes>
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<pane id="PackagesPane">
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<subPane>
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<PATH>
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<PATH_ELEMENT>
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<option name="myItemId" value="cmi-gatk" />
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<option name="myItemType" value="com.intellij.ide.projectView.impl.nodes.PackageViewProjectNode" />
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</PATH_ELEMENT>
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<PATH_ELEMENT>
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<option name="myItemId" value="cmi-gatk" />
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<option name="myItemType" value="com.intellij.ide.projectView.impl.nodes.PackageViewModuleNode" />
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</PATH_ELEMENT>
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</PATH>
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</subPane>
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</pane>
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<pane id="ProjectPane">
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<subPane>
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<PATH>
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<PATH_ELEMENT>
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<option name="myItemId" value="cmi-gatk" />
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<option name="myItemType" value="com.intellij.ide.projectView.impl.nodes.ProjectViewProjectNode" />
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</PATH_ELEMENT>
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</PATH>
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</subPane>
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</pane>
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<pane id="Scope" />
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</panes>
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<panes />
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</component>
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<component name="PropertiesComponent">
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<property name="GoToFile.includeJavaFiles" value="false" />
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@ -147,7 +149,7 @@
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<property name="options.splitter.main.proportions" value="0.3" />
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<property name="MemberChooser.sorted" value="false" />
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<property name="options.lastSelected" value="project.propVCSSupport.VCSs.Git" />
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<property name="project.structure.side.proportion" value="0.0" />
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<property name="project.structure.side.proportion" value="0.2" />
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<property name="GoToClass.includeJavaFiles" value="false" />
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<property name="MemberChooser.copyJavadoc" value="false" />
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<property name="GoToClass.toSaveIncludeLibraries" value="false" />
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@ -228,8 +230,9 @@
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<component name="ShelveChangesManager" show_recycled="false" />
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<component name="ToolWindowManager">
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<frame x="-1200" y="-870" width="1200" height="1562" extended-state="0" />
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<editor active="true" />
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<editor active="false" />
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<layout>
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<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" />
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<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" />
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<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" />
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<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" />
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@ -286,7 +289,7 @@
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<option name="SHOW_VCS_ERROR_NOTIFICATIONS" value="true" />
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<option name="FORCE_NON_EMPTY_COMMENT" value="false" />
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<option name="CLEAR_INITIAL_COMMIT_MESSAGE" value="false" />
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<option name="LAST_COMMIT_MESSAGE" />
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<option name="LAST_COMMIT_MESSAGE" value="Updating working environment and adding scala to the project" />
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<option name="MAKE_NEW_CHANGELIST_ACTIVE" value="false" />
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<option name="OPTIMIZE_IMPORTS_BEFORE_PROJECT_COMMIT" value="false" />
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<option name="CHECK_FILES_UP_TO_DATE_BEFORE_COMMIT" value="false" />
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@ -299,21 +302,149 @@
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<option name="UPDATE_GROUP_BY_CHANGELIST" value="false" />
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<option name="SHOW_FILE_HISTORY_AS_TREE" value="false" />
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<option name="FILE_HISTORY_SPLITTER_PROPORTION" value="0.6" />
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<MESSAGE value="Generic input file name recognition (still need to implement support to FastQ, but it now can at least accept it)" />
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<MESSAGE value="Updating working environment and adding scala to the project" />
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</component>
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<component name="XDebuggerManager">
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<breakpoint-manager />
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</component>
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<component name="antWorkspaceConfiguration">
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<option name="IS_AUTOSCROLL_TO_SOURCE" value="false" />
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<option name="FILTER_TARGETS" value="false" />
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<buildFile url="file://$PROJECT_DIR$/build.xml">
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<antCommandLine value="" />
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<runInBackground value="true" />
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<targetFilters>
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<filter targetName="queue" isVisible="false" />
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<filter targetName="queuelite.binary.release.tests" isVisible="false" />
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<filter targetName="test" isVisible="false" />
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<filter targetName="generate.build.version" isVisible="false" />
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<filter targetName="clean.gsalib" isVisible="false" />
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<filter targetName="package" isVisible="true" />
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<filter targetName="gatklite.binary.release.tests" isVisible="false" />
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<filter targetName="javadoc" isVisible="false" />
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<filter targetName="init.scaladoc" isVisible="false" />
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<filter targetName="sting-utils.manifests" isVisible="false" />
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<filter targetName="test.init.compile" isVisible="false" />
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<filter targetName="queue.manifests" isVisible="false" />
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<filter targetName="release.queue.full" isVisible="false" />
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||||
<filter targetName="init.scala.compile" isVisible="true" />
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||||
<filter targetName="extracthelp" isVisible="true" />
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||||
<filter targetName="R.public.tar" isVisible="false" />
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||||
<filter targetName="init.manifests" isVisible="false" />
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||||
<filter targetName="gsalib" isVisible="false" />
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||||
<filter targetName="init.buildqueuefull" isVisible="false" />
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||||
<filter targetName="test.init" isVisible="false" />
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||||
<filter targetName="package.queue.lite" isVisible="false" />
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||||
<filter targetName="test.java.internal.compile" isVisible="false" />
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||||
<filter targetName="integrationtest" isVisible="true" />
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||||
<filter targetName="queue.jar" isVisible="false" />
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||||
<filter targetName="scala.compile" isVisible="false" />
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||||
<filter targetName="clean.gatkdocs" isVisible="false" />
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||||
<filter targetName="scaladoc" isVisible="false" />
|
||||
<filter targetName="init.publicprotectedonly" isVisible="false" />
|
||||
<filter targetName="init" isVisible="false" />
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||||
<filter targetName="gatkfull.binary.release.tests" isVisible="false" />
|
||||
<filter targetName="failed-pipeline" isVisible="false" />
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||||
<filter targetName="require.executable" isVisible="false" />
|
||||
<filter targetName="tagged.build.version" isVisible="false" />
|
||||
<filter targetName="init.publiconly" isVisible="false" />
|
||||
<filter targetName="unittest" isVisible="true" />
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||||
<filter targetName="test.scala.compile" isVisible="false" />
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||||
<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" />
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||||
<filter targetName="scala.jar" isVisible="false" />
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||||
<filter targetName="release" isVisible="true" />
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||||
<filter targetName="test.java.compile" isVisible="false" />
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||||
<filter targetName="init.testqueuejar" isVisible="false" />
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||||
<filter targetName="dist" isVisible="false" />
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||||
<filter targetName="failed-largescale" isVisible="false" />
|
||||
<filter targetName="untagged.build.version" isVisible="false" />
|
||||
<filter targetName="gatk.contracts" isVisible="false" />
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||||
<filter targetName="release.gatk.full" isVisible="false" />
|
||||
<filter targetName="stage" isVisible="true" />
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||||
<filter targetName="scala" isVisible="true" />
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||||
<filter targetName="failed-integration" isVisible="false" />
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||||
<filter targetName="queuefull.binary.release.tests" isVisible="false" />
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||||
<filter targetName="test.java.external.compile" isVisible="false" />
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||||
<filter targetName="init.queue-extensions.generate" isVisible="false" />
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||||
<filter targetName="largescaletest" isVisible="true" />
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||||
<filter targetName="init.javaandscala" isVisible="false" />
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||||
<filter targetName="init.usecontracts" isVisible="false" />
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||||
<filter targetName="git.rev-parse" isVisible="false" />
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||||
<filter targetName="clean" isVisible="true" />
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||||
<filter targetName="sting.manifests" isVisible="false" />
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||||
<filter targetName="clean.javadoc" isVisible="false" />
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||||
<filter targetName="pipelinetest" isVisible="true" />
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||||
<filter targetName="init.javaonly" isVisible="false" />
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||||
<filter targetName="vcf.jar" isVisible="false" />
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||||
<filter targetName="gatk.compile.external.source" isVisible="false" />
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||||
<filter targetName="resolve" isVisible="true" />
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||||
<filter targetName="init.buildgatkfull" isVisible="false" />
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||||
<filter targetName="fasttest" isVisible="false" />
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||||
<filter targetName="sting-utils.jar" isVisible="false" />
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||||
<filter targetName="gatk.compile" isVisible="false" />
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||||
<filter targetName="gatkdocs" isVisible="true" />
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||||
<filter targetName="clean.scaladoc" isVisible="false" />
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||||
<filter targetName="init.extracthelp" isVisible="false" />
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||||
<filter targetName="gatk.jar" isVisible="true" />
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||||
<filter targetName="gatk.compile.internal.source" isVisible="false" />
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||||
<filter targetName="committests" isVisible="false" />
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||||
<filter targetName="git.describe" isVisible="false" />
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||||
<filter targetName="package.gatk.lite" isVisible="false" />
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||||
<filter targetName="init.testgatkjar" isVisible="false" />
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||||
<filter targetName="init.jar" isVisible="false" />
|
||||
<filter targetName="queue-extensions.generate" isVisible="true" />
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||||
<filter targetName="test.compile" isVisible="false" />
|
||||
<filter targetName="gatk.manifests" isVisible="false" />
|
||||
<filter targetName="sting.jar" isVisible="false" />
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||||
<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" />
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||||
</targetFilters>
|
||||
<treeView value="true" />
|
||||
<verbose value="true" />
|
||||
<viewClosedWhenNoErrors value="false" />
|
||||
<expanded value="true" />
|
||||
</buildFile>
|
||||
</component>
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||||
<component name="editorHistoryManager">
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||||
<entry file="file://$PROJECT_DIR$/public/scala/src/org/broadinstitute/sting/queue/util/QScriptUtils.scala">
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||||
<provider selected="true" editor-type-id="text-editor">
|
||||
<state line="46" column="6" selection-start="1607" selection-end="1607" vertical-scroll-proportion="0.0">
|
||||
<state line="46" column="6" selection-start="1607" selection-end="1607" vertical-scroll-proportion="0.21216407">
|
||||
<folding />
|
||||
</state>
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||||
</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">
|
||||
<folding />
|
||||
</state>
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||||
</provider>
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||||
</entry>
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||||
<entry file="file://$PROJECT_DIR$/private/java/src/org/broadinstitute/sting/tools/CompareBAMAlignments.java">
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||||
<provider selected="true" editor-type-id="text-editor">
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||||
<state line="47" column="81" selection-start="1757" selection-end="1757" vertical-scroll-proportion="0.0">
|
||||
<folding>
|
||||
<element signature="imports" expanded="true" />
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||||
</folding>
|
||||
</state>
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||||
</provider>
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||||
</entry>
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||||
<entry file="file://$PROJECT_DIR$/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala">
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||||
<provider selected="true" editor-type-id="text-editor">
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||||
<state line="234" column="40" selection-start="10480" selection-end="10480" vertical-scroll-proportion="0.40685225">
|
||||
<state line="211" column="39" selection-start="9612" selection-end="9612" vertical-scroll-proportion="1.4740821">
|
||||
<folding />
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||||
</state>
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||||
</provider>
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||||
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@ -333,6 +464,18 @@
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|||
</splitter-proportions>
|
||||
</settings>
|
||||
</state>
|
||||
<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>
|
||||
<state key="GlobalLibrariesConfigurable.UI">
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||||
<settings>
|
||||
<splitter-proportions>
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||||
|
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@ -346,6 +489,7 @@
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|||
</state>
|
||||
<state key="JdkListConfigurable.UI">
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||||
<settings>
|
||||
<last-edited>1.6</last-edited>
|
||||
<splitter-proportions>
|
||||
<option name="proportions">
|
||||
<list>
|
||||
|
|
@ -362,7 +506,6 @@
|
|||
<option name="proportions">
|
||||
<list>
|
||||
<option value="0.2" />
|
||||
<option value="0.5" />
|
||||
</list>
|
||||
</option>
|
||||
</splitter-proportions>
|
||||
|
|
|
|||
10
cmi-gatk.iml
10
cmi-gatk.iml
|
|
@ -1,5 +1,13 @@
|
|||
<?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://$MODULE_DIR$">
|
||||
|
|
@ -17,7 +25,7 @@
|
|||
</content>
|
||||
<orderEntry type="inheritedJdk" />
|
||||
<orderEntry type="sourceFolder" forTests="false" />
|
||||
<orderEntry type="library" name="lib" level="project" />
|
||||
<orderEntry type="library" name="GATK libraries" level="project" />
|
||||
</component>
|
||||
</module>
|
||||
|
||||
|
|
|
|||
Loading…
Reference in New Issue