Commit 85e5d3c1 authored by Sander Bollen's avatar Sander Bollen

warning messages

parent bddec662
......@@ -52,6 +52,9 @@ class Tarmac(val parent: Configurable) extends QScript with PedigreeQscript with
val outFile = new File(sampleDir + File.separator + s"$name.dcov")
(inputXhmmCountFile, bamFile) match {
case (Some(f), _) => {
if (bamFile.isDefined) {
logger.warn(s"Both BAM and Xhmm count files are given for sample $name. The BAM file will be ignored")
}
val ln = new Ln(root)
ln.input = f
ln.output = outFile
......@@ -86,6 +89,9 @@ class Tarmac(val parent: Configurable) extends QScript with PedigreeQscript with
val outFile = new File(sampleDir + File.separator + s"$name.wisecondor.bed")
(inputWisecondorCountFile, bamFile) match {
case (Some(f), _) => {
if (bamFile.isDefined) {
logger.warn(s"Both BAM and Wisecondor count files are given for sample $name. The BAM file will be ignored")
}
val ln = new Ln(root)
ln.input = f
ln.output = outFile
......
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