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Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable

This commit is contained in:
Eric Banks 2011-08-04 12:49:02 -04:00
parent e48492f3c3 0739b7f75b
commit 406982284c
1 changed files with 13 additions and 14 deletions
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27
public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala
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@ -2,7 +2,6 @@ package org.broadinstitute.sting.queue.qscripts
import org.broadinstitute.sting.queue.extensions.gatk._
import org.broadinstitute.sting.queue.QScript
import org.broadinstitute.sting.queue.function.ListWriterFunction
import org.broadinstitute.sting.queue.extensions.picard._
import org.broadinstitute.sting.gatk.walkers.indels.IndelRealigner.ConsensusDeterminationModel
import org.broadinstitute.sting.utils.baq.BAQ.CalculationMode
@ -12,6 +11,7 @@ import net.sf.samtools.SAMFileReader
import net.sf.samtools.SAMFileHeader.SortOrder
import org.broadinstitute.sting.queue.util.QScriptUtils
import org.broadinstitute.sting.queue.function.{CommandLineFunction, ListWriterFunction}
class DataProcessingPipeline extends QScript {
qscript =>
@ -283,12 +283,6 @@ class DataProcessingPipeline extends QScript {
****************************************************************************/
// General arguments to GATK walkers
trait CommandLineGATKArgs extends CommandLineGATK {
this.reference_sequence = qscript.reference
this.memoryLimit = 4
this.isIntermediate = true
}
// General arguments to non-GATK tools
trait ExternalCommonArgs extends CommandLineFunction {
@ -296,6 +290,14 @@ class DataProcessingPipeline extends QScript {
this.isIntermediate = true
}
// General arguments to GATK walkers
trait CommandLineGATKArgs extends CommandLineGATK with ExternalCommonArgs {
this.reference_sequence = qscript.reference
}
trait SAMargs extends PicardBamFunction with ExternalCommonArgs {
this.maxRecordsInRam = 100000
}
case class target (inBams: File, outIntervals: File) extends RealignerTargetCreator with CommandLineGATKArgs {
if (cleaningModel != ConsensusDeterminationModel.KNOWNS_ONLY)
@ -303,7 +305,7 @@ class DataProcessingPipeline extends QScript {
this.out = outIntervals
this.mismatchFraction = 0.0
this.rodBind :+= RodBind("dbsnp", "VCF", dbSNP)
if (!indels.isEmpty)
if (indels != null)
this.rodBind :+= RodBind("indels", "VCF", indels)
this.scatterCount = nContigs
this.analysisName = queueLogDir + outIntervals + ".target"
@ -315,7 +317,7 @@ class DataProcessingPipeline extends QScript {
this.targetIntervals = tIntervals
this.out = outBam
this.rodBind :+= RodBind("dbsnp", "VCF", dbSNP)
if (!qscript.indels.isEmpty)
if (qscript.indels != null)
this.rodBind :+= RodBind("indels", "VCF", qscript.indels)
this.consensusDeterminationModel = consensusDeterminationModel
this.compress = 0
@ -393,7 +395,6 @@ class DataProcessingPipeline extends QScript {
case class validate (inBam: File, outLog: File) extends ValidateSamFile with ExternalCommonArgs {
this.input = List(inBam)
this.output = outLog
this.maxRecordsInRam = 100000
this.REFERENCE_SEQUENCE = qscript.reference
this.isIntermediate = false
this.analysisName = queueLogDir + outLog + ".validate"
@ -412,8 +413,6 @@ class DataProcessingPipeline extends QScript {
this.RGPL = readGroup.pl
this.RGPU = readGroup.pu
this.RGSM = readGroup.sm
this.memoryLimit = 4
this.isIntermediate = true
this.analysisName = queueLogDir + outBam + ".rg"
this.jobName = queueLogDir + outBam + ".rg"
}
@ -439,6 +438,7 @@ class DataProcessingPipeline extends QScript {
@Input(doc="bwa alignment index file") var sai = inSai
@Output(doc="output aligned bam file") var alignedBam = outBam
def commandLine = bwaPath + " samse " + reference + " " + sai + " " + bam + " > " + alignedBam
this.memoryLimit = 6
this.analysisName = queueLogDir + outBam + ".bwa_sam_se"
this.jobName = queueLogDir + outBam + ".bwa_sam_se"
}
@ -449,6 +449,7 @@ class DataProcessingPipeline extends QScript {
@Input(doc="bwa alignment index file for 2nd mating pair") var sai2 = inSai2
@Output(doc="output aligned bam file") var alignedBam = outBam
def commandLine = bwaPath + " sampe " + reference + " " + sai1 + " " + sai2 + " " + bam + " " + bam + " > " + alignedBam
this.memoryLimit = 6
this.analysisName = queueLogDir + outBam + ".bwa_sam_pe"
this.jobName = queueLogDir + outBam + ".bwa_sam_pe"
}
@ -459,6 +460,4 @@ class DataProcessingPipeline extends QScript {
this.analysisName = queueLogDir + outBamList + ".bamList"
this.jobName = queueLogDir + outBamList + ".bamList"
}
}