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Commit 9a5a8577 authored by Wai Yi Leung's avatar Wai Yi Leung
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Merge branch 'patch-ide_files' into 'develop' 

Patch ide files

This patch excludes existing IDE-specific files from the git index. I'm not sure yet if this solution works clean for everybody, so please test it first locally.

@wyleung & @p.j.van_t_hof , this is what we discussed earlier with the `*.iml` files and `.idea/*` files.

See merge request !98
parents a92d12f8 286a975f
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.gitignore
View file @ 9a5a8577
......@@ -7,7 +7,8 @@ git.properties
# Vim
*.swp
# IntelliJ
.idea/workspace.xml
.idea/*
*.iml
/target/
/public/target/
/protected/target/
.idea/compiler.xml deleted 100644 → 0
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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="true">
<sourceOutputDir name="target/generated-sources/annotations" />
<sourceTestOutputDir name="target/generated-test-sources/test-annotations" />
<outputRelativeToContentRoot value="true" />
<processorPath useClasspath="true" />
<module name="Bam2Wig" />
<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>
\ No newline at end of file
.idea/copyright/profiles_settings.xml deleted 100644 → 0
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<component name="CopyrightManager">
<settings default="" />
</component>
\ No newline at end of file
.idea/encodings.xml deleted 100644 → 0
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<?xml version="1.0" encoding="UTF-8"?>
<project version="4">
<component name="Encoding" useUTFGuessing="true" native2AsciiForPropertiesFiles="false">
<file url="file://$PROJECT_DIR$" 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/bam2wig" 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>
\ No newline at end of file
.idea/libraries/Maven__colt_colt_1_2_0.xml deleted 100644 → 0
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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_beust_jcommander_1_27.xml deleted 100644 → 0
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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>
\ No newline at end of file
.idea/libraries/Maven__com_github_julien_truffaut_monocle_core_2_11_0_5_0.xml deleted 100644 → 0
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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>
\ No newline at end of file
.idea/libraries/Maven__com_github_scopt_scopt_2_10_3_2_0.xml deleted 100644 → 0
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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_code_cofoja_cofoja_1_0_r139.xml deleted 100644 → 0
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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 deleted 100644 → 0
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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_google_guava_guava_18_0.xml deleted 100644 → 0
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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__com_jamesmurty_utils_java_xmlbuilder_0_4.xml deleted 100644 → 0
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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 deleted 100644 → 0
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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 deleted 100644 → 0
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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 deleted 100644 → 0
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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 deleted 100644 → 0
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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 deleted 100644 → 0
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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 deleted 100644 → 0
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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 deleted 100644 → 0
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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 deleted 100644 → 0
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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
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