From f2645096efbdf32d6f9c0292e15f0cf54c7e8a9e Mon Sep 17 00:00:00 2001
From: Peter van 't Hof
Date: Mon, 8 Jun 2015 13:06:14 +0200
Subject: [PATCH] Fix insertsize table
---
.../nl/lumc/sasc/biopet/pipelines/bammetrics/insertSize.ssp | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/insertSize.ssp b/public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/insertSize.ssp
index d67bd4efd..266c63876 100644
--- a/public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/insertSize.ssp
+++ b/public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/insertSize.ssp
@@ -45,7 +45,7 @@
Sample |
#if (!sampleLevel) Library | #end
#for (field <- fields)
- ${field} |
+ ${field.replaceAll("_", " ")} |
#end
@@ -65,7 +65,7 @@
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(metricsTag, "stats", "insert_size_metrics", field)):_*)
+ summary.getValue((prefixPath ::: List("CollectInsertSizeMetrics", "metrics", field.toUpperCase)):_*).getOrElse(prefixPath ::: metricsTag :: Nil)
}
}#
#for (value <- fieldValues)
--
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