Merge pull request #49 from biopet/fix-pipes

Fix pipes

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsFlagstat.scala

@@ -28,7 +28,9 @@ class SamtoolsFlagstat(val root: Configurable) extends Samtools {
   var output: File = _
 
   /** Returns command to execute */
-  def cmdLine = required(executable) + required("flagstat") + required(input) + " > " + required(output)
+  def cmdLine = required(executable) + required("flagstat") +
+    (if (inputAsStdin) "-" else required(input)) +
+    (if (outputAsStsout) "" else " > " + required(output))
 }
 
 object SamtoolsFlagstat {

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsView.scala

@@ -33,18 +33,20 @@ class SamtoolsView(val root: Configurable) extends Samtools {
   var f: List[String] = config("f", default = List.empty[String])
   var F: List[String] = config("F", default = List.empty[String])
 
-  def cmdBase = required(executable) +
+  @Input(required = false)
+  var L: Option[File] = None
+
+  /** Returns command to execute */
+  def cmdLine = required(executable) +
     required("view") +
     optional("-q", q) +
+    optional("-L", L) +
     repeat("-f", f) +
     repeat("-F", F) +
     conditional(b, "-b") +
-    conditional(h, "-h")
-  def cmdPipeInput = cmdBase + "-"
-  def cmdPipe = cmdBase + required(input)
-
-  /** Returns command to execute */
-  def cmdLine = cmdPipe + " > " + required(output)
+    conditional(h, "-h") +
+    (if (inputAsStdin) "-" else required(input)) +
+    (if (outputAsStsout) "" else " > " + required(output))
 }
 
 object SamtoolsView {