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James P says this change worked for him, so I'm committing it. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5795 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
chartl 2011-05-12 16:55:18 +00:00
parent a22e98a2c4
commit 66c8fa5c48
1 changed files with 19 additions and 21 deletions
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40
scala/qscript/playground/BatchMerge.q
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@ -1,6 +1,4 @@
import java.io.{FileReader, BufferedReader}
import org.broadinstitute.sting.commandline.Hidden
import org.broadinstitute.sting.datasources.pipeline.Pipeline
import org.broadinstitute.sting.gatk.walkers.genotyper.{GenotypeLikelihoodsCalculationModel, UnifiedGenotyperEngine}
import org.broadinstitute.sting.queue.extensions.gatk._
import org.broadinstitute.sting.queue.library.ipf.vcf.{VCFSimpleMerge, VCFExtractSites,VCFExtractIntervals}
@ -8,7 +6,6 @@ import org.broadinstitute.sting.queue.{QException, QScript}
import collection.JavaConversions._
import org.broadinstitute.sting.utils.baq.BAQ
import org.broadinstitute.sting.utils.text.XReadLines
import org.broadinstitute.sting.utils.yaml.YamlUtils
class batchMergePipeline extends QScript {
batchMerge =>
@ -34,14 +31,29 @@ class batchMergePipeline extends QScript {
this.keepQual = false
}
trait CombineVariantsArgs extends CombineVariants {
this.reference_sequence = batchMerge.ref
this.jarFile = new File(batchMerge.stingDir+"/dist/GenomeAnalysisTK.jar")
this.scatterCount = 10
this.memoryLimit=4
}
var combine : CombineVariants = new CombineVariants with CombineVariantsArgs
combine.out = swapExt(batchOut,".vcf",".variant.combined.vcf")
combine.rodBind ++= vcfs.map( u => new RodBind(u.getName,"vcf",u) )
add(combine)
var getVariantAlleles : List[VCFExtractSites] = vcfs.map( u => new VCFExtractSites(u, swapExt(batchOut.getParent,u,".vcf",".alleles.vcf")) with ExtractArgs)
var combineVCFs : VCFSimpleMerge = new VCFSimpleMerge
combineVCFs.vcfs = getVariantAlleles.map(u => u.outVCF)
combineVCFs.fai = new File(ref.getAbsolutePath+".fai")
combineVCFs.outVCF = swapExt(batchOut,".vcf",".pf.alleles.vcf")
var extractIntervals : VCFExtractIntervals = new VCFExtractIntervals(combineVCFs.outVCF,swapExt(combineVCFs.outVCF,".vcf",".intervals.list"),true)
addAll(getVariantAlleles)
add(combineVCFs,extractIntervals)
var extractIntervals : VCFExtractIntervals = new VCFExtractIntervals(combine.out,swapExt(combine.out,".vcf",".intervals.list"),true)
//addAll(getVariantAlleles)
//add(combineVCFs,extractIntervals)
add(extractIntervals)
trait CalcLikelihoodArgs extends UGCalcLikelihoods {
this.reference_sequence = batchMerge.ref
@ -52,7 +64,7 @@ class batchMergePipeline extends QScript {
this.baq = BAQ.CalculationMode.CALCULATE_AS_NECESSARY
}
this.intervals :+= extractIntervals.listOut
this.allelesVCF = combineVCFs.outVCF
this.allelesVCF = combine.out
this.jarFile = new File(stingDir+"/dist/GenomeAnalysisTK.jar")
this.memoryLimit = 4
this.scatterCount = 60
@ -84,20 +96,6 @@ class batchMergePipeline extends QScript {
cVars.rodBind ++= calcs.map( a => new RodBind("variant"+a.out.getName.replace(".vcf",""),"vcf",a.out) )
cVars.out = batchOut
add(cVars)
trait CombineVariantsArgs extends CombineVariants {
this.reference_sequence = batchMerge.ref
this.intervals :+= extractIntervals.listOut
this.jarFile = new File(batchMerge.stingDir+"/dist/GenomeAnalysisTK.jar")
this.scatterCount = 10
this.memoryLimit=4
}
var combine : CombineVariants = new CombineVariants with CombineVariantsArgs
combine.out = swapExt(batchOut,".vcf",".variant.combined.vcf")
combine.rodBind ++= vcfs.map( u => new RodBind(u.getName,"vcf",u) )
add(combine)
}
override def extractFileEntries(in: File): List[File] = {