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Added the capability of running count covariates only on a given interval. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5717 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
carneiro 2011-04-29 21:30:14 +00:00
parent 34092fd32f
commit 2384e23274
2 changed files with 10 additions and 7 deletions
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11
scala/qscript/oneoffs/carneiro/dataProcessingV2.scala
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@ -9,6 +9,7 @@ import net.sf.samtools.{SAMFileReader,SAMReadGroupRecord}
import scala.io.Source._ import scala.io.Source._
import collection.JavaConversions._ import collection.JavaConversions._
import org.broadinstitute.sting.queue.function.scattergather.ScatterFunction
class dataProcessingV2 extends QScript { class dataProcessingV2 extends QScript {
@ -192,6 +193,8 @@ class dataProcessingV2 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
nContigs = getNumberOfContigs(perLaneAlignedBamFiles(0)) nContigs = getNumberOfContigs(perLaneAlignedBamFiles(0))
println("nContigs: " + nContigs)
// Final output list of processed bam files // Final output list of processed bam files
var cohortList: List[File] = List() var cohortList: List[File] = List()
@ -279,9 +282,9 @@ class dataProcessingV2 extends QScript {
this.rodBind :+= RodBind("dbsnp", "VCF", dbSNP) this.rodBind :+= RodBind("dbsnp", "VCF", dbSNP)
this.rodBind :+= RodBind("indels", "VCF", qscript.indels) this.rodBind :+= RodBind("indels", "VCF", qscript.indels)
this.useOnlyKnownIndels = knownsOnly this.useOnlyKnownIndels = knownsOnly
this.doNotUseSW = useSW this.doNotUseSW = !useSW
this.compress = 0 this.compress = 0
this.U = org.broadinstitute.sting.gatk.arguments.ValidationExclusion.TYPE.NO_READ_ORDER_VERIFICATION // todo -- update this with the last consensus between Tim, Matt and Eric. This is ugly! // this.U = org.broadinstitute.sting.gatk.arguments.ValidationExclusion.TYPE.NO_READ_ORDER_VERIFICATION // todo -- update this with the last consensus between Tim, Matt and Eric. This is ugly!
this.scatterCount = nContigs this.scatterCount = nContigs
this.analysisName = queueLogDir + outBam + ".clean" this.analysisName = queueLogDir + outBam + ".clean"
this.jobName = queueLogDir + outBam + ".clean" this.jobName = queueLogDir + outBam + ".clean"
@ -292,6 +295,8 @@ class dataProcessingV2 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 (!qscript.intervalString.isEmpty()) this.intervalsString ++= List(qscript.intervalString)
else if (qscript.intervals != null) this.intervals :+= qscript.intervals
this.scatterCount = nContigs this.scatterCount = nContigs
this.analysisName = queueLogDir + outRecalFile + ".covariates" this.analysisName = queueLogDir + outRecalFile + ".covariates"
this.jobName = queueLogDir + outRecalFile + ".covariates" this.jobName = queueLogDir + outRecalFile + ".covariates"
@ -304,7 +309,7 @@ class dataProcessingV2 extends QScript {
this.out = outBam this.out = outBam
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.U = org.broadinstitute.sting.gatk.arguments.ValidationExclusion.TYPE.NO_READ_ORDER_VERIFICATION // todo -- update this with the last consensus between Tim, Matt and Eric. This is ugly! // this.U = org.broadinstitute.sting.gatk.arguments.ValidationExclusion.TYPE.NO_READ_ORDER_VERIFICATION // todo -- update this with the last consensus between Tim, Matt and Eric. This is ugly!
// this.index_output_bam_on_the_fly = true // this.index_output_bam_on_the_fly = true
this.scatterCount = nContigs this.scatterCount = nContigs
this.isIntermediate = false this.isIntermediate = false

6
scala/qscript/oneoffs/carneiro/justClean.scala
View File

@ -35,7 +35,7 @@ class justClean extends QScript {
println(GATKjar) println(GATKjar)
val outBam = swapExt(input, ".bam", ".Qclean.bam") val outBam = swapExt(input, ".bam", ".clean.bam")
val tIntervals = swapExt(input, ".bam", ".all_indels.intervals") val tIntervals = swapExt(input, ".bam", ".all_indels.intervals")
val target = new RealignerTargetCreator() val target = new RealignerTargetCreator()
@ -60,11 +60,9 @@ class justClean extends QScript {
clean.rodBind :+= RodBind("dbsnp", "VCF", dbSNP) clean.rodBind :+= RodBind("dbsnp", "VCF", dbSNP)
clean.rodBind :+= RodBind("indels", "VCF", indels) clean.rodBind :+= RodBind("indels", "VCF", indels)
clean.doNotUseSW = false clean.doNotUseSW = false
clean.compress = 0
// clean.U = org.broadinstitute.sting.gatk.arguments.ValidationExclusion.TYPE.NO_READ_ORDER_VERIFICATION // todo -- update clean with the last consensus between Tim, Matt and Eric. This is ugly!
clean.jobName = queueLogDir + outBam + ".clean" clean.jobName = queueLogDir + outBam + ".clean"
clean.jarFile = GATKjar clean.jarFile = GATKjar
clean.memoryLimit = 6 clean.memoryLimit = 24
clean.scatterCount = 84 clean.scatterCount = 84
add(target, clean); add(target, clean);