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biopet.biopet
Commits
8923196d
Commit
8923196d
authored
Dec 03, 2015
by
Peter van 't Hof
Browse files
Fixed report with regions
parent
692208f2
Changes
1
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Inline
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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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