Added sampe

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaSampe.scala

+package nl.lumc.sasc.biopet.extensions.bwa
+
+import java.io.File
+
+import nl.lumc.sasc.biopet.core.config.Configurable
+import org.broadinstitute.gatk.utils.commandline.{Output, Input}
+
+/**
+ * Created by pjvan_thof on 1/16/15.
+ */
+class BwaSampe (val root: Configurable) extends Bwa {
+  @Input(doc = "Fastq file R1", required = true)
+  var fastqR1: File = _
+
+  @Input(doc = "Fastq file R2", required = true)
+  var fastqR2: File = _
+
+  @Input(doc = "Sai file R1", required = true)
+  var saiR1: File = _
+
+  @Input(doc = "Sai file R2", required = true)
+  var saiR2: File = _
+
+  @Input(doc = "The reference file for the bam files.", required = true)
+  var reference: File = config("reference", required = true)
+
+  @Output(doc = "Output file SAM", required = false)
+  var output: File = _
+
+  var a: Option[Int] = config("a")
+  var o: Option[Int] = config("o")
+  var n: Option[Int] = config("n")
+  var N: Option[Int] = config("N")
+  var c: Option[Float] = config("c")
+  var P: Boolean = config("P", default = false)
+  var s: Boolean = config("s", default = false)
+  var A: Boolean = config("A", default = false)
+
+  var r: String = _
+
+  def cmdLine = required(executable) +
+    required("samse") +
+    optional("-n", n) +
+    optional("-f", output) +
+    optional("-r", r) +
+    optional("-c", c) +
+    conditional(P, "-P") +
+    conditional(s, "-s") +
+    conditional(A, "-A") +
+    required(reference) +
+    required(saiR1) +
+    required(saiR2) +
+    required(fastqR1) +
+    required(fastqR2)
+}