From 002dd1c3d248604b5c5ce29a321c4d38d570cf37 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Wed, 12 Aug 2015 16:17:04 +0200
Subject: [PATCH] Added a better error handling on a missing reference.
---
.../src/main/scala/nl/lumc/sasc/biopet/core/Reference.scala | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/Reference.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/Reference.scala
index d6aca7975..d3ae0023a 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/Reference.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/Reference.scala
@@ -94,12 +94,12 @@ trait Reference extends Configurable {
)
}
- //TODO: this become obsolete when index get autogenerated
+ //TODO: this become obsolete when index get auto generated
/** Check fasta file if file exist and index file are there */
def checkFasta(file: File): Unit = {
if (!Reference.checked.contains(file)) {
- require(file.exists(), "Reference not found: " + file)
+ if (!file.exists()) BiopetQScript.addError(s"Reference not found: $file, species: $referenceSpecies, name: $referenceName, configValue: " + config("reference_fasta"))
if (dictRequired) Reference.requireDict(file)
if (faiRequired) Reference.requireFai(file)
--
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