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Adding hidden options to the DPP 

controlling the default platform parameter to Count Covariates and the number of scatter gather jobs to generate are now available under hidden parameters
This commit is contained in:
Mauricio Carneiro 2011-10-11 13:56:00 -04:00
parent 0429b38021
commit 66b5646f95
1 changed files with 17 additions and 2 deletions
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19
public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala
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@ -12,6 +12,7 @@ import net.sf.samtools.SAMFileHeader.SortOrder
import org.broadinstitute.sting.queue.util.QScriptUtils import org.broadinstitute.sting.queue.util.QScriptUtils
import org.broadinstitute.sting.queue.function.ListWriterFunction import org.broadinstitute.sting.queue.function.ListWriterFunction
import org.broadinstitute.sting.commandline.Hidden
class DataProcessingPipeline extends QScript { class DataProcessingPipeline extends QScript {
qscript => qscript =>
@ -71,12 +72,24 @@ class DataProcessingPipeline extends QScript {
var noValidation: Boolean = false var noValidation: Boolean = false
/****************************************************************************
* Hidden Parameters
****************************************************************************/
@Hidden
@Input(doc="How many ways to scatter/gather", fullName="scatter_gather", shortName="sg", required=false)
var nContigs: Int = -1
@Hidden
@Input(doc="Define the default platform for Count Covariates -- useful for techdev purposes only.", fullName="default_platform", shortName="dp", required=false)
var defaultPlatform: String = _
/**************************************************************************** /****************************************************************************
* Global Variables * Global Variables
****************************************************************************/ ****************************************************************************/
val queueLogDir: String = ".qlog/" // Gracefully hide Queue's output val queueLogDir: String = ".qlog/" // Gracefully hide Queue's output
var nContigs: Int = 0 // Use the number of contigs for scatter gathering jobs
var cleanModelEnum: ConsensusDeterminationModel = ConsensusDeterminationModel.USE_READS var cleanModelEnum: ConsensusDeterminationModel = ConsensusDeterminationModel.USE_READS
@ -210,7 +223,8 @@ class DataProcessingPipeline extends QScript {
// keep a record of the number of contigs in the first bam file in the list // keep a record of the number of contigs in the first bam file in the list
val bams = QScriptUtils.createListFromFile(input) val bams = QScriptUtils.createListFromFile(input)
nContigs = QScriptUtils.getNumberOfContigs(bams(0)) if (nContigs < 0)
nContigs = QScriptUtils.getNumberOfContigs(bams(0))
val realignedBAMs = if (useBWApe || useBWAse) {performAlignment(bams)} else {revertBams(bams)} val realignedBAMs = if (useBWApe || useBWAse) {performAlignment(bams)} else {revertBams(bams)}
@ -325,6 +339,7 @@ class DataProcessingPipeline extends QScript {
this.covariate ++= List("ReadGroupCovariate", "QualityScoreCovariate", "CycleCovariate", "DinucCovariate") this.covariate ++= List("ReadGroupCovariate", "QualityScoreCovariate", "CycleCovariate", "DinucCovariate")
this.input_file :+= inBam this.input_file :+= inBam
this.recal_file = outRecalFile this.recal_file = outRecalFile
if (!defaultPlatform.isEmpty) this.default_platform = defaultPlatform
if (!qscript.intervalString.isEmpty()) this.intervalsString ++= List(qscript.intervalString) if (!qscript.intervalString.isEmpty()) this.intervalsString ++= List(qscript.intervalString)
else if (qscript.intervals != null) this.intervals :+= qscript.intervals else if (qscript.intervals != null) this.intervals :+= qscript.intervals
this.scatterCount = nContigs this.scatterCount = nContigs