diff --git a/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/rnaHistogram.ssp b/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/rnaHistogram.ssp
index 944c9fbdbe0dfef49d3d840dd399945a77df00c2..3b7b02727ee1c930e3af48f9b0d37d0278bc3f8c 100644
--- a/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/rnaHistogram.ssp
+++ b/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/rnaHistogram.ssp
@@ -1,4 +1,5 @@
-#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
}
}#
-
${sample} |
+
${sample.name} |
#for (libId <- libs)
#{ val libName = libId.map(l => allLibraries.find(_.id == l).get.name) }#
#if (libs.head != libId)
#end
#if (!sampleLevel) ${libName} | #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)
${results(field)} |
diff --git a/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/wgsHistogram.ssp b/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/wgsHistogram.ssp
index ea2e2dab1f7f78a4dc665d3ab3b011dad8983b8b..3e0147e89c94eb6e6239e56ccc5dc61c0b1c804a 100644
--- a/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/wgsHistogram.ssp
+++ b/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/wgsHistogram.ssp
@@ -1,4 +1,5 @@
-#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._)
diff --git a/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala b/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala
index a7929e471f6ad5dbef277600a9d3fbab7375ea60..f5eb76650c0fa8a268808ea3fed4fbf61dd6016b 100644
--- a/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala
+++ b/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")
}
diff --git a/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/summary/db/SummaryDb.scala b/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/summary/db/SummaryDb.scala
index f24feb43cd6697f8d77e899b54ea3819e7acf7bd..63773032def8c6650faaec9191a09c0b9de3b872 100644
--- a/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/summary/db/SummaryDb.scala
+++ b/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 {