Commit b43464ed authored by Peter van 't Hof's avatar Peter van 't Hof

Give a warning in de logwhen a variantcaller is used that does not support this.

parent 06a147a3
......@@ -245,6 +245,14 @@ class Shiva(val parent: Configurable) extends QScript with MultisampleMappingTra
if (!usePrintReads)
vc.inputBqsrFiles = samples.flatMap { case (sampleId, sample) => sample.bqsrFile.map(sampleId -> _) }
add(vc)
if (!usePrintReads) {
import variantcallers._
if (vc.callers.exists(_ match {
case _:HaplotypeCaller | _:HaplotypeCallerAllele | _:HaplotypeCallerGvcf => false
case _:UnifiedGenotyper | _:UnifiedGenotyperAllele => false
case _ => true
})) logger.warn("Not all variantcallers chosen can read BQSR files, All non-GATK")
}
annotation.foreach { toucan =>
toucan.outputDir = new File(outputDir, "annotation")
......
Markdown is supported
0% or
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment