Commit d793f5dd authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Fixing ConTest

parent 9890b968
......@@ -11,20 +11,6 @@ class ContEst(val parent: Configurable) extends CommandLineGATK {
def analysis_type: String = "ContEst"
/** Getter and setter for tumor sample bam file. */
def tumorSampleBam = input_file.find(file => isFileWithTag(file, "eval")).getOrElse(null)
def tumorSampleBam_= (value:File):Unit = {
input_file = input_file.filterNot(file => isFileWithTag(file, "eval"))
input_file :+= TaggedFile(value, "eval")
}
/** Getter and setter for normal sample bam file. */
def normalSampleBam = input_file.find(file => isFileWithTag(file, "genotype")).getOrElse(null)
def normalSampleBam_= (value:File):Unit = {
input_file = input_file.filterNot(file => isFileWithTag(file, "genotype"))
input_file :+= TaggedFile(value, "genotype")
}
/** Variant file containing information about the population allele frequencies. */
@Input(fullName = "popfile", shortName="pf", required = true)
var popFile: File = config("popfile")
......@@ -89,13 +75,3 @@ class ContEst(val parent: Configurable) extends CommandLineGATK {
optional("--trim_fraction", trimFraction)
}
object ContEst {
def apply(parent: Configurable, tumorSampleBam: File, normalSampleBam: File, output: File): ContEst = {
val conest = new ContEst(parent)
conest.tumorSampleBam = tumorSampleBam
conest.normalSampleBam = normalSampleBam
conest.output = output
conest
}
}
\ No newline at end of file
......@@ -46,8 +46,8 @@ class MuTect2(val parent: Configurable) extends SomaticVariantCaller {
if (runConEst) {
val namePrefix = outputFile.getAbsolutePath.stripSuffix(".vcf.gz")
val contEst = new gatk.ContEst(this)
inputBams.get(pair.tumorSample).foreach(contEst.input_file :+= _)
inputBams.get(pair.normalSample).foreach(contEst.input_file :+= _)
inputBams.get(pair.tumorSample).foreach(contEst.input_file :+= TaggedFile(_, "eval"))
inputBams.get(pair.normalSample).foreach(contEst.input_file :+= TaggedFile(_, "genotype"))
contEst.output = new File(s"$namePrefix.contamination.txt")
contEst.BQSR = bqsrFile
add(contEst)
......
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