Commit ae1b86f2 authored by Peter van 't Hof's avatar Peter van 't Hof

Added rna

parent 19a8e5d7
......@@ -29,7 +29,7 @@
<div class="col-md-1"></div>
<div class="col-md-6">
<p>
Here we show the total number of positions in the reference that are covered with a given coverage. This plot is whole-genome based, and will therefore be highly skewed in the case of an exome or targeted approach.
This Show the relative coverage for all transcripts. De data here is generated by picard CollectRnaMetrics
</p>
</div>
</div>
......
......@@ -57,9 +57,13 @@ object BammetricsReport extends ReportBuilder {
sampleId: Option[String],
libId: Option[String],
metricsTag: String = "bammetrics") = {
val wgsExecuted = summary.getValue(sampleId, libId, metricsTag, "stats", "wgs").isDefined
val rnaExecuted = summary.getValue(sampleId, libId, metricsTag, "stats", "rna").isDefined
val targets = (
summary.getValue(sampleId, libId, "bammetrics", "settings", "amplicon_name"),
summary.getValue(sampleId, libId, "bammetrics", "settings", "roi_name")
summary.getValue(sampleId, libId, metricsTag, "settings", "amplicon_name"),
summary.getValue(sampleId, libId, metricsTag, "settings", "roi_name")
) match {
case (Some(amplicon: String), Some(roi: List[_])) => amplicon :: roi.map(_.toString)
case (_, Some(roi: List[_])) => roi.map(_.toString)
......@@ -74,9 +78,11 @@ object BammetricsReport extends ReportBuilder {
Map())),
List(
"Summary" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp"),
"Insert Size" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/insertSize.ssp", Map("showPlot" -> true)),
"Whole genome coverage" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/wgsHistogram.ssp", Map("showPlot" -> true))
),
"Insert Size" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/insertSize.ssp", Map("showPlot" -> true))
) ++ ( if (wgsExecuted) List("Whole genome coverage" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/wgsHistogram.ssp",
Map("showPlot" -> true))) else Nil) ++
( if (rnaExecuted) List("Rna coverage" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/rnaHistogram.ssp",
Map("showPlot" -> true))) else Nil),
Map("metricsTag" -> metricsTag)
)
}
......
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