Scala protected is more akin to Java private than Java protected. Not typing these defs.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4470 348d0f76-0448-11de-a6fe-93d51630548a
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@ -33,7 +33,7 @@ class BamProcessing(yaml: File, gatkJar: File, fixMatesJar: File) {
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* @Doc: Creates a standard realigner target creator CLF given a bam, an output file, and the contigs over which to run
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* @Returns: A CLF for the realigner target creator job
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*/
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protected def StandardRealignerTargetCreator(bam: File, contigs: List[String], output: File) : RealignerTargetCreator = {
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def StandardRealignerTargetCreator(bam: File, contigs: List[String], output: File) : RealignerTargetCreator = {
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var rtc = new RealignerTargetCreator with StandardCommandLineGATK
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rtc.intervals = null
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rtc.intervalsString = contigs
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@ -48,7 +48,7 @@ class BamProcessing(yaml: File, gatkJar: File, fixMatesJar: File) {
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* @Doc: Creates a standard indel cleaner CLF given a bam, the results of the target creator, and an output .bam file
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* @Returns: A CLF for the indel cleaning job
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*/
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protected def StandardIndelCleaner(bam: File, contigs: List[String], targets: File, outBam: File) : IndelRealigner = {
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def StandardIndelCleaner(bam: File, contigs: List[String], targets: File, outBam: File) : IndelRealigner = {
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var realigner = new IndelRealigner with StandardCommandLineGATK
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realigner.intervalsString = contigs
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realigner.intervals = null
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@ -65,7 +65,7 @@ class BamProcessing(yaml: File, gatkJar: File, fixMatesJar: File) {
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* @Doc: Creates a standard split-by-contig indel cleaner job for a given bam file, RTC output, and bam to merge everything to
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* @Returns: A list of CLFs (todo -- wrapped in a Pipeline)
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*/
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protected def StandardIndelCleanBam(bam: File, jobContigs: List[List[String]], targets: File, cleanedBam: File) : List[CommandLineFunction] = {
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def StandardIndelCleanBam(bam: File, jobContigs: List[List[String]], targets: File, cleanedBam: File) : List[CommandLineFunction] = {
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var cmds : List[CommandLineFunction] = Nil
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var jobSpecs : List[(File,File,List[String])] = jobContigs.map[(File,File,List[String]),List[(File,File,List[String])]](
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ctigs => { (bam, swapExt(bam,".bam",".%s.bam".format(ctigs.mkString("_"))), ctigs) }
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@ -89,7 +89,7 @@ class BamProcessing(yaml: File, gatkJar: File, fixMatesJar: File) {
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* @Returns: A list of command line functions for the full indel realignment pipeline from the collection
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* of uncleaned bams to the collection of cleaned bams
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*/
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protected def StandardIndelRealign( bamsUncleanCleanPairs: List[(File,File)], nJobs: Int = 1 ) : List[CommandLineFunction] = {
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def StandardIndelRealign( bamsUncleanCleanPairs: List[(File,File)], nJobs: Int = 1 ) : List[CommandLineFunction] = {
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val contigsForJobs : List[List[String]] = PipelineUtils.smartSplitContigs(library.attributes.getProject.getReferenceFile, library.attributes.getProject.getIntervalList, nJobs)
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var commands : List[CommandLineFunction] = Nil
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for ( bamPair <- bamsUncleanCleanPairs ) {
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@ -110,7 +110,7 @@ class BamProcessing(yaml: File, gatkJar: File, fixMatesJar: File) {
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* @Doc: Merges N bam files into one bam file, fixing mate pairs in the process; does not assume they are sorted
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* @Returns: Command line function for the merge, fix-mate, and sort operation
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*/
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protected def StandardPicardFixMates(inBams: List[File], outBam: File, picardJar: File) : CommandLineFunction = {
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def StandardPicardFixMates(inBams: List[File], outBam: File, picardJar: File) : CommandLineFunction = {
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var pfm : PicardFixMates = new PicardFixMates
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pfm.bams = inBams
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pfm.outBam = outBam
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@ -35,7 +35,7 @@ class VariantCalling(yaml: File,gatkJar: File) {
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* @Return: UnifiedGenotyper with the standard GSA arguments
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* @TODO: Add a formula: f(#bams)=memory; allow yaml to specify triggers and perhaps other information
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*/
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protected def StandardUnifiedGenotyper(bams : List[File], output : File) : UnifiedGenotyper = {
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def StandardUnifiedGenotyper(bams : List[File], output : File) : UnifiedGenotyper = {
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var ug = new UnifiedGenotyper with StandardCommandLineGATK
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ug.analysisName = "UnifiedGenotyper"
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ug.input_file = bams
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@ -63,7 +63,7 @@ class VariantCalling(yaml: File,gatkJar: File) {
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* @Doc: Creates a CLF to call indels on a specific .bam file, outputting to a given output file
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* @Returns: An IndelGenotyperV2 CLF with standard GSA arguments
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*/
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protected def StandardIndelGenotyper(bam : File, output: File) : IndelGenotyperV2 = {
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def StandardIndelGenotyper(bam : File, output: File) : IndelGenotyperV2 = {
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var ig = new IndelGenotyperV2 with StandardCommandLineGATK
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ig.analysisName = "IndelGenotyper"
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ig.input_file :+= bam
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@ -86,7 +86,7 @@ class VariantCalling(yaml: File,gatkJar: File) {
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* @Doc: Combines a list of indel VCFs to a single output file
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* @Returns: A CombineVariants CLF with standard GSA arguments
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*/
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protected def StandardIndelCombine( igList : List[IndelGenotyperV2], output : File ) : CombineVariants = {
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def StandardIndelCombine( igList : List[IndelGenotyperV2], output : File ) : CombineVariants = {
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var cv = new CombineVariants with StandardCommandLineGATK
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cv.out = output
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cv.genotypemergeoption = Some(org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils.GenotypeMergeType.UNIQUIFY)
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@ -105,7 +105,7 @@ class VariantCalling(yaml: File,gatkJar: File) {
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* @Doc: Generates indel calls on a list of .bam files, and merges those calls into an output file. This is a small pipeline.
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* @Returns: A list of CLFs that run indel calls and indel merging. User has zero control over individual indel VCF names.
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*/
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protected def StandardIndelCalls ( bams : List[File], output : File ) : List[CommandLineGATK] = {
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def StandardIndelCalls ( bams : List[File], output : File ) : List[CommandLineGATK] = {
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var genotypers = bams.foldLeft[List[IndelGenotyperV2]](Nil)( (igs,bam) => igs ::: List(this.StandardIndelGenotyper(bam, swapExt(bam,".bam",".indels.vcf"), false)))
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var combine = this.StandardIndelCombine( genotypers, output )
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var callFunctions: List[CommandLineGATK] = genotypers
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@ -114,7 +114,7 @@ class VariantCalling(yaml: File,gatkJar: File) {
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return callFunctions
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}
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protected def StandardFilterAtIndels ( snps: File, indels: File, output : File ) : VariantFiltration = {
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def StandardFilterAtIndels ( snps: File, indels: File, output : File ) : VariantFiltration = {
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var iFil = new VariantFiltration with StandardCommandLineGATK
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iFil.analysisName = "FilterAtIndels"
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iFil.out = output
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@ -128,7 +128,7 @@ class VariantCalling(yaml: File,gatkJar: File) {
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return iFil
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}
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protected def StandardHandfilter( snps: File, output: File ) : VariantFiltration = {
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def StandardHandfilter( snps: File, output: File ) : VariantFiltration = {
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var hFil = new VariantFiltration with StandardCommandLineGATK
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hFil.analysisName = "HandFilter"
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hFil.out = output
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@ -143,7 +143,7 @@ class VariantCalling(yaml: File,gatkJar: File) {
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return hFil
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}
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protected def StandardVariantCluster( snps: File, output: File ) : GenerateVariantClusters = {
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def StandardVariantCluster( snps: File, output: File ) : GenerateVariantClusters = {
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var genC = new GenerateVariantClusters with StandardCommandLineGATK
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genC.analysisName = "VariantQualityRecalibration"
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genC.rodBind :+= new RodBind("input","VCF",snps)
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@ -157,7 +157,7 @@ class VariantCalling(yaml: File,gatkJar: File) {
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return genC
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}
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protected def StandardVariantRecalibrator ( raw_vcf: File, cluster: File, target_titv: scala.Double, out_vcf: File,
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def StandardVariantRecalibrator ( raw_vcf: File, cluster: File, target_titv: scala.Double, out_vcf: File,
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out_tranches: File, out_dat: File) : VariantRecalibrator = {
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var vr = new VariantRecalibrator with StandardCommandLineGATK
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vr.analysisName = "VariantQualityRecalibration"
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@ -176,7 +176,7 @@ class VariantCalling(yaml: File,gatkJar: File) {
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}
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protected def StandardApplyVariantCuts( snpRecal: File, tranches: File, output: File) : ApplyVariantCuts = {
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def StandardApplyVariantCuts( snpRecal: File, tranches: File, output: File) : ApplyVariantCuts = {
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var avc = new ApplyVariantCuts with StandardCommandLineGATK
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avc.analysisName = "VariantQualityRecalibration"
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avc.rodBind :+= new RodBind("input","VCF",snpRecal)
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@ -187,7 +187,7 @@ class VariantCalling(yaml: File,gatkJar: File) {
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return avc
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}
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protected def StandardRecalibrateVariants( snps: File, targetTiTv: scala.Double, recalVcf: File) : List[CommandLineGATK] = {
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def StandardRecalibrateVariants( snps: File, targetTiTv: scala.Double, recalVcf: File) : List[CommandLineGATK] = {
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var clust = StandardVariantCluster(snps, swapExt(snps,".vcf",".cluster"))
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var recal = StandardVariantRecalibrator(snps,clust.clusterFile,targetTiTv,swapExt(snps,".vcf",".recal.vcf"),
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swapExt(snps,".vcf",".recal.tranch"),swapExt(snps,".vcf",".recal.dat"))
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@ -201,7 +201,7 @@ class VariantCalling(yaml: File,gatkJar: File) {
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return cmds
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}
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protected def StandardGenomicAnnotation ( snps: File, refseqFile: File, outputVCF: File) : GenomicAnnotator = {
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def StandardGenomicAnnotation ( snps: File, refseqFile: File, outputVCF: File) : GenomicAnnotator = {
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var ga = new GenomicAnnotator with StandardCommandLineGATK
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ga.analysisName = "GenomicAnnotator"
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ga.variantVCF = snps
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@ -212,7 +212,7 @@ class VariantCalling(yaml: File,gatkJar: File) {
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return ga
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}
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protected def StandardSNPCalls( bams: List[File], output: File, targetTiTv: scala.Double, refGene: File = null ) : List[CommandLineGATK] = {
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def StandardSNPCalls( bams: List[File], output: File, targetTiTv: scala.Double, refGene: File = null ) : List[CommandLineGATK] = {
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var commands : List[CommandLineGATK] = Nil
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var dir = ""
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@ -250,7 +250,7 @@ class VariantCalling(yaml: File,gatkJar: File) {
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return commands
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}
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protected def StandardSNPCallsBothFilterTypes(bams: List[File], recalOut: File, handFilteredOut: File, targetTiTv: scala.Double, refGene: File = null ) : List[CommandLineGATK] = {
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def StandardSNPCallsBothFilterTypes(bams: List[File], recalOut: File, handFilteredOut: File, targetTiTv: scala.Double, refGene: File = null ) : List[CommandLineGATK] = {
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var commands : List[CommandLineGATK] = Nil
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var dir = ""
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@ -292,7 +292,7 @@ class VariantCalling(yaml: File,gatkJar: File) {
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return commands
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}
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protected def StandardCallingPipeline(bams: List[File], indelOut: File, recalOut: File, handFilteredOut: File, targetTiTv: scala.Double, refGene: File = null ) : List[CommandLineGATK] = {
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def StandardCallingPipeline(bams: List[File], indelOut: File, recalOut: File, handFilteredOut: File, targetTiTv: scala.Double, refGene: File = null ) : List[CommandLineGATK] = {
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var commands : List[CommandLineGATK] = Nil
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var dir = ""
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