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Consensus mode and new RodBinding framework. 

The DPP was not using the parameter correctly. It didn't matter for the default option (which is the only one we have been testing) but it would not work for knowns only or smith waterman. It is fixed now.

It now complies with the new rod binding framework.
This commit is contained in:
Mauricio Carneiro 2011-08-22 14:05:13 -04:00
parent 85c5a6f890
commit caebc88e9a
1 changed files with 19 additions and 13 deletions
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32
public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala
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@ -84,12 +84,6 @@ class DataProcessingPipeline extends QScript {
var nContigs: Int = 0 // Use the number of contigs for scatter gathering jobs
var cleanModelEnum: ConsensusDeterminationModel = ConsensusDeterminationModel.USE_READS
if (cleaningModel == "KNOWNS_ONLY") {
cleanModelEnum = ConsensusDeterminationModel.KNOWNS_ONLY
}
else if (cleaningModel == "USE_SW") {
cleanModelEnum = ConsensusDeterminationModel.USE_SW
}
@ -200,6 +194,15 @@ class DataProcessingPipeline extends QScript {
return realignedBams
}
def getIndelCleaningModel(): ConsensusDeterminationModel = {
if (cleaningModel == "KNOWNS_ONLY")
ConsensusDeterminationModel.KNOWNS_ONLY
else if (cleaningModel == "USE_SW")
ConsensusDeterminationModel.USE_SW
else
ConsensusDeterminationModel.USE_READS
}
/****************************************************************************
* Main script
@ -208,6 +211,8 @@ class DataProcessingPipeline extends QScript {
def script = {
cleanModelEnum = getIndelCleaningModel()
// keep a record of the number of contigs in the first bam file in the list
val bams = QScriptUtils.createListFromFile(input)
nContigs = QScriptUtils.getNumberOfContigs(bams(0))
@ -300,13 +305,13 @@ class DataProcessingPipeline extends QScript {
}
case class target (inBams: File, outIntervals: File) extends RealignerTargetCreator with CommandLineGATKArgs {
if (cleaningModel != ConsensusDeterminationModel.KNOWNS_ONLY)
if (cleanModelEnum != ConsensusDeterminationModel.KNOWNS_ONLY)
this.input_file :+= inBams
this.out = outIntervals
this.mismatchFraction = 0.0
this.rodBind :+= RodBind("dbsnp", "VCF", dbSNP)
this.known :+= qscript.dbSNP
if (indels != null)
this.rodBind :+= RodBind("indels", "VCF", indels)
this.known :+= qscript.indels
this.scatterCount = nContigs
this.analysisName = queueLogDir + outIntervals + ".target"
this.jobName = queueLogDir + outIntervals + ".target"
@ -317,10 +322,10 @@ class DataProcessingPipeline extends QScript {
this.input_file :+= inBams
this.targetIntervals = tIntervals
this.out = outBam
this.rodBind :+= RodBind("dbsnp", "VCF", dbSNP)
this.known :+= qscript.dbSNP
if (qscript.indels != null)
this.rodBind :+= RodBind("indels", "VCF", qscript.indels)
this.consensusDeterminationModel = consensusDeterminationModel
this.known :+= qscript.indels
this.consensusDeterminationModel = cleanModelEnum
this.compress = 0
this.scatterCount = nContigs
this.analysisName = queueLogDir + outBam + ".clean"
@ -328,7 +333,7 @@ class DataProcessingPipeline extends QScript {
}
case class cov (inBam: File, outRecalFile: File) extends CountCovariates with CommandLineGATKArgs {
this.rodBind :+= RodBind("dbsnp", "VCF", dbSNP)
this.knownSites :+= qscript.dbSNP
this.covariate ++= List("ReadGroupCovariate", "QualityScoreCovariate", "CycleCovariate", "DinucCovariate")
this.input_file :+= inBam
this.recal_file = outRecalFile
@ -372,6 +377,7 @@ class DataProcessingPipeline extends QScript {
this.input = List(inBam)
this.output = outBam
this.metrics = metricsFile
this.memoryLimit = 16
this.analysisName = queueLogDir + outBam + ".dedup"
this.jobName = queueLogDir + outBam + ".dedup"
}