Support clipping-mode and upgrade-clipipng in ClipBam.

See: fulcrumgenomics/fgbio#337

tasks/src/main/scala/dagr/tasks/fgbio/ClipBam.scala

@@ -32,21 +32,28 @@ import scala.collection.mutable.ListBuffer
 class ClipBam(val input: PathToBam,
               val output: PathToBam,
               val ref: PathToFasta,
+              @deprecated("Use clipping-mode instead.", since="0.2.1")
               val softClip: Option[Boolean] = None,
+              val clippingMode: Option[String] = None,
               val autoClipAttributes: Option[Boolean] = None,
+              val upgradeClipping: Option[Boolean] = None,
               val readOneFivePrime: Option[Int] = None,
               val readOneThreePrime: Option[Int] = None,
               val readTwoFivePrime: Option[Int] = None,
               val readTwoThreePrime: Option[Int] = None,
               val clipOverlappingReads: Option[Boolean] = None
              ) extends FgBioTask {
 
+  require(softClip.isEmpty || clippingMode.isEmpty, "Both softClip and clippingMode cannot both be used.")
+
   override protected def addFgBioArgs(buffer: ListBuffer[Any]): Unit = {
     buffer.append("-i", input)
     buffer.append("-o", output)
     buffer.append("-r", ref)
     softClip.foreach          (s => buffer.append("-s", s))
+    clippingMode.foreach      (c => buffer.append("-c", c))
     autoClipAttributes.foreach(a => buffer.append("-a", a))
+    upgradeClipping.foreach   (u => buffer.append("--upgrade-clipping", u))
     readOneFivePrime.foreach  (b => buffer.append("--read-one-five-prime", b))
     readOneThreePrime.foreach (c => buffer.append("--read-one-three-prime", c))
     readTwoFivePrime.foreach  (d => buffer.append("--read-two-five-prime", d))