From 6368a46babf39fcaea1ecd9e85bf37b8bb5bfa13 Mon Sep 17 00:00:00 2001 From: chartl Date: Fri, 8 Oct 2010 19:36:23 +0000 Subject: [PATCH] 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 --- .../sting/queue/pipeline/BamProcessing.scala | 10 +++---- .../sting/queue/pipeline/VariantCalling.scala | 28 +++++++++---------- 2 files changed, 19 insertions(+), 19 deletions(-) diff --git a/scala/src/org/broadinstitute/sting/queue/pipeline/BamProcessing.scala b/scala/src/org/broadinstitute/sting/queue/pipeline/BamProcessing.scala index 15c0183ac..bbee47f44 100755 --- a/scala/src/org/broadinstitute/sting/queue/pipeline/BamProcessing.scala +++ b/scala/src/org/broadinstitute/sting/queue/pipeline/BamProcessing.scala @@ -33,7 +33,7 @@ class BamProcessing(yaml: File, gatkJar: File, fixMatesJar: File) { * @Doc: Creates a standard realigner target creator CLF given a bam, an output file, and the contigs over which to run * @Returns: A CLF for the realigner target creator job */ - protected def StandardRealignerTargetCreator(bam: File, contigs: List[String], output: File) : RealignerTargetCreator = { + def StandardRealignerTargetCreator(bam: File, contigs: List[String], output: File) : RealignerTargetCreator = { var rtc = new RealignerTargetCreator with StandardCommandLineGATK rtc.intervals = null rtc.intervalsString = contigs @@ -48,7 +48,7 @@ class BamProcessing(yaml: File, gatkJar: File, fixMatesJar: File) { * @Doc: Creates a standard indel cleaner CLF given a bam, the results of the target creator, and an output .bam file * @Returns: A CLF for the indel cleaning job */ - protected def StandardIndelCleaner(bam: File, contigs: List[String], targets: File, outBam: File) : IndelRealigner = { + def StandardIndelCleaner(bam: File, contigs: List[String], targets: File, outBam: File) : IndelRealigner = { var realigner = new IndelRealigner with StandardCommandLineGATK realigner.intervalsString = contigs realigner.intervals = null @@ -65,7 +65,7 @@ class BamProcessing(yaml: File, gatkJar: File, fixMatesJar: File) { * @Doc: Creates a standard split-by-contig indel cleaner job for a given bam file, RTC output, and bam to merge everything to * @Returns: A list of CLFs (todo -- wrapped in a Pipeline) */ - protected def StandardIndelCleanBam(bam: File, jobContigs: List[List[String]], targets: File, cleanedBam: File) : List[CommandLineFunction] = { + def StandardIndelCleanBam(bam: File, jobContigs: List[List[String]], targets: File, cleanedBam: File) : List[CommandLineFunction] = { var cmds : List[CommandLineFunction] = Nil var jobSpecs : List[(File,File,List[String])] = jobContigs.map[(File,File,List[String]),List[(File,File,List[String])]]( ctigs => { (bam, swapExt(bam,".bam",".%s.bam".format(ctigs.mkString("_"))), ctigs) } @@ -89,7 +89,7 @@ class BamProcessing(yaml: File, gatkJar: File, fixMatesJar: File) { * @Returns: A list of command line functions for the full indel realignment pipeline from the collection * of uncleaned bams to the collection of cleaned bams */ - protected def StandardIndelRealign( bamsUncleanCleanPairs: List[(File,File)], nJobs: Int = 1 ) : List[CommandLineFunction] = { + def StandardIndelRealign( bamsUncleanCleanPairs: List[(File,File)], nJobs: Int = 1 ) : List[CommandLineFunction] = { val contigsForJobs : List[List[String]] = PipelineUtils.smartSplitContigs(library.attributes.getProject.getReferenceFile, library.attributes.getProject.getIntervalList, nJobs) var commands : List[CommandLineFunction] = Nil for ( bamPair <- bamsUncleanCleanPairs ) { @@ -110,7 +110,7 @@ class BamProcessing(yaml: File, gatkJar: File, fixMatesJar: File) { * @Doc: Merges N bam files into one bam file, fixing mate pairs in the process; does not assume they are sorted * @Returns: Command line function for the merge, fix-mate, and sort operation */ - protected def StandardPicardFixMates(inBams: List[File], outBam: File, picardJar: File) : CommandLineFunction = { + def StandardPicardFixMates(inBams: List[File], outBam: File, picardJar: File) : CommandLineFunction = { var pfm : PicardFixMates = new PicardFixMates pfm.bams = inBams pfm.outBam = outBam diff --git a/scala/src/org/broadinstitute/sting/queue/pipeline/VariantCalling.scala b/scala/src/org/broadinstitute/sting/queue/pipeline/VariantCalling.scala index d25df3284..81d1ee1ab 100755 --- a/scala/src/org/broadinstitute/sting/queue/pipeline/VariantCalling.scala +++ b/scala/src/org/broadinstitute/sting/queue/pipeline/VariantCalling.scala @@ -35,7 +35,7 @@ class VariantCalling(yaml: File,gatkJar: File) { * @Return: UnifiedGenotyper with the standard GSA arguments * @TODO: Add a formula: f(#bams)=memory; allow yaml to specify triggers and perhaps other information */ - protected def StandardUnifiedGenotyper(bams : List[File], output : File) : UnifiedGenotyper = { + def StandardUnifiedGenotyper(bams : List[File], output : File) : UnifiedGenotyper = { var ug = new UnifiedGenotyper with StandardCommandLineGATK ug.analysisName = "UnifiedGenotyper" ug.input_file = bams @@ -63,7 +63,7 @@ class VariantCalling(yaml: File,gatkJar: File) { * @Doc: Creates a CLF to call indels on a specific .bam file, outputting to a given output file * @Returns: An IndelGenotyperV2 CLF with standard GSA arguments */ - protected def StandardIndelGenotyper(bam : File, output: File) : IndelGenotyperV2 = { + def StandardIndelGenotyper(bam : File, output: File) : IndelGenotyperV2 = { var ig = new IndelGenotyperV2 with StandardCommandLineGATK ig.analysisName = "IndelGenotyper" ig.input_file :+= bam @@ -86,7 +86,7 @@ class VariantCalling(yaml: File,gatkJar: File) { * @Doc: Combines a list of indel VCFs to a single output file * @Returns: A CombineVariants CLF with standard GSA arguments */ - protected def StandardIndelCombine( igList : List[IndelGenotyperV2], output : File ) : CombineVariants = { + def StandardIndelCombine( igList : List[IndelGenotyperV2], output : File ) : CombineVariants = { var cv = new CombineVariants with StandardCommandLineGATK cv.out = output cv.genotypemergeoption = Some(org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils.GenotypeMergeType.UNIQUIFY) @@ -105,7 +105,7 @@ class VariantCalling(yaml: File,gatkJar: File) { * @Doc: Generates indel calls on a list of .bam files, and merges those calls into an output file. This is a small pipeline. * @Returns: A list of CLFs that run indel calls and indel merging. User has zero control over individual indel VCF names. */ - protected def StandardIndelCalls ( bams : List[File], output : File ) : List[CommandLineGATK] = { + def StandardIndelCalls ( bams : List[File], output : File ) : List[CommandLineGATK] = { var genotypers = bams.foldLeft[List[IndelGenotyperV2]](Nil)( (igs,bam) => igs ::: List(this.StandardIndelGenotyper(bam, swapExt(bam,".bam",".indels.vcf"), false))) var combine = this.StandardIndelCombine( genotypers, output ) var callFunctions: List[CommandLineGATK] = genotypers @@ -114,7 +114,7 @@ class VariantCalling(yaml: File,gatkJar: File) { return callFunctions } - protected def StandardFilterAtIndels ( snps: File, indels: File, output : File ) : VariantFiltration = { + def StandardFilterAtIndels ( snps: File, indels: File, output : File ) : VariantFiltration = { var iFil = new VariantFiltration with StandardCommandLineGATK iFil.analysisName = "FilterAtIndels" iFil.out = output @@ -128,7 +128,7 @@ class VariantCalling(yaml: File,gatkJar: File) { return iFil } - protected def StandardHandfilter( snps: File, output: File ) : VariantFiltration = { + def StandardHandfilter( snps: File, output: File ) : VariantFiltration = { var hFil = new VariantFiltration with StandardCommandLineGATK hFil.analysisName = "HandFilter" hFil.out = output @@ -143,7 +143,7 @@ class VariantCalling(yaml: File,gatkJar: File) { return hFil } - protected def StandardVariantCluster( snps: File, output: File ) : GenerateVariantClusters = { + def StandardVariantCluster( snps: File, output: File ) : GenerateVariantClusters = { var genC = new GenerateVariantClusters with StandardCommandLineGATK genC.analysisName = "VariantQualityRecalibration" genC.rodBind :+= new RodBind("input","VCF",snps) @@ -157,7 +157,7 @@ class VariantCalling(yaml: File,gatkJar: File) { return genC } - protected def StandardVariantRecalibrator ( raw_vcf: File, cluster: File, target_titv: scala.Double, out_vcf: File, + def StandardVariantRecalibrator ( raw_vcf: File, cluster: File, target_titv: scala.Double, out_vcf: File, out_tranches: File, out_dat: File) : VariantRecalibrator = { var vr = new VariantRecalibrator with StandardCommandLineGATK vr.analysisName = "VariantQualityRecalibration" @@ -176,7 +176,7 @@ class VariantCalling(yaml: File,gatkJar: File) { } - protected def StandardApplyVariantCuts( snpRecal: File, tranches: File, output: File) : ApplyVariantCuts = { + def StandardApplyVariantCuts( snpRecal: File, tranches: File, output: File) : ApplyVariantCuts = { var avc = new ApplyVariantCuts with StandardCommandLineGATK avc.analysisName = "VariantQualityRecalibration" avc.rodBind :+= new RodBind("input","VCF",snpRecal) @@ -187,7 +187,7 @@ class VariantCalling(yaml: File,gatkJar: File) { return avc } - protected def StandardRecalibrateVariants( snps: File, targetTiTv: scala.Double, recalVcf: File) : List[CommandLineGATK] = { + def StandardRecalibrateVariants( snps: File, targetTiTv: scala.Double, recalVcf: File) : List[CommandLineGATK] = { var clust = StandardVariantCluster(snps, swapExt(snps,".vcf",".cluster")) var recal = StandardVariantRecalibrator(snps,clust.clusterFile,targetTiTv,swapExt(snps,".vcf",".recal.vcf"), swapExt(snps,".vcf",".recal.tranch"),swapExt(snps,".vcf",".recal.dat")) @@ -201,7 +201,7 @@ class VariantCalling(yaml: File,gatkJar: File) { return cmds } - protected def StandardGenomicAnnotation ( snps: File, refseqFile: File, outputVCF: File) : GenomicAnnotator = { + def StandardGenomicAnnotation ( snps: File, refseqFile: File, outputVCF: File) : GenomicAnnotator = { var ga = new GenomicAnnotator with StandardCommandLineGATK ga.analysisName = "GenomicAnnotator" ga.variantVCF = snps @@ -212,7 +212,7 @@ class VariantCalling(yaml: File,gatkJar: File) { return ga } - protected def StandardSNPCalls( bams: List[File], output: File, targetTiTv: scala.Double, refGene: File = null ) : List[CommandLineGATK] = { + def StandardSNPCalls( bams: List[File], output: File, targetTiTv: scala.Double, refGene: File = null ) : List[CommandLineGATK] = { var commands : List[CommandLineGATK] = Nil var dir = "" @@ -250,7 +250,7 @@ class VariantCalling(yaml: File,gatkJar: File) { return commands } - protected def StandardSNPCallsBothFilterTypes(bams: List[File], recalOut: File, handFilteredOut: File, targetTiTv: scala.Double, refGene: File = null ) : List[CommandLineGATK] = { + def StandardSNPCallsBothFilterTypes(bams: List[File], recalOut: File, handFilteredOut: File, targetTiTv: scala.Double, refGene: File = null ) : List[CommandLineGATK] = { var commands : List[CommandLineGATK] = Nil var dir = "" @@ -292,7 +292,7 @@ class VariantCalling(yaml: File,gatkJar: File) { return commands } - protected def StandardCallingPipeline(bams: List[File], indelOut: File, recalOut: File, handFilteredOut: File, targetTiTv: scala.Double, refGene: File = null ) : List[CommandLineGATK] = { + def StandardCallingPipeline(bams: List[File], indelOut: File, recalOut: File, handFilteredOut: File, targetTiTv: scala.Double, refGene: File = null ) : List[CommandLineGATK] = { var commands : List[CommandLineGATK] = Nil var dir = ""