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Commit 1676c967 authored by wyleung's avatar wyleung
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Merge branch 'develop' of git.lumc.nl:biopet/biopet into feature-yamsvp

parents bbe3ee3d 5abe8248
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.gitignore
View file @ 1676c967
# Project-related
dependency-reduced-pom.xml
/biopet-framework/src/main/resources/git.properties
git.properties
# gedit
*~
......@@ -8,3 +8,6 @@ dependency-reduced-pom.xml
*.swp
# IntelliJ
.idea/workspace.xml
/target/
/public/target/
/protected/target/
.idea/.name deleted 100644 → 0
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Biopet
\ No newline at end of file
.idea/compiler.xml
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......@@ -17,14 +17,24 @@
<profile default="true" name="Default" enabled="false">
<processorPath useClasspath="true" />
</profile>
<profile default="false" name="Maven default annotation processors profile" enabled="false">
<profile default="false" name="Maven default annotation processors profile" enabled="true">
<sourceOutputDir name="target/generated-sources/annotations" />
<sourceTestOutputDir name="target/generated-test-sources/test-annotations" />
<outputRelativeToContentRoot value="true" />
<processorPath useClasspath="true" />
<module name="BamMetrics" />
<module name="Basty" />
<module name="BiopetFramework" />
<module name="BiopetGatkExtensions" />
<module name="BiopetGatkPipelines" />
<module name="BiopetProtectedPackage" />
<module name="BiopetPublicPackage" />
<module name="Flexiprep" />
<module name="Gentrap" />
<module name="Mapping" />
<module name="Sage" />
<module name="Yamsvp" />
</profile>
</annotationProcessing>
</component>
</project>
</project>
\ No newline at end of file
.idea/dictionaries/warindrarto.xml deleted 100644 → 0
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<component name="ProjectDictionaryState">
<dictionary name="warindrarto">
<words>
<w>arindrarto</w>
<w>biopet</w>
<w>chrom</w>
<w>cufflinks</w>
<w>exon</w>
<w>fastq</w>
<w>gentrap</w>
<w>gsnap</w>
<w>snvmix</w>
<w>tophat</w>
<w>transcriptome</w>
<w>varcaller</w>
<w>varscan</w>
<w>warindrarto</w>
<w>wibowo</w>
</words>
</dictionary>
</component>
\ No newline at end of file
.idea/encodings.xml
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<?xml version="1.0" encoding="UTF-8"?>
<project version="4">
<component name="Encoding" useUTFGuessing="true" native2AsciiForPropertiesFiles="false">
<file url="file://$PROJECT_DIR$/biopet-framework" charset="UTF-8" />
<file url="file://$PROJECT_DIR$" charset="UTF-8" />
<file url="file://$PROJECT_DIR$/protected" charset="UTF-8" />
<file url="file://$PROJECT_DIR$/protected/basty" charset="UTF-8" />
<file url="file://$PROJECT_DIR$/protected/biopet-gatk-extensions" charset="UTF-8" />
<file url="file://$PROJECT_DIR$/protected/biopet-gatk-pipelines" charset="UTF-8" />
<file url="file://$PROJECT_DIR$/protected/biopet-protected-package" charset="UTF-8" />
<file url="file://$PROJECT_DIR$/public" charset="UTF-8" />
<file url="file://$PROJECT_DIR$/public/bammetrics" charset="UTF-8" />
<file url="file://$PROJECT_DIR$/public/biopet-framework" charset="UTF-8" />
<file url="file://$PROJECT_DIR$/public/biopet-public-package" charset="UTF-8" />
<file url="file://$PROJECT_DIR$/public/flexiprep" charset="UTF-8" />
<file url="file://$PROJECT_DIR$/public/gentrap" charset="UTF-8" />
<file url="file://$PROJECT_DIR$/public/mapping" charset="UTF-8" />
<file url="file://$PROJECT_DIR$/public/sage" charset="UTF-8" />
<file url="file://$PROJECT_DIR$/public/yamsvp" charset="UTF-8" />
</component>
</project>
</project>
\ No newline at end of file
.idea/inspectionProfiles/Project_Default.xml deleted 100644 → 0
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<component name="InspectionProjectProfileManager">
<profile version="1.0" is_locked="false">
<option name="myName" value="Project Default" />
<option name="myLocal" value="false" />
<inspection_tool class="LoggerInitializedWithForeignClass" enabled="false" level="WARNING" enabled_by_default="false">
<option name="loggerClassName" value="org.apache.log4j.Logger,org.slf4j.LoggerFactory,org.apache.commons.logging.LogFactory,java.util.logging.Logger" />
<option name="loggerFactoryMethodName" value="getLogger,getLogger,getLog,getLogger" />
</inspection_tool>
<inspection_tool class="MatchToPartialFunction" enabled="false" level="WARNING" enabled_by_default="false" />
<inspection_tool class="SpellCheckingInspection" enabled="false" level="TYPO" enabled_by_default="false">
<option name="processCode" value="true" />
<option name="processLiterals" value="true" />
<option name="processComments" value="true" />
</inspection_tool>
</profile>
</component>
\ No newline at end of file
.idea/inspectionProfiles/profiles_settings.xml deleted 100644 → 0
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<component name="InspectionProjectProfileManager">
<settings>
<option name="PROJECT_PROFILE" value="Project Default" />
<option name="USE_PROJECT_PROFILE" value="true" />
<version value="1.0" />
</settings>
</component>
\ No newline at end of file
.idea/libraries/Maven__colt_colt_1_2_0.xml 0 → 100644
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<component name="libraryTable">
<library name="Maven: colt:colt:1.2.0">
<CLASSES>
<root url="jar://$MAVEN_REPOSITORY$/colt/colt/1.2.0/colt-1.2.0.jar!/" />
</CLASSES>
<JAVADOC>
<root url="jar://$MAVEN_REPOSITORY$/colt/colt/1.2.0/colt-1.2.0-javadoc.jar!/" />
</JAVADOC>
<SOURCES>
<root url="jar://$MAVEN_REPOSITORY$/colt/colt/1.2.0/colt-1.2.0-sources.jar!/" />
</SOURCES>
</library>
</component>
\ No newline at end of file
.idea/libraries/Maven__com_google_code_cofoja_cofoja_1_0_r139.xml 0 → 100644
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<component name="libraryTable">
<library name="Maven: com.google.code.cofoja:cofoja:1.0-r139">
<CLASSES>
<root url="jar://$MAVEN_REPOSITORY$/com/google/code/cofoja/cofoja/1.0-r139/cofoja-1.0-r139.jar!/" />
</CLASSES>
<JAVADOC>
<root url="jar://$MAVEN_REPOSITORY$/com/google/code/cofoja/cofoja/1.0-r139/cofoja-1.0-r139-javadoc.jar!/" />
</JAVADOC>
<SOURCES>
<root url="jar://$MAVEN_REPOSITORY$/com/google/code/cofoja/cofoja/1.0-r139/cofoja-1.0-r139-sources.jar!/" />
</SOURCES>
</library>
</component>
\ No newline at end of file
.idea/libraries/Maven__com_google_code_gson_gson_2_2_2.xml 0 → 100644
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<component name="libraryTable">
<library name="Maven: com.google.code.gson:gson:2.2.2">
<CLASSES>
<root url="jar://$MAVEN_REPOSITORY$/com/google/code/gson/gson/2.2.2/gson-2.2.2.jar!/" />
</CLASSES>
<JAVADOC>
<root url="jar://$MAVEN_REPOSITORY$/com/google/code/gson/gson/2.2.2/gson-2.2.2-javadoc.jar!/" />
</JAVADOC>
<SOURCES>
<root url="jar://$MAVEN_REPOSITORY$/com/google/code/gson/gson/2.2.2/gson-2.2.2-sources.jar!/" />
</SOURCES>
</library>
</component>
\ No newline at end of file
.idea/libraries/Maven__com_jamesmurty_utils_java_xmlbuilder_0_4.xml 0 → 100644
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<component name="libraryTable">
<library name="Maven: com.jamesmurty.utils:java-xmlbuilder:0.4">
<CLASSES>
<root url="jar://$MAVEN_REPOSITORY$/com/jamesmurty/utils/java-xmlbuilder/0.4/java-xmlbuilder-0.4.jar!/" />
</CLASSES>
<JAVADOC>
<root url="jar://$MAVEN_REPOSITORY$/com/jamesmurty/utils/java-xmlbuilder/0.4/java-xmlbuilder-0.4-javadoc.jar!/" />
</JAVADOC>
<SOURCES>
<root url="jar://$MAVEN_REPOSITORY$/com/jamesmurty/utils/java-xmlbuilder/0.4/java-xmlbuilder-0.4-sources.jar!/" />
</SOURCES>
</library>
</component>
\ No newline at end of file
.idea/libraries/Maven__commons_codec_commons_codec_1_3.xml 0 → 100644
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<component name="libraryTable">
<library name="Maven: commons-codec:commons-codec:1.3">
<CLASSES>
<root url="jar://$MAVEN_REPOSITORY$/commons-codec/commons-codec/1.3/commons-codec-1.3.jar!/" />
</CLASSES>
<JAVADOC>
<root url="jar://$MAVEN_REPOSITORY$/commons-codec/commons-codec/1.3/commons-codec-1.3-javadoc.jar!/" />
</JAVADOC>
<SOURCES>
<root url="jar://$MAVEN_REPOSITORY$/commons-codec/commons-codec/1.3/commons-codec-1.3-sources.jar!/" />
</SOURCES>
</library>
</component>
\ No newline at end of file
.idea/libraries/Maven__commons_collections_commons_collections_3_2_1.xml 0 → 100644
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<component name="libraryTable">
<library name="Maven: commons-collections:commons-collections:3.2.1">
<CLASSES>
<root url="jar://$MAVEN_REPOSITORY$/commons-collections/commons-collections/3.2.1/commons-collections-3.2.1.jar!/" />
</CLASSES>
<JAVADOC>
<root url="jar://$MAVEN_REPOSITORY$/commons-collections/commons-collections/3.2.1/commons-collections-3.2.1-javadoc.jar!/" />
</JAVADOC>
<SOURCES>
<root url="jar://$MAVEN_REPOSITORY$/commons-collections/commons-collections/3.2.1/commons-collections-3.2.1-sources.jar!/" />
</SOURCES>
</library>
</component>
\ No newline at end of file
.idea/libraries/Maven__commons_httpclient_commons_httpclient_3_1.xml 0 → 100644
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<component name="libraryTable">
<library name="Maven: commons-httpclient:commons-httpclient:3.1">
<CLASSES>
<root url="jar://$MAVEN_REPOSITORY$/commons-httpclient/commons-httpclient/3.1/commons-httpclient-3.1.jar!/" />
</CLASSES>
<JAVADOC>
<root url="jar://$MAVEN_REPOSITORY$/commons-httpclient/commons-httpclient/3.1/commons-httpclient-3.1-javadoc.jar!/" />
</JAVADOC>
<SOURCES>
<root url="jar://$MAVEN_REPOSITORY$/commons-httpclient/commons-httpclient/3.1/commons-httpclient-3.1-sources.jar!/" />
</SOURCES>
</library>
</component>
\ No newline at end of file
.idea/libraries/Maven__commons_io_commons_io_2_1.xml 0 → 100644
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<component name="libraryTable">
<library name="Maven: commons-io:commons-io:2.1">
<CLASSES>
<root url="jar://$MAVEN_REPOSITORY$/commons-io/commons-io/2.1/commons-io-2.1.jar!/" />
</CLASSES>
<JAVADOC>
<root url="jar://$MAVEN_REPOSITORY$/commons-io/commons-io/2.1/commons-io-2.1-javadoc.jar!/" />
</JAVADOC>
<SOURCES>
<root url="jar://$MAVEN_REPOSITORY$/commons-io/commons-io/2.1/commons-io-2.1-sources.jar!/" />
</SOURCES>
</library>
</component>
\ No newline at end of file
.idea/libraries/Maven__commons_lang_commons_lang_2_5.xml 0 → 100644
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<component name="libraryTable">
<library name="Maven: commons-lang:commons-lang:2.5">
<CLASSES>
<root url="jar://$MAVEN_REPOSITORY$/commons-lang/commons-lang/2.5/commons-lang-2.5.jar!/" />
</CLASSES>
<JAVADOC>
<root url="jar://$MAVEN_REPOSITORY$/commons-lang/commons-lang/2.5/commons-lang-2.5-javadoc.jar!/" />
</JAVADOC>
<SOURCES>
<root url="jar://$MAVEN_REPOSITORY$/commons-lang/commons-lang/2.5/commons-lang-2.5-sources.jar!/" />
</SOURCES>
</library>
</component>
\ No newline at end of file
.idea/libraries/Maven__commons_logging_commons_logging_1_1_1.xml 0 → 100644
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<component name="libraryTable">
<library name="Maven: commons-logging:commons-logging:1.1.1">
<CLASSES>
<root url="jar://$MAVEN_REPOSITORY$/commons-logging/commons-logging/1.1.1/commons-logging-1.1.1.jar!/" />
</CLASSES>
<JAVADOC>
<root url="jar://$MAVEN_REPOSITORY$/commons-logging/commons-logging/1.1.1/commons-logging-1.1.1-javadoc.jar!/" />
</JAVADOC>
<SOURCES>
<root url="jar://$MAVEN_REPOSITORY$/commons-logging/commons-logging/1.1.1/commons-logging-1.1.1-sources.jar!/" />
</SOURCES>
</library>
</component>
\ No newline at end of file
.idea/libraries/Maven__concurrent_concurrent_1_3_4.xml 0 → 100644
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<component name="libraryTable">
<library name="Maven: concurrent:concurrent:1.3.4">
<CLASSES>
<root url="jar://$MAVEN_REPOSITORY$/concurrent/concurrent/1.3.4/concurrent-1.3.4.jar!/" />
</CLASSES>
<JAVADOC>
<root url="jar://$MAVEN_REPOSITORY$/concurrent/concurrent/1.3.4/concurrent-1.3.4-javadoc.jar!/" />
</JAVADOC>
<SOURCES>
<root url="jar://$MAVEN_REPOSITORY$/concurrent/concurrent/1.3.4/concurrent-1.3.4-sources.jar!/" />
</SOURCES>
</library>
</component>
\ No newline at end of file
.idea/libraries/Maven__dom4j_dom4j_1_6_1.xml 0 → 100644
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<component name="libraryTable">
<library name="Maven: dom4j:dom4j:1.6.1">
<CLASSES>
<root url="jar://$MAVEN_REPOSITORY$/dom4j/dom4j/1.6.1/dom4j-1.6.1.jar!/" />
</CLASSES>
<JAVADOC>
<root url="jar://$MAVEN_REPOSITORY$/dom4j/dom4j/1.6.1/dom4j-1.6.1-javadoc.jar!/" />
</JAVADOC>
<SOURCES>
<root url="jar://$MAVEN_REPOSITORY$/dom4j/dom4j/1.6.1/dom4j-1.6.1-sources.jar!/" />
</SOURCES>
</library>
</component>
\ No newline at end of file
.idea/libraries/Maven__gov_nist_math_jama_1_0_2.xml 0 → 100644
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<component name="libraryTable">
<library name="Maven: gov.nist.math:jama:1.0.2">
<CLASSES>
<root url="jar://$MAVEN_REPOSITORY$/gov/nist/math/jama/1.0.2/jama-1.0.2.jar!/" />
</CLASSES>
<JAVADOC>
<root url="jar://$MAVEN_REPOSITORY$/gov/nist/math/jama/1.0.2/jama-1.0.2-javadoc.jar!/" />
</JAVADOC>
<SOURCES>
<root url="jar://$MAVEN_REPOSITORY$/gov/nist/math/jama/1.0.2/jama-1.0.2-sources.jar!/" />
</SOURCES>
</library>
</component>
\ No newline at end of file
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