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bug fix in MDCP 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5613 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
rpoplin 2011-04-11 18:27:47 +00:00
parent 004f5295ea
commit 05ad6ecf72
1 changed files with 2 additions and 1 deletions
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3
scala/qscript/core/MethodsDevelopmentCallingPipeline.scala
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@ -209,6 +209,7 @@ class MethodsDevelopmentCallingPipeline extends QScript {
if (qscript.deletions >= 0) if (qscript.deletions >= 0)
this.max_deletion_fraction = qscript.deletions this.max_deletion_fraction = qscript.deletions
this.out = t.rawVCF this.out = t.rawVCF
this.glm = org.broadinstitute.sting.gatk.walkers.genotyper.GenotypeLikelihoodsCalculationModel.Model.SNP
this.baq = if (noBAQ) {org.broadinstitute.sting.utils.baq.BAQ.CalculationMode.OFF} else {org.broadinstitute.sting.utils.baq.BAQ.CalculationMode.CALCULATE_AS_NECESSARY} this.baq = if (noBAQ) {org.broadinstitute.sting.utils.baq.BAQ.CalculationMode.OFF} else {org.broadinstitute.sting.utils.baq.BAQ.CalculationMode.CALCULATE_AS_NECESSARY}
this.analysisName = t.name + "_UGs" this.analysisName = t.name + "_UGs"
this.jobName = queueLogDir + t.name + ".snpcall" this.jobName = queueLogDir + t.name + ".snpcall"
@ -217,7 +218,7 @@ class MethodsDevelopmentCallingPipeline extends QScript {
// 1b.) Call Indels with UG // 1b.) Call Indels with UG
class indelCall (t: Target) extends GenotyperBase(t) { class indelCall (t: Target) extends GenotyperBase(t) {
this.out = t.rawIndelVCF this.out = t.rawIndelVCF
this.glm = org.broadinstitute.sting.gatk.walkers.genotyper.GenotypeLikelihoodsCalculationModel.Model.DINDEL this.glm = org.broadinstitute.sting.gatk.walkers.genotyper.GenotypeLikelihoodsCalculationModel.Model.INDEL
this.baq = org.broadinstitute.sting.utils.baq.BAQ.CalculationMode.OFF this.baq = org.broadinstitute.sting.utils.baq.BAQ.CalculationMode.OFF
this.analysisName = t.name + "_UGi" this.analysisName = t.name + "_UGi"
this.jobName = queueLogDir + t.name + ".indelcall" this.jobName = queueLogDir + t.name + ".indelcall"