Commit 58c2b606 authored by rhpvorderman's avatar rhpvorderman

Defutured Bammetricsreport

parent e5b7192d
......@@ -126,10 +126,49 @@ object BammetricsReport extends ReportBuilder {
for (t <- targets) {
covstatsPlotValuesArray += Tuple2(t,BammetricsReportPage.covstatsPlotValues(summary, runId, sampleId, libId, Some(t)))
}
val covstatsPlotValuesList = covstatsPlotValuesArray.toList
val alignmentSummaryReportValues = BammetricsReportPage.alignmentSummaryValues(
summary,
runId,
samples,
libraries,
sampleId,
libId
)
val mappingQualityReportValues = BammetricsReportPage.mappingQualityValues(
summary,
runId,
samples,
libraries,
sampleId,
libId,
showPlot = true
)
val clippingReportValues = BammetricsReportPage.clippingValues(
summary,
runId,
samples,
libraries,
sampleId,
libId,
showPlot= true
)
val insertSizeReportValues = BammetricsReportPage.insertSizeValues(
summary,
runId,
samples,
libraries,
sampleId,
libId,
showPlot= true
)
val wgsHistogramReportValues = BammetricsReportPage.wgsHistogramValues(
summary,runId, samples, libraries, sampleId, libId, showPlot = true
)
val rnaHistogramReportValues = BammetricsReportPage.rnaHistogramValues(
summary,runId, samples, libraries, sampleId, libId, showPlot = true
)
Future {
ReportPage(
if (targets.isEmpty) List()
......@@ -144,29 +183,29 @@ object BammetricsReport extends ReportBuilder {
Map()))),
List(
"Summary" -> ReportSection(
"/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp"),
"/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp",alignmentSummaryReportValues),
"Mapping Quality" -> ReportSection(
"/nl/lumc/sasc/biopet/pipelines/bammetrics/mappingQuality.ssp",
Map("showPlot" -> true)),
mappingQualityReportValues),
"Clipping" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/clipping.ssp",
Map("showPlot" -> true))
clippingReportValues)
) ++
(if (insertsizeMetrics)
List(
"Insert Size" -> ReportSection(
"/nl/lumc/sasc/biopet/pipelines/bammetrics/insertSize.ssp",
Map("showPlot" -> true)))
insertSizeReportValues))
else Nil) ++ (if (wgsExecuted)
List(
"Whole genome coverage" -> ReportSection(
"/nl/lumc/sasc/biopet/pipelines/bammetrics/wgsHistogram.ssp",
Map("showPlot" -> true)))
wgsHistogramReportValues))
else Nil) ++
(if (rnaExecuted)
List(
"Rna coverage" -> ReportSection(
"/nl/lumc/sasc/biopet/pipelines/bammetrics/rnaHistogram.ssp",
Map("showPlot" -> true)))
rnaHistogramReportValues))
else Nil),
Map("metricsTag" -> metricsTag)
)
......
Markdown is supported
0% or
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment