Completely defutured mappingQuality.ssp

bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/mappingQuality.ssp

 #import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb)
-#import(nl.lumc.sasc.biopet.utils.summary.db.Schema._)
+#import(nl.lumc.sasc.biopet.utils.summary.db.Schema.Sample)
+#import(nl.lumc.sasc.biopet.utils.summary.db.Schema.Library)
 #import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb._)
 #import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb.Implicts._)
 #import(nl.lumc.sasc.biopet.core.report.ReportPage)
@@ -19,6 +20,7 @@
 <%@ var allSamples: Seq[Sample] %>
 <%@ var allLibraries: Seq[Library] %>
 <%@ var mappingQualityPlotTables: Array[Map[String, Array[Any]]] %>
+<%@ var mappingQualityTableResults: Map[(Int, Int), Map[String, Option[Any]]] %>
 #{
     val samples = sampleId match {
     case Some(id) => allSamples.filter(_.id == id).toList
@@ -87,8 +89,7 @@
                 #if (libs.head != libId) <tr> #end
                     #if (!sampleLevel) <td><a href="${rootPath}Samples/${sample.name}/Libraries/${libName}/index.html">${libName}</a></td> #end
                     #{
-                        val statsPaths = fields.map(x => x -> List("mapping_quality", "general", x)).toMap
-                        val results = summary.getStatKeys(runId, "bammetrics", "bamstats", sample = sample.id, library = libId.map(LibraryId).getOrElse(NoLibrary), keyValues = statsPaths)
+                        val results: Map[String, Option[Any]] = mappingQualityTableResults(sample.id, libId)
                     }#
                     #for (field <- fields)
                         <td>${results(field)}</td>

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

@@ -569,10 +569,11 @@ object BammetricsReport extends ReportBuilder {
              allLibraries: Seq[Library],
              sampleId: Option[Int],
              libId: Option[Int],
+              fields: List[String] = List("min", "max", "mean", "median", "modal"),
              sampleLevel: Boolean = false,
              showPlot: Boolean = false,
              showIntro: Boolean = true,
-             showTable: Boolean = true
+             showTable: Boolean = true)
                : Map[String, Any] = {
 
     val samples = sampleId match {
@@ -580,7 +581,11 @@ object BammetricsReport extends ReportBuilder {
       case _ => allSamples.toList
     }
     val mapQualityPlotTables = mappingQualityPlotTables(summary,!sampleLevel,sampleId,libId)
+
+    val statsPaths = fields.map(x => x -> List("mapping_quality", "general", x)).toMap
+    val mappingQualityTableResults: Map[(Int, Int), Map[String, Option[Any]]]: = summary.getStatsForLibraries(runId, "bammetrics", "bamstats", sampleId, statsPaths)
     Map("mappingQualityPlotTables" -> mapQualityPlotTables,
+      "mappingQualityTableResults" -> mappingQualityTableResults,
     "showIntro" -> showIntro,
     "showTable" -> showTable,
       "showPlot" -> showPlot,