From fd5d1f9cfc19b5abaadad9f83851807f9b29503d Mon Sep 17 00:00:00 2001 From: carneiro Date: Fri, 25 Feb 2011 21:56:35 +0000 Subject: [PATCH] minor cosmetic changes. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5322 348d0f76-0448-11de-a6fe-93d51630548a --- .../MethodsDevelopmentCallingPipeline.scala | 14 +++++------ .../oneoffs/carneiro/dataProcessing.scala | 25 ++++++++----------- 2 files changed, 16 insertions(+), 23 deletions(-) diff --git a/scala/qscript/core/MethodsDevelopmentCallingPipeline.scala b/scala/qscript/core/MethodsDevelopmentCallingPipeline.scala index 3ca9e39ca..4fa503ce8 100755 --- a/scala/qscript/core/MethodsDevelopmentCallingPipeline.scala +++ b/scala/qscript/core/MethodsDevelopmentCallingPipeline.scala @@ -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 diff --git a/scala/qscript/oneoffs/carneiro/dataProcessing.scala b/scala/qscript/oneoffs/carneiro/dataProcessing.scala index a3ea3168b..52fe2ee8e 100755 --- a/scala/qscript/oneoffs/carneiro/dataProcessing.scala +++ b/scala/qscript/oneoffs/carneiro/dataProcessing.scala @@ -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)