Added bwa aln extension

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/bwa/BwaAln.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 BwaAln(val root: Configurable) extends Bwa {
+  @Input(doc = "Fastq file", required = true)
+  var fastq: 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 n: Option[Int] = config("n")
+  var o: Option[Int] = config("o")
+  var e: Option[Int] = config("e")
+  var i: Option[Int] = config("i")
+  var d: Option[Int] = config("d")
+  var l: Option[Int] = config("l")
+  var k: Option[Int] = config("k")
+  var m: Option[Int] = config("m")
+  var M: Option[Int] = config("M")
+  var O: Option[Int] = config("O")
+  var E: Option[Int] = config("E")
+  var R: Option[Int] = config("R")
+  var q: Option[Int] = config("q")
+  var B: Option[Int] = config("B")
+  var L: Boolean = config("L", default = false)
+  var N: Boolean = config("N", default = false)
+  var I: Boolean = config("I", default = false)
+  var b: Boolean = config("b", default = false)
+  var n0: Boolean = config("0", default = false)
+  var n1: Boolean = config("1", default = false)
+  var n2: Boolean = config("2", default = false)
+  var Y: Boolean = config("Y", default = false)
+
+  override val defaultVmem = "5G"
+  override val defaultThreads = 8
+
+  def cmdLine = required(executable) +
+    required("aln") +
+    optional("-n", n) +
+    optional("-o", o) +
+    optional("-e", e) +
+    optional("-i", i) +
+    optional("-d", d) +
+    optional("-l", l) +
+    optional("-k", k) +
+    optional("-m", m) +
+    optional("-M", M) +
+    optional("-O", O) +
+    optional("-E", E) +
+    optional("-R", R) +
+    optional("-q", q) +
+    optional("-B", B) +
+    conditional(L, "-L") +
+    conditional(N, "-N") +
+    conditional(I, "-I") +
+    conditional(b, "-b") +
+    conditional(n0, "-0") +
+    conditional(n1, "-1") +
+    conditional(n2, "-2") +
+    conditional(Y, "-Y") +
+    required("-f", output) +
+    required(reference) +
+    required(fastq)
+}