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join all per-lane Bams before doing target realigning and indel cleaning. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5435 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
carneiro 2011-03-14 16:11:03 +00:00
parent 5406e779d2
commit 42f70d9e07
1 changed files with 14 additions and 5 deletions
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19
scala/qscript/oneoffs/carneiro/dataProcessing.scala
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@ -72,6 +72,7 @@ class dataProcessing extends QScript {
// BAM files generated by the pipeline // BAM files generated by the pipeline
val bamList: String = outDir + outName + ".list" val bamList: String = outDir + outName + ".list"
val joinedBams: String = outDir + outName + ".join.bam"
val cleanedBam: String = outDir + outName + ".clean.bam" val cleanedBam: String = outDir + outName + ".clean.bam"
val fixedBam: String = outDir + outName + ".processed.bam" val fixedBam: String = outDir + outName + ".processed.bam"
@ -119,8 +120,9 @@ class dataProcessing extends QScript {
add(new writeList(recalibratedBamList, bamList), add(new writeList(recalibratedBamList, bamList),
new allTargets(bamList, allTargetIntervals), new joinBams(bamList, joinedBams),
new clean(bamList, allTargetIntervals, cleanedBam, !knownsOnly, !intermediate)) new allTargets(joinedBams, allTargetIntervals),
new clean(joinedBams, allTargetIntervals, cleanedBam, !knownsOnly, !intermediate))
} }
class TargetBase (outIntervals: String) extends RealignerTargetCreator with CommandLineGATKArgs { class TargetBase (outIntervals: String) extends RealignerTargetCreator with CommandLineGATKArgs {
@ -137,6 +139,7 @@ class dataProcessing extends QScript {
class allTargets (inBams: String, outIntervals: String) extends TargetBase(outIntervals) { class allTargets (inBams: String, outIntervals: String) extends TargetBase(outIntervals) {
this.input_file :+= new File(inBams) this.input_file :+= new File(inBams)
this.memoryLimit = Some(6)
this.jobName = queueLogDir + outIntervals + ".atarget" this.jobName = queueLogDir + outIntervals + ".atarget"
} }
@ -199,8 +202,14 @@ class dataProcessing extends QScript {
} }
class writeList(inBams: List[File], outBamList: String) extends ListWriterFunction { class writeList(inBams: List[File], outBamList: String) extends ListWriterFunction {
this.inputFiles = inBams this.inputFiles = inBams
this.listFile = new File(outBamList) this.listFile = new File(outBamList)
this.jobName = queueLogDir + outBamList + ".bamList" this.jobName = queueLogDir + outBamList + ".bamList"
}
class joinBams(inBams: File, outBam: String) extends PrintReads {
this.input_file :+= inBams
this.out = new File(outBam)
this.jobName = queueLogDir + inBams + ".joinBams"
} }
} }