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Bug fixes in MDCP 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5561 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
rpoplin 2011-04-03 00:04:38 +00:00
parent 98798eb276
commit 40a25af58e
1 changed files with 1 additions and 2 deletions
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3
scala/qscript/core/MethodsDevelopmentCallingPipeline.scala
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@ -103,7 +103,6 @@ class MethodsDevelopmentCallingPipeline extends QScript {
val lowPass: Boolean = true val lowPass: Boolean = true
val indels: Boolean = true val indels: Boolean = true
val useCut: Boolean = !noCut
val queueLogDir = ".qlog/" val queueLogDir = ".qlog/"
@ -275,7 +274,7 @@ class MethodsDevelopmentCallingPipeline extends QScript {
this.rodBind :+= RodBind("input", "VCF", if ( goldStandard ) { t.goldStandard_VCF } else { t.rawVCF } ) this.rodBind :+= RodBind("input", "VCF", if ( goldStandard ) { t.goldStandard_VCF } else { t.rawVCF } )
this.tranches_file = if ( goldStandard ) { t.goldStandardTranchesFile } else { t.tranchesFile} this.tranches_file = if ( goldStandard ) { t.goldStandardTranchesFile } else { t.tranchesFile}
this.recal_file = if ( goldStandard ) { t.goldStandardRecalFile } else { t.recalFile } this.recal_file = if ( goldStandard ) { t.goldStandardRecalFile } else { t.recalFile }
this.fdr_filter_level = t.trancheTarget this.ts_filter_level = t.trancheTarget
this.out = t.recalibratedVCF this.out = t.recalibratedVCF
this.analysisName = t.name + "_AVQSR" this.analysisName = t.name + "_AVQSR"
this.jobName = queueLogDir + t.name + ".applyVQSR" this.jobName = queueLogDir + t.name + ".applyVQSR"