Graph structure must be known at compile time. Removing GroupIntervals until a future point where in-process-functions can predict their output based on inputs [though this is probably forever: the inputs may not exist at compile time!]
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4886 348d0f76-0448-11de-a6fe-93d51630548a
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chartl
parent
61d5daa65c
commit
fc33901810
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@ -1,6 +1,7 @@
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import org.broadinstitute.sting.commandline.ArgumentCollection
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import org.broadinstitute.sting.queue.extensions.gatk._
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import org.broadinstitute.sting.queue.library.ipf.ExpandIntervals
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import org.broadinstitute.sting.queue.library.ipf.intervals.GroupIntervals
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import org.broadinstitute.sting.queue.pipeline.PipelineArgumentCollection
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import org.broadinstitute.sting.queue.QScript
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import org.broadinstitute.sting.utils.text.XReadLines
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@ -14,52 +15,91 @@ class expanded_targets extends QScript {
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def script = {
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val intervalExpands : List[ExpandIntervals] = (new Range(0,40,1)).toList.map( u => {
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new ExpandIntervals(args.projectIntervals,1+5*u,5,new File(System.getProperty("user.dir")+"/"+args.projectName+"_expanded_%d_%d.interval_list".format(1+5*u,6+5*u)),args.projectRef,"INTERVALS")
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new ExpandIntervals(args.projectIntervals,1+5*u,5,new File(System.getProperty("user.dir")+"/"+args.projectName+"_expanded_%d_%d.interval_list".format(1+5*u,6+5*u)),args.projectRef,"TSV","INTERVALS")
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})
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trait GATKArgs extends CommandLineGATK {
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this.reference_sequence = args.projectRef
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this.DBSNP = args.projectDBSNP
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this.jarFile = args.gatkJar
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}
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val userDir = System.getProperty("user.dir")
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addAll(intervalExpands)
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val callFiles: List[File] = intervalExpands.map(_.outList).map(makeCalls(_,20))
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val cleanIntervals : ExpandIntervals = new ExpandIntervals(args.projectIntervals,1,210,new File(userDir+"/"+args.projectName+"_expanded_full.interval_list"),args.projectRef,"TSV","INTERVALS")
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add(cleanIntervals)
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val uncleanBams : List[File] = asScalaIterable(new XReadLines(args.projectBams)).toList.map(u => new File(u))
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val realign : List[RealignerTargetCreator] = uncleanBams.map(u => {
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var rtc : RealignerTargetCreator = new RealignerTargetCreator with GATKArgs
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rtc.out = swapExt(userDir,u,".bam",".expanded.targets.txt")
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rtc.input_file :+= u.getAbsoluteFile
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rtc.intervals :+= cleanIntervals.outList
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rtc
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})
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val clean : List[IndelRealigner] = realign.map( u => {
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var clean : IndelRealigner = new IndelRealigner with GATKArgs
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clean.targetIntervals = u.out
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clean.input_file = u.input_file
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clean.memoryLimit = Some(4)
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clean.out = new File(userDir+"/"+swapExt(u.out,".bam",".expanded.targets.bam").getName)
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clean
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})
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addAll(realign)
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addAll(clean)
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val callFiles: List[File] = intervalExpands.map(u => makeCalls(u.outList,20,clean.map(h => h.out)))
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}
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def makeCalls(iList: File, scatterNo: Int): List[File] = {
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var scatters : List[(File,File)] = _
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def makeCalls(iList: File, scatterNo: Int, bams: List[File]): File = {
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var scatters : GroupIntervals = new GroupIntervals(iList,20,true,Some(System.getProperty("user.dir")))
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var filtered : List[(File,File)] = scatters.outputList.zipWithIndex.map(v => reallyMakeCalls(v._1,bams,v._2))
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var gatherStandard : VcfGatherFunction = new VcfGatherFunction
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gatherStandard.gatherParts = filtered.map(u => u._1)
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gatherStandard.originalOutput = swapExt(iList,".interval_list",".filtered.calls.vcf")
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var gatherHiseq : VcfGatherFunction = new VcfGatherFunction
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gatherHiseq.gatherParts = filtered.map(u => u._2)
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gatherHiseq.originalOutput = swapExt(iList,".interval_list",".filtered.hiseq.vcf")
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var eval : VariantEval = new VariantEval
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eval.rodBind :+= new RodBind("evalInterval","vcf",filter.out)
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eval.rodBind :+= new RodBind("compHiSeq","vcf",new File("/humgen/gsa-hpprojects/GATK/data/Comparisons/Unvalidated/NA12878/NA12878.hg19.HiSeq.WGS.cleaned.ug.snpfiltered.indelfiltered.optimized.cut.vcf"))
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eval.rodBind :+= new RodBind("compHiSeq_atSites","vcf",callHiseq.out)
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eval.rodBind :+= new RodBind("compOMNI","vcf",new File("/humgen/gsa-hpprojects/GATK/data/Comparisons/Validated/Omni2.5_chip/Omni_2.5_764_samples.b37.deduped.annot.vcf"))
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eval.out = swapExt(iList,".interval_list",".eval")
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eval.reportType = Option(org.broadinstitute.sting.utils.report.VE2ReportFactory.VE2TemplateType.CSV)
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}
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def makeCalls(iList: File) : File = {
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var bams : List[File] = asScalaIterable(new XReadLines(args.projectBams)).toList.map(u => new File(u))
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add(scatters)
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add(gatherStandard)
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add(gatherHiseq)
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trait GATKArgs extends CommandLineGATK {
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this.reference_sequence = args.projectRef
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this.DBSNP = args.projectDBSNP
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this.intervals = List(iList)
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this.jarFile = args.gatkJar
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this.memoryLimit = Some(6)
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}
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var rtc : RealignerTargetCreator = new RealignerTargetCreator with GATKArgs
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rtc.out = swapExt(iList,".interval_list",".targets.txt")
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rtc.input_file = bams
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var clean : IndelRealigner = new IndelRealigner with GATKArgs
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clean.targetIntervals = rtc.out
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clean.out = swapExt(iList,".interval_list",".cleaned.bam")
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clean.input_file = bams
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clean.maxReads = Some(100000)
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var eval : VariantEval = new VariantEval with GATKArgs
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eval.rodBind :+= new RodBind("evalInterval","vcf",gatherStandard.originalOutput)
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eval.rodBind :+= new RodBind("compHiSeq","vcf",new File("/humgen/gsa-hpprojects/GATK/data/Comparisons/Unvalidated/NA12878/NA12878.hg19.HiSeq.WGS.cleaned.ug.snpfiltered.indelfiltered.optimized.cut.vcf"))
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eval.rodBind :+= new RodBind("compHiSeq_atSites","vcf",gatherHiseq.originalOutput)
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eval.rodBind :+= new RodBind("compOMNI","vcf",new File("/humgen/gsa-hpprojects/GATK/data/Comparisons/Validated/Omni2.5_chip/Omni_2.5_764_samples.b37.deduped.annot.vcf"))
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eval.out = swapExt(iList,".interval_list",".eval")
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eval.reportType = Option(org.broadinstitute.sting.utils.report.VE2ReportFactory.VE2TemplateType.CSV)
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eval.out
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}
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def reallyMakeCalls(iList: File, bams : List[File], scatterNo: Int) : (File,File) = {
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trait GATKArgs extends CommandLineGATK {
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this.reference_sequence = args.projectRef
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this.DBSNP = args.projectDBSNP
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this.jarFile = args.gatkJar
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this.intervals :+= iList
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}
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var call : UnifiedGenotyper = new UnifiedGenotyper with GATKArgs
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call.scatterCount = 4
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call.input_file = List(clean.out)
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call.out = swapExt(iList,".interval_list",".raw.vcf")
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call.input_file = bams
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call.out = swapExt(iList,".interval_list",".scatter%d.raw.vcf".format(scatterNo))
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call.trig_emit_conf = Some(0.0)
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call.rodBind :+= new RodBind("trigger","vcf",thisTrigger)
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var filter : VariantFiltration = new VariantFiltration with GATKArgs
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@ -68,16 +108,16 @@ class expanded_targets extends QScript {
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filter.filterName :+= "LowQualByDepth"
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filter.filterExpression :+= "\"SB>-0.10\""
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filter.filterName :+= "HighStrandBias"
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filter.out = swapExt(iList,".interval_list",".filtered.vcf")
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filter.out = swapExt(iList,".interval_list",".scatter%d.filtered.vcf".format(scatterNo))
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var callHiseq : UnifiedGenotyper = new UnifiedGenotyper with GATKArgs
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callHiseq.input_file = List(new File("/humgen/1kg/analysis/bamsForDataProcessingPapers/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam"))
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callHiseq.rodBind :+= new RodBind("trigger","vcf",filter.out)
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callHiseq.out = swapExt(iList,".interval_list",".hiSeq.genotypes.vcf")
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callHiseq.out = swapExt(iList,".interval_list",".scatter%d.hiSeq.genotypes.vcf".format(scatterNo))
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callHiseq.trig_emit_conf = Some(0.0)
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add(rtc,clean,call,filter,callHiseq)
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add(call,filter,callHiseq)
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return (filter.out,callHiSeq.out)
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return (filter.out,callHiseq.out)
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}
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}
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@ -1,48 +0,0 @@
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package org.broadinstitute.sting.queue.library.ipf.intervals
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import org.broadinstitute.sting.queue.function.InProcessFunction
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import org.broadinstitute.sting.commandline.{Argument, Output, Input}
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import collection.JavaConversions._
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import org.broadinstitute.sting.utils.text.XReadLines
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import java.io.{PrintStream, File}
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/**
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* Utility for explicitly grouping intervals together in sets of size num
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* @Author chartl
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*/
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class GroupIntervals(iList: File, num: Int, head: Boolean, dir: Option[String]) extends InProcessFunction {
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@Input(doc="Interval list to split into groups") var intervalList : File = iList
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@Output(doc="The output interval lists created") var outputList : List[File] = Nil
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@Argument(doc="The number of groups wanted") var nGroups : Int = num
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@Argument(doc="The base location you want the files") var directory : Option[String] = dir
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@Argument(doc="Has header (@ lines)") var hasHeader : Boolean = head
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var written : Int = 0
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var header : List[String] = Nil
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def run = {
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written = 0
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header = Nil
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asScalaIterator(new XReadLines(intervalList)).filter(u => ! isHeader(u)).grouped(num).foreach(n => write(n))
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}
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def write(lines : Seq[String]) = {
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val oFile : File = if ( dir.isEmpty) new File(intervalList.getAbsolutePath+".group%d".format(written))else new File(dir.get+"/"+intervalList.getAbsolutePath+".group%d".format(written))
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outputList :+= oFile
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val output : PrintStream = new PrintStream(oFile)
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header.foreach( u => output.print("%s%n".format(u)))
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lines.foreach(u => output.print("%s%n".format(u)))
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output.close()
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}
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def isHeader(s : String) : Boolean = {
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if ( hasHeader && s.startsWith("@") ) {
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header :+= s
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return true
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} else {
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return false
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}
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}
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}
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