Add IntelliJ project files

.idea/.name

+Biopet
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.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="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

+<component name="CopyrightManager">
+  <settings default="" />
+</component>
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.idea/dictionaries/warindrarto.xml

+<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

+<?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

+<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

+<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_baqend_bloom_filter_1_02.xml

+<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>
\ 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

.idea/libraries/Maven__com_github_julien_truffaut_monocle_core_2_11_0_5_0.xml

+<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

+<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_gson_gson_2_2_4.xml

+<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>
\ No newline at end of file

.idea/libraries/Maven__com_google_guava_guava_17_0.xml

+<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>
\ No newline at end of file

.idea/libraries/Maven__io_argonaut_argonaut_2_11_6_1_M4.xml

+<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

+<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_apache_commons_commons_pool2_2_2.xml

+<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>
\ No newline at end of file

.idea/libraries/Maven__org_beanshell_bsh_2_0b4.xml

+<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

+<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

+<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

+<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