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biopet.biopet
Commit 8923196d authored by Peter van 't Hof's avatar Peter van 't Hof
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Fixed report with regions

parent 692208f2
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Showing with 4 additions and 4 deletions
public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/covstatsPlot.ssp
View file @ 8923196d
......@@ -8,13 +8,13 @@
<%@ var libId: Option[String] = None %>
<%@ var outputDir: File %>
<%@ var metricsTag: String = "bammetrics" %>
<%@ var target: String %>
<%@ var target: Option[String] %>
#{
val originalPlot = new File(summary.getValue(sampleId, libId, metricsTag, "files", target + "_cov_stats", "plot", "path")
val originalPlot = new File(summary.getValue(sampleId, libId, metricsTag, "files", target.get + "_cov_stats", "plot", "path")
.getOrElse(throw new IllegalArgumentException("No plot found in summary")).toString)
val plot = new File(outputDir, target + "_cov_stats.png")
val plot = new File(outputDir, target.get + "_cov_stats.png")
val values = summary.getValue(sampleId, libId, metricsTag, "stats", target + "_cov_stats", "coverage", "_all")
val values = summary.getValue(sampleId, libId, metricsTag, "stats", target.get + "_cov_stats", "coverage", "_all")
.getOrElse(throw new IllegalArgumentException("No plot found in summary")).asInstanceOf[Map[String, Any]]
if (originalPlot.exists()) IoUtils.copyFile(originalPlot, plot)
......
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