Added tabix

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Tabix.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 3/4/15.
+ */
+class Tabix(val root: Configurable) extends BiopetCommandLineFunction {
+
+  @Input(doc = "Input files", required = true)
+  var input: File = null
+
+  @Output(doc = "Compressed output file", required = true)
+  protected var output: File = null
+
+  var p: Option[String] = config("p")
+  executable = config("exe", default = "bgzip")
+
+  override def beforeGraph: Unit = {
+    output = new File(input.getAbsolutePath + ".tbi")
+  }
+
+  def cmdLine = required(executable) +
+    optional("-p", p) +
+    required(input)
+}
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