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biopet.biopet
Commits
1676c967
Commit
1676c967
authored
Nov 25, 2014
by
wyleung
Browse files
Merge branch 'develop' of git.lumc.nl:biopet/biopet into feature-yamsvp
parents
bbe3ee3d
5abe8248
Changes
308
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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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bbe3ee3d
Biopet
\ No newline at end of file
.idea/compiler.xml
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1676c967
...
...
@@ -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=
"
fals
e"
>
<profile
default=
"false"
name=
"Maven default annotation processors profile"
enabled=
"
tru
e"
>
<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
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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=
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>
<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
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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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1676c967
<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
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<component
name=
"libraryTable"
>
<library
name=
"Maven: commons-httpclient:commons-httpclient:3.1"
>
<CLASSES>
<root
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"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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1676c967
<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
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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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1676c967
<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=
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/>
</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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