From 5d8fb79d700c3d3d0bd8e8245fd361824d234326 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Fri, 18 Sep 2015 14:13:13 +0200
Subject: [PATCH] skip canRead when file does not exist
---
.../src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
index bcaf9dc77..366fc0b78 100644
--- a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
+++ b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetQScript.scala
@@ -92,7 +92,7 @@ trait BiopetQScript extends Configurable with GatkLogging {
inputFiles.foreach { i =>
if (!i.file.exists()) Logging.addError(s"Input file does not exist: ${i.file}")
- if (!i.file.canRead()) Logging.addError(s"Input file can not be read: ${i.file}")
+ else if (!i.file.canRead()) Logging.addError(s"Input file can not be read: ${i.file}")
}
reportClass.foreach(add(_))
--
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