Added samtools sort

public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsSort.scala

+package nl.lumc.sasc.biopet.extensions.samtools
+
+import java.io.File
+
+import nl.lumc.sasc.biopet.utils.config.Configurable
+import org.broadinstitute.gatk.utils.commandline.{Output, Input}
+
+/**
+ * Created by pjvanthof on 22/09/15.
+ */
+class SamtoolsSort(val root: Configurable) extends Samtools {
+
+  @Input(required = true)
+  var input: File = _
+
+  @Output
+  var output: File = _
+
+  val compresion: Option[Int] = config("l")
+  val outputFormat: Option[String] = config("O")
+  val sortByName: Boolean = config("sort_by_name", default = false)
+  val prefix: String = config("prefix", default = new File(qSettings.tempDirectory, output.getAbsolutePath))
+
+  def cmdLine = optional("-m", (coreMemeory + "G")) +
+    optional("-@", threads) +
+    optional("-O", outputFormat) +
+    conditional(sortByName, "-n") +
+    (if (outputAsStsout) "" else  required("-o", output)) +
+    (if (inputAsStdin) "" else required(input))
+}