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Commit b7521058 authored by bow's avatar bow
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Merge branch 'develop' into feature-wipereads

parents 9c3639f6 35dba66e
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.gitignore
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# Project-related
dependency-reduced-pom.xml
/biopet-framework/src/main/resources/git.properties
# gedit
*~
# Vim
*.swp
/biopet-framework/src/main/resources/git.properties
# IntelliJ
.idea/workspace.xml
.idea/.name 0 → 100644
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Biopet
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.idea/compiler.xml 0 → 100644
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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 0 → 100644
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<component name="CopyrightManager">
<settings default="" />
</component>
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.idea/dictionaries/warindrarto.xml 0 → 100644
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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>
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.idea/encodings.xml 0 → 100644
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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 0 → 100644
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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>
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.idea/inspectionProfiles/profiles_settings.xml 0 → 100644
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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>
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<component name="libraryTable">
<library name="Maven: com.baqend:bloom-filter:1.02">
<CLASSES>
<root url="jar://$MAVEN_REPOSITORY$/com/baqend/bloom-filter/1.02/bloom-filter-1.02.jar!/" />
</CLASSES>
<JAVADOC>
<root url="jar://$MAVEN_REPOSITORY$/com/baqend/bloom-filter/1.02/bloom-filter-1.02-javadoc.jar!/" />
</JAVADOC>
<SOURCES>
<root url="jar://$MAVEN_REPOSITORY$/com/baqend/bloom-filter/1.02/bloom-filter-1.02-sources.jar!/" />
</SOURCES>
</library>
</component>
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.idea/libraries/Maven__com_beust_jcommander_1_27.xml 0 → 100644
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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 0 → 100644
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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 0 → 100644
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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>
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.idea/libraries/Maven__com_google_code_gson_gson_2_2_4.xml 0 → 100644
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<component name="libraryTable">
<library name="Maven: com.google.code.gson:gson:2.2.4">
<CLASSES>
<root url="jar://$MAVEN_REPOSITORY$/com/google/code/gson/gson/2.2.4/gson-2.2.4.jar!/" />
</CLASSES>
<JAVADOC>
<root url="jar://$MAVEN_REPOSITORY$/com/google/code/gson/gson/2.2.4/gson-2.2.4-javadoc.jar!/" />
</JAVADOC>
<SOURCES>
<root url="jar://$MAVEN_REPOSITORY$/com/google/code/gson/gson/2.2.4/gson-2.2.4-sources.jar!/" />
</SOURCES>
</library>
</component>
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.idea/libraries/Maven__com_google_guava_guava_17_0.xml 0 → 100644
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<component name="libraryTable">
<library name="Maven: com.google.guava:guava:17.0">
<CLASSES>
<root url="jar://$MAVEN_REPOSITORY$/com/google/guava/guava/17.0/guava-17.0.jar!/" />
</CLASSES>
<JAVADOC>
<root url="jar://$MAVEN_REPOSITORY$/com/google/guava/guava/17.0/guava-17.0-javadoc.jar!/" />
</JAVADOC>
<SOURCES>
<root url="jar://$MAVEN_REPOSITORY$/com/google/guava/guava/17.0/guava-17.0-sources.jar!/" />
</SOURCES>
</library>
</component>
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.idea/libraries/Maven__io_argonaut_argonaut_2_11_6_1_M4.xml 0 → 100644
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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>
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.idea/libraries/Maven__junit_junit_4_10.xml 0 → 100644
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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>
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.idea/libraries/Maven__org_apache_commons_commons_pool2_2_2.xml 0 → 100644
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<component name="libraryTable">
<library name="Maven: org.apache.commons:commons-pool2:2.2">
<CLASSES>
<root url="jar://$MAVEN_REPOSITORY$/org/apache/commons/commons-pool2/2.2/commons-pool2-2.2.jar!/" />
</CLASSES>
<JAVADOC>
<root url="jar://$MAVEN_REPOSITORY$/org/apache/commons/commons-pool2/2.2/commons-pool2-2.2-javadoc.jar!/" />
</JAVADOC>
<SOURCES>
<root url="jar://$MAVEN_REPOSITORY$/org/apache/commons/commons-pool2/2.2/commons-pool2-2.2-sources.jar!/" />
</SOURCES>
</library>
</component>
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.idea/libraries/Maven__org_beanshell_bsh_2_0b4.xml 0 → 100644
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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>
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.idea/libraries/Maven__org_biojava_biojava3_core_3_1_0.xml 0 → 100644
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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>
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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!/" />
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<JAVADOC>
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<SOURCES>
<root url="jar://$MAVEN_REPOSITORY$/org/biojava/biojava3-sequencing/3.1.0/biojava3-sequencing-3.1.0-sources.jar!/" />
</SOURCES>
</library>
</component>
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