From cf4d0b827b8ef685b2b2fef40722e790146acc3e Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Thu, 29 Oct 2015 14:38:18 +0100
Subject: [PATCH] Changed error handeling
---
.../scala/nl/lumc/sasc/biopet/core/Reference.scala | 10 +++++-----
1 file changed, 5 insertions(+), 5 deletions(-)
diff --git a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/Reference.scala b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/Reference.scala
index be479a8fa..ed5a4492e 100644
--- a/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/Reference.scala
+++ b/public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/Reference.scala
@@ -118,22 +118,22 @@ object Reference {
/**
* Raise an exception when given fasta file has no fai file
* @param fastaFile Fasta file
- * @throws IllegalArgumentException
*/
def requireFai(fastaFile: File): Unit = {
val fai = new File(fastaFile.getAbsolutePath + ".fai")
require(fai.exists(), "Reference is missing a fai file")
- require(IndexedFastaSequenceFile.canCreateIndexedFastaReader(fastaFile),
- "Index of reference cannot be loaded, reference: " + fastaFile)
+ if (fai.exists()) {
+ if (!IndexedFastaSequenceFile.canCreateIndexedFastaReader(fastaFile))
+ Logging.addError(s"Index of reference cannot be loaded, reference: $fastaFile")
+ } else Logging.addError("Reference is missing a fai file")
}
/**
* Raise an exception when given fasta file has no dict file
* @param fastaFile Fasta file
- * @throws IllegalArgumentException
*/
def requireDict(fastaFile: File): Unit = {
val dict = new File(fastaFile.getAbsolutePath.stripSuffix(".fa").stripSuffix(".fasta") + ".dict")
- require(dict.exists(), "Reference is missing a dict file")
+ if (!dict.exists()) Logging.addError("Reference is missing a dict file")
}
}
--
GitLab