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Updating to use new rod system syntax plus name change for CountRODs

This commit is contained in:
Eric Banks 2011-09-19 13:30:32 -04:00
parent 5e832254a4
commit ba150570f3
1 changed files with 3 additions and 3 deletions
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6
public/scala/qscript/org/broadinstitute/sting/queue/qscripts/GATKResourcesBundle.scala
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@ -300,9 +300,9 @@ class GATKResourcesBundle extends QScript {
bamFile = bamIn bamFile = bamIn
} }
class IndexVCF(@Input vcf: File, @Input ref: File) extends CountRod with UNIVERSAL_GATK_ARGS { class IndexVCF(@Input vcf: File, @Input ref: File) extends CountRODs with UNIVERSAL_GATK_ARGS {
//@Output val vcfIndex: File = swapExt(vcf.getParent, vcf, ".vcf", ".vcf.idx") //@Output val vcfIndex: File = swapExt(vcf.getParent, vcf, ".vcf", ".vcf.idx")
this.rodBind :+= RodBind(vcf.getName, "VCF", vcf) this.rod :+= vcf
this.reference_sequence = ref this.reference_sequence = ref
} }
@ -313,7 +313,7 @@ class GATKResourcesBundle extends QScript {
} }
class MakeDBSNP129(@Input dbsnp: File, @Input ref: File, @Output dbsnp129: File) extends SelectVariants with UNIVERSAL_GATK_ARGS { class MakeDBSNP129(@Input dbsnp: File, @Input ref: File, @Output dbsnp129: File) extends SelectVariants with UNIVERSAL_GATK_ARGS {
this.rodBind :+= RodBind("variant", "VCF", dbsnp) this.variant = dbsnp
this.select ++= List("\"dbSNPBuildID <= 129\"") this.select ++= List("\"dbSNPBuildID <= 129\"")
this.reference_sequence = ref this.reference_sequence = ref
this.out = dbsnp129 this.out = dbsnp129