Merge branch 'develop' into feature-license

.idea/compiler.xml

+<?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="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

+<component name="CopyrightManager">
+  <settings default="" />
+</component>
\ No newline at end of file

.idea/encodings.xml

+<?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/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

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+<component name="libraryTable">
+  <library name="Maven: colt:colt:1.2.0">
+    <CLASSES>
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+    </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

+<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

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+    <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

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+    </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

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+  <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

+<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

+<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

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+  <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

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+    </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

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+    </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

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+    </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!/" />
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+</component>
\ No newline at end of file

.idea/libraries/Maven__commons_io_commons_io_2_1.xml

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+    <JAVADOC>
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+    <SOURCES>
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+</component>
\ No newline at end of file

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+    </CLASSES>
+    <JAVADOC>
+      <root url="jar://$MAVEN_REPOSITORY$/commons-lang/commons-lang/2.5/commons-lang-2.5-javadoc.jar!/" />
+    </JAVADOC>
+    <SOURCES>
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+    <JAVADOC>
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+    <SOURCES>
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\ No newline at end of file

.idea/libraries/Maven__concurrent_concurrent_1_3_4.xml

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+    <JAVADOC>
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+</component>
\ No newline at end of file