From 6a362745e7b1a4ec729954aa3594a36cc330345f Mon Sep 17 00:00:00 2001 From: Peter van 't Hof Date: Thu, 24 Nov 2016 17:34:11 +0100 Subject: [PATCH] Fixed field names --- .../nl/lumc/sasc/biopet/pipelines/bammetrics/clipping.ssp | 2 +- .../nl/lumc/sasc/biopet/pipelines/bammetrics/mappingQuality.ssp | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/clipping.ssp b/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/clipping.ssp index 5a25be35b..19f7edd3f 100644 --- a/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/clipping.ssp +++ b/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/clipping.ssp @@ -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("bamstats", "clipping", "general", field.toUpperCase)):_*).getOrElse("N/A") + summary.getValue((prefixPath ::: List("bamstats", "clipping", "general", field)):_*).getOrElse("N/A") } }# #for (value <- fieldValues) diff --git a/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/mappingQuality.ssp b/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/mappingQuality.ssp index fd651d002..517806911 100644 --- a/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/mappingQuality.ssp +++ b/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/mappingQuality.ssp @@ -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("bamstats", "clipping", "general", field.toUpperCase)):_*).getOrElse("N/A") + summary.getValue((prefixPath ::: List("bamstats", "mapping_quality", "general", field)):_*).getOrElse("N/A") } }# #for (value <- fieldValues) -- GitLab