Commit e2f5ad58 authored by Peter van 't Hof's avatar Peter van 't Hof

Changed reports summary values

parent 2e049a98
...@@ -83,10 +83,10 @@ ...@@ -83,10 +83,10 @@
#if (!sampleLevel) <td><a href="${rootPath}Samples/${sample}/Libraries/${libId}/index.html">${libId}</a></td> #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("bammetrics", "stats") val prefixPath = List("samples", sample) ::: (if (libId.isEmpty) Nil else List("libraries", libId)) ::: List("bammetrics", "stats")
val total = summary.getValue((prefixPath ::: List("biopet_flagstat", "All")):_*).getOrElse(0L).asInstanceOf[Long] val total = summary.getValue((prefixPath ::: List("bamstats", "flagstats", "All")):_*).getOrElse(0L).asInstanceOf[Long]
val mapped = summary.getValue((prefixPath ::: List("biopet_flagstat", "Mapped")):_*).getOrElse(0L).asInstanceOf[Long] val mapped = summary.getValue((prefixPath ::: List("bamstats", "flagstats", "Mapped")):_*).getOrElse(0L).asInstanceOf[Long]
val duplicates = summary.getValue((prefixPath ::: List("biopet_flagstat", "Duplicates")):_*).getOrElse(0L).asInstanceOf[Long] val duplicates = summary.getValue((prefixPath ::: List("bamstats", "flagstats", "Duplicates")):_*).getOrElse(0L).asInstanceOf[Long]
val secondary = summary.getValue((prefixPath ::: List("biopet_flagstat", "NotPrimaryAlignment")):_*).getOrElse(0L).asInstanceOf[Long] val secondary = summary.getValue((prefixPath ::: List("bamstats", "flagstats", "NotPrimaryAlignment")):_*).getOrElse(0L).asInstanceOf[Long]
}# }#
<td>${total}</td> <td>${total}</td>
<td>${mapped}</td> <td>${mapped}</td>
......
...@@ -12,9 +12,9 @@ ...@@ -12,9 +12,9 @@
#for (field <- fields) #for (field <- fields)
<tr><th>${field}</th><td> <tr><th>${field}</th><td>
#if (libId.isDefined) #if (libId.isDefined)
${summary.getLibraryValue(sampleId.get, libId.get, metricsTag, "stats", "biopet_flagstat", field)} ${summary.getLibraryValue(sampleId.get, libId.get, metricsTag, "stats", "bamstats", "flagstats", field)}
#else #else
${summary.getSampleValue(sampleId.get, metricsTag, "stats", "biopet_flagstat", field)} ${summary.getSampleValue(sampleId.get, metricsTag, "stats", "bamstats", "flagstats", field)}
#end #end
</td></tr> </td></tr>
#end #end
......
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