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biopet.biopet
Commits
e685c701
Commit
e685c701
authored
Nov 25, 2014
by
Peter van 't Hof
Browse files
Remove unused files
parent
20b3a06d
Changes
40
Hide whitespace changes
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.idea/.name
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Biopet
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.idea/compiler.xml
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<?xml version="1.0" encoding="UTF-8"?>
<project
version=
"4"
>
<component
name=
"CompilerConfiguration"
>
<option
name=
"DEFAULT_COMPILER"
value=
"Javac"
/>
<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"
/>
</wildcardResourcePatterns>
<annotationProcessing>
<profile
default=
"true"
name=
"Default"
enabled=
"false"
>
<processorPath
useClasspath=
"true"
/>
</profile>
<profile
default=
"false"
name=
"Maven default annotation processors profile"
enabled=
"false"
>
<sourceOutputDir
name=
"target/generated-sources/annotations"
/>
<sourceTestOutputDir
name=
"target/generated-test-sources/test-annotations"
/>
<outputRelativeToContentRoot
value=
"true"
/>
<processorPath
useClasspath=
"true"
/>
<module
name=
"BiopetFramework"
/>
</profile>
</annotationProcessing>
</component>
</project>
.idea/copyright/profiles_settings.xml
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<component
name=
"CopyrightManager"
>
<settings
default=
""
/>
</component>
\ 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=
"false"
>
<file
url=
"file://$PROJECT_DIR$/biopet-framework"
charset=
"UTF-8"
/>
</component>
</project>
.idea/inspectionProfiles/Project_Default.xml
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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__com_beust_jcommander_1_27.xml
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<component
name=
"libraryTable"
>
<library
name=
"Maven: com.beust:jcommander:1.27"
>
<CLASSES>
<root
url=
"jar://$MAVEN_REPOSITORY$/com/beust/jcommander/1.27/jcommander-1.27.jar!/"
/>
</CLASSES>
<JAVADOC>
<root
url=
"jar://$MAVEN_REPOSITORY$/com/beust/jcommander/1.27/jcommander-1.27-javadoc.jar!/"
/>
</JAVADOC>
<SOURCES>
<root
url=
"jar://$MAVEN_REPOSITORY$/com/beust/jcommander/1.27/jcommander-1.27-sources.jar!/"
/>
</SOURCES>
</library>
</component>
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.idea/libraries/Maven__com_github_julien_truffaut_monocle_core_2_11_0_5_0.xml
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<component
name=
"libraryTable"
>
<library
name=
"Maven: com.github.julien-truffaut:monocle-core_2.11:0.5.0"
>
<CLASSES>
<root
url=
"jar://$MAVEN_REPOSITORY$/com/github/julien-truffaut/monocle-core_2.11/0.5.0/monocle-core_2.11-0.5.0.jar!/"
/>
</CLASSES>
<JAVADOC>
<root
url=
"jar://$MAVEN_REPOSITORY$/com/github/julien-truffaut/monocle-core_2.11/0.5.0/monocle-core_2.11-0.5.0-javadoc.jar!/"
/>
</JAVADOC>
<SOURCES>
<root
url=
"jar://$MAVEN_REPOSITORY$/com/github/julien-truffaut/monocle-core_2.11/0.5.0/monocle-core_2.11-0.5.0-sources.jar!/"
/>
</SOURCES>
</library>
</component>
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.idea/libraries/Maven__com_github_scopt_scopt_2_10_3_2_0.xml
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<component
name=
"libraryTable"
>
<library
name=
"Maven: com.github.scopt:scopt_2.10:3.2.0"
>
<CLASSES>
<root
url=
"jar://$MAVEN_REPOSITORY$/com/github/scopt/scopt_2.10/3.2.0/scopt_2.10-3.2.0.jar!/"
/>
</CLASSES>
<JAVADOC>
<root
url=
"jar://$MAVEN_REPOSITORY$/com/github/scopt/scopt_2.10/3.2.0/scopt_2.10-3.2.0-javadoc.jar!/"
/>
</JAVADOC>
<SOURCES>
<root
url=
"jar://$MAVEN_REPOSITORY$/com/github/scopt/scopt_2.10/3.2.0/scopt_2.10-3.2.0-sources.jar!/"
/>
</SOURCES>
</library>
</component>
\ No newline at end of file
.idea/libraries/Maven__com_google_guava_guava_18_0.xml
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<component
name=
"libraryTable"
>
<library
name=
"Maven: com.google.guava:guava:18.0"
>
<CLASSES>
<root
url=
"jar://$MAVEN_REPOSITORY$/com/google/guava/guava/18.0/guava-18.0.jar!/"
/>
</CLASSES>
<JAVADOC>
<root
url=
"jar://$MAVEN_REPOSITORY$/com/google/guava/guava/18.0/guava-18.0-javadoc.jar!/"
/>
</JAVADOC>
<SOURCES>
<root
url=
"jar://$MAVEN_REPOSITORY$/com/google/guava/guava/18.0/guava-18.0-sources.jar!/"
/>
</SOURCES>
</library>
</component>
\ No newline at end of file
.idea/libraries/Maven__io_argonaut_argonaut_2_11_6_1_M4.xml
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<component
name=
"libraryTable"
>
<library
name=
"Maven: io.argonaut:argonaut_2.11:6.1-M4"
>
<CLASSES>
<root
url=
"jar://$MAVEN_REPOSITORY$/io/argonaut/argonaut_2.11/6.1-M4/argonaut_2.11-6.1-M4.jar!/"
/>
</CLASSES>
<JAVADOC>
<root
url=
"jar://$MAVEN_REPOSITORY$/io/argonaut/argonaut_2.11/6.1-M4/argonaut_2.11-6.1-M4-javadoc.jar!/"
/>
</JAVADOC>
<SOURCES>
<root
url=
"jar://$MAVEN_REPOSITORY$/io/argonaut/argonaut_2.11/6.1-M4/argonaut_2.11-6.1-M4-sources.jar!/"
/>
</SOURCES>
</library>
</component>
\ No newline at end of file
.idea/libraries/Maven__junit_junit_4_10.xml
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<component
name=
"libraryTable"
>
<library
name=
"Maven: junit:junit:4.10"
>
<CLASSES>
<root
url=
"jar://$MAVEN_REPOSITORY$/junit/junit/4.10/junit-4.10.jar!/"
/>
</CLASSES>
<JAVADOC>
<root
url=
"jar://$MAVEN_REPOSITORY$/junit/junit/4.10/junit-4.10-javadoc.jar!/"
/>
</JAVADOC>
<SOURCES>
<root
url=
"jar://$MAVEN_REPOSITORY$/junit/junit/4.10/junit-4.10-sources.jar!/"
/>
</SOURCES>
</library>
</component>
\ No newline at end of file
.idea/libraries/Maven__org_beanshell_bsh_2_0b4.xml
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<component
name=
"libraryTable"
>
<library
name=
"Maven: org.beanshell:bsh:2.0b4"
>
<CLASSES>
<root
url=
"jar://$MAVEN_REPOSITORY$/org/beanshell/bsh/2.0b4/bsh-2.0b4.jar!/"
/>
</CLASSES>
<JAVADOC>
<root
url=
"jar://$MAVEN_REPOSITORY$/org/beanshell/bsh/2.0b4/bsh-2.0b4-javadoc.jar!/"
/>
</JAVADOC>
<SOURCES>
<root
url=
"jar://$MAVEN_REPOSITORY$/org/beanshell/bsh/2.0b4/bsh-2.0b4-sources.jar!/"
/>
</SOURCES>
</library>
</component>
\ No newline at end of file
.idea/libraries/Maven__org_biojava_biojava3_core_3_1_0.xml
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<component
name=
"libraryTable"
>
<library
name=
"Maven: org.biojava:biojava3-core:3.1.0"
>
<CLASSES>
<root
url=
"jar://$MAVEN_REPOSITORY$/org/biojava/biojava3-core/3.1.0/biojava3-core-3.1.0.jar!/"
/>
</CLASSES>
<JAVADOC>
<root
url=
"jar://$MAVEN_REPOSITORY$/org/biojava/biojava3-core/3.1.0/biojava3-core-3.1.0-javadoc.jar!/"
/>
</JAVADOC>
<SOURCES>
<root
url=
"jar://$MAVEN_REPOSITORY$/org/biojava/biojava3-core/3.1.0/biojava3-core-3.1.0-sources.jar!/"
/>
</SOURCES>
</library>
</component>
\ No newline at end of file
.idea/libraries/Maven__org_biojava_biojava3_sequencing_3_1_0.xml
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<component
name=
"libraryTable"
>
<library
name=
"Maven: org.biojava:biojava3-sequencing:3.1.0"
>
<CLASSES>
<root
url=
"jar://$MAVEN_REPOSITORY$/org/biojava/biojava3-sequencing/3.1.0/biojava3-sequencing-3.1.0.jar!/"
/>
</CLASSES>
<JAVADOC>
<root
url=
"jar://$MAVEN_REPOSITORY$/org/biojava/biojava3-sequencing/3.1.0/biojava3-sequencing-3.1.0-javadoc.jar!/"
/>
</JAVADOC>
<SOURCES>
<root
url=
"jar://$MAVEN_REPOSITORY$/org/biojava/biojava3-sequencing/3.1.0/biojava3-sequencing-3.1.0-sources.jar!/"
/>
</SOURCES>
</library>
</component>
\ No newline at end of file
.idea/libraries/Maven__org_broadinstitute_gatk_gatk_queue_package_distribution_3_2.xml
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<component
name=
"libraryTable"
>
<library
name=
"Maven: org.broadinstitute.gatk:gatk-queue-package-distribution:3.2"
>
<CLASSES>
<root
url=
"jar://$MAVEN_REPOSITORY$/org/broadinstitute/gatk/gatk-queue-package-distribution/3.2/gatk-queue-package-distribution-3.2.jar!/"
/>
</CLASSES>
<JAVADOC>
<root
url=
"jar://$MAVEN_REPOSITORY$/org/broadinstitute/gatk/gatk-queue-package-distribution/3.2/gatk-queue-package-distribution-3.2-javadoc.jar!/"
/>
</JAVADOC>
<SOURCES>
<root
url=
"jar://$MAVEN_REPOSITORY$/org/broadinstitute/gatk/gatk-queue-package-distribution/3.2/gatk-queue-package-distribution-3.2-sources.jar!/"
/>
<root
url=
"file://$PROJECT_DIR$/../htsjdk/src/java"
/>
<root
url=
"file://$PROJECT_DIR$/../htsjdk/src/tests/java"
/>
</SOURCES>
</library>
</component>
\ No newline at end of file
.idea/libraries/Maven__org_broadinstitute_gatk_gatk_queue_package_distribution_3_3.xml
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<component
name=
"libraryTable"
>
<library
name=
"Maven: org.broadinstitute.gatk:gatk-queue-package-distribution:3.3"
>
<CLASSES>
<root
url=
"jar://$MAVEN_REPOSITORY$/org/broadinstitute/gatk/gatk-queue-package-distribution/3.3/gatk-queue-package-distribution-3.3.jar!/"
/>
</CLASSES>
<JAVADOC>
<root
url=
"jar://$MAVEN_REPOSITORY$/org/broadinstitute/gatk/gatk-queue-package-distribution/3.3/gatk-queue-package-distribution-3.3-javadoc.jar!/"
/>
</JAVADOC>
<SOURCES>
<root
url=
"jar://$MAVEN_REPOSITORY$/org/broadinstitute/gatk/gatk-queue-package-distribution/3.3/gatk-queue-package-distribution-3.3-sources.jar!/"
/>
</SOURCES>
</library>
</component>
\ No newline at end of file
.idea/libraries/Maven__org_hamcrest_hamcrest_core_1_1.xml
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<component
name=
"libraryTable"
>
<library
name=
"Maven: org.hamcrest:hamcrest-core:1.1"
>
<CLASSES>
<root
url=
"jar://$MAVEN_REPOSITORY$/org/hamcrest/hamcrest-core/1.1/hamcrest-core-1.1.jar!/"
/>
</CLASSES>
<JAVADOC>
<root
url=
"jar://$MAVEN_REPOSITORY$/org/hamcrest/hamcrest-core/1.1/hamcrest-core-1.1-javadoc.jar!/"
/>
</JAVADOC>
<SOURCES>
<root
url=
"jar://$MAVEN_REPOSITORY$/org/hamcrest/hamcrest-core/1.1/hamcrest-core-1.1-sources.jar!/"
/>
</SOURCES>
</library>
</component>
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.idea/libraries/Maven__org_mockito_mockito_all_1_9_5.xml
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<component
name=
"libraryTable"
>
<library
name=
"Maven: org.mockito:mockito-all:1.9.5"
>
<CLASSES>
<root
url=
"jar://$MAVEN_REPOSITORY$/org/mockito/mockito-all/1.9.5/mockito-all-1.9.5.jar!/"
/>
</CLASSES>
<JAVADOC>
<root
url=
"jar://$MAVEN_REPOSITORY$/org/mockito/mockito-all/1.9.5/mockito-all-1.9.5-javadoc.jar!/"
/>
</JAVADOC>
<SOURCES>
<root
url=
"jar://$MAVEN_REPOSITORY$/org/mockito/mockito-all/1.9.5/mockito-all-1.9.5-sources.jar!/"
/>
</SOURCES>
</library>
</component>
\ No newline at end of file
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