From 24205501a774b901b658c1f8332b96753b7259b3 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Mon, 9 Nov 2015 08:30:20 +0100
Subject: [PATCH] Fixed small bug
---
.../biopet/pipelines/gentrap/extensions/RawBaseCounter.scala | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/extensions/RawBaseCounter.scala b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/extensions/RawBaseCounter.scala
index efd7de06e..8be307a9d 100644
--- a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/extensions/RawBaseCounter.scala
+++ b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/extensions/RawBaseCounter.scala
@@ -83,7 +83,7 @@ class RawBaseCounter(val root: Configurable) extends BiopetCommandLineFunction {
}
override def beforeGraph(): Unit = {
- if (annotationBed != null) Logging.addError("Annotation BED must be supplied")
+ if (annotationBed == null) Logging.addError("Annotation BED must be supplied")
require(output != null, "Output must be defined")
require((mixedStrand && !distinctStrand) || (!mixedStrand && distinctStrand),
"Invalid input BAM combinations for RawBaseCounter")
--
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