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No more default callsets, they're now mandatory arguments. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5858 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
carneiro 2011-05-23 21:56:43 +00:00
parent 133712faec
commit 2efd807952
1 changed files with 5 additions and 5 deletions
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10
scala/qscript/oneoffs/carneiro/mendelianViolation.scala
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@ -1,6 +1,6 @@
import java.io.File
import org.broadinstitute.sting.commandline.Argument
import org.broadinstitute.sting.queue.extensions.gatk.{SelectVariants, RodBind}
import org.broadinstitute.sting.queue.extensions.gatk.{SelectVariants, RodBind, VariantsToTable}
import org.broadinstitute.sting.queue.QScript
/*
@ -13,11 +13,11 @@ import org.broadinstitute.sting.queue.QScript
class mendelianViolation extends QScript
{
@Argument(shortName="trio", doc="input trio VCF file", required=false)
var trio: File = new File("/home/radon00/carneiro/prj/trio/analysis/calls/CEUTrio.WEx.recalibrated.vcf")
@Argument(shortName="trio", doc="input trio VCF file", required=true)
var trio: File = _
@Argument(shortName="daughter", doc="daughter input VCF file", required=false)
var daughter: File = "/humgen/gsa-hpprojects/dev/rpoplin/perfectCalls/NA12878/chart/sting/NA12878.HiSeq19.recalibrated.hapmapCut.vcf"
@Argument(shortName="daughter", doc="daughter input VCF file", required=true)
var daughter: File = _
@Argument(shortName="family", doc="family string", required=false)
var family: String = "NA12891+NA12892=NA12878"