Added BedToIntervalList extension

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

+package nl.lumc.sasc.biopet.extensions.picard
+
+import java.io.File
+
+import nl.lumc.sasc.biopet.core.config.Configurable
+import org.broadinstitute.gatk.utils.commandline.{Output, Input}
+
+/**
+ * Created by pjvan_thof on 4/15/15.
+ */
+class BedToIntervalList(val root: Configurable) extends Picard {
+  javaMainClass = new picard.util.BedToIntervalList().getClass.getName
+
+  @Input(doc = "Input bed file", required = true)
+  var input: File = null
+
+  @Input(doc = "Reference dict file", required = true)
+  var dict: File = new File(config("reference").asString.stripSuffix(".fa").stripSuffix(".fasta") + ".dict")
+
+  @Output(doc = "Output interval list", required = true)
+  var output: File = null
+
+  override def commandLine = super.commandLine +
+    required("SEQUENCE_DICTIONARY=", dict, spaceSeparated = false) +
+    required("INPUT=", input, spaceSeparated = false) +
+    required("OUTPUT=", output, spaceSeparated = false)
+}
+
+object BedToIntervalList {
+  def apply(root:Configurable, input:File, output:File): BedToIntervalList = {
+    val bi = new BedToIntervalList(root)
+    bi.input = input
+    bi.output = output
+    bi
+  }
+}
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