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Allowing multiple dnsnp and indel files in the DPP

This commit is contained in:
Mauricio Carneiro 2011-09-02 13:38:35 -04:00
parent 8da36a965e
commit 28d782b4c7
1 changed files with 8 additions and 8 deletions
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16
public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala
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@ -11,7 +11,7 @@ import net.sf.samtools.SAMFileReader
import net.sf.samtools.SAMFileHeader.SortOrder 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.{CommandLineFunction, ListWriterFunction} import org.broadinstitute.sting.queue.function.ListWriterFunction
class DataProcessingPipeline extends QScript { class DataProcessingPipeline extends QScript {
qscript => qscript =>
@ -31,7 +31,7 @@ class DataProcessingPipeline extends QScript {
var reference: File = _ var reference: File = _
@Input(doc="dbsnp ROD to use (must be in VCF format)", fullName="dbsnp", shortName="D", required=true) @Input(doc="dbsnp ROD to use (must be in VCF format)", fullName="dbsnp", shortName="D", required=true)
var dbSNP: File = _ var dbSNP: List[File] = List()
/**************************************************************************** /****************************************************************************
* Optional Parameters * Optional Parameters
@ -43,7 +43,7 @@ class DataProcessingPipeline extends QScript {
// //
@Input(doc="extra VCF files to use as reference indels for Indel Realignment", fullName="extra_indels", shortName="indels", required=false) @Input(doc="extra VCF files to use as reference indels for Indel Realignment", fullName="extra_indels", shortName="indels", required=false)
var indels: File = _ var indels: List[File] = List()
@Input(doc="The path to the binary of bwa (usually BAM files have already been mapped - but if you want to remap this is the option)", fullName="path_to_bwa", shortName="bwa", required=false) @Input(doc="The path to the binary of bwa (usually BAM files have already been mapped - but if you want to remap this is the option)", fullName="path_to_bwa", shortName="bwa", required=false)
var bwaPath: File = _ var bwaPath: File = _
@ -321,9 +321,9 @@ class DataProcessingPipeline extends QScript {
this.input_file = inBams this.input_file = inBams
this.out = outIntervals this.out = outIntervals
this.mismatchFraction = 0.0 this.mismatchFraction = 0.0
this.known :+= qscript.dbSNP this.known ++= qscript.dbSNP
if (indels != null) if (indels != null)
this.known :+= qscript.indels this.known ++= qscript.indels
this.scatterCount = nContigs this.scatterCount = nContigs
this.analysisName = queueLogDir + outIntervals + ".target" this.analysisName = queueLogDir + outIntervals + ".target"
this.jobName = queueLogDir + outIntervals + ".target" this.jobName = queueLogDir + outIntervals + ".target"
@ -333,9 +333,9 @@ class DataProcessingPipeline extends QScript {
this.input_file = inBams this.input_file = inBams
this.targetIntervals = tIntervals this.targetIntervals = tIntervals
this.out = outBam this.out = outBam
this.known :+= qscript.dbSNP this.known ++= qscript.dbSNP
if (qscript.indels != null) if (qscript.indels != null)
this.known :+= qscript.indels this.known ++= qscript.indels
this.consensusDeterminationModel = cleanModelEnum this.consensusDeterminationModel = cleanModelEnum
this.compress = 0 this.compress = 0
this.scatterCount = nContigs this.scatterCount = nContigs
@ -344,7 +344,7 @@ class DataProcessingPipeline extends QScript {
} }
case class cov (inBam: File, outRecalFile: File) extends CountCovariates with CommandLineGATKArgs { case class cov (inBam: File, outRecalFile: File) extends CountCovariates with CommandLineGATKArgs {
this.knownSites :+= qscript.dbSNP this.knownSites ++= qscript.dbSNP
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