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minor cosmetic changes. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5322 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
carneiro 2011-02-25 21:56:35 +00:00
parent 7ff8d23c64
commit fd5d1f9cfc
2 changed files with 16 additions and 23 deletions
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14
scala/qscript/core/MethodsDevelopmentCallingPipeline.scala
View File

@ -172,7 +172,6 @@ class MethodsDevelopmentCallingPipeline extends QScript {
add(new snpCall(target))
add(new snpFilter(target))
add(new GenerateClusters(target, !goldStandard))
add(new VariantRecalibratorTiTv(target, !goldStandard))
add(new VariantRecalibratorNRS(target, !goldStandard))
if (!noCut) add(new VariantCut(target))
if (eval) add(new snpEvaluation(target))
@ -205,7 +204,7 @@ class MethodsDevelopmentCallingPipeline extends QScript {
}
// 1a.) Call SNPs with UG
class snpCall (t: Target) extends GenotyperBase {
class snpCall (t: Target) extends GenotyperBase(t) {
this.out = t.rawVCF
this.baq = Some( 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"
@ -213,7 +212,7 @@ class MethodsDevelopmentCallingPipeline extends QScript {
}
// 1b.) Call Indels with UG
class indelCall (t: Target) extends GenotyperBase {
class indelCall (t: Target) extends GenotyperBase(t) {
this.out = t.rawIndelVCF
this.glm = Some(org.broadinstitute.sting.gatk.walkers.genotyper.GenotypeLikelihoodsCalculationModel.Model.DINDEL)
this.baq = Some(org.broadinstitute.sting.utils.baq.BAQ.CalculationMode.OFF)
@ -231,7 +230,7 @@ class MethodsDevelopmentCallingPipeline extends QScript {
}
// 2a.) Hard Filter for SNPs (soon to be obsolete)
class snpFilter (t: Target) extends FilterBase {
class snpFilter (t: Target) extends FilterBase(t) {
this.variantVCF = t.rawVCF
this.out = t.filteredVCF
if (useMask) {
@ -243,7 +242,7 @@ class MethodsDevelopmentCallingPipeline extends QScript {
}
// 2b.) Hard Filter for Indels
class indelFilter (t: Target) extends FilterBase {
class indelFilter (t: Target) extends FilterBase(t) {
this.variantVCF = t.rawIndelVCF
this.out = t.filteredIndelVCF
this.filterName ++= List("LowQual", "StrandBias", "QualByDepth", "HomopolymerRun")
@ -347,17 +346,16 @@ class MethodsDevelopmentCallingPipeline extends QScript {
}
// 6a.) SNP Evaluation (OPTIONAL) based on the cut vcf
class snpEvaluation(t: Target) extends EvalBase {
class snpEvaluation(t: Target) extends EvalBase(t) {
if (t.reference == b37 || t.reference == hg19) this.rodBind :+= RodBind("compomni", "VCF", omni_b37)
this.rodBind :+= RodBind("eval", "VCF", if (useCut) {t.cutVCF} else {t.tsRecalibratedVCF} )
this.evalModule :+= "GenotypeConcordance"
this.out = t.evalFile
this.analysisName = t.name + "_VEs"
this.jobName = queueLogDir + t.name + ".snp.eval"
}
// 6b.) Indel Evaluation (OPTIONAL)
class indelEvaluation(t: Target) extends EvalBase {
class indelEvaluation(t: Target) extends EvalBase(t) {
this.rodBind :+= RodBind("eval", "VCF", t.filteredIndelVCF)
this.evalModule :+= "IndelStatistics"
this.out = t.evalIndelFile

25
scala/qscript/oneoffs/carneiro/dataProcessing.scala
View File

@ -130,19 +130,7 @@ class dataProcessing extends QScript {
new clean(bamList, allTargetIntervals, cleanedBam, !knownsOnly, !intermediate))
}
class knownTargets (outIntervals: String) extends RealignerTargetCreator with CommandLineGATKArgs {
this.out = new File(outIntervals)
this.mismatchFraction = Some(0.0)
this.rodBind :+= RodBind("dbsnp", "VCF", dbSNP)
this.rodBind :+= RodBind("indels1", "VCF", dindelPilotCalls)
this.rodBind :+= RodBind("indels2", "VCF", dindelAFRCalls)
this.rodBind :+= RodBind("indels3", "VCF", dindelEURCalls)
this.rodBind :+= RodBind("indels4", "VCF", dindelASNCalls)
this.jobName = queueLogDir + outIntervals + ".ktarget"
}
class allTargets (inBams: String, outIntervals: String) extends knownTargets(outIntervals) {
this.input_file :+= new File(inBams)
class TargetBase (outIntervals: String) extends RealignerTargetCreator with CommandLineGATKArgs {
this.out = new File(outIntervals)
this.mismatchFraction = Some(0.0)
this.rodBind :+= RodBind("dbsnp", "VCF", dbSNP)
@ -151,6 +139,15 @@ class dataProcessing extends QScript {
this.rodBind :+= RodBind("indels3", "VCF", dindelEURCalls)
this.rodBind :+= RodBind("indels4", "VCF", dindelASNCalls)
if (qscript.indels != null) this.rodBind :+= RodBind("indels5", "VCF", qscript.indels)
}
class knownTargets (outIntervals: String) extends TargetBase {
this.jobName = queueLogDir + outIntervals + ".ktarget"
}
class allTargets (inBams: String, outIntervals: String) extends TargetBase(outIntervals) {
this.input_file :+= new File(inBams)
this.jobName = queueLogDir + outIntervals + ".atarget"
}
@ -165,8 +162,6 @@ class dataProcessing extends QScript {
this.rodBind :+= RodBind("indels4", "VCF", dindelASNCalls)
if (qscript.indels != null) this.rodBind :+= RodBind("indels5", "VCF", qscript.indels)
this.useOnlyKnownIndels = knownsOnly
this.sortInCoordinateOrderEvenThoughItIsHighlyUnsafe = true
this.constrainMovement = true
this.doNotUseSW = true
this.baq = Some(org.broadinstitute.sting.utils.baq.BAQ.CalculationMode.CALCULATE_AS_NECESSARY)
this.compress = Some(0)