now only accepts intervals files if the user specifically requests to report bams at interval only.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5291 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
carneiro
parent
ecfb51bcd8
commit
2a48ec1307
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@ -25,13 +25,13 @@ class dataProcessing extends QScript {
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var input: String = _
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@Input(doc="Reference fasta file", shortName="R", required=false)
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var reference: File = new File("/humgen/1kg/reference/human_g1k_v37.fasta")
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var reference: File = new File("/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19")
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@Input(doc="dbsnp ROD to use (VCF)", shortName="D", required=false) // todo -- accept any format. Not only VCF.
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val dbSNP: File = new File("/humgen/gsa-hpprojects/GATK/data/dbsnp_132_b37.leftAligned.vcf")
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@Input(doc="extra VCF files to use as reference indels for Indel Realignment", shortName="indels", required=false) //todo -- once vcfs are merged, this will become the only indel vcf to be used and the merged file will be the default.
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val indels: File = _
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val indels: File = null
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@Input(doc="the project name determines the final output (BAM file) base name. Example NA12878 yields NA12878.processed.bam", shortName="p", required=false)
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var projectName: String = "combined"
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@ -39,12 +39,11 @@ class dataProcessing extends QScript {
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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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@Input(doc="the -L interval string to be used by GATK - output bams at interval only", 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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@Input(doc="output bams at intervals only", shortName="intervals", required=false)
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var intervals: File = _
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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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@ -71,6 +70,22 @@ class dataProcessing extends QScript {
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var perLaneBamList: List[String] = Nil
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var recalibratedBamList: List[File] = Nil
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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 + ".clean.bam"
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val fixedBam: String = outDir + outName + ".processed.bam"
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// Accessory files
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val knownTargetIntervals: String = outDir + outName + ".known_indels.intervals"
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val allTargetIntervals: String = outDir + outName + ".all_indels.intervals"
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add(new knownTargets(knownTargetIntervals))
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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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@ -78,9 +93,6 @@ class dataProcessing extends QScript {
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for (bam <- Source.fromFile(input).getLines())
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perLaneBamList :+= bam
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perLaneBamList.foreach { perLaneBam =>
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// Helpful variables
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@ -93,15 +105,13 @@ class dataProcessing extends QScript {
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val recalBam: String = baseName + ".clean.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, intermediate),
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add(new clean(perLaneBam, knownTargetIntervals, cleanedBam, knownsOnly, intermediate),
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new dedup(cleanedBam, dedupedBam, metricsFile),
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new cov(dedupedBam, preRecalFile),
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new recal(dedupedBam, preRecalFile, recalBam),
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@ -112,24 +122,23 @@ class dataProcessing extends QScript {
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recalibratedBamList :+= new File(recalBam)
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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 + ".clean.bam"
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val fixedBam: String = outDir + outName + ".processed.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),
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new target(bamList, targetIntervals), // todo -- reuse previously generated intervals (see how to do that)
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new clean(bamList, targetIntervals, cleanedBam, !knownsOnly, !intermediate))
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new allTargets(bamList, allTargetIntervals),
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new clean(bamList, allTargetIntervals, cleanedBam, !knownsOnly, !intermediate))
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}
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class target (inBams: String, outIntervals: String) extends RealignerTargetCreator with CommandLineGATKArgs {
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class knownTargets (outIntervals: String) extends RealignerTargetCreator with CommandLineGATKArgs {
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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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}
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class allTargets (inBams: String, outIntervals: String) extends knownTargets(outIntervals) {
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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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@ -139,17 +148,13 @@ class dataProcessing extends QScript {
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this.rodBind :+= RodBind("indels3", "VCF", dindelEURCalls)
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this.rodBind :+= RodBind("indels4", "VCF", dindelASNCalls)
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if (qscript.indels != null) this.rodBind :+= RodBind("indels5", "VCF", qscript.indels)
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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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this.jobName = outIntervals + ".target"
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}
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class clean (inBams: String, tIntervals: String, outBam: String, knownsOnly: Boolean, intermediate: 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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@ -159,27 +164,20 @@ class dataProcessing extends QScript {
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this.useOnlyKnownIndels = knownsOnly
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this.sortInCoordinateOrderEvenThoughItIsHighlyUnsafe = true
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this.constrainMovement = true
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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.compress = Some(0)
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this.isIntermediate = intermediate
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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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override def commandLine = super.commandLine + " CREATE_INDEX=true"
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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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this.jobName = outBam + ".clean"
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if (!intermediate && !qscript.intervalString.isEmpty()) this.intervalsString ++= List(qscript.intervalString)
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if (!intermediate && qscript.intervals != null) this.intervals :+= qscript.intervals
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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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@Output(doc="deduped bam index") var dedupedIndex: File = new File(outBam + ".bai")
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@Output(doc="metrics file") var metrics: File = new File(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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@ -187,7 +185,7 @@ class dataProcessing extends QScript {
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this.memoryLimit = Some(6)
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this.jarFile = qscript.dedupJar
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this.isIntermediate = true
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this.jobName = inBam + ".dedup"
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this.jobName = outBam + ".dedup"
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}
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class cov (inBam: String, outRecalFile: String) extends CountCovariates with CommandLineGATKArgs {
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@ -195,13 +193,16 @@ class dataProcessing extends QScript {
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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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this.jobName = outRecalFile + ".covariates"
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}
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class recal (inBam: String, inRecalFile: String, outBam: String) extends TableRecalibration with CommandLineGATKArgs {
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@Output(doc="recalibrated bam index") var recalIndex: File = new File(outBam + ".bai")
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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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this.index_output_bam_on_the_fly = Some(true)
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this.jobName = outBam + ".recalibration"
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}
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class analyzeCovariates (inRecalFile: String, outPath: String) extends AnalyzeCovariates {
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@ -209,11 +210,12 @@ class dataProcessing extends QScript {
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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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this.jobName = inRecalFile + ".analyze_covariates"
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}
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class writeList(inBams: List[File], outBamList: String) extends ListWriterFunction {
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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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this.jobName = outBamList + ".bamList"
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}
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}
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}
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