Added bedtools sorted flag as default

bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala

@@ -41,6 +41,8 @@ class BamMetrics(val root: Configurable) extends QScript
   @Input(doc = "Bam File", shortName = "BAM", required = true)
   var inputBam: File = _
 
+  override def defaults = Map("bedtoolscoverage" -> Map("sorted" -> true))
+
   /** return location of summary file */
   def summaryFile = (sampleId, libId) match {
     case (Some(s), Some(l)) => new File(outputDir, s + "-" + l + ".BamMetrics.summary.json")

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsCoverage.scala

@@ -41,6 +41,8 @@ class BedtoolsCoverage(val root: Configurable) extends Bedtools {
   @Argument(doc = "diffStrand", required = false)
   var diffStrand: Boolean = false
 
+  var sorted: Boolean = config("sorted", default = false, freeVar = false)
+
   override def defaultCoreMemory = 4.0
 
   /** Returns command to execute */
@@ -50,6 +52,7 @@ class BedtoolsCoverage(val root: Configurable) extends Bedtools {
     conditional(depth, "-d") +
     conditional(sameStrand, "-s") +
     conditional(diffStrand, "-S") +
+    conditional(sorted, "-sorted") +
     (if (outputAsStsout) "" else " > " + required(output))
 }