Commit 5760560d authored by Peter van 't Hof's avatar Peter van 't Hof

Fixing compile issues

parent e8609425
......@@ -3,9 +3,7 @@ package nl.lumc.sasc.biopet.extensions.gatk
import java.io.File
import nl.lumc.sasc.biopet.core.ScatterGatherableFunction
import nl.lumc.sasc.biopet.extensions.gatk.CommandLineGATK.isFileWithTag
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.queue.extensions.gatk.TaggedFile
import org.broadinstitute.gatk.utils.commandline.{Argument, Gather, Input, Output}
class MuTect2(val parent: Configurable) extends CommandLineGATK with ScatterGatherableFunction {
......@@ -181,8 +179,7 @@ class MuTect2(val parent: Configurable) extends CommandLineGATK with ScatterGath
@Argument(fullName = "useNewAFCalculator", shortName = "newQual", required = false)
var useNewAFCalculator: Boolean = config("use_new_af_calculator", default = false)
override def cmdLine = super.cmdLine +
override def cmdLine: String = super.cmdLine +
optional("--cosmic", cosmic) +
optional("--dbsnp", dbsnp) +
optional("--normal_panel", ponFile) +
......@@ -213,13 +210,3 @@ class MuTect2(val parent: Configurable) extends CommandLineGATK with ScatterGath
conditional(useNewAFCalculator, "--useNewAFCalculator") +
(if (outputAsStdout) "" else required("--out", outputVcf))
}
object MuTect2 {
def apply(parent: Configurable, tumorSampleBam: File, normalSampleBam: File, output: File): MuTect2 = {
val mutect2 = new MuTect2(parent)
mutect2.tumorSampleBam = tumorSampleBam
mutect2.normalSampleBam = normalSampleBam
mutect2.outputVcf = output
mutect2
}
}
......@@ -416,8 +416,8 @@ object ConfigUtils extends Logging {
Logging.addError(
"Value does not exist but is required, key: " + value.requestIndex.key +
" namespace: " + value.requestIndex.module,
if (value.requestIndex.path != Nil) " path: " + value.requestIndex.path.mkString("->")
else null
if (value.requestIndex.path != Nil) Some(" path: " + value.requestIndex.path.mkString("->"))
else None
)
exist
}
......
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