Merge branch 'release-0.2.0' into 'master'

Release 0.2.0 See merge request !64

Merge branch 'release-0.2.0' into 'master'
Release 0.2.0 See merge request !64
19d495c5 · Peter van 't Hof · 187bae8b · 1572cb02 · 19d495c5 · 19d495c5
Commit 19d495c5 authored Dec 09, 2014 by Peter van 't Hof
--- a/.idea/libraries/Maven__org_slf4j_slf4j_api_1_6_1.xml
+++ b/.idea/libraries/Maven__org_slf4j_slf4j_api_1_6_1.xml
+<component name="libraryTable">
+  <library name="Maven: org.slf4j:slf4j-api:1.6.1">
+    <CLASSES>
+      <root url="jar://$MAVEN_REPOSITORY$/org/slf4j/slf4j-api/1.6.1/slf4j-api-1.6.1.jar!/" />
+    </CLASSES>
+    <JAVADOC>
+      <root url="jar://$MAVEN_REPOSITORY$/org/slf4j/slf4j-api/1.6.1/slf4j-api-1.6.1-javadoc.jar!/" />
+    </JAVADOC>
+    <SOURCES>
+      <root url="jar://$MAVEN_REPOSITORY$/org/slf4j/slf4j-api/1.6.1/slf4j-api-1.6.1-sources.jar!/" />
+    </SOURCES>
+  </library>
+</component>
\ No newline at end of file
--- a/.idea/libraries/Maven__org_slf4j_slf4j_log4j12_1_6_1.xml
+++ b/.idea/libraries/Maven__org_slf4j_slf4j_log4j12_1_6_1.xml
+<component name="libraryTable">
+  <library name="Maven: org.slf4j:slf4j-log4j12:1.6.1">
+    <CLASSES>
+      <root url="jar://$MAVEN_REPOSITORY$/org/slf4j/slf4j-log4j12/1.6.1/slf4j-log4j12-1.6.1.jar!/" />
+    </CLASSES>
+    <JAVADOC>
+      <root url="jar://$MAVEN_REPOSITORY$/org/slf4j/slf4j-log4j12/1.6.1/slf4j-log4j12-1.6.1-javadoc.jar!/" />
+    </JAVADOC>
+    <SOURCES>
+      <root url="jar://$MAVEN_REPOSITORY$/org/slf4j/slf4j-log4j12/1.6.1/slf4j-log4j12-1.6.1-sources.jar!/" />
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+</component>
\ No newline at end of file
--- a/.idea/libraries/Maven__org_testng_testng_6_8.xml
+++ b/.idea/libraries/Maven__org_testng_testng_6_8.xml
+<component name="libraryTable">
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+    </JAVADOC>
+    <SOURCES>
+      <root url="jar://$MAVEN_REPOSITORY$/org/testng/testng/6.8/testng-6.8-sources.jar!/" />
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+</component>
\ No newline at end of file
--- a/.idea/libraries/Maven__org_xerial_snappy_snappy_java_1_0_3_rc3.xml
+++ b/.idea/libraries/Maven__org_xerial_snappy_snappy_java_1_0_3_rc3.xml
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+    <JAVADOC>
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+    <SOURCES>
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\ No newline at end of file
--- a/.idea/libraries/Maven__org_yaml_snakeyaml_1_6.xml
+++ b/.idea/libraries/Maven__org_yaml_snakeyaml_1_6.xml
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+</component>
\ No newline at end of file
--- a/.idea/libraries/Maven__picard_picard_1_120_1579.xml
+++ b/.idea/libraries/Maven__picard_picard_1_120_1579.xml
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+    <SOURCES>
+      <root url="jar://$MAVEN_REPOSITORY$/picard/picard/1.120.1579/picard-1.120.1579-sources.jar!/" />
+    </SOURCES>
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+</component>
\ No newline at end of file
--- a/.idea/libraries/Maven__samtools_htsjdk_1_120_1620.xml
+++ b/.idea/libraries/Maven__samtools_htsjdk_1_120_1620.xml
+<component name="libraryTable">
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+    <JAVADOC>
+      <root url="jar://$MAVEN_REPOSITORY$/samtools/htsjdk/1.120.1620/htsjdk-1.120.1620-javadoc.jar!/" />
+    </JAVADOC>
+    <SOURCES>
+      <root url="jar://$MAVEN_REPOSITORY$/samtools/htsjdk/1.120.1620/htsjdk-1.120.1620-sources.jar!/" />
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+</component>
\ No newline at end of file
--- a/.idea/libraries/Maven__stax_stax_1_2_0.xml
+++ b/.idea/libraries/Maven__stax_stax_1_2_0.xml
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+    </JAVADOC>
+    <SOURCES>
+      <root url="jar://$MAVEN_REPOSITORY$/stax/stax/1.2.0/stax-1.2.0-sources.jar!/" />
+    </SOURCES>
+  </library>
+</component>
\ No newline at end of file
--- a/.idea/libraries/Maven__stax_stax_api_1_0_1.xml
+++ b/.idea/libraries/Maven__stax_stax_api_1_0_1.xml
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+    </CLASSES>
+    <JAVADOC>
+      <root url="jar://$MAVEN_REPOSITORY$/stax/stax-api/1.0.1/stax-api-1.0.1-javadoc.jar!/" />
+    </JAVADOC>
+    <SOURCES>
+      <root url="jar://$MAVEN_REPOSITORY$/stax/stax-api/1.0.1/stax-api-1.0.1-sources.jar!/" />
+    </SOURCES>
+  </library>
+</component>
\ No newline at end of file
--- a/.idea/libraries/Maven__us_levk_drmaa_common_1_0.xml
+++ b/.idea/libraries/Maven__us_levk_drmaa_common_1_0.xml
+<component name="libraryTable">
+  <library name="Maven: us.levk:drmaa-common:1.0">
+    <CLASSES>
+      <root url="jar://$MAVEN_REPOSITORY$/us/levk/drmaa-common/1.0/drmaa-common-1.0.jar!/" />
+    </CLASSES>
+    <JAVADOC>
+      <root url="jar://$MAVEN_REPOSITORY$/us/levk/drmaa-common/1.0/drmaa-common-1.0-javadoc.jar!/" />
+    </JAVADOC>
+    <SOURCES>
+      <root url="jar://$MAVEN_REPOSITORY$/us/levk/drmaa-common/1.0/drmaa-common-1.0-sources.jar!/" />
+    </SOURCES>
+  </library>
+</component>
\ No newline at end of file
--- a/.idea/libraries/Maven__us_levk_drmaa_gridengine_6_2u5.xml
+++ b/.idea/libraries/Maven__us_levk_drmaa_gridengine_6_2u5.xml
+<component name="libraryTable">
+  <library name="Maven: us.levk:drmaa-gridengine:6.2u5">
+    <CLASSES>
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+    </CLASSES>
+    <JAVADOC>
+      <root url="jar://$MAVEN_REPOSITORY$/us/levk/drmaa-gridengine/6.2u5/drmaa-gridengine-6.2u5-javadoc.jar!/" />
+    </JAVADOC>
+    <SOURCES>
+      <root url="jar://$MAVEN_REPOSITORY$/us/levk/drmaa-gridengine/6.2u5/drmaa-gridengine-6.2u5-sources.jar!/" />
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+</component>
\ No newline at end of file
--- a/.idea/libraries/Maven__xml_apis_xml_apis_1_0_b2.xml
+++ b/.idea/libraries/Maven__xml_apis_xml_apis_1_0_b2.xml
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+    <JAVADOC>
+      <root url="jar://$MAVEN_REPOSITORY$/xml-apis/xml-apis/1.0.b2/xml-apis-1.0.b2-javadoc.jar!/" />
+    </JAVADOC>
+    <SOURCES>
+      <root url="jar://$MAVEN_REPOSITORY$/xml-apis/xml-apis/1.0.b2/xml-apis-1.0.b2-sources.jar!/" />
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\ No newline at end of file
--- a/.idea/misc.xml
+++ b/.idea/misc.xml
+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
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+    <option name="originalFiles">
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+  <component name="ProjectRootManager" version="2" languageLevel="JDK_1_6" assert-keyword="true" jdk-15="true" project-jdk-name="1.7" project-jdk-type="JavaSDK" />
+</project>
\ No newline at end of file
--- a/.idea/modules.xml
+++ b/.idea/modules.xml
+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+  <component name="ProjectModuleManager">
+    <modules>
+      <module fileurl="file://$PROJECT_DIR$/public/bammetrics/BamMetrics.iml" filepath="$PROJECT_DIR$/public/bammetrics/BamMetrics.iml" />
+      <module fileurl="file://$PROJECT_DIR$/protected/basty/Basty.iml" filepath="$PROJECT_DIR$/protected/basty/Basty.iml" />
+      <module fileurl="file://$PROJECT_DIR$/public/Biopet.iml" filepath="$PROJECT_DIR$/public/Biopet.iml" />
+      <module fileurl="file://$PROJECT_DIR$/public/biopet-framework/BiopetFramework.iml" filepath="$PROJECT_DIR$/public/biopet-framework/BiopetFramework.iml" />
+      <module fileurl="file://$PROJECT_DIR$/protected/BiopetGatk.iml" filepath="$PROJECT_DIR$/protected/BiopetGatk.iml" />
+      <module fileurl="file://$PROJECT_DIR$/protected/biopet-gatk-extensions/BiopetGatkExtensions.iml" filepath="$PROJECT_DIR$/protected/biopet-gatk-extensions/BiopetGatkExtensions.iml" />
+      <module fileurl="file://$PROJECT_DIR$/protected/biopet-gatk-pipelines/BiopetGatkPipelines.iml" filepath="$PROJECT_DIR$/protected/biopet-gatk-pipelines/BiopetGatkPipelines.iml" />
+      <module fileurl="file://$PROJECT_DIR$/protected/biopet-protected-package/BiopetProtectedPackage.iml" filepath="$PROJECT_DIR$/protected/biopet-protected-package/BiopetProtectedPackage.iml" />
+      <module fileurl="file://$PROJECT_DIR$/public/biopet-public-package/BiopetPublicPackage.iml" filepath="$PROJECT_DIR$/public/biopet-public-package/BiopetPublicPackage.iml" />
+      <module fileurl="file://$PROJECT_DIR$/BiopetRoot.iml" filepath="$PROJECT_DIR$/BiopetRoot.iml" />
+      <module fileurl="file://$PROJECT_DIR$/public/flexiprep/Flexiprep.iml" filepath="$PROJECT_DIR$/public/flexiprep/Flexiprep.iml" />
+      <module fileurl="file://$PROJECT_DIR$/public/gentrap/Gentrap.iml" filepath="$PROJECT_DIR$/public/gentrap/Gentrap.iml" />
+      <module fileurl="file://$PROJECT_DIR$/public/mapping/Mapping.iml" filepath="$PROJECT_DIR$/public/mapping/Mapping.iml" />
+      <module fileurl="file://$PROJECT_DIR$/public/sage/Sage.iml" filepath="$PROJECT_DIR$/public/sage/Sage.iml" />
+      <module fileurl="file://$PROJECT_DIR$/public/yamsvp/Yamsvp.iml" filepath="$PROJECT_DIR$/public/yamsvp/Yamsvp.iml" />
+    </modules>
+  </component>
+</project>
\ No newline at end of file
--- a/.idea/scala_compiler.xml
+++ b/.idea/scala_compiler.xml
+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+  <component name="ScalaCompilerConfiguration">
+    <option name="deprecationWarnings" value="true" />
+    <option name="featureWarnings" value="true" />
+    <parameters>
+      <parameter value="-dependencyfile" />
+      <parameter value="$MODULE_DIR$/target/.scala_dependencies" />
+      <parameter value="-feature" />
+      <parameter value="$PROJECT_DIR$/biopet-framework/target/.scala_dependencies" />
+      <parameter value="$PROJECT_DIR$/protected/biopet-protected-package/target/.scala_dependencies" />
+      <parameter value="$PROJECT_DIR$/protected/basty/target/.scala_dependencies" />
+      <parameter value="$PROJECT_DIR$/public/biopet-public-package/target/.scala_dependencies" />
+      <parameter value="$PROJECT_DIR$/public/gentrap/target/.scala_dependencies" />
+      <parameter value="$PROJECT_DIR$/public/sage/target/.scala_dependencies" />
+      <parameter value="$PROJECT_DIR$/public/yamsvp/target/.scala_dependencies" />
+      <parameter value="$PROJECT_DIR$/protected/biopet-gatk-pipelines/target/.scala_dependencies" />
+      <parameter value="$PROJECT_DIR$/public/bammetrics/target/.scala_dependencies" />
+      <parameter value="$PROJECT_DIR$/public/biopet-framework/target/.scala_dependencies" />
+      <parameter value="$PROJECT_DIR$/public/flexiprep/target/.scala_dependencies" />
+      <parameter value="$PROJECT_DIR$/public/mapping/target/.scala_dependencies" />
+      <parameter value="$PROJECT_DIR$/protected/biopet-gatk-extensions/target/.scala_dependencies" />
+    </parameters>
+  </component>
+</project>
\ No newline at end of file
--- a/.idea/scopes/scope_settings.xml
+++ b/.idea/scopes/scope_settings.xml
+<component name="DependencyValidationManager">
+  <state>
+    <option name="SKIP_IMPORT_STATEMENTS" value="false" />
+  </state>
+</component>
\ No newline at end of file
--- a/.idea/vcs.xml
+++ b/.idea/vcs.xml
+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+  <component name="VcsDirectoryMappings">
+    <mapping directory="" vcs="" />
+    <mapping directory="$PROJECT_DIR$" vcs="Git" />
+  </component>
+</project>
\ No newline at end of file
--- a/BiopetRoot.iml
+++ b/BiopetRoot.iml
+<?xml version="1.0" encoding="UTF-8"?>
+<module org.jetbrains.idea.maven.project.MavenProjectsManager.isMavenModule="true" type="JAVA_MODULE" version="4">
+  <component name="NewModuleRootManager" inherit-compiler-output="false">
+    <output url="file://$MODULE_DIR$/target/classes" />
+    <output-test url="file://$MODULE_DIR$/target/test-classes" />
+    <content url="file://$MODULE_DIR$">
+      <sourceFolder url="file://$MODULE_DIR$/src/main/resources" type="java-resource" />
+      <excludeFolder url="file://$MODULE_DIR$/target" />
+    </content>
+    <orderEntry type="inheritedJdk" />
+    <orderEntry type="sourceFolder" forTests="false" />
+  </component>
+</module>
\ No newline at end of file
--- a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunction.scala
+++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunction.scala
-package nl.lumc.sasc.biopet.core
-
-abstract class BiopetCommandLineFunction extends BiopetCommandLineFunctionTrait {
-  protected def cmdLine: String
-  final def commandLine: String = {
-    preCmdInternal
-    val cmd = cmdLine
-    addJobReportBinding("command", cmd)
-    return cmd
-  }
-}
--- a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/MainCommand.scala
+++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/MainCommand.scala
-package nl.lumc.sasc.biopet.core
-
-trait MainCommand {
-
-  lazy val commandName = this.getClass.getSimpleName
-    .split("\\$").last
-
-  def main(args: Array[String])
-}