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made ApplyVariantCut a default part of the pipeline, added the -noCut option if you don't want to use it. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5189 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
carneiro 2011-02-03 19:29:36 +00:00
parent ce2866122d
commit 358a400474
1 changed files with 4 additions and 4 deletions
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8
scala/qscript/oneoffs/rpoplin/MethodsDevelopmentCallingPipeline.scala
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@ -28,8 +28,8 @@ class MethodsDevelopmentCallingPipeline extends QScript {
@Argument(shortName="eval", doc="adds the VariantEval walker to the pipeline", required=false)
var eval: Boolean = false
@Argument(shortName="cut", doc="adds the ApplyVariantCut walker to the pipeline", required=false)
var cut: Boolean = false
@Argument(shortName="noCut", doc="adds the ApplyVariantCut walker to the pipeline", required=false)
var noCut: Boolean = false
trait UNIVERSAL_GATK_ARGS extends CommandLineGATK { logging_level = "INFO"; jarFile = gatkJarFile; memoryLimit = Some(3); }
@ -140,7 +140,7 @@ class MethodsDevelopmentCallingPipeline extends QScript {
add(new GenerateVariantClusters(target, !goldStandard))
add(new VariantRecalibratorTiTv(target, !goldStandard))
add(new VariantRecalibratorNRS(target, !goldStandard))
if (cut) add (new VariantCut(target))
if (!noCut) add (new VariantCut(target))
if (eval) add(new VariantEvaluation(target))
}
if ( !skipGoldStandard ) {
@ -270,7 +270,7 @@ class MethodsDevelopmentCallingPipeline extends QScript {
val name: String = t.name
this.reference_sequence = t.reference
this.rodBind :+= RodBind("comphapmap", "VCF", t.hapmapFile)
this.rodBind :+= RodBind("eval", "VCF", if (cut) {t.cutVCF} else {t.tsRecalibratedVCF} )
this.rodBind :+= RodBind("eval", "VCF", if (!noCut) {t.cutVCF} else {t.tsRecalibratedVCF} )
this.analysisName = name + "_VE"
this.intervalsString ++= List(t.intervals)
this.EV ++= List("GenotypeConcordance")