diff --git a/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp b/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp index e836fb2faa975ac8d43afcf363859bef601a1252..8e35b9035271b6dae70fbfac855690d61e718c07 100644 --- a/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp +++ b/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp @@ -83,10 +83,10 @@ #if (!sampleLevel) ${libId} #end #{ 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 mapped = summary.getValue((prefixPath ::: List("biopet_flagstat", "Mapped")):_*).getOrElse(0L).asInstanceOf[Long] - val duplicates = summary.getValue((prefixPath ::: List("biopet_flagstat", "Duplicates")):_*).getOrElse(0L).asInstanceOf[Long] - val secondary = summary.getValue((prefixPath ::: List("biopet_flagstat", "NotPrimaryAlignment")):_*).getOrElse(0L).asInstanceOf[Long] + val total = summary.getValue((prefixPath ::: List("bamstats", "flagstats", "All")):_*).getOrElse(0L).asInstanceOf[Long] + val mapped = summary.getValue((prefixPath ::: List("bamstats", "flagstats", "Mapped")):_*).getOrElse(0L).asInstanceOf[Long] + val duplicates = summary.getValue((prefixPath ::: List("bamstats", "flagstats", "Duplicates")):_*).getOrElse(0L).asInstanceOf[Long] + val secondary = summary.getValue((prefixPath ::: List("bamstats", "flagstats", "NotPrimaryAlignment")):_*).getOrElse(0L).asInstanceOf[Long] }# ${total} ${mapped} diff --git a/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/bamStats.ssp b/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/bamStats.ssp index aab83e541800b520b4b871689536aff6fba84d0c..f1540198d243068ab863d8bf65a8a72219d08c3f 100644 --- a/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/bamStats.ssp +++ b/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/bamStats.ssp @@ -12,9 +12,9 @@ #for (field <- fields) ${field} #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 - ${summary.getSampleValue(sampleId.get, metricsTag, "stats", "biopet_flagstat", field)} + ${summary.getSampleValue(sampleId.get, metricsTag, "stats", "bamstats", "flagstats", field)} #end #end