-

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

@@ -102,12 +102,8 @@ class ShivaSvCalling(val parent: Configurable) extends QScript with SummaryQScri
       addSummarizable(new Summarizable {
         def summaryFiles = Map("output_vcf" -> mergedResultFile)
         def summaryStats = counts
-      }, "variantsBySizeAndType", Some(sample))
+      }, "parse_sv_vcf", Some(sample))
     }
-    addSummarizable(new Summarizable {
-      def summaryFiles = Map.empty
-      def summaryStats = ShivaSvCallingReport.histogramBinBoundaries
-    }, "histBreaksForCounts")
 
     addSummaryJobs()
   }
@@ -116,7 +112,7 @@ 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)
+  def summarySettings = Map("sv_callers" -> configCallers.toList, "hist_bin_boundaries" -> ShivaSvCallingReport.histogramBinBoundaries)
 
   /** Files for the summary */
   def summaryFiles: Map[String, File] = if (inputBams.size > 1) Map("final_mergedvcf" -> outputMergedVCF) else Map.empty

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

@@ -19,7 +19,7 @@ object ShivaSvCallingReport {
     var delCounts, insCounts, dupCounts, invCounts: Map[String, Array[Long]] = Map()
 
     for (sampleName <- sampleNames) {
-      val sampleCounts: Map[String, Any] = Await.result(summary.getStat(runId, PipelineName("shivasvcalling"), ModuleName("variantsBySizeAndType"), SampleName(sampleName)), Duration.Inf).get
+      val sampleCounts: Map[String, Any] = Await.result(summary.getStat(runId, PipelineName("shivasvcalling"), ModuleName("parse_sv_vcf"), SampleName(sampleName)), Duration.Inf).get
       for ((svType, counts) <- sampleCounts.collect({ case (k, v: List[_]) => (k, v.toArray[Any]) })) {
         val elem: Tuple2[String, Array[Long]] = (sampleName, counts.collect({ case x: Long => x }))
         svType match {
@@ -42,7 +42,7 @@ object ShivaSvCallingReport {
   def parseSummaryForTranslocations(summary: SummaryDb, runId: Int, sampleNames: Seq[String]): Map[String, Long] = {
     var traCounts: Map[String, Long] = Map()
     for (sampleName <- sampleNames) {
-      val counts: Map[String, Any] = Await.result(summary.getStat(runId, PipelineName("shivasvcalling"), ModuleName("variantsBySizeAndType"), SampleName(sampleName)), Duration.Inf).get
+      val counts: Map[String, Any] = Await.result(summary.getStat(runId, PipelineName("shivasvcalling"), ModuleName("parse_sv_vcf"), SampleName(sampleName)), Duration.Inf).get
       traCounts += (sampleName -> counts.get("TRA").get.asInstanceOf[Long])
     }
     if (traCounts.exists(elem => elem._2 > 0)) traCounts else Map.empty