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biopet.biopet
Commit c8521fb6 authored by Ruben Vorderman's avatar Ruben Vorderman
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Defutured bammetricsPage

parent 3df673e7
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Showing with 24 additions and 110 deletions
bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala
View file @ c8521fb6
...@@ -73,7 +73,7 @@ object BammetricsReport extends ReportBuilder { ...@@ -73,7 +73,7 @@ object BammetricsReport extends ReportBuilder {
def bamMetricsPageValues(summary: SummaryDb, def bamMetricsPageValues(summary: SummaryDb,
sampleId: Option[Int], sampleId: Option[Int],
libId: Option[Int], libId: Option[Int],
metricsTag: String = "bammetrics"): Map[String, Any] = { metricsTag: String = "bammetrics"): (Map[String, Boolean], Map[String, List[String]], Map[String, List[(String, Map[String, Any])]], Map[String, Map[String, Any]]) = {
val wgsExecuted = summary.getStatsSize(runId, val wgsExecuted = summary.getStatsSize(runId,
metricsTag, metricsTag,
"wgs", "wgs",
...@@ -174,128 +174,42 @@ object BammetricsReport extends ReportBuilder { ...@@ -174,128 +174,42 @@ object BammetricsReport extends ReportBuilder {
libId, libId,
showPlot = true showPlot = true
) )
Tuple5(
Map( Map(
"wgsExecuted" -> wgsExecuted, "wgsExecuted" -> wgsExecuted,
"rnaExecuted" -> rnaExecuted, "rnaExecuted" -> rnaExecuted,
"insertsizeMetrics" -> insertsizeMetrics, "insertsizeMetrics" -> insertsizeMetrics),
"targetSettings" -> targetSettings, Map("targets" -> targets),
"covstatsPlotValuesList" -> covstatsPlotValuesList, Map("covstatsPlotValuesList" -> covstatsPlotValuesList),
Map(
"alignmentSummaryReportValues" -> alignmentSummaryReportValues, "alignmentSummaryReportValues" -> alignmentSummaryReportValues,
"mappingQualityReportValues" -> mappingQualityReportValues,
"clippingReportValues" -> clippingReportValues, "clippingReportValues" -> clippingReportValues,
"insertSizeReportValues" -> insertSizeReportValues, "insertSizeReportValues" -> insertSizeReportValues,
"wgsHistogramReportValues" -> wgsHistogramReportValues, "wgsHistogramReportValues" -> wgsHistogramReportValues,
"rnaHistogramReportValues" -> rnaHistogramReportValues "rnaHistogramReportValues" -> rnaHistogramReportValues
),
metricsTag
) )
} }
/** Generates a page with alignment stats */ /** Generates a page with alignment stats */
def bamMetricsPage(summary: SummaryDb, def bamMetricsPage(bamMetricsPageValues:(Map[String, Boolean], Map[String, List[String]], Map[String, List[(String, Map[String, Any])]], Map[String, Map[String, Any]], String)): Future[ReportPage] = {
sampleId: Option[Int],
libId: Option[Int], val wgsExecuted = bamMetricsPageValues._1("wgsExecuted")
metricsTag: String = "bammetrics"): Future[ReportPage] = { val rnaExecuted = bamMetricsPageValues._1("rnaExecuted")
val insertsizeMetrics = bamMetricsPageValues._1("insertsizeMetrics")
val wgsExecuted: Boolean = summary.getStatsSize(runId, val targets = bamMetricsPageValues._2("targets")
metricsTag, val covstatsPlotValuesList = bamMetricsPageValues._3("covstatsPlotValuesList")
"wgs", val alignmentSummaryReportValues = bamMetricsPageValues._4("alignmentSummaryReportValues")
sample = sampleId.map(SampleId), val mappingQualityReportValues = bamMetricsPageValues._4("mappingQualityReportValues")
library = libId.map(LibraryId)) >= 1 val clippingReportValues = bamMetricsPageValues._4("clippingReportValues")
val rnaExecuted: Boolean = summary.getStatsSize(runId, val insertSizeReportValues = bamMetricsPageValues._4("insertSizeReportValues")
metricsTag, val wgsHistogramReportValues = bamMetricsPageValues._4("wgsHistogramReportValues")
"rna", val rnaHistogramReportValues = bamMetricsPageValues._4("rnaHistogramReportValues")
sample = sampleId.map(SampleId), val metricsTag = bamMetricsPageValues._5
library = libId.map(LibraryId)) >= 1
val insertsizeMetrics: Boolean = summary
.getStatKeys(
runId,
metricsTag,
"CollectInsertSizeMetrics",
sampleId.map(SampleId).getOrElse(NoSample),
libId.map(LibraryId).getOrElse(NoLibrary),
Map("metrics" -> List("metrics"))
)
.exists(_._2.isDefined)
val targetSettings: Map[String, Option[Any]] = summary.getSettingKeys(
runId,
metricsTag,
NoModule,
sample = sampleId.map(SampleId).getOrElse(NoSample),
library = libId.map(LibraryId).getOrElse(NoLibrary),
Map("amplicon_name" -> List("amplicon_name"), "roi_name" -> List("roi_name"))
)
val targets = (
targetSettings("amplicon_name"),
targetSettings("roi_name")
) match {
case (Some(amplicon: String), Some(roi: List[_])) => amplicon :: roi.map(_.toString)
case (_, Some(roi: List[_])) => roi.map(_.toString)
case _ => Nil
}
val covstatsPlotValuesArray = ArrayBuffer[(String, Map[String, Any])]()
for (t <- targets) {
covstatsPlotValuesArray += Tuple2(
t,
BammetricsReportPage.covstatsPlotValues(summary, runId, sampleId, libId, Some(t)))
}
val covstatsPlotValuesList: List[(String, Map[String, Any])] = covstatsPlotValuesArray.toList
val alignmentSummaryReportValues: Map[String, Any] =
BammetricsReportPage.alignmentSummaryValues(
summary,
runId,
samples,
libraries,
sampleId,
libId
)
val mappingQualityReportValues: Map[String, Any] = BammetricsReportPage.mappingQualityValues(
summary,
runId,
samples,
libraries,
sampleId,
libId,
showPlot = true
)
val clippingReportValues: Map[String, Any] = BammetricsReportPage.clippingValues(
summary,
runId,
samples,
libraries,
sampleId,
libId,
showPlot = true
)
val insertSizeReportValues: Map[String, Any] = BammetricsReportPage.insertSizeValues(
summary,
runId,
samples,
libraries,
sampleId,
libId,
showPlot = true
)
val wgsHistogramReportValues: Map[String, Any] = BammetricsReportPage.wgsHistogramValues(
summary,
runId,
samples,
libraries,
sampleId,
libId,
showPlot = true
)
val rnaHistogramReportValues: Map[String, Any] = BammetricsReportPage.rnaHistogramValues(
summary,
runId,
samples,
libraries,
sampleId,
libId,
showPlot = true
)
Future { Future {
ReportPage( ReportPage(
if (targets.isEmpty) List() if (targets.isEmpty) List()
......
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