Fixed rna coverage plot

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

-#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._)
 #import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb.Implicts._)
@@ -72,14 +73,14 @@
                 case _ => allLibraries.filter(_.sampleId == sample.id).map(x => Some(x.id)).toList
                 }
             }#
-            <tr><td rowspan="${libs.size}"><a href="${rootPath}Samples/${sample}/index.html">${sample}</a></td>
+            <tr><td rowspan="${libs.size}"><a href="${rootPath}Samples/${sample.name}/index.html">${sample.name}</a></td>
             #for (libId <- libs)
                 #{ val libName = libId.map(l => allLibraries.find(_.id == l).get.name) }#
                 #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("metrics", x.toUpperCase)).toMap
-                        val results = summary.getStatKeys(runId, "bammetrics", "wgs", sample = sample.id, library = libId.map(LibraryId).getOrElse(NoLibrary), keyValues = statsPaths)
+                        val results = summary.getStatKeys(runId, "bammetrics", "rna", sample = sample.id, library = libId.map(LibraryId).getOrElse(NoLibrary), keyValues = statsPaths)
                     }#
                     #for (field <- fields)
                         <td>${results(field)}</td>

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

-#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._)
 #import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb.Implicts._)

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

@@ -306,12 +306,12 @@ object BammetricsReport extends ReportBuilder {
                        sampleId: Option[Int] = None,
                        libraryId: Option[Int] = None): Unit = {
     val statsPaths = Map(
-      "position" -> List("rna", "histogram", "normalized_position"),
-      "count" -> List("rna", "histogram", "All_Reads.normalized_coverage")
+      "position" -> List("histogram", "normalized_position"),
+      "count" -> List("histogram", "All_Reads.normalized_coverage")
     )
 
     writePlotFromSummary(outputDir, prefix, summary, libraryLevel, sampleId, libraryId, statsPaths,
-      "coverage", "count", "bammetrics", "rna",
+      "position", "count", "bammetrics", "rna",
       "Relative position", "Coverage", "Rna coverage")
   }
 

biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/summary/db/SummaryDb.scala

@@ -251,6 +251,9 @@ trait SummaryDb extends Closeable {
                   library: LibraryQuery = NoLibrary,
                   keyValues: Map[String, List[String]]): Map[String, Option[Any]] = {
     val stats = Await.result(getStat(runId, pipeline, module, sample, library), Duration.Inf)
+    if (module == ModuleName("rna")) {
+      ""
+    }
     keyValues.map {
       case (key, path) =>
         stats match {