From 17d627b86d96ab244c262ad09f9e965129fc2436 Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Tue, 17 Jul 2012 13:15:32 -0400 Subject: [PATCH] Update the DPP and PBPP to use the BQSRv2 walkers --- .../qscripts/DataProcessingPipeline.scala | 25 ++++++------------- .../qscripts/PacbioProcessingPipeline.scala | 25 ++++++------------- 2 files changed, 16 insertions(+), 34 deletions(-) diff --git a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala index 677d973f5..b6560876b 100755 --- a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala +++ b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala @@ -258,8 +258,8 @@ class DataProcessingPipeline extends QScript { // Accessory files val targetIntervals = if (cleaningModel == ConsensusDeterminationModel.KNOWNS_ONLY) {globalIntervals} else {swapExt(bam, ".bam", ".intervals")} val metricsFile = swapExt(bam, ".bam", ".metrics") - val preRecalFile = swapExt(bam, ".bam", ".pre_recal.csv") - val postRecalFile = swapExt(bam, ".bam", ".post_recal.csv") + val preRecalFile = swapExt(bam, ".bam", ".pre_recal.table") + val postRecalFile = swapExt(bam, ".bam", ".post_recal.table") val preOutPath = swapExt(bam, ".bam", ".pre") val postOutPath = swapExt(bam, ".bam", ".post") val preValidateLog = swapExt(bam, ".bam", ".pre.validation") @@ -281,9 +281,7 @@ class DataProcessingPipeline extends QScript { dedup(cleanedBam, dedupedBam, metricsFile), cov(dedupedBam, preRecalFile), recal(dedupedBam, preRecalFile, recalBam), - cov(recalBam, postRecalFile), - analyzeCovariates(preRecalFile, preOutPath), - analyzeCovariates(postRecalFile, postOutPath)) + cov(recalBam, postRecalFile)) cohortList :+= recalBam @@ -345,11 +343,11 @@ class DataProcessingPipeline extends QScript { this.jobName = queueLogDir + outBam + ".clean" } - case class cov (inBam: File, outRecalFile: File) extends CountCovariates with CommandLineGATKArgs { + case class cov (inBam: File, outRecalFile: File) extends BaseQualityScoreRecalibrator with CommandLineGATKArgs { this.knownSites ++= qscript.dbSNP this.covariate ++= Seq("ReadGroupCovariate", "QualityScoreCovariate", "CycleCovariate", "DinucCovariate") this.input_file :+= inBam - this.recal_file = outRecalFile + this.out = outRecalFile if (!defaultPlatform.isEmpty) this.default_platform = defaultPlatform if (!qscript.intervalString.isEmpty) this.intervalsString ++= Seq(qscript.intervalString) else if (qscript.intervals != null) this.intervals :+= qscript.intervals @@ -358,14 +356,14 @@ class DataProcessingPipeline extends QScript { this.jobName = queueLogDir + outRecalFile + ".covariates" } - case class recal (inBam: File, inRecalFile: File, outBam: File) extends TableRecalibration with CommandLineGATKArgs { + case class recal (inBam: File, inRecalFile: File, outBam: File) extends PrintReads with CommandLineGATKArgs { this.input_file :+= inBam - this.recal_file = inRecalFile + this.BQSR = inRecalFile + this.disable_indel_quals = true this.baq = CalculationMode.CALCULATE_AS_NECESSARY this.out = outBam if (!qscript.intervalString.isEmpty) this.intervalsString ++= Seq(qscript.intervalString) else if (qscript.intervals != null) this.intervals :+= qscript.intervals - this.no_pg_tag = qscript.testMode this.scatterCount = nContigs this.isIntermediate = false this.analysisName = queueLogDir + outBam + ".recalibration" @@ -379,13 +377,6 @@ class DataProcessingPipeline extends QScript { ****************************************************************************/ - case class analyzeCovariates (inRecalFile: File, outPath: File) extends AnalyzeCovariates { - this.recal_file = inRecalFile - this.output_dir = outPath.toString - this.analysisName = queueLogDir + inRecalFile + ".analyze_covariates" - this.jobName = queueLogDir + inRecalFile + ".analyze_covariates" - } - case class dedup (inBam: File, outBam: File, metricsFile: File) extends MarkDuplicates with ExternalCommonArgs { this.input :+= inBam this.output = outBam diff --git a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/PacbioProcessingPipeline.scala b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/PacbioProcessingPipeline.scala index 46587c5b6..f3894c5cc 100755 --- a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/PacbioProcessingPipeline.scala +++ b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/PacbioProcessingPipeline.scala @@ -80,8 +80,8 @@ class PacbioProcessingPipeline extends QScript { // BAM Steps val mqBAM: File = swapExt(bamBase, ".bam", ".mq.bam") - val recalFile1: File = swapExt(bamBase, ".bam", ".recal1.csv") - val recalFile2: File = swapExt(bamBase, ".bam", ".recal2.csv") + val recalFile1: File = swapExt(bamBase, ".bam", ".recal1.table") + val recalFile2: File = swapExt(bamBase, ".bam", ".recal2.table") val recalBam: File = swapExt(bamBase, ".bam", ".recal.bam") val path1: String = recalBam + ".before" val path2: String = recalBam + ".after" @@ -102,9 +102,7 @@ class PacbioProcessingPipeline extends QScript { add(cov(bam, recalFile1, resetQuals), recal(bam, recalFile1, recalBam), - cov(recalBam, recalFile2, false), - analyzeCovariates(recalFile1, path1), - analyzeCovariates(recalFile2, path2)) + cov(recalBam, recalFile2, false)) } } @@ -162,36 +160,29 @@ class PacbioProcessingPipeline extends QScript { this.jobName = queueLogDir + outBam + ".rg" } - case class cov (inBam: File, outRecalFile: File, resetQuals: Boolean) extends CountCovariates with CommandLineGATKArgs { + case class cov (inBam: File, outRecalFile: File, resetQuals: Boolean) extends BaseQualityScoreRecalibrator with CommandLineGATKArgs { if (resetQuals) this.DBQ = dbq this.knownSites :+= dbSNP this.covariate ++= List("ReadGroupCovariate", "QualityScoreCovariate", "CycleCovariate", "DinucCovariate") this.input_file :+= inBam - this.recal_file = outRecalFile + this.out = outRecalFile this.analysisName = queueLogDir + outRecalFile + ".covariates" this.jobName = queueLogDir + outRecalFile + ".covariates" this.scatterCount = threads this.read_filter :+= "BadCigar" } - case class recal (inBam: File, inRecalFile: File, outBam: File) extends TableRecalibration with CommandLineGATKArgs { + case class recal (inBam: File, inRecalFile: File, outBam: File) extends PrintReads with CommandLineGATKArgs { this.DBQ = dbq this.input_file :+= inBam - this.recal_file = inRecalFile + this.BQSR = inRecalFile this.out = outBam - this.no_pg_tag = testMode + this.disable_indel_quals = true this.isIntermediate = false this.analysisName = queueLogDir + outBam + ".recalibration" this.jobName = queueLogDir + outBam + ".recalibration" this.read_filter :+= "BadCigar" this.scatterCount = threads } - - case class analyzeCovariates (inRecalFile: File, outPath: String) extends AnalyzeCovariates { - this.recal_file = inRecalFile - this.output_dir = outPath - this.analysisName = queueLogDir + inRecalFile + ".analyze_covariates" - this.jobName = queueLogDir + inRecalFile + ".analyze_covariates" - } }