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Library-ized pipeline now functions 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4759 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
chartl 2010-11-30 21:34:59 +00:00
parent 2ac938fe4e
commit 06a0fb4489
2 changed files with 12 additions and 20 deletions
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30
scala/qscript/chartl/fullCallingPipelineV2.q
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@ -1,23 +1,15 @@
import com.sun.tools.doclets.internal.toolkit.util.DocFinder.Input
import org.broadinstitute.sting.gatk.{CommandLineGATK, DownsampleType}
import java.io.File
import net.sf.picard.reference.FastaSequenceFile
import org.broadinstitute.sting.commandline.Argument
import org.broadinstitute.sting.datasources.pipeline.Pipeline
import org.broadinstitute.sting.gatk.walkers.genotyper.GenotypeCalculationModel.Model
import org.broadinstitute.sting.queue.extensions.gatk._
import org.broadinstitute.sting.queue.extensions.picard.PicardBamJarFunction
import org.broadinstitute.sting.queue.extensions.samtools._
import org.broadinstitute.sting.queue.extensions.gatk.CommandLineGATK
import org.broadinstitute.sting.queue.pipeline.{BamProcessing,VariantCalling}
import org.broadinstitute.sting.queue.{QException, QScript}
import collection.JavaConversions._
import org.broadinstitute.sting.utils.yaml.YamlUtils
import org.broadinstitute.sting.utils.report.VE2ReportFactory.VE2TemplateType
class fullCallingPipelineV2 extends QScript {
qscript =>
@Argument(doc="Number of cleaning jobs", shortName="cleaningJobs")
var cleaningJobs: Int = _
@Argument(doc="Number of cleaning jobs", shortName="cleaningJobs", required=false)
var cleaningJobs: Int = 1
@Argument(doc="the YAML file specifying inputs, interval lists, reference sequence, etc.", shortName="Y")
var yamlFile: File = _
@ -31,7 +23,7 @@ class fullCallingPipelineV2 extends QScript {
@Input(doc="path to Picard FixMateInformation.jar. See http://picard.sourceforge.net/ .", required=false)
var picardFixMatesJar: File = new java.io.File("/seq/software/picard/current/bin/FixMateInformation.jar")
@Input(doc="path to GATK jar")
@Input(doc="path to GATK jar", shortName="gatk")
var gatkJar: File = _
@Input(doc="target Ti/Tv ratio for recalibration", shortName="titv", required=true)
@ -61,7 +53,7 @@ class fullCallingPipelineV2 extends QScript {
private var pipeline: Pipeline = _
trait CommandLineGATKArgs extends CommandLineGATK {
this.intervals = qscript.pipeline.getProject.getIntervalList
this.intervals :+= qscript.pipeline.getProject.getIntervalList
this.jarFile = qscript.gatkJar
this.reference_sequence = qscript.pipeline.getProject.getReferenceFile
this.memoryLimit = Some(4)
@ -103,17 +95,17 @@ class fullCallingPipelineV2 extends QScript {
}
if (!qscript.skip_cleaning) {
endToEnd(cleanedBase, cleanedBams, lib)
endToEnd(cleanedBase, cleanedBams, callingLib)
} else {
endToEnd(uncleanedBase, recalBams, lib)
endToEnd(uncleanedBase, recalBams, callingLib)
}
}
def endToEnd(base: String, bamFiles: List[File], lib: VariantCalling) = {
var recal_vcf = base+"_snps.recal.annotated.tranched.vcf"
var handfilt_vcf = base+"_snps.handfiltered.annotated.vcf"
var indel_vcf = base+"_indel_calls.vcf"
var recal_vcf = new File(base+"_snps.recal.annotated.tranched.vcf")
var handfilt_vcf = new File(base+"_snps.handfiltered.annotated.vcf")
var indel_vcf = new File(base+"_indel_calls.vcf")
for ( c <- lib.StandardCallingPipeline(bamFiles,indel_vcf,recal_vcf,handfilt_vcf,qscript.target_titv,qscript.refseqTable) ) {
add(c)

2
scala/src/org/broadinstitute/sting/queue/pipeline/VariantCalling.scala
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@ -182,7 +182,7 @@ class VariantCalling(yaml: File,gatkJar: File) {
var clust = StandardVariantCluster(snps, swapExt(snps,".vcf",".cluster"))
var recal = StandardVariantRecalibrator(snps,clust.clusterFile,targetTiTv,swapExt(snps,".vcf",".recal.vcf"),
swapExt(snps,".vcf",".recal.tranch"))
var cut = StandardApplyVariantCuts(recal.out,recal.tranches_file,recal.out)
var cut = StandardApplyVariantCuts(recal.out,recal.tranches_file,swapExt(recal.out,".vcf",".tranched.vcf"))
var cmds: List[CommandLineGATK] = Nil
cmds :+= clust