
@@ -78,9 +80,8 @@
#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 = wgsHistogramTableResults(sample.id, libId)
+ }#
#for (field <- fields)
${results(field)} |
#end
diff --git a/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReportPage.scala b/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReportPage.scala
index 0582cc7a9e1116b33c94a3d3ef74ce2b1f1ea8b3..8f425f646f1a1d5acf4ed9ae576e3c381a6d1c81 100644
--- a/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReportPage.scala
+++ b/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReportPage.scala
@@ -144,5 +144,71 @@ object BammetricsReportPage {
"libId" -> libId
)
}
+ def rnaHistogramValues(summary: SummaryDb,
+ runId: Int,
+ allSamples: Seq[Sample],
+ allLibraries: Seq[Library],
+ sampleId: Option[Int],
+ libId: Option[Int],
+ fields: List[String] = List("PF_ALIGNED_BASES", "MEDIAN_5PRIME_BIAS", "MEDIAN_3PRIME_BIAS", "MEDIAN_5PRIME_TO_3PRIME_BIAS"),
+ sampleLevel: Boolean = false,
+ showPlot: Boolean = false,
+ showIntro: Boolean = true,
+ showTable: Boolean = true): Map[String, Any] = {
+
+ val samples = sampleId match {
+ case Some(id) => allSamples.filter(_.id == id).toList
+ case _ => allSamples.toList
+ }
+ val rnaHistogramPlotTables: Option[Array[Map[String, Array[Any]]]] =
+ if (showPlot)
+ Some(BammetricsReport.rnaHistogramPlotTables(summary, !sampleLevel, sampleId, libId))
+ else None
+
+ val statsPaths = fields.map(x => x -> List("metrics", x.toUpperCase)).toMap
+ val rnaHistogramTableResults = summary.getStatsForLibraries(runId, "bammetrics", "rna", sampleId, statsPaths)
+ Map(
+ "rnaHistogramPlotTables" -> rnaHistogramPlotTables,
+ "rnaHistogramTableResults" -> rnaHistogramTableResults,
+ "showIntro" -> showIntro,
+ "showTable" -> showTable,
+ "showPlot" -> showPlot,
+ "sampleId" -> sampleId,
+ "libId" -> libId
+ )
+ }
+ def wgsHistogramValues(summary: SummaryDb,
+ runId: Int,
+ allSamples: Seq[Sample],
+ allLibraries: Seq[Library],
+ sampleId: Option[Int],
+ libId: Option[Int],
+ fields: List[String] = List("mean_coverage", "pct_5x", "pct_10x", "pct_15x", "pct_20x", "pct_25x", "pct_30x", "pct_40x", "pct_50x", "pct_60x", "pct_70x", "pct_80x", "pct_90x", "pct_100x"),
+ sampleLevel: Boolean = false,
+ showPlot: Boolean = false,
+ showIntro: Boolean = true,
+ showTable: Boolean = true): Map[String, Any] = {
+
+ val samples = sampleId match {
+ case Some(id) => allSamples.filter(_.id == id).toList
+ case _ => allSamples.toList
+ }
+ val wgsHistogramPlotTables: Option[Array[Map[String, Array[Any]]]] =
+ if (showPlot)
+ Some(BammetricsReport.wgsHistogramPlotTables(summary, !sampleLevel, sampleId, libId))
+ else None
+
+ val statsPaths = fields.map(x => x -> List("metrics", x.toUpperCase)).toMap
+ val wgsHistogramTableResults = summary.getStatsForLibraries(runId, "bammetrics", "wgs", sampleId, statsPaths)
+ Map(
+ "wgsHistogramPlotTables" -> wgsHistogramPlotTables,
+ "wgsHistogramTableResults" -> wgsHistogramTableResults,
+ "showIntro" -> showIntro,
+ "showTable" -> showTable,
+ "showPlot" -> showPlot,
+ "sampleId" -> sampleId,
+ "libId" -> libId
+ )
+ }
}