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Right. The issue was not setting the scatter/gather classes appropriately. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5501 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
chartl 2011-03-23 20:08:53 +00:00
parent 3c1bf40a45
commit cd90fdeca1
1 changed files with 17 additions and 2 deletions
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19
scala/qscript/oneoffs/chartl/ScatterGatherAssociation.q
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@ -1,5 +1,5 @@
import org.broadinstitute.sting.commandline.{Argument, Output, Input} import org.broadinstitute.sting.commandline.{Argument, Output, Input}
import org.broadinstitute.sting.queue.extensions.gatk.CommandLineGATK import org.broadinstitute.sting.queue.extensions.gatk.{IntervalScatterFunction, CommandLineGATK}
import org.broadinstitute.sting.queue.QScript import org.broadinstitute.sting.queue.QScript
import org.broadinstitute.sting.utils.text.XReadLines import org.broadinstitute.sting.utils.text.XReadLines
import collection.JavaConversions._ import collection.JavaConversions._
@ -36,35 +36,49 @@ class ScatterGatherAssociation extends QScript {
// the rest are output files implicitly constructed by the multiplexer // the rest are output files implicitly constructed by the multiplexer
@Output(doc="bqs") @Output(doc="bqs")
@Gather(classOf[SimpleTextGatherFunction])
var bqs : File = new File(String.format("%s.%s.%s", base, "BaseQualityScore", ext)) var bqs : File = new File(String.format("%s.%s.%s", base, "BaseQualityScore", ext))
@Output(doc="isd") @Output(doc="isd")
@Gather(classOf[SimpleTextGatherFunction])
var isd : File = new File(String.format("%s.%s.%s",base,"InsertSizeDistribution",ext)) var isd : File = new File(String.format("%s.%s.%s",base,"InsertSizeDistribution",ext))
@Output(doc="mq0") @Output(doc="mq0")
@Gather(classOf[SimpleTextGatherFunction])
var mq0 : File = new File(String.format("%s.%s.%s",base,"MappingQuality0",ext)) var mq0 : File = new File(String.format("%s.%s.%s",base,"MappingQuality0",ext))
@Output(doc="mmq") @Output(doc="mmq")
@Gather(classOf[SimpleTextGatherFunction])
var mmq : File = new File(String.format("%s.%s.%s",base,"MateMappingQuality",ext)) var mmq : File = new File(String.format("%s.%s.%s",base,"MateMappingQuality",ext))
@Output(doc="moc") @Output(doc="moc")
@Gather(classOf[SimpleTextGatherFunction])
var moc : File = new File(String.format("%s.%s.%s",base,"MateOtherContig",ext)) var moc : File = new File(String.format("%s.%s.%s",base,"MateOtherContig",ext))
@Output(doc="mss") @Output(doc="mss")
@Gather(classOf[SimpleTextGatherFunction])
var mss : File = new File(String.format("%s.%s.%s",base,"MateSameStrand",ext)) var mss : File = new File(String.format("%s.%s.%s",base,"MateSameStrand",ext))
@Output(doc="mu") @Output(doc="mu")
@Gather(classOf[SimpleTextGatherFunction])
var mu : File = new File(String.format("%s.%s.%s",base,"MateUnmapped",ext)) var mu : File = new File(String.format("%s.%s.%s",base,"MateUnmapped",ext))
@Output(doc="mmr") @Output(doc="mmr")
@Gather(classOf[SimpleTextGatherFunction])
var mmr : File = new File(String.format("%s.%s.%s",base,"MismatchRate",ext)) var mmr : File = new File(String.format("%s.%s.%s",base,"MismatchRate",ext))
@Output(doc="pp") @Output(doc="pp")
@Gather(classOf[SimpleTextGatherFunction])
var pp : File = new File(String.format("%s.%s.%s",base,"ProperPairs",ext)) var pp : File = new File(String.format("%s.%s.%s",base,"ProperPairs",ext))
@Output(doc="rc") @Output(doc="rc")
@Gather(classOf[SimpleTextGatherFunction])
var rc : File = new File(String.format("%s.%s.%s",base,"ReadClipping",ext)) var rc : File = new File(String.format("%s.%s.%s",base,"ReadClipping",ext))
@Output(doc="ri") @Output(doc="ri")
@Gather(classOf[SimpleTextGatherFunction])
var ri : File = new File(String.format("%s.%s.%s",base,"ReadIndels",ext)) var ri : File = new File(String.format("%s.%s.%s",base,"ReadIndels",ext))
@Output(doc="rmq") @Output(doc="rmq")
@Gather(classOf[SimpleTextGatherFunction])
var rmq : File = new File(String.format("%s.%s.%s",base,"ReadMappingQuality",ext)) var rmq : File = new File(String.format("%s.%s.%s",base,"ReadMappingQuality",ext))
@Output(doc="rm") @Output(doc="rm")
@Gather(classOf[SimpleTextGatherFunction])
var rm : File = new File(String.format("%s.%s.%s",base,"ReferenceMismatches",ext)) var rm : File = new File(String.format("%s.%s.%s",base,"ReferenceMismatches",ext))
@Output(doc="sd") @Output(doc="sd")
@Gather(classOf[SimpleTextGatherFunction])
var sd : File = new File(String.format("%s.%s.%s",base,"SampleDepth",ext)) var sd : File = new File(String.format("%s.%s.%s",base,"SampleDepth",ext))
override def commandLine = super.commandLine + " -o %s".format(base) override def commandLine = super.commandLine + " -AT ALL -o %s".format(base)
} }
def script = { def script = {
@ -83,6 +97,7 @@ class ScatterGatherAssociation extends QScript {
association.input_file ++= asScalaIterable((new XReadLines(bamList)).readLines).map(u => new File(u)).toList association.input_file ++= asScalaIterable((new XReadLines(bamList)).readLines).map(u => new File(u)).toList
association.scatterCount = scatterJobs association.scatterCount = scatterJobs
association.memoryLimit = Some(memLimit) association.memoryLimit = Some(memLimit)
association.scatterClass = classOf[IntervalScatterFunction]
add(association) add(association)
} }