Merge branch 'develop' into feature-unittest_core

Conflicts:
	protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantcalling.scala
	public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala
	public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/igvtools/IGVToolsCount.scala
	public/mapping/pom.xml

.idea/compiler.xml

@@ -22,6 +22,7 @@
         <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" />

.idea/encodings.xml

@@ -8,6 +8,7 @@
     <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" />

.idea/libraries/Maven__nl_lumc_sasc_Bam2Wig_0_3_0_DEV.xml

+<component name="libraryTable">
+  <library name="Maven: nl.lumc.sasc:Bam2Wig:0.3.0-DEV">
+    <CLASSES>
+      <root url="jar://$MAVEN_REPOSITORY$/nl/lumc/sasc/Bam2Wig/0.3.0-DEV/Bam2Wig-0.3.0-DEV.jar!/" />
+    </CLASSES>
+    <JAVADOC>
+      <root url="jar://$MAVEN_REPOSITORY$/nl/lumc/sasc/Bam2Wig/0.3.0-DEV/Bam2Wig-0.3.0-DEV-javadoc.jar!/" />
+    </JAVADOC>
+    <SOURCES>
+      <root url="jar://$MAVEN_REPOSITORY$/nl/lumc/sasc/Bam2Wig/0.3.0-DEV/Bam2Wig-0.3.0-DEV-sources.jar!/" />
+    </SOURCES>
+  </library>
+</component>
\ No newline at end of file

.idea/modules.xml

@@ -2,6 +2,7 @@
 <project version="4">
   <component name="ProjectModuleManager">
     <modules>
+      <module fileurl="file://$PROJECT_DIR$/public/bam2wig/Bam2Wig.iml" filepath="$PROJECT_DIR$/public/bam2wig/Bam2Wig.iml" />
       <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" />

.idea/scala_compiler.xml

@@ -20,6 +20,8 @@
       <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" />
+      <parameter value="$PROJECT_DIR$/public/bamtobigwig/target/.scala_dependencies" />
+      <parameter value="$PROJECT_DIR$/public/bam2wig/target/.scala_dependencies" />
     </parameters>
   </component>
 </project>
\ No newline at end of file

protected/basty/Basty.iml

@@ -93,5 +93,6 @@
     <orderEntry type="module" module-name="Mapping" />
     <orderEntry type="module" module-name="Flexiprep" />
     <orderEntry type="module" module-name="BamMetrics" />
+    <orderEntry type="module" module-name="Bam2Wig" />
   </component>
 </module>
\ No newline at end of file

protected/biopet-gatk-pipelines/BiopetGatkPipelines.iml

@@ -92,5 +92,6 @@
     <orderEntry type="module" module-name="Mapping" />
     <orderEntry type="module" module-name="Flexiprep" />
     <orderEntry type="module" module-name="BamMetrics" />
+    <orderEntry type="module" module-name="Bam2Wig" />
   </component>
 </module>
\ No newline at end of file

protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkPipeline.scala

@@ -9,6 +9,7 @@ import nl.lumc.sasc.biopet.core.MultiSampleQScript
 import nl.lumc.sasc.biopet.core.PipelineCommand
 import nl.lumc.sasc.biopet.core.config.Configurable
 import htsjdk.samtools.SamReaderFactory
+import nl.lumc.sasc.biopet.pipelines.bamtobigwig.Bam2Wig
 import scala.collection.JavaConversions._
 import nl.lumc.sasc.biopet.extensions.gatk.{ CombineVariants, CombineGVCFs }
 import nl.lumc.sasc.biopet.extensions.picard.AddOrReplaceReadGroups
@@ -50,6 +51,7 @@ class GatkPipeline(val root: Configurable) extends QScript with MultiSampleQScri
 
       /** Library variantcalling */
       val gatkVariantcalling = new GatkVariantcalling(qscript)
+      gatkVariantcalling.doublePreProces = false
       gatkVariantcalling.sampleID = sampleId
       gatkVariantcalling.outputDir = new File(libDir, "variantcalling")
 
@@ -112,7 +114,6 @@ class GatkPipeline(val root: Configurable) extends QScript with MultiSampleQScri
         if (bamFile.isDefined) {
           gatkVariantcalling.inputBams = List(bamFile.get)
           gatkVariantcalling.variantcalling = config("library_variantcalling", default = false)
-          gatkVariantcalling.preProcesBams = true
           gatkVariantcalling.init
           gatkVariantcalling.biopetScript
           addAll(gatkVariantcalling.functions)
@@ -136,6 +137,8 @@ class GatkPipeline(val root: Configurable) extends QScript with MultiSampleQScri
       gatkVariantcalling.init
       gatkVariantcalling.biopetScript
       addAll(gatkVariantcalling.functions)
+
+      gatkVariantcalling.inputBams.foreach(x => addAll(Bam2Wig(qscript, x).functions))
     }
   }
 

protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantcalling.scala

@@ -7,6 +7,7 @@ package nl.lumc.sasc.biopet.pipelines.gatk
 
 import nl.lumc.sasc.biopet.core.{ BiopetQScript, PipelineCommand }
 import java.io.File
+import nl.lumc.sasc.biopet.extensions.Ln
 import nl.lumc.sasc.biopet.tools.{ VcfStats, MpileupToVcf, VcfFilter, MergeAlleles }
 import nl.lumc.sasc.biopet.core.config.Configurable
 import nl.lumc.sasc.biopet.extensions.gatk.{ AnalyzeCovariates, BaseRecalibrator, GenotypeGVCFs, HaplotypeCaller, IndelRealigner, PrintReads, RealignerTargetCreator, SelectVariants, CombineVariants, UnifiedGenotyper }
@@ -38,12 +39,12 @@ class GatkVariantcalling(val root: Configurable) extends QScript with BiopetQScr
   @Argument(doc = "Sample name", required = false)
   var sampleID: String = _
 
-  var preProcesBams: Option[Boolean] = config("pre_proces_bams", default = true)
+  var preProcesBams: Boolean = config("pre_proces_bams", default = true)
   var variantcalling: Boolean = true
-  var doublePreProces: Option[Boolean] = config("double_pre_proces", default = true)
-  var useHaplotypecaller: Option[Boolean] = config("use_haplotypecaller", default = true)
-  var useUnifiedGenotyper: Option[Boolean] = config("use_unifiedgenotyper", default = false)
-  var useAllelesOption: Option[Boolean] = config("use_alleles_option", default = false)
+  var doublePreProces: Boolean = config("double_pre_proces", default = true)
+  var useHaplotypecaller: Boolean = config("use_haplotypecaller", default = true)
+  var useUnifiedGenotyper: Boolean = config("use_unifiedgenotyper", default = false)
+  var useAllelesOption: Boolean = config("use_alleles_option", default = false)
   var useMpileup: Boolean = config("use_mpileup", default = true)
   var useIndelRealigner: Boolean = config("use_indel_realign", default = true)
   var useBaseRecalibration: Boolean = config("use_base_recalibration", default = true)
@@ -60,42 +61,53 @@ class GatkVariantcalling(val root: Configurable) extends QScript with BiopetQScr
   }
 
   private def doublePreProces(files: List[File]): List[File] = {
-    if (files.size == 1) return files
     if (files.isEmpty) throw new IllegalStateException("Files can't be empty")
-    if (!doublePreProces.get) return files
-    val markDup = MarkDuplicates(this, files, new File(outputDir, outputName + ".dedup.bam"))
-    markDup.isIntermediate = useIndelRealigner
-    add(markDup)
-    if (useIndelRealigner) {
-      List(addIndelRealign(markDup.output, outputDir, isIntermediate = false))
+    else if (!doublePreProces) files
+    else if (files.size == 1) {
+      val bamFile = new File(outputDir, files.head.getName)
+      if (bamFile != files.head) {
+        val oldIndex: File = files.head.getAbsolutePath.stripSuffix(".bam") + ".bai"
+        val newIndex: File = bamFile.getAbsolutePath.stripSuffix(".bam") + ".bai"
+        add(Ln(this, oldIndex, newIndex))
+
+        val bamLn = Ln(this, files.head, bamFile)
+        bamLn.deps :+= newIndex
+        add(bamLn)
+      }
+      List(bamFile)
     } else {
-      List(markDup.output)
+      val markDup = MarkDuplicates(this, files, new File(outputDir + outputName + ".dedup.bam"))
+      markDup.isIntermediate = useIndelRealigner
+      add(markDup)
+      if (useIndelRealigner) {
+        List(addIndelRealign(markDup.output, outputDir, isIntermediate = false))
+      } else {
+        List(markDup.output)
+      }
     }
   }
 
   def biopetScript() {
-    scriptOutput.bamFiles = if (preProcesBams.get) {
-      var bamFiles: List[File] = Nil
-      for (inputBam <- inputBams) {
-        var bamFile = inputBam
-        if (useIndelRealigner) {
-          bamFile = addIndelRealign(bamFile, outputDir, isIntermediate = useBaseRecalibration)
-        }
-        if (useBaseRecalibration) {
-          bamFile = addBaseRecalibrator(bamFile, outputDir, isIntermediate = bamFiles.size > 1)
+    scriptOutput.bamFiles = {
+      doublePreProces(if (preProcesBams) {
+        for (inputBam <- inputBams) yield {
+          var bamFile = inputBam
+          if (useIndelRealigner)
+            bamFile = addIndelRealign(bamFile, outputDir, isIntermediate = useBaseRecalibration)
+          if (useBaseRecalibration)
+            bamFile = addBaseRecalibrator(bamFile, outputDir, isIntermediate = inputBams.size > 1)
+          bamFile
         }
-        bamFiles :+= bamFile
-      }
-      doublePreProces(bamFiles)
-    } else if (inputBams.size > 1 && doublePreProces.get) {
-      doublePreProces(inputBams)
-    } else inputBams
+      } else {
+        inputBams
+      })
+    }
 
     if (variantcalling) {
       var mergBuffer: SortedMap[String, File] = SortedMap()
       def mergeList = mergBuffer map { case (key, file) => TaggedFile(removeNoneVariants(file), "name=" + key) }
 
-      if (sampleID != null && (useHaplotypecaller.get || config("joint_genotyping", default = false).asBoolean)) {
+      if (sampleID != null && (useHaplotypecaller || config("joint_genotyping", default = false).asBoolean)) {
         val hcGvcf = new HaplotypeCaller(this)
         hcGvcf.useGvcf
         hcGvcf.input_file = scriptOutput.bamFiles
@@ -104,7 +116,7 @@ class GatkVariantcalling(val root: Configurable) extends QScript with BiopetQScr
         scriptOutput.gvcfFile = hcGvcf.out
       }
 
-      if (useHaplotypecaller.get) {
+      if (useHaplotypecaller) {
         if (sampleID != null) {
           val genotypeGVCFs = GenotypeGVCFs(this, List(scriptOutput.gvcfFile), new File(outputDir, outputName + ".hc.discovery.vcf.gz"))
           add(genotypeGVCFs)
@@ -119,7 +131,7 @@ class GatkVariantcalling(val root: Configurable) extends QScript with BiopetQScr
         mergBuffer += ("1.HC-Discovery" -> scriptOutput.hcVcfFile)
       }
 
-      if (useUnifiedGenotyper.get) {
+      if (useUnifiedGenotyper) {
         val ugVcf = new UnifiedGenotyper(this)
         ugVcf.input_file = scriptOutput.bamFiles
         ugVcf.out = new File(outputDir, outputName + ".ug.discovery.vcf.gz")
@@ -154,12 +166,12 @@ class GatkVariantcalling(val root: Configurable) extends QScript with BiopetQScr
       }
 
       // Allele mode
-      if (useAllelesOption.get) {
+      if (useAllelesOption) {
         val mergeAlleles = MergeAlleles(this, mergeList.toList, outputDir + "raw.allele__temp_only.vcf.gz")
         mergeAlleles.isIntermediate = true
         add(mergeAlleles)
 
-        if (useHaplotypecaller.get) {
+        if (useHaplotypecaller) {
           val hcAlleles = new HaplotypeCaller(this)
           hcAlleles.input_file = scriptOutput.bamFiles
           hcAlleles.out = new File(outputDir, outputName + ".hc.allele.vcf.gz")
@@ -170,7 +182,7 @@ class GatkVariantcalling(val root: Configurable) extends QScript with BiopetQScr
           mergBuffer += ("3.HC-alleles" -> hcAlleles.out)
         }
 
-        if (useUnifiedGenotyper.get) {
+        if (useUnifiedGenotyper) {
           val ugAlleles = new UnifiedGenotyper(this)
           ugAlleles.input_file = scriptOutput.bamFiles
           ugAlleles.out = new File(outputDir, outputName + ".ug.allele.vcf.gz")

protected/biopet-protected-package/BiopetProtectedPackage.iml

@@ -95,6 +95,7 @@
     <orderEntry type="module" module-name="Gentrap" />
     <orderEntry type="module" module-name="Sage" />
     <orderEntry type="module" module-name="Yamsvp" />
+    <orderEntry type="module" module-name="Bam2Wig" />
     <orderEntry type="module" module-name="BiopetGatkPipelines" />
     <orderEntry type="module" module-name="BiopetGatkExtensions" />
     <orderEntry type="module" module-name="Basty" />

public/bam2wig/Bam2Wig.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" />
+      <sourceFolder url="file://$MODULE_DIR$/src/main/scala" isTestSource="false" />
+      <excludeFolder url="file://$MODULE_DIR$/target" />
+    </content>
+    <orderEntry type="inheritedJdk" />
+    <orderEntry type="sourceFolder" forTests="false" />
+    <orderEntry type="module" module-name="BiopetFramework" />
+    <orderEntry type="library" name="Maven: org.scala-lang:scala-library:2.11.2" level="project" />
+    <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-queue:3.3" level="project" />
+    <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-tools-public:3.3" level="project" />
+    <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-engine:3.3" level="project" />
+    <orderEntry type="library" name="Maven: org.scala-lang:scala-compiler:2.10.2" level="project" />
+    <orderEntry type="library" name="Maven: org.scala-lang:scala-reflect:2.10.2" level="project" />
+    <orderEntry type="library" name="Maven: log4j:log4j:1.2.15" level="project" />
+    <orderEntry type="library" name="Maven: net.sf.jgrapht:jgrapht:0.8.3" level="project" />
+    <orderEntry type="library" name="Maven: org.apache.commons:commons-email:1.2" level="project" />
+    <orderEntry type="library" name="Maven: javax.activation:activation:1.1" level="project" />
+    <orderEntry type="library" name="Maven: javax.mail:mail:1.4.4" level="project" />
+    <orderEntry type="module-library">
+      <library name="Maven: com.sun:tools:1.4.2">
+        <CLASSES>
+          <root url="jar:///usr/lib/jvm/java-1.7.0-openjdk-amd64/lib/tools.jar!/" />
+        </CLASSES>
+        <JAVADOC />
+        <SOURCES />
+      </library>
+    </orderEntry>
+    <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-queue-extensions-distribution:3.3" level="project" />
+    <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-tools-protected:3.3" level="project" />
+    <orderEntry type="library" name="Maven: gov.nist.math:jama:1.0.2" level="project" />
+    <orderEntry type="library" scope="RUNTIME" name="Maven: org.broadinstitute.gatk:gatk-queue-extensions-generator:3.3" level="project" />
+    <orderEntry type="library" name="Maven: org.broadinstitute.gatk:gatk-utils:3.3" level="project" />
+    <orderEntry type="library" name="Maven: samtools:htsjdk:1.120.1620" level="project" />
+    <orderEntry type="library" name="Maven: org.xerial.snappy:snappy-java:1.0.3-rc3" level="project" />
+    <orderEntry type="library" name="Maven: picard:picard:1.120.1579" level="project" />
+    <orderEntry type="library" name="Maven: org.apache.ant:ant:1.8.2" level="project" />
+    <orderEntry type="module-library">
+      <library name="Maven: com.sun:tools.jar:1.5">
+        <CLASSES>
+          <root url="jar:///usr/lib/jvm/java-1.7.0-openjdk-amd64/lib/tools.jar!/" />
+        </CLASSES>
+        <JAVADOC />
+        <SOURCES />
+      </library>
+    </orderEntry>
+    <orderEntry type="library" name="Maven: colt:colt:1.2.0" level="project" />
+    <orderEntry type="library" name="Maven: concurrent:concurrent:1.3.4" level="project" />
+    <orderEntry type="library" name="Maven: it.unimi.dsi:fastutil:6.5.3" level="project" />
+    <orderEntry type="library" name="Maven: org.simpleframework:simple-xml:2.0.4" level="project" />
+    <orderEntry type="library" name="Maven: stax:stax-api:1.0.1" level="project" />
+    <orderEntry type="library" name="Maven: stax:stax:1.2.0" level="project" />
+    <orderEntry type="library" name="Maven: org.reflections:reflections:0.9.9-RC1" level="project" />
+    <orderEntry type="library" name="Maven: org.javassist:javassist:3.16.1-GA" level="project" />
+    <orderEntry type="library" name="Maven: dom4j:dom4j:1.6.1" level="project" />
+    <orderEntry type="library" name="Maven: xml-apis:xml-apis:1.0.b2" level="project" />
+    <orderEntry type="library" name="Maven: org.slf4j:slf4j-log4j12:1.6.1" level="project" />
+    <orderEntry type="library" name="Maven: org.slf4j:slf4j-api:1.6.1" level="project" />
+    <orderEntry type="library" name="Maven: org.freemarker:freemarker:2.3.18" level="project" />
+    <orderEntry type="library" name="Maven: org.apache.commons:commons-jexl:2.1.1" level="project" />
+    <orderEntry type="library" name="Maven: commons-logging:commons-logging:1.1.1" level="project" />
+    <orderEntry type="library" name="Maven: commons-lang:commons-lang:2.5" level="project" />
+    <orderEntry type="library" name="Maven: commons-io:commons-io:2.1" level="project" />
+    <orderEntry type="library" name="Maven: commons-collections:commons-collections:3.2.1" level="project" />
+    <orderEntry type="library" name="Maven: org.apache.commons:commons-math:2.2" level="project" />
+    <orderEntry type="library" name="Maven: net.java.dev.jna:jna:3.2.7" level="project" />
+    <orderEntry type="library" name="Maven: net.java.dev.jets3t:jets3t:0.8.1" level="project" />
+    <orderEntry type="library" name="Maven: commons-codec:commons-codec:1.3" level="project" />
+    <orderEntry type="library" name="Maven: commons-httpclient:commons-httpclient:3.1" level="project" />
+    <orderEntry type="library" name="Maven: com.jamesmurty.utils:java-xmlbuilder:0.4" level="project" />
+    <orderEntry type="library" name="Maven: us.levk:drmaa-gridengine:6.2u5" level="project" />
+    <orderEntry type="library" name="Maven: us.levk:drmaa-common:1.0" level="project" />
+    <orderEntry type="library" name="Maven: com.google.code.gson:gson:2.2.2" level="project" />
+    <orderEntry type="library" name="Maven: org.apache.httpcomponents:httpclient:4.1.1" level="project" />
+    <orderEntry type="library" name="Maven: org.apache.httpcomponents:httpcore:4.1" level="project" />
+    <orderEntry type="library" name="Maven: com.google.code.cofoja:cofoja:1.0-r139" level="project" />
+    <orderEntry type="library" name="Maven: io.argonaut:argonaut_2.11:6.1-M4" level="project" />
+    <orderEntry type="library" name="Maven: org.scalaz:scalaz-core_2.11:7.1.0" level="project" />
+    <orderEntry type="library" name="Maven: org.scala-lang.modules:scala-parser-combinators_2.11:1.0.2" level="project" />
+    <orderEntry type="library" name="Maven: org.scala-lang.modules:scala-xml_2.11:1.0.2" level="project" />
+    <orderEntry type="library" name="Maven: com.github.julien-truffaut:monocle-core_2.11:0.5.0" level="project" />
+    <orderEntry type="library" name="Maven: org.biojava:biojava3-core:3.1.0" level="project" />
+    <orderEntry type="library" name="Maven: org.biojava:biojava3-sequencing:3.1.0" level="project" />
+    <orderEntry type="library" name="Maven: com.google.guava:guava:18.0" level="project" />
+    <orderEntry type="library" name="Maven: com.github.scopt:scopt_2.10:3.2.0" level="project" />
+  </component>
+</module>
\ No newline at end of file

public/bam2wig/pom.xml

+<?xml version="1.0" encoding="UTF-8"?>
+<project xmlns="http://maven.apache.org/POM/4.0.0"
+         xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+         xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+    <modelVersion>4.0.0</modelVersion>
+
+    <groupId>nl.lumc.sasc</groupId>
+    <artifactId>Bam2Wig</artifactId>
+    <packaging>jar</packaging>
+
+    <parent>
+        <groupId>nl.lumc.sasc</groupId>
+        <artifactId>Biopet</artifactId>
+        <version>0.3.0-DEV</version>
+        <relativePath>../</relativePath>
+    </parent>
+
+    <inceptionYear>2014</inceptionYear>
+    <name>Bam2Wig</name>
+
+    <dependencies>
+        <dependency>
+            <groupId>nl.lumc.sasc</groupId>
+            <artifactId>BiopetFramework</artifactId>
+            <version>${project.version}</version>
+        </dependency>
+    </dependencies>
+
+</project>
\ No newline at end of file

public/bam2wig/src/main/scala/nl/lumc/sasc/biopet/pipelines/bamtobigwig/Bam2Wig.scala

+package nl.lumc.sasc.biopet.pipelines.bamtobigwig
+
+import java.io.File
+
+import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.core.{ BiopetQScript, PipelineCommand }
+import nl.lumc.sasc.biopet.extensions.WigToBigWig
+import nl.lumc.sasc.biopet.extensions.igvtools.IGVToolsCount
+import org.broadinstitute.gatk.queue.QScript
+import org.broadinstitute.gatk.utils.commandline.{ Output, Input }
+
+/**
+ * Created by pjvan_thof on 1/29/15.
+ */
+class Bam2Wig(val root: Configurable) extends QScript with BiopetQScript {
+  def this() = this(null)
+
+  @Input(doc = "Input bam file", required = true)
+  var bamFile: File = null
+
+  def init(): Unit = {
+  }
+
+  def biopetScript(): Unit = {
+    val bs = new BamToChromSizes(this)
+    bs.bamFile = bamFile
+    bs.chromSizesFile = bamFile.getAbsoluteFile + ".chrom.sizes"
+    bs.isIntermediate = true
+    add(bs)
+
+    val igvCount = new IGVToolsCount(this)
+    igvCount.input = bamFile
+    igvCount.genomeChromSizes = bs.chromSizesFile
+    igvCount.wig = Some(swapExt(outputDir, bamFile, ".bam", ".wig"))
+    igvCount.tdf = Some(swapExt(outputDir, bamFile, ".bam", ".tdf"))
+    add(igvCount)
+
+    val wigToBigWig = new WigToBigWig(this)
+    wigToBigWig.inputWigFile = igvCount.wig.get
+    wigToBigWig.inputChromSizesFile = bs.chromSizesFile
+    wigToBigWig.outputBigWig = swapExt(outputDir, bamFile, ".bam", ".bigwig")
+    add(wigToBigWig)
+  }
+}
+
+object Bam2Wig extends PipelineCommand {
+  def apply(root: Configurable, bamFile: File): Bam2Wig = {
+    val bamToBigWig = new Bam2Wig(root)
+    bamToBigWig.outputDir = bamFile.getParent
+    bamToBigWig.bamFile = bamFile
+    bamToBigWig.init()
+    bamToBigWig.biopetScript()
+    bamToBigWig
+  }
+}
\ No newline at end of file

public/bam2wig/src/main/scala/nl/lumc/sasc/biopet/pipelines/bamtobigwig/BamToChromSizes.scala

+package nl.lumc.sasc.biopet.pipelines.bamtobigwig
+
+import java.io.{ PrintWriter, File }
+
+import htsjdk.samtools.SamReaderFactory
+import nl.lumc.sasc.biopet.core.config.Configurable
+import org.broadinstitute.gatk.queue.function.InProcessFunction
+import org.broadinstitute.gatk.utils.commandline.{ Output, Input }
+import scala.collection.JavaConversions._
+
+/**
+ * Created by pjvan_thof on 1/29/15.
+ */
+class BamToChromSizes(val root: Configurable) extends InProcessFunction with Configurable {
+  @Input
+  var bamFile: File = _
+
+  @Output
+  var chromSizesFile: File = _
+
+  def run(): Unit = {
+    val bamReader = SamReaderFactory.makeDefault().open(bamFile)
+    val writer = new PrintWriter(chromSizesFile)
+    for (ref <- bamReader.getFileHeader.getSequenceDictionary.getSequences) {
+      writer.println(ref.getSequenceName + "\t" + ref.getSequenceLength)
+    }
+    bamReader.close()
+    writer.close
+  }
+}

public/biopet-framework/BiopetFramework.iml

 <?xml version="1.0" encoding="UTF-8"?>
 <module org.jetbrains.idea.maven.project.MavenProjectsManager.isMavenModule="true" type="JAVA_MODULE" version="4">
+  <component name="FacetManager">
+    <facet type="Python" name="Python">
+      <configuration sdkName="" />
+    </facet>
+  </component>
   <component name="NewModuleRootManager" inherit-compiler-output="false">
     <output url="file://$MODULE_DIR$/target/classes" />
     <output-test url="file://$MODULE_DIR$/target/test-classes" />

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala

@@ -58,7 +58,7 @@ trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurab
   override def freezeFieldValues() {
     preProcesExecutable
     beforeGraph
-    if (jobOutputFile == null) jobOutputFile = new File(firstOutput.getParent + "/." + firstOutput.getName + "." + configName + ".out")
+    if (jobOutputFile == null) jobOutputFile = new File(firstOutput.getAbsoluteFile.getParent, "." + firstOutput.getName + "." + configName + ".out")
 
     if (threads == 0) threads = getThreads(defaultThreads)
     if (threads > 1) nCoresRequest = Option(threads)

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Ln.scala

@@ -30,6 +30,9 @@ class Ln(val root: Configurable) extends InProcessFunction with Configurable {
   @Output(doc = "Link destination")
   var out: File = _
 
+  @Output
+  var deps: List[File] = Nil
+
   var relative: Boolean = true
 
   lazy val cmd: String = {

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/WigToBigWig.scala

@@ -14,10 +14,10 @@ class WigToBigWig(val root: Configurable) extends BiopetCommandLineFunction {
   @Input(doc = "Input wig file")
   var inputWigFile: File = _
 
-  @Input(doc = "Input chrom sizes file")
+  @Input(doc = "Input chrom sizes file", required = true)
   var inputChromSizesFile: File = _
 
-  @Output(doc = "Output BigWig file")
+  @Output(doc = "Output BigWig file", required = true)
   var outputBigWig: File = _
 
   executable = config("exe", default = "wigToBigWig")

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/igvtools/IGVTools.scala

@@ -9,6 +9,6 @@ import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
 abstract class IGVTools extends BiopetCommandLineFunction {
   executable = config("exe", default = "igvtools", submodule = "igvtools", freeVar = false)
   override def versionCommand = executable + " version"
-  override val versionRegex = """IGV Version: ([\d\.]) .*""".r
+  override val versionRegex = """IGV Version:? ([\w\.]*) .*""".r
   override val versionExitcode = List(0)
 }
\ No newline at end of file

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/igvtools/IGVToolsCount.scala

 
 package nl.lumc.sasc.biopet.extensions.igvtools
 
-import java.nio.file.InvalidPathException
-
 import nl.lumc.sasc.biopet.core.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output, Argument }
 import java.io.{ FileNotFoundException, File }
@@ -13,19 +11,18 @@ import java.io.{ FileNotFoundException, File }
  * @constructor create a new IGVTools instance from a `.bam` file
  *
  */
-
 class IGVToolsCount(val root: Configurable) extends IGVTools {
   @Input(doc = "Bam File")
   var input: File = _
 
-  @Input(doc = "<genome>.chrom.sizes File")
+  @Input(doc = "<genome>.chrom.sizes File", required = true)
   var genomeChromSizes: File = _
 
   @Output
-  var tdf: Option[File] = _
+  var tdf: Option[File] = None
 
   @Output
-  var wig: Option[File] = _
+  var wig: Option[File] = None
 
   var maxZoom: Option[Int] = config("maxZoom")
   var windowSize: Option[Int] = config("windowSize")
@@ -48,8 +45,10 @@ class IGVToolsCount(val root: Configurable) extends IGVTools {
     super.beforeGraph
     if (!input.exists()) throw new FileNotFoundException("Input bam is required for IGVToolsCount")
 
-    if (!wig.isEmpty && !wig.get.getAbsolutePath.endsWith(".wig")) throw new IllegalArgumentException("Wiggle file should have a .wig file-extension")
-    if (!tdf.isEmpty && !tdf.get.getAbsolutePath.endsWith(".tdf")) throw new IllegalArgumentException("TDF file should have a .tdf file-extension")
+    wig.foreach(x => if (!x.getAbsolutePath.endsWith(".wig"))
+      throw new IllegalArgumentException("WIG file should have a .wig file-extension"))
+    tdf.foreach(x => if (!x.getAbsolutePath.endsWith(".tdf"))
+      throw new IllegalArgumentException("TDF file should have a .tdf file-extension"))
   }