Adapting to the new RodBinding framework

2011-08-23 15:38:19 -04:00 · 2011-08-23 15:38:19 -04:00 · 219252a566
parent 1ecbf05aae
commit 219252a566
1 changed files with 1 additions and 1 deletions
--- a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/PacbioProcessingPipeline.scala
+++ b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/PacbioProcessingPipeline.scala
@ -145,7 +145,7 @@ class RecalibrateBaseQualities extends QScript {
  }

  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.input_file :+= inBam
    this.recal_file = outRecalFile