changes Bowo and Peter suggested

shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaSvCalling.scala

@@ -18,11 +18,14 @@ import htsjdk.variant.vcf.VCFFileReader
 import nl.lumc.sasc.biopet.core.summary.{ Summarizable, SummaryQScript }
 import nl.lumc.sasc.biopet.core.{ PipelineCommand, Reference }
 import nl.lumc.sasc.biopet.extensions.Pysvtools
+import nl.lumc.sasc.biopet.pipelines.shiva.ShivaSvCallingReport.histogramBinBoundaries
 import nl.lumc.sasc.biopet.pipelines.shiva.svcallers._
 import nl.lumc.sasc.biopet.utils.config.Configurable
 import nl.lumc.sasc.biopet.utils.{ BamUtils, Logging }
 import org.broadinstitute.gatk.queue.QScript
 
+import scala.collection.JavaConversions._
+
 /**
  * Common trait for ShivaVariantcalling
  *
@@ -98,7 +101,7 @@ class ShivaSvCalling(val parent: Configurable) extends QScript with SummaryQScri
     // sample tagging is however not available within this pipeline
 
     for ((sample, mergedResultFile) <- outputMergedVCFbySample) {
-      lazy val counts = getVariantCounts(mergedResultFile, ShivaSvCallingReport.histogramBinBoundaries)
+      lazy val counts = getVariantCounts(mergedResultFile)
       addSummarizable(new Summarizable {
         def summaryFiles = Map("output_vcf" -> mergedResultFile)
         def summaryStats = counts
@@ -112,35 +115,35 @@ class ShivaSvCalling(val parent: Configurable) extends QScript with SummaryQScri
   protected def callersList: List[SvCaller] = List(new Breakdancer(this), new Clever(this), new Delly(this), new Pindel(this))
 
   /** Settings for the summary */
-  def summarySettings = Map("sv_callers" -> configCallers.toList, "hist_bin_boundaries" -> ShivaSvCallingReport.histogramBinBoundaries)
+  def summarySettings = Map("sv_callers" -> configCallers.toList, "hist_bin_boundaries" -> histogramBinBoundaries)
 
   /** Files for the summary */
   def summaryFiles: Map[String, File] = if (inputBams.size > 1) Map("final_mergedvcf" -> outputMergedVCF) else Map.empty
 
-  def getVariantCounts(vcfFile: File, breaks: Array[Int]): Map[String, Any] = {
-    val delCounts, insCounts, dupCounts, invCounts = Array.fill(breaks.size + 1) { 0 }
+  /** Parses a vcf-file and counts sv-s by type and size. Sv-s are divided to different size classes, the boundaries between these classes are those given in ShivaSvCallingReport.histogramBinBoundaries. */
+  def getVariantCounts(vcfFile: File): Map[String, Any] = {
+    val delCounts, insCounts, dupCounts, invCounts = Array.fill(histogramBinBoundaries.size + 1) { 0 }
     var traCount = 0
 
-    val iterator = new VCFFileReader(vcfFile, false).iterator
-    while (iterator.hasNext) {
-      val record = iterator.next
-      val svType = record.getAttributeAsString("SVTYPE", "")
-      if (svType == "TRA" || svType == "CTX" || svType == "ITX") {
-        traCount += 1
-      } else {
-        val size = record.getEnd - record.getStart
-        var i = 0
-        while (i < breaks.size && size > breaks(i)) i += 1
-        svType match {
-          case "DEL" => delCounts(i) += 1
-          case "INS" => insCounts(i) += 1
-          case "DUP" => dupCounts(i) += 1
-          case "INV" => invCounts(i) += 1
-          case _     => logger.warn(s"Vcf file contains a record of unknown type: file-$vcfFile, type-$svType")
+    val reader = new VCFFileReader(vcfFile, false)
+    for (record <- reader) {
+      record.getAttributeAsString("SVTYPE", "") match {
+        case "TRA" | "CTX" | "ITX" => traCount += 1
+        case svType => {
+          val size = record.getEnd - record.getStart
+          var i = 0
+          while (i < histogramBinBoundaries.size && size > histogramBinBoundaries(i)) i += 1
+          svType match {
+            case "DEL" => delCounts(i) += 1
+            case "INS" => insCounts(i) += 1
+            case "DUP" => dupCounts(i) += 1
+            case "INV" => invCounts(i) += 1
+            case _     => logger.warn(s"Vcf file contains a record of unknown type: file-$vcfFile, type-$svType")
+          }
         }
       }
     }
-    iterator.close()
+    reader.close()
 
     Map("DEL" -> delCounts, "INS" -> insCounts, "DUP" -> dupCounts, "INV" -> invCounts, "TRA" -> traCount)
   }