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Adapting to the new RodBinding framework

This commit is contained in:
Mauricio Carneiro 2011-08-23 15:38:19 -04:00
parent 1ecbf05aae
commit 219252a566
1 changed files with 1 additions and 1 deletions
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2
public/scala/qscript/org/broadinstitute/sting/queue/qscripts/PacbioProcessingPipeline.scala
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@ -145,7 +145,7 @@ class RecalibrateBaseQualities extends QScript {
} }
case class cov (inBam: File, outRecalFile: File) extends CountCovariates with CommandLineGATKArgs { case class cov (inBam: File, outRecalFile: File) extends CountCovariates with CommandLineGATKArgs {
this.rodBind :+= RodBind("dbsnp", "VCF", dbSNP) this.knownSites :+= dbSNP
this.covariate ++= List("ReadGroupCovariate", "QualityScoreCovariate", "CycleCovariate", "DinucCovariate") this.covariate ++= List("ReadGroupCovariate", "QualityScoreCovariate", "CycleCovariate", "DinucCovariate")
this.input_file :+= inBam this.input_file :+= inBam
this.recal_file = outRecalFile this.recal_file = outRecalFile