Merge branch 'develop' into toucan-groups

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Grep.scala

+package nl.lumc.sasc.biopet.extensions
+
+import java.io.File
+
+import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
+import nl.lumc.sasc.biopet.utils.config.Configurable
+import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
+
+/**
+  * Created by pjvanthof on 30/03/16.
+  */
+class Grep(val root: Configurable) extends BiopetCommandLineFunction {
+  @Input(doc = "Input file", required = true)
+  var input: File = _
+
+  @Output(doc = "Output file", required = true)
+  var output: File = _
+
+  executable = config("exe", default = "grep")
+
+  var grepFor: String = null
+
+  var invertMatch: Boolean = false
+  var regex: Boolean = false
+  var perlRegexp: Boolean = false
+
+  /** return commandline to execute */
+  def cmdLine = required(executable) +
+    conditional(invertMatch, "-v") +
+    conditional(regex, "-e") +
+    conditional(perlRegexp, "-P") +
+    required(grepFor) +
+    (if (inputAsStdin) "" else required(input)) +
+    (if (outputAsStsout) "" else " > " + required(output))
+}
+
+object Grep {
+  def apply(root: Configurable,
+            grepFor: String,
+            regex: Boolean = false,
+            invertMatch: Boolean = false,
+            perlRegexp: Boolean = false): Grep = {
+    val grep = new Grep(root)
+    grep.grepFor = grepFor
+    grep.regex = regex
+    grep.perlRegexp = perlRegexp
+    grep.invertMatch = invertMatch
+    grep
+  }
+}