From e714e45dcb937222c8280e3e245b910468f10404 Mon Sep 17 00:00:00 2001
From: bow <bow@bow.web.id>
Date: Thu, 5 Mar 2015 18:42:32 +0100
Subject: [PATCH] Avoid NullPointerException when checking for R2 in Gentrap
---
.../scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala
index 7abfc7593..77e5abbc2 100644
--- a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala
+++ b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala
@@ -790,7 +790,7 @@ class Gentrap(val root: Configurable) extends QScript with MultiSampleQScript wi
)
/** Convenience method to check whether the library is paired or not */
- def paired: Boolean = Option(config("R2").asFile).isDefined
+ def paired: Boolean = config.contains("R2")
/** Alignment results of this library ~ can only be accessed after addJobs is run! */
def alnFile: File = mappingJob.outputFiles("finalBamFile")
--
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