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Be smarter if the beagle output is set such that getParent() returns null. Up the memory limit. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4389 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
chartl 2010-09-30 12:48:47 +00:00
parent 0142047da9
commit f34b4c6b82
1 changed files with 10 additions and 5 deletions
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15
scala/qscript/chartl/RefineGenotypesAndMerge.q
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@ -36,11 +36,16 @@ class BeagleGenotypeRefinement extends QScript {
@Output(doc="The beagle phased file") var beaglePhasedFile: File = _
@Output(doc="The beagle likelihood file") var beagleLikelihoods: File = _
@Output(doc="The beagle r2 file") var beagleRSquared: File = _
var beagleOutputDir: String = _
def freezeOutputs = {
val beagleOutputDir = beagleInput.getParent
beaglePhasedFile = new File(beagleOutputDir+beagleOutputBase+"."+beagleInput.getName+".phased")
beagleLikelihoods = new File(beagleOutputDir+beagleOutputBase+"."+beagleInput.getName+".gprobs")
if ( beagleInput.getParent == null ) {
beagleOutputDir = ""
} else {
beagleOutputDir = beagleInput.getParent
}
beaglePhasedFile = new File(beagleOutputDir+beagleOutputBase+"."+beagleInput.getName+".phased.gz")
beagleLikelihoods = new File(beagleOutputDir+beagleOutputBase+"."+beagleInput.getName+".gprobs.gz")
beagleRSquared = new File(beagleOutputDir+beagleOutputBase+"."+beagleInput.getName+".r2")
}
@ -57,8 +62,8 @@ class BeagleGenotypeRefinement extends QScript {
var refine = new BeagleRefinement
refine.beagleInput = beagleInput.out
refine.beagleOutputBase = beagleBase
refine.beagleMemoryGigs = 4
refine.memoryLimit = Some(4)
refine.beagleMemoryGigs = 6
refine.memoryLimit = Some(6)
refine.freezeOutputs
var vcfConvert = new BeagleOutputToVCF with GATKArgs