88 lines
3.8 KiB
Scala
Executable File
88 lines
3.8 KiB
Scala
Executable File
import org.broadinstitute.sting.queue.extensions.gatk._
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import org.broadinstitute.sting.queue.extensions.samtools.SamtoolsIndexFunction
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import org.broadinstitute.sting.queue.QScript
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import org.apache.commons.io.FilenameUtils;
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class recalibrate extends QScript {
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@Input(doc="bamIn", shortName="I")
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var bamIns: List[File] = Nil
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@Argument(doc="scatter")
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var scatter = false
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@Argument(doc="gatk jar file")
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var gatkJarFile: File = _
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@Argument(doc="Assume initial count covariates has completed", required=false)
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var skipInitialCountCovariates: Boolean = false
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@Argument(shortName = "R", doc="ref")
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var referenceFile: File = _
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trait UNIVERSAL_GATK_ARGS extends CommandLineGATK { logging_level = "INFO"; jarFile = gatkJarFile; reference_sequence = referenceFile; }
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def script = {
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for (bamIn <- bamIns) {
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val root = bamIn.getPath()
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val bamRoot = FilenameUtils.removeExtension(root);
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val recalData = new File(bamRoot + ".recal_data.csv")
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val recalBam = new File(bamRoot + ".recal.bam")
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val recalRecalData = new File(bamRoot + ".recal.recal_data.csv")
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if ( ! skipInitialCountCovariates )
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add(new CountCovariates(bamIn, recalData) { useOriginalQualities = true } )
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val tableRecal = new TableRecalibrate(bamIn, recalData, recalBam) { useOriginalQualities = true }
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if ( scatter ) {
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tableRecal.intervals = new File("/humgen/gsa-hpprojects/GATK/data/chromosomes.hg18.interval_list")
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tableRecal.scatterCount = 25
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}
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add(tableRecal)
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add(new Index(recalBam))
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add(new CountCovariates(recalBam, recalRecalData) { num_threads = Some(4) })
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add(new AnalyzeCovariates(recalData, new File(recalData.getPath() + ".analyzeCovariates")))
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add(new AnalyzeCovariates(recalRecalData, new File(recalRecalData.getPath() + ".analyzeCovariates")))
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}
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}
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def bai(bam: File) = new File(bam + ".bai")
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class Index(bamIn: File) extends SamtoolsIndexFunction {
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bamFile = bamIn
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}
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class CountCovariates(bamIn: File, recalDataIn: File) extends org.broadinstitute.sting.queue.extensions.gatk.CountCovariates with UNIVERSAL_GATK_ARGS {
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this.jarFile = gatkJarFile
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this.input_file :+= bamIn
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this.recal_file = recalDataIn
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this.DBSNP = new File("/humgen/gsa-hpprojects/GATK/data/dbsnp_129_hg18.rod")
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this.logging_level = "INFO"
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this.max_reads_at_locus = Some(20000)
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this.covariate ++= List("ReadGroupCovariate", "QualityScoreCovariate", "CycleCovariate", "DinucCovariate")
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this.memoryLimit = Some(3)
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override def dotString = "CountCovariates: %s [args %s]".format(bamIn.getName, if (this.num_threads.isDefined) "-nt " + this.num_threads else "")
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}
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class TableRecalibrate(bamInArg: File, recalDataIn: File, bamOutArg: File) extends org.broadinstitute.sting.queue.extensions.gatk.TableRecalibration with UNIVERSAL_GATK_ARGS {
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this.jarFile = gatkJarFile
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this.input_file :+= bamInArg
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this.recal_file = recalDataIn
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this.output_bam = bamOutArg
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this.logging_level = "INFO"
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this.memoryLimit = Some(2)
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override def dotString = "TableRecalibrate: %s => %s".format(bamInArg.getName, bamOutArg.getName, if (this.useOriginalQualities) " -OQ" else "")
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}
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class AnalyzeCovariates(recalDataIn: File, outputDir: File) extends org.broadinstitute.sting.queue.extensions.gatk.AnalyzeCovariates {
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this.jarFile = new File("/home/radon01/depristo/dev/GenomeAnalysisTK/trunk/dist/AnalyzeCovariates.jar")
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this.recal_file = recalDataIn
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this.output_dir = outputDir.toString
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this.path_to_resources = "/home/radon01/depristo/dev/GenomeAnalysisTK/trunk/R/"
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this.ignoreQ = Some(5)
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this.path_to_Rscript = "/broad/software/free/Linux/redhat_5_x86_64/pkgs/r_2.7.2/bin/Rscript"
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this.memoryLimit = Some(2)
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override def dotString = "AnalyzeCovariates: %s".format(recalDataIn.getName)
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}
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}
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