229 lines
11 KiB
Scala
Executable File
229 lines
11 KiB
Scala
Executable File
import org.broadinstitute.sting.queue.extensions.gatk._
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import org.broadinstitute.sting.queue.extensions.picard.PicardBamJarFunction
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import org.broadinstitute.sting.queue.QScript
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import org.broadinstitute.sting.queue.extensions.samtools.SamtoolsIndexFunction
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import org.broadinstitute.sting.queue.function.ListWriterFunction
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import scala.io.Source
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class dataProcessing extends QScript {
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qscript =>
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@Input(doc="path to GATK jar", shortName="gatk", required=true)
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var GATKjar: File = _
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@Input(doc="path to AnalyzeCovariates.jar", shortName="ac", required=true)
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var ACJar: File = _
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// todo -- we should support the standard GATK arguments -R, -D [dbsnp],
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// todo -- and indel files. Those should be defaulted to hg19 but providable on command line
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@Input(doc="path to R resources folder inside Sting", shortName="r", required=true)
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var R: String = _
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@Input(doc="path to Picard FixMateInformation.jar. See http://picard.sourceforge.net/ .", shortName="fixmates", required=false)
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var fixMatesJar: File = new java.io.File("/seq/software/picard/current/bin/FixMateInformation.jar")
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@Input(doc="path to MarkDuplicates jar", shortName="dedup", required=false)
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var dedupJar: File = new java.io.File("/seq/software/picard/current/bin/MarkDuplicates.jar")
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@Input(doc="input BAM file", shortName="i", required=true)
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var input: String = _
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@Input(doc="final output BAM file base name", shortName="p", required=false)
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var projectName: String = "combined"
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@Input(doc="output path", shortName="outputDir", required=false)
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var outputDir: String = ""
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@Input(doc="the -L interval string to be used by GATK", shortName="L", required=false)
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var intervalString: String = ""
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// todo -- this shouldn't be allowed. We want a flag that says "output bams at intervals only" or not
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@Input(doc="provide a .intervals file with the list of target intervals", shortName="intervals", required=false)
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var intervals: File = new File("/humgen/1kg/processing/pipeline_test_bams/whole_genome_chunked.hg19.intervals")
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// Reference sequence, dbsnps and RODs used by the pipeline
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val reference: File = new File("/humgen/1kg/reference/human_g1k_v37.fasta")
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val dbSNP: File = new File("/humgen/gsa-hpprojects/GATK/data/dbsnp_132_b37.leftAligned.vcf")
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// TODO -- let's create a pre-merged single VCF and put it into /humgen/gsa-hpprojects/GATK/data please
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val dindelPilotCalls: String = "/humgen/gsa-hpprojects/GATK/data/Comparisons/Unvalidated/1kg.pilot_release.merged.indels.sites.hg19.vcf"
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val dindelAFRCalls: String = "/humgen/1kg/DCC/ftp/technical/working/20110126_dindel_august/AFR.dindel_august_release_merged_pilot1.20110126.sites.vcf.gz"
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val dindelASNCalls: String = "/humgen/1kg/DCC/ftp/technical/working/20110126_dindel_august/ASN.dindel_august_release_merged_pilot1.20110126.sites.vcf.gz"
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val dindelEURCalls: String = "/humgen/1kg/DCC/ftp/technical/working/20110126_dindel_august/EUR.dindel_august_release_merged_pilot1.20110126.sites.vcf.gz"
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// Simple boolean definitions for code clarity
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val knownsOnly: Boolean = true
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val intermediate: Boolean = true
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// General arguments to all programs
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trait CommandLineGATKArgs extends CommandLineGATK {
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this.jarFile = qscript.GATKjar
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this.reference_sequence = reference
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this.memoryLimit = Some(4)
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this.isIntermediate = true
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}
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def script = {
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var perLaneBamList: List[String] = Nil
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var recalibratedBamList: List[File] = Nil
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var recalibratedBamIndexList: List[File] = Nil
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// Populates the list of per lane bam files to process (single bam or list of bams).
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if (input.endsWith("bam")) {
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perLaneBamList :+= input
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}
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else {
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for (bam <- Source.fromFile(input).getLines())
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perLaneBamList :+= bam
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}
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perLaneBamList.foreach { perLaneBam =>
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// Helpful variables
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val baseName: String = swapExt(new File(perLaneBam.substring(perLaneBam.lastIndexOf("/")+1)), ".bam", "").toString()
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val baseDir: String = perLaneBam.substring(0, perLaneBam.lastIndexOf("/")+1)
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// BAM files generated by the pipeline
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val cleanedBam: String = baseName + ".cleaned.bam"
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val fixedBam: String = baseName + ".cleaned.fixed.bam"
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val dedupedBam: String = baseName + ".cleaned.fixed.dedup.bam"
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val recalBam: String = baseName + ".cleaned.fixed.dedup.recal.bam"
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// Accessory files
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val targetIntervals: String = baseName + ".indel.intervals"
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val metricsFile: String = baseName + ".metrics"
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val preRecalFile: String = baseName + ".pre_recal.csv"
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val postRecalFile: String = baseName + ".post_recal.csv"
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val preOutPath: String = baseName + ".pre"
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val postOutPath: String = baseName + ".post"
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add(new target(perLaneBam, targetIntervals),
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new clean(perLaneBam, targetIntervals, cleanedBam, knownsOnly), // todo -- use constrained movement mode to skip this
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new fixMates(cleanedBam, fixedBam, intermediate), // todo -- use constrained movement mode to skip this
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new dedup(fixedBam, dedupedBam, metricsFile), // todo -- generate index on fly here
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new index(dedupedBam), // todo -- remove for on the fly index
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new cov(dedupedBam, preRecalFile),
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new recal(dedupedBam, preRecalFile, recalBam), // todo -- use GATK on the fly indexing?
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new index(recalBam), // todo remove for on the fly indexing
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new cov(recalBam, postRecalFile),
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new analyzeCovariates(preRecalFile, preOutPath),
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new analyzeCovariates(postRecalFile, postOutPath))
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recalibratedBamList :+= new File(recalBam)
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recalibratedBamIndexList :+= new File(recalBam + ".bai") // to hold next process by this dependency
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}
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// Helpful variables
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val outName: String = qscript.projectName
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val outDir: String = qscript.outputDir
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// BAM files generated by the pipeline
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val bamList: String = outDir + outName + ".list"
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val cleanedBam: String = outDir + outName + ".cleaned.bam"
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val fixedBam: String = outDir + outName + ".final.bam"
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// Accessory files
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val targetIntervals: String = outDir + outName + ".indel.intervals"
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add(new writeList(recalibratedBamList, bamList, recalibratedBamIndexList),
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new target(bamList, targetIntervals),
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new clean(bamList, targetIntervals, cleanedBam, !knownsOnly), // todo -- use constrained movement mode to skip fix mates
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new fixMates(cleanedBam, fixedBam, !intermediate)) // todo -- use constrained movement mode to skip this
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}
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class target (inBams: String, outIntervals: String) extends RealignerTargetCreator with CommandLineGATKArgs {
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this.input_file :+= new File(inBams)
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this.out = new File(outIntervals)
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this.mismatchFraction = Some(0.0)
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this.rodBind :+= RodBind("dbsnp", "VCF", dbSNP)
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this.rodBind :+= RodBind("indels1", "VCF", dindelPilotCalls)
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this.rodBind :+= RodBind("indels2", "VCF", dindelAFRCalls)
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this.rodBind :+= RodBind("indels3", "VCF", dindelEURCalls)
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this.rodBind :+= RodBind("indels4", "VCF", dindelASNCalls)
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this.jobName = inBams + ".tgt"
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if (!qscript.intervalString.isEmpty()) this.intervalsString :+= qscript.intervalString
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else this.intervals :+= qscript.intervals
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}
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class clean (inBams: String, tIntervals: String, outBam: String, knownsOnly: Boolean) extends IndelRealigner with CommandLineGATKArgs {
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this.input_file :+= new File(inBams)
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this.targetIntervals = new File(tIntervals)
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this.out = new File(outBam)
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this.doNotUseSW = true
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this.baq = Some(org.broadinstitute.sting.utils.baq.BAQ.CalculationMode.CALCULATE_AS_NECESSARY)
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this.rodBind :+= RodBind("dbsnp", "VCF", dbSNP)
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this.rodBind :+= RodBind("indels1", "VCF", dindelPilotCalls)
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this.rodBind :+= RodBind("indels2", "VCF", dindelAFRCalls)
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this.rodBind :+= RodBind("indels3", "VCF", dindelEURCalls)
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this.rodBind :+= RodBind("indels4", "VCF", dindelASNCalls)
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this.useOnlyKnownIndels = knownsOnly
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this.sortInCoordinateOrderEvenThoughItIsHighlyUnsafe = true
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this.jobName = inBams + ".clean"
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if (!qscript.intervalString.isEmpty()) this.intervalsString ++= List(qscript.intervalString)
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else this.intervals :+= qscript.intervals
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}
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class fixMates (inBam: String, outBam: String, intermediate: Boolean) extends PicardBamJarFunction {
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@Input(doc="cleaned bam") var cleaned: File = new File(inBam)
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@Output(doc="fixed bam") var fixed: File = new File(outBam)
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override def inputBams = List(cleaned)
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override def outputBam = fixed
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this.jarFile = qscript.fixMatesJar
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this.isIntermediate = intermediate
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this.memoryLimit = Some(6)
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this.jobName = inBam + ".fix"
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}
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class dedup (inBam: String, outBam: String, metricsFile: String) extends PicardBamJarFunction {
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@Input(doc="fixed bam") var clean: File = new File(inBam)
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@Output(doc="deduped bam") var deduped: File = new File(outBam)
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override def inputBams = List(clean)
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override def outputBam = deduped
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override def commandLine = super.commandLine + " M=" + metricsFile
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sortOrder = null
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this.memoryLimit = Some(6)
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this.jarFile = qscript.dedupJar
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this.jobName = inBam + ".dedup"
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}
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// todo -- may we should use the picard version instead? What about telling all of the picard tools to
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// todo -- generate BAM indices on the fly? That would be even better
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class index (inBam: String) extends SamtoolsIndexFunction {
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@Output(doc="bam index file") var outIndex: File = new File(inBam + ".bai")
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this.bamFile = new File(inBam)
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this.analysisName = inBam + ".index"
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}
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class cov (inBam: String, outRecalFile: String) extends CountCovariates with CommandLineGATKArgs {
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this.rodBind :+= RodBind("dbsnp", "VCF", dbSNP)
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this.covariate ++= List("ReadGroupCovariate", "QualityScoreCovariate", "CycleCovariate", "DinucCovariate")
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this.input_file :+= new File(inBam)
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this.recal_file = new File(outRecalFile)
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}
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class recal (inBam: String, inRecalFile: String, outBam: String) extends TableRecalibration with CommandLineGATKArgs {
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this.input_file :+= new File (inBam)
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this.recal_file = new File(inRecalFile)
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this.out = new File(outBam)
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}
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class analyzeCovariates (inRecalFile: String, outPath: String) extends AnalyzeCovariates {
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this.jarFile = qscript.ACJar
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this.resources = qscript.R
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this.recal_file = new File(inRecalFile)
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this.output_dir = outPath
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}
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class writeList(inBams: List[File], outBamList: String, depIndices: List[File]) extends ListWriterFunction {
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@Input(doc="bam indexes") var indexes: List[File] = depIndices // I need this dependency to hold creation of the list until all indices are done
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this.inputFiles = inBams
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this.listFile = new File(outBamList)
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this.jobName = "bamList"
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}
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} |