add BuildBamIndex to biopet

public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/BuildBamIndex.scala

+package nl.lumc.sasc.biopet.extensions.picard
+
+import java.io.File
+
+import nl.lumc.sasc.biopet.utils.config.Configurable
+import org.broadinstitute.gatk.utils.commandline.{Output, Input}
+
+/**
+ * Created by sajvanderzeeuw on 6-10-15.
+ */
+class BuildBamIndex (val root: Configurable) extends Picard {
+
+  javaMainClass = new picard.sam.BuildBamIndex().getClass.getName
+
+  @Input(doc = "The input SAM or BAM files to analyze.", required = true)
+  var input: File = _
+
+  @Output(doc = "The output file to bam file to", required = true)
+  var output: File = _
+
+  override def cmdLine = super.cmdLine +
+    required("INPUT=", input, spaceSeparated = false) +
+    required("OUTPUT=", output, spaceSeparated = false)
+}