Commit b3454f23 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Fix compile error

parent 8cab8c38
......@@ -46,8 +46,6 @@ class GwasTest(val root: Configurable) extends QScript with BiopetQScript with R
case _ => Nil
})
lazy val referenceDict = new FastaSequenceFile(referenceFasta(), true).getSequenceDictionary
override def dictRequired = true
override def defaults = Map("snptest" -> Map("genotype_field" -> "GP"))
......@@ -55,6 +53,7 @@ class GwasTest(val root: Configurable) extends QScript with BiopetQScript with R
/** Init for pipeline */
def init(): Unit = {
inputGens.foreach { g =>
val referenceDict = new FastaSequenceFile(referenceFasta(), true).getSequenceDictionary
if (referenceDict.getSequenceIndex(g.contig) == -1)
Logging.addError(s"Contig '${g.contig}' does not exist on reference: ${referenceFasta()}")
}
......
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