Commit 1ba08563 authored by Peter van 't Hof's avatar Peter van 't Hof

Adding general stats to report

parent d8a71161
......@@ -10,7 +10,7 @@
<%@ var metricsTag: String = "bammetrics" %>
<%@ var sampleLevel: Boolean = false %>
<%@ var outputDir: File %>
<%@ var fields: List[String] = List("mean_insert_size", "standard_deviation", "median_insert_size")%>
<%@ var fields: List[String] = List("min", "max", "mean", "median", "modal")%>
<%@ var showPlot: Boolean = false %>
<%@ var showTable: Boolean = true %>
<%@ var showIntro: Boolean = true%>
......@@ -87,7 +87,7 @@
val prefixPath = List("samples", sample) ::: (if (libId.isEmpty) Nil else List("libraries", libId)) ::: List("bammetrics", "stats")
val fieldValues = for (field <- fields) yield {
summary.getValue((prefixPath ::: List("CollectInsertSizeMetrics", "metrics", field.toUpperCase)):_*).getOrElse("N/A")
summary.getValue((prefixPath ::: List("bamstats", "clipping", "general", field.toUpperCase)):_*).getOrElse("N/A")
}
}#
#for (value <- fieldValues)
......
......@@ -10,7 +10,7 @@
<%@ var metricsTag: String = "bammetrics" %>
<%@ var sampleLevel: Boolean = false %>
<%@ var outputDir: File %>
<%@ var fields: List[String] = List("mean_insert_size", "standard_deviation", "median_insert_size")%>
<%@ var fields: List[String] = List("min", "max", "mean", "median", "modal")%>
<%@ var showPlot: Boolean = false %>
<%@ var showTable: Boolean = true %>
<%@ var showIntro: Boolean = true%>
......@@ -87,7 +87,7 @@
val prefixPath = List("samples", sample) ::: (if (libId.isEmpty) Nil else List("libraries", libId)) ::: List("bammetrics", "stats")
val fieldValues = for (field <- fields) yield {
summary.getValue((prefixPath ::: List("CollectInsertSizeMetrics", "metrics", field.toUpperCase)):_*).getOrElse("N/A")
summary.getValue((prefixPath ::: List("bamstats", "clipping", "general", field.toUpperCase)):_*).getOrElse("N/A")
}
}#
#for (value <- fieldValues)
......
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