Fixing ConTest

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/ContEst.scala

@@ -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

shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/somatic/MuTect2.scala

@@ -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)