Commit cf4d0b82 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Changed error handeling

parent ef5ea6ce
...@@ -118,22 +118,22 @@ object Reference { ...@@ -118,22 +118,22 @@ object Reference {
/** /**
* Raise an exception when given fasta file has no fai file * Raise an exception when given fasta file has no fai file
* @param fastaFile Fasta file * @param fastaFile Fasta file
* @throws IllegalArgumentException
*/ */
def requireFai(fastaFile: File): Unit = { def requireFai(fastaFile: File): Unit = {
val fai = new File(fastaFile.getAbsolutePath + ".fai") val fai = new File(fastaFile.getAbsolutePath + ".fai")
require(fai.exists(), "Reference is missing a fai file") require(fai.exists(), "Reference is missing a fai file")
require(IndexedFastaSequenceFile.canCreateIndexedFastaReader(fastaFile), if (fai.exists()) {
"Index of reference cannot be loaded, reference: " + fastaFile) 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 * Raise an exception when given fasta file has no dict file
* @param fastaFile Fasta file * @param fastaFile Fasta file
* @throws IllegalArgumentException
*/ */
def requireDict(fastaFile: File): Unit = { def requireDict(fastaFile: File): Unit = {
val dict = new File(fastaFile.getAbsolutePath.stripSuffix(".fa").stripSuffix(".fasta") + ".dict") 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")
} }
} }
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