showing translocation counts aswell

shiva/src/main/resources/nl/lumc/sasc/biopet/pipelines/shiva/sampleVariantsSv.ssp

@@ -11,6 +11,7 @@
     val sampleNames: List[String] = summary.samples.toList.sorted
 
     val counts: Map[String, Map[String, Array[Long]]] = ShivaSvCallingReport.parseSummaryForSvCounts(summary)
+    val traCounts: Map[String, Long] = ShivaSvCallingReport.parseSummaryForTranslocations(summary)
 
     var svTypes = List(
     SvTypeForReport("DEL", "Deletions", "svSummaryDeletions.tsv", "svSummaryDeletions.png"),
@@ -31,12 +32,29 @@
         <img src="${sv.pngFileName}" />
     #end
     </div>
+    #if (traCounts.nonEmpty)
+        <div class="panel-body">
+        <h5>Number of translocation events detected:</h5>
+        <table class="table table-condensed" style="width:auto">
+            <thead><tr>
+            #for (sampleName <- sampleNames)
+                <th>${sampleName}</th>
+            #end
+            </tr></thead>
+            <tbody><tr>
+            #for (sampleName <- sampleNames)
+                <td>${traCounts.get(sampleName).get}</td>
+            #end
+            </tr></tbody>
+        </table>
+        </div>
+    #end
     <div class="panel-footer">
         <button type="button" class="btn btn-info" data-toggle="collapse" data-target="#svSummaryTable">
             #if (showTable)
-                <i class="glyphicon glyphicon-eye-close"></i> Hide table
+                <i class="glyphicon glyphicon-eye-close"></i> Hide tables
             #else
-                <i class="glyphicon glyphicon-eye-open"></i> Show table
+                <i class="glyphicon glyphicon-eye-open"></i> Show tables
             #end
         </button>
         <a href="${tsvAllTypes}"><button type="button" class="btn btn-info"><i class="glyphicon glyphicon-cloud-download"></i> TSV file</button></a>

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

@@ -15,12 +15,12 @@
 package nl.lumc.sasc.biopet.pipelines.shiva
 
 import htsjdk.variant.vcf.VCFFileReader
-import nl.lumc.sasc.biopet.core.summary.{Summarizable, SummaryQScript}
-import nl.lumc.sasc.biopet.core.{PipelineCommand, Reference, SampleLibraryTag}
+import nl.lumc.sasc.biopet.core.summary.{ Summarizable, SummaryQScript }
+import nl.lumc.sasc.biopet.core.{ PipelineCommand, Reference, SampleLibraryTag }
 import nl.lumc.sasc.biopet.extensions.Pysvtools
 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 nl.lumc.sasc.biopet.utils.{ BamUtils, Logging }
 import org.broadinstitute.gatk.queue.QScript
 
 /**

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

@@ -35,6 +35,15 @@ object ShivaSvCallingReport {
     result
   }
 
+  def parseSummaryForTranslocations(summary: Summary): Map[String, Long] = {
+    var traCounts: Map[String, Long] = Map()
+    for (sampleName <- summary.samples) {
+      var counts: Map[String, Any] = summary.getSampleValue(sampleName, "shivasvcalling", "stats", "variantsBySizeAndType").get.asInstanceOf[Map[String, Any]]
+      traCounts += (sampleName -> counts.get("TRA").get.asInstanceOf[Long])
+    }
+    if (traCounts.exists(elem => elem._2 > 0)) traCounts else Map.empty
+  }
+
   def writeTsvFiles(sampleNames: List[String], counts: Map[String, Map[String, Array[Long]]], svTypes: List[SvTypeForReport], outFileAllTypes: String, outDir: File): Unit = {
 
     val tsvWriter = new PrintWriter(new File(outDir, outFileAllTypes))