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Re-enabling indel cleaning, explicitly calling fix mates in the case where indel cleaning is not scatter/gathered 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4324 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
chartl 2010-09-21 20:37:49 +00:00
parent 522830fb01
commit 6dec042288
1 changed files with 51 additions and 9 deletions
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60
scala/qscript/fullCallingPipeline.q
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@ -1,8 +1,9 @@
import org.broadinstitute.sting.gatk.DownsampleType
import org.broadinstitute.sting.gatk.walkers.genotyper.GenotypeCalculationModel.Model
import org.broadinstitute.sting.queue.extensions.gatk._
import org.broadinstitute.sting.queue.extensions.picard.PicardBamJarFunction
import org.broadinstitute.sting.queue.extensions.samtools._
import org.broadinstitute.sting.queue.QScript
import org.broadinstitute.sting.queue.{QException, QScript}
class fullCallingPipeline extends QScript {
qscript =>
@ -102,26 +103,67 @@ class fullCallingPipeline extends QScript {
realigner.intervals = qscript.contigIntervals
realigner.targetIntervals = new java.io.File(targetCreator.out.getAbsolutePath)
realigner.scatterCount = qscript.numContigs
realigner.out = cleaned_bam
realigner.scatterClass = classOf[ContigScatterFunction]
realigner.setupGatherFunction = { case (f: BamGatherFunction, _) => f.jarFile = qscript.picardFixMatesJar }
realigner.jobQueue = "week"
// may need to explicitly run fix mates
var fixMates = new PicardBamJarFunction {
// Declare inputs/outputs for dependency tracking.
@Input(doc="unfixed bam") var unfixed: File = _
@Output(doc="fixed bam") var fixed: File = _
def inputBams = List(unfixed)
def outputBam = fixed
}
// realigner.out = cleaned_bam
// realigner.scatterClass = classOf[ContigScatterFunction]
// realigner.setupGatherFunction = { case (f: BamGatherFunction, _) => f.jarFile = qscript.picardFixMatesJar }
// realigner.jobQueue = "week"
// if scatter count is > 1, do standard scatter gather, if not, explicitly set up fix mates
if (realigner.scatterCount > 1) {
realigner.out = cleaned_bam
// While gathering run fix mates.
realigner.scatterClass = classOf[ContigScatterFunction]
realigner.setupGatherFunction = {
case (gather: BamGatherFunction, _) =>
gather.memoryLimit = Some(4)
gather.jarFile = qscript.picardFixMatesJar
// Don't pass this AS=true to fix mates!
gather.assumeSorted = None
case (gather: SimpleTextGatherFunction, _) =>
throw new QException("Cannot text-gather a realignment job")
}
} else {
realigner.out = swapExt(bam,"bam","unfixed.cleaned.bam")
// Explicitly run fix mates if the function won't be scattered.
fixMates.memoryLimit = Some(4)
fixMates.jarFile = qscript.picardFixMatesJar
fixMates.unfixed = realigner.out
fixMates.fixed = cleaned_bam
// Add the fix mates explicitly
}
var samtoolsindex = new SamtoolsIndexFunction
samtoolsindex.bamFile = cleaned_bam
// put clean bams in clean genotypers
cleanBamFiles :+= realigner.out
cleanBamFiles :+= cleaned_bam
// COMMENT THIS NEXT LINE TO SKIP CLEANING
//add(targetCreator,realigner,samtoolsindex)
// COMMENT THIS NEXT BLOCK TO SKIP CLEANING
if ( realigner.scatterCount > 1 )
add(targetCreator,realigner,samtoolsindex)
else
add(targetCreator,realigner,fixMates,samtoolsindex)
}
// actually make calls
endToEnd(uncleanedBase,qscript.bamFiles)
// COMMENT THIS NEXT LINE TO AVOID CALLING ON CLEANED FILES
//endToEnd(cleanedBase,cleanBamFiles)
endToEnd(cleanedBase,cleanBamFiles)
}
def endToEnd(base: String, bamFiles: List[File]) = {