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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) @Argument(shortName="eval", doc="adds the VariantEval walker to the pipeline", required=false)
var eval: Boolean = false var eval: Boolean = false
@Argument(shortName="cut", doc="adds the ApplyVariantCut walker to the pipeline", required=false) @Argument(shortName="noCut", doc="adds the ApplyVariantCut walker to the pipeline", required=false)
var cut: Boolean = false var noCut: Boolean = false
trait UNIVERSAL_GATK_ARGS extends CommandLineGATK { logging_level = "INFO"; jarFile = gatkJarFile; memoryLimit = Some(3); } 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 GenerateVariantClusters(target, !goldStandard))
add(new VariantRecalibratorTiTv(target, !goldStandard)) add(new VariantRecalibratorTiTv(target, !goldStandard))
add(new VariantRecalibratorNRS(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 (eval) add(new VariantEvaluation(target))
} }
if ( !skipGoldStandard ) { if ( !skipGoldStandard ) {
@ -270,7 +270,7 @@ class MethodsDevelopmentCallingPipeline extends QScript {
val name: String = t.name val name: String = t.name
this.reference_sequence = t.reference this.reference_sequence = t.reference
this.rodBind :+= RodBind("comphapmap", "VCF", t.hapmapFile) 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.analysisName = name + "_VE"
this.intervalsString ++= List(t.intervals) this.intervalsString ++= List(t.intervals)
this.EV ++= List("GenotypeConcordance") this.EV ++= List("GenotypeConcordance")