Merge branch 'develop' into feature-Chipcap

Conflicts:
	public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala

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

@@ -129,9 +129,7 @@ trait MultiSampleQScript extends BiopetQScript {
     ConfigUtils.any2map(Config.global.map("samples")).keySet
   }
 
-  /**
-   * Runs addAndTrackJobs method for each sample
-   */
+  /** Runs addAndTrackJobs method for each sample */
   final def addSamplesJobs() {
     for ((sampleId, sample) <- samples) {
       sample.addAndTrackJobs()

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

+package nl.lumc.sasc.biopet.extensions
+
+import java.io.File
+
+import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
+import nl.lumc.sasc.biopet.core.config.Configurable
+import org.broadinstitute.gatk.utils.commandline.{ Output, Input }
+
+/**
+ * Created by pjvan_thof on 1/29/15.
+ * Versions from the executable are not reliable, this extension is based on md5 '3d033ff8a1f4ea9cb3ede12939561141' from the executable
+ */
+class WigToBigWig(val root: Configurable) extends BiopetCommandLineFunction {
+  @Input(doc = "Input wig file")
+  var inputWigFile: File = _
+
+  @Input(doc = "Input chrom sizes file")
+  var inputChromSizesFile: File = _
+
+  @Output(doc = "Output BigWig file")
+  var outputBigWig: File = _
+
+  executable = config("exe", default = "wigToBigWig")
+
+  var blockSize: Option[Int] = config("blockSize")
+  var itemsPerSlot: Option[Int] = config("itemsPerSlot")
+  var clip: Boolean = config("clip", default = false)
+  var unc: Boolean = config("unc", default = false)
+
+  def cmdLine = required(executable) +
+    optional("-blockSize=", blockSize, spaceSeparated = false) +
+    optional("-itemsPerSlot=", itemsPerSlot, spaceSeparated = false) +
+    conditional(clip, "-clip") +
+    conditional(unc, "-unc") +
+    required(inputWigFile) +
+    required(inputChromSizesFile) +
+    required(outputBigWig)
+}
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