67 lines
2.6 KiB
Plaintext
Executable File
67 lines
2.6 KiB
Plaintext
Executable File
import org.broadinstitute.sting.commandline.ArgumentCollection
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import org.broadinstitute.sting.datasources.pipeline.Pipeline
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import org.broadinstitute.sting.queue.extensions.gatk.CommandLineGATK
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import org.broadinstitute.sting.queue.pipeline._
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import org.broadinstitute.sting.queue.util.PipelineUtils
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import org.broadinstitute.sting.queue.{QException, QScript}
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import collection.JavaConversions._
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import org.broadinstitute.sting.utils.yaml.YamlUtils
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class fullCallingPipelineV2 extends QScript {
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fcp =>
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@ArgumentCollection var pipelineArgs = new PipelineArgumentCollection
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private var pipeline: Pipeline = _
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def script = {
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pipelineArgs.verifyArguments
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pipeline = PipelineUtils.loadPipelineFromPAC(pipelineArgs)
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var callingLib: VariantCalling = new VariantCalling(pipeline,fcp.pipelineArgs.gatkJar)
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var cleaningLib: BamProcessing = new BamProcessing(pipeline,fcp.pipelineArgs.gatkJar,fcp.pipelineArgs.picardFixMatesJar)
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val projectBase: String = fcp.pipeline.getProject.getName
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val cleanedBase: String = projectBase + ".cleaned"
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val uncleanedBase: String = projectBase + ".uncleaned"
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// there are commands that use all the bam files
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val recalibratedSamples = fcp.pipeline.getSamples.filter( u => ( u.getBamFiles.contains("recalibrated") || u.getBamFiles.contains("cleaned") ) )
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var bamsToClean: List[(File,File)] = Nil
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var recalBams: List[File] = Nil
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var cleanedBams: List[File] = Nil
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for ( sample <- recalibratedSamples ) {
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val bam = sample.getBamFiles.get("recalibrated")
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recalBams :+= bam
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if (!sample.getBamFiles.contains("cleaned")) {
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sample.getBamFiles.put("cleaned", swapExt(bam,"bam","cleaned.bam"))
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bamsToClean :+= (bam,sample.getBamFiles.get("cleaned"))
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}
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cleanedBams :+= sample.getBamFiles.get("cleaned")
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}
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if ( !fcp.pipelineArgs.skip_cleaning ) {
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addAll(cleaningLib.StandardIndelRealign(bamsToClean,fcp.pipelineArgs.cleaningJobs))
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}
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if (!fcp.pipelineArgs.skip_cleaning ) {
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endToEnd(cleanedBase, cleanedBams, callingLib)
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} else {
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endToEnd(uncleanedBase, recalBams, callingLib)
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}
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}
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def endToEnd(base: String, bamFiles: List[File], lib: VariantCalling) = {
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var recal_vcf = new File(base+"_snps.recal.annotated.tranched.vcf")
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var handfilt_vcf = new File(base+"_snps.handfiltered.annotated.vcf")
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var indel_vcf = new File(base+"_indel_calls.vcf")
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addAll(lib.StandardCallingPipeline(bamFiles,indel_vcf,recal_vcf,handfilt_vcf,fcp.pipelineArgs.target_titv,fcp.pipelineArgs.refseqTable))
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}
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def addAll(clfs: List[CommandLineFunction]) = { clfs.foreach(c => add(c)) }
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}
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