quick updates to conform with the new picard bam function structure
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5505 348d0f76-0448-11de-a6fe-93d51630548a
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carneiro
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@ -46,7 +46,7 @@ class dataProcessingV2 extends QScript {
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@Input(doc="the project name determines the final output (BAM file) base name. Example NA12878 yields NA12878.processed.bam", fullName="project", shortName="p", required=false)
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var projectName: String = "project"
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@Input(doc="Perform cleaning on knowns only", fullname="knowns_only", shortName="knowns", required=false)
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@Input(doc="Perform cleaning on knowns only", fullName="knowns_only", shortName="knowns", required=false)
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var knownsOnly: Boolean = false
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@Input(doc="Perform cleaning using Smith Waterman", fullName="use_smith_waterman", shortName="sw", required=false)
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@ -78,6 +78,18 @@ class dataProcessingV2 extends QScript {
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return nContigs == n
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}
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def hasMultipleSamples(readGroups: java.util.List[SAMReadGroupRecord]): Boolean = {
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var sample: String = ""
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for (r <- readGroups) {
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if (sample.isEmpty)
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sample = r.getSample()
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else if (sample != r.getSample())
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return true;
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}
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return false
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}
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def createSampleFiles(): Map[String, File] = {
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val outName: String = qscript.outputDir + qscript.projectName
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@ -93,7 +105,7 @@ class dataProcessingV2 extends QScript {
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// only allow one sample per file. Bam files with multiple samples would require pre-processing of the file
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// with PrintReads to separate the samples. Tell user to do it himself!
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assert(hasMultipleSamples(readGroups), "The pipeline requires that only one sample is present in a BAM file. Please separate the samples in " + bam)
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assert(!hasMultipleSamples(readGroups), "The pipeline requires that only one sample is present in a BAM file. Please separate the samples in " + bam)
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// Fill out the sample table with the readgroups in this file
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for (rg <- readGroups) {
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@ -169,32 +181,19 @@ class dataProcessingV2 extends QScript {
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add(writeList(cohortList, cohortFile))
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}
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// General arguments to all programs
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// General arguments to GATK walkers
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trait CommandLineGATKArgs extends CommandLineGATK {
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this.jarFile = qscript.GATKjar
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this.reference_sequence = qscript.reference
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this.memoryLimit = 4
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this.memoryLimit = Some(4)
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this.isIntermediate = true
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}
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case class joinBams (inBams: List[File], outBam: File) extends PicardBamFunction {
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@Input(doc="input bam list") var join = inBams
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@Output(doc="joined bam") var joined = outBam
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@Output(doc="joined bam index") var joinedIndex = new File(outBam + "bai")
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override def inputBams = join
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override def outputBam = joined
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override def commandLine = super.commandLine + " CREATE_INDEX=true"
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this.jarFile = qscript.mergeBamJar
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this.isIntermediate = true
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this.analysisName = queueLogDir + outBam + ".joinBams"
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this.jobName = queueLogDir + outBam + ".joinBams"
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}
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case class target (inBams: File, outIntervals: File) extends RealignerTargetCreator with CommandLineGATKArgs {
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if (!knownsOnly)
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this.input_file :+= inBams
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this.out = outIntervals
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this.mismatchFraction = 0.0
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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("indels", "VCF", indels)
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this.scatterCount = nContigs
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@ -210,28 +209,13 @@ class dataProcessingV2 extends QScript {
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this.rodBind :+= RodBind("indels", "VCF", qscript.indels)
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this.useOnlyKnownIndels = knownsOnly
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this.doNotUseSW = useSW
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this.compress = 0
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this.U = org.broadinstitute.sting.gatk.arguments.ValidationExclusion.TYPE.NO_READ_ORDER_VERIFICATION // todo -- update this with the last consensus between Tim, Matt and Eric. This is ugly!
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this.compress = Some(0)
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this.U = Some(org.broadinstitute.sting.gatk.arguments.ValidationExclusion.TYPE.NO_READ_ORDER_VERIFICATION) // todo -- update this with the last consensus between Tim, Matt and Eric. This is ugly!
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this.scatterCount = nContigs
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this.analysisName = queueLogDir + outBam + ".clean"
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this.jobName = queueLogDir + outBam + ".clean"
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}
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case class dedup (inBam: File, outBam: File, metricsFile: File) extends PicardBamFunction {
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@Input(doc="fixed bam") var clean = inBam
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@Output(doc="deduped bam") var deduped = outBam
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@Output(doc="deduped bam index") var dedupedIndex = new File(outBam + ".bai")
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@Output(doc="metrics file") var metrics = metricsFile
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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 + " CREATE_INDEX=true"
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sortOrder = null
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this.memoryLimit = 6
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this.jarFile = qscript.dedupJar
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this.analysisName = queueLogDir + outBam + ".dedup"
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this.jobName = queueLogDir + outBam + ".dedup"
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}
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//todo -- add scatter gather capability (waiting for khalid's modifications to the queue base
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case class cov (inBam: File, outRecalFile: File) extends CountCovariates with CommandLineGATKArgs {
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this.rodBind :+= RodBind("dbsnp", "VCF", dbSNP)
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@ -246,17 +230,20 @@ class dataProcessingV2 extends QScript {
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@Output(doc="recalibrated bam index") var recalIndex = new File(outBam + ".bai")
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this.input_file :+= inBam
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this.recal_file = inRecalFile
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this.baq = org.broadinstitute.sting.utils.baq.BAQ.CalculationMode.CALCULATE_AS_NECESSARY
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this.baq = Some(org.broadinstitute.sting.utils.baq.BAQ.CalculationMode.CALCULATE_AS_NECESSARY)
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this.out = outBam
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if (!qscript.intervalString.isEmpty()) this.intervalsString ++= List(qscript.intervalString)
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else if (qscript.intervals != null) this.intervals :+= qscript.intervals
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this.U = org.broadinstitute.sting.gatk.arguments.ValidationExclusion.TYPE.NO_READ_ORDER_VERIFICATION // todo -- update this with the last consensus between Tim, Matt and Eric. This is ugly!
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this.index_output_bam_on_the_fly = true
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this.U = Some(org.broadinstitute.sting.gatk.arguments.ValidationExclusion.TYPE.NO_READ_ORDER_VERIFICATION) // todo -- update this with the last consensus between Tim, Matt and Eric. This is ugly!
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this.index_output_bam_on_the_fly = Some(true)
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this.isIntermediate = false
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this.analysisName = queueLogDir + outBam + ".recalibration"
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this.jobName = queueLogDir + outBam + ".recalibration"
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}
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// Outside tools (not GATK walkers)
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case class analyzeCovariates (inRecalFile: File, outPath: File) extends AnalyzeCovariates {
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this.jarFile = qscript.ACJar
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this.resources = qscript.R
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@ -266,6 +253,35 @@ class dataProcessingV2 extends QScript {
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this.jobName = queueLogDir + inRecalFile + ".analyze_covariates"
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}
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case class dedup (inBam: File, outBam: File, metricsFile: File) extends PicardBamFunction {
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@Input(doc="fixed bam") var clean = inBam
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@Output(doc="deduped bam") var deduped = outBam
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@Output(doc="deduped bam index") var dedupedIndex = new File(outBam + ".bai")
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@Output(doc="metrics file") var metrics = metricsFile
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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 + " CREATE_INDEX=true"
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sortOrder = null
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this.memoryLimit = Some(6)
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this.isIntermediate = true
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this.jarFile = qscript.dedupJar
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this.analysisName = queueLogDir + outBam + ".dedup"
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this.jobName = queueLogDir + outBam + ".dedup"
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}
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case class joinBams (inBams: List[File], outBam: File) extends PicardBamFunction {
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@Input(doc="input bam list") var join = inBams
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@Output(doc="joined bam") var joined = outBam
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@Output(doc="joined bam index") var joinedIndex = new File(outBam + "bai")
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override def inputBams = join
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override def outputBam = joined
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override def commandLine = super.commandLine + " CREATE_INDEX=true"
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this.jarFile = qscript.mergeBamJar
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this.isIntermediate = true
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this.analysisName = queueLogDir + outBam + ".joinBams"
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this.jobName = queueLogDir + outBam + ".joinBams"
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}
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case class writeList(inBams: List[File], outBamList: File) extends ListWriterFunction {
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this.inputFiles = inBams
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this.listFile = outBamList
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