Commit 9e3b5000 authored by Peter van 't Hof's avatar Peter van 't Hof

Added multisample coverage table

parent c2b02cda
#import(nl.lumc.sasc.biopet.utils.IoUtils)
#import(nl.lumc.sasc.biopet.core.summary.Summary)
#import(nl.lumc.sasc.biopet.core.report.ReportPage)
#import(org.apache.commons.io.FileUtils)
#import(java.io.File)
<%@ var summary: Summary %>
<%@ var sampleId: Option[String] = None %>
<%@ var libId: Option[String] = None %>
<%@ var sampleLevel: Boolean = true %>
<%@ var rootPath: String %>
<%@ var outputDir: File %>
<%@ var metricsTag: String = "bammetrics" %>
<%@ var target: String %>
#{
val samples = sampleId match {
case Some(sample) => List(sample.toString)
case _ => summary.samples.toList
}
}#
<table class="table">
<thead><tr>
<th>mean</th>
<th>median</th>
<th>max</th>
<th>horizontal</th>
<th>frac min 10x</th>
<th>frac min 20x</th>
<th>frac min 30x</th>
<th>frac min 40x</th>
<th>frac min 50x</th>
</tr></thead>
<tbody>
#for (sample <- samples.toList.sorted)
#{
val libs = (libId, sampleLevel) match {
case (_, true) => List("")
case (Some(libId), _) => List(libId.toString)
case _ => summary.libraries(sample).toList
}
}#
<tr><td rowspan="${libs.size}"><a href="${rootPath}Samples/${sample}/index.html">${sample}</a></td>
#for (libId <- libs)
#if (libs.head != libId) <tr> #end
#if (!sampleLevel) <td><a href="${rootPath}Samples/${sample}/Libraries/${libId}/index.html">${libId}</a></td> #end
#{
val prefixPath = List("samples", sample) ::: (if (libId.isEmpty) Nil else List("libraries", libId)) ::: List(metricsTag, "stats", target + "_cov_stats", "coverage", "_all")
val total = summary.getValue((prefixPath ::: List("biopet_flagstat", "All")):_*).getOrElse(0L).asInstanceOf[Long]
val mapped = summary.getValue((prefixPath ::: List("biopet_flagstat", "Mapped")):_*).getOrElse(0L).asInstanceOf[Long]
val duplicates = summary.getValue((prefixPath ::: List("biopet_flagstat", "Duplicates")):_*).getOrElse(0L).asInstanceOf[Long]
}#
<td>${summary.getValue((prefixPath ::: "mean" :: Nil):_*)}</td>
<td>${summary.getValue((prefixPath ::: "median" :: Nil):_*)}</td>
<td>${summary.getValue((prefixPath ::: "max" :: Nil):_*)}</td>
<td>${summary.getValue((prefixPath ::: "horizontal" :: Nil):_*)}</td>
<td>${summary.getValue((prefixPath ::: "frac_min_10x" :: Nil):_*)}</td>
<td>${summary.getValue((prefixPath ::: "frac_min_20x" :: Nil):_*)}</td>
<td>${summary.getValue((prefixPath ::: "frac_min_30x" :: Nil):_*)}</td>
<td>${summary.getValue((prefixPath ::: "frac_min_40x" :: Nil):_*)}</td>
<td>${summary.getValue((prefixPath ::: "frac_min_50x" :: Nil):_*)}</td>
</tr>
#end
#end
</tbody>
</table>
......@@ -58,7 +58,7 @@ object ShivaReport extends MultisampleReportBuilder {
def createPage(name: String, amplicon: Boolean = false): ReportPage = {
//TODO: get target content
ReportPage(Map(), List(), Map())
ReportPage(Map(), List("Coverage" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/covstatsMultiTable.ssp")), Map("target" -> name))
}
amplicon match {
......
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