covstatsPlot.ssp 725 Bytes
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#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] %>
<%@ var libId: Option[String] = None %>
<%@ var outputDir: File %>
<%@ var target: String %>
#{
    val originalPlot = new File(summary.getLibraryValue(sampleId, libId, "bammetrics", "files", target + "_cov_stats", "plot", "path")
        .getOrElse(throw new IllegalArgumentException("No plot found in summary")).toString)

    val plot = new File(outputDir, target + "_cov_stats.png")

    IoUtils.copyFile(originalPlot, plot)
}#

<img src="${plot}">