From 219252a5661d7f00bff5237c040d55d813f9c24c Mon Sep 17 00:00:00 2001 From: Mauricio Carneiro Date: Tue, 23 Aug 2011 15:38:19 -0400 Subject: [PATCH] Adapting to the new RodBinding framework --- .../sting/queue/qscripts/PacbioProcessingPipeline.scala | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/PacbioProcessingPipeline.scala b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/PacbioProcessingPipeline.scala index 9f3dd9a2c..accc5c7f0 100755 --- 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