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Added memory limit parameter 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5855 348d0f76-0448-11de-a6fe-93d51630548a
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fromer 2011-05-23 21:11:44 +00:00
parent c7f4674fe2
commit bc4305c956
1 changed files with 4 additions and 0 deletions
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4
scala/qscript/oneoffs/fromer/ScatteredFullVariantAnnotator.scala
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@ -28,6 +28,8 @@ class ScatteredFullVariantAnnotator extends QScript {
@Output(doc = "annotated file to output", shortName = "o", required = true) @Output(doc = "annotated file to output", shortName = "o", required = true)
var outputAnnotated: File = _ var outputAnnotated: File = _
@Output(doc = "Memory limit", fullName = "memoryLimit", shortName = "m", required = false)
var memoryLimit = 3
def script = { def script = {
add(new ScatteredFullVariantAnnotator()) add(new ScatteredFullVariantAnnotator())
@ -38,6 +40,8 @@ class ScatteredFullVariantAnnotator extends QScript {
this.jarFile = qscript.gatkJarFile this.jarFile = qscript.gatkJarFile
this.reference_sequence = qscript.referenceFile this.reference_sequence = qscript.referenceFile
this.input_file = List(qscript.bams) this.input_file = List(qscript.bams)
this.memoryLimit = qscript.memoryLimit
this.logging_level = "INFO" this.logging_level = "INFO"
this.rodToIntervalTrackName = "variant" this.rodToIntervalTrackName = "variant"