From 863eb5b5c068252b0b781b95ee189b39765878e2 Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Tue, 17 Jul 2012 15:18:11 -0400
Subject: [PATCH] Use Context not Dinuc covariate

---
 .../sting/queue/qscripts/DataProcessingPipeline.scala           | 2 +-
 .../sting/queue/qscripts/PacbioProcessingPipeline.scala         | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala
index b6560876b..70c89ac31 100755
--- a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala
+++ b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala
@@ -345,7 +345,7 @@ class DataProcessingPipeline extends QScript {
 
   case class cov (inBam: File, outRecalFile: File) extends BaseQualityScoreRecalibrator with CommandLineGATKArgs {
     this.knownSites ++= qscript.dbSNP
-    this.covariate ++= Seq("ReadGroupCovariate", "QualityScoreCovariate", "CycleCovariate", "DinucCovariate")
+    this.covariate ++= Seq("ReadGroupCovariate", "QualityScoreCovariate", "CycleCovariate", "ContextCovariate")
     this.input_file :+= inBam
     this.out = outRecalFile
     if (!defaultPlatform.isEmpty) this.default_platform = defaultPlatform
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 f3894c5cc..86f2d4969 100755
--- a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/PacbioProcessingPipeline.scala
+++ b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/PacbioProcessingPipeline.scala
@@ -164,7 +164,7 @@ class PacbioProcessingPipeline extends QScript {
     if (resetQuals) 
       this.DBQ = dbq
     this.knownSites :+= dbSNP
-    this.covariate ++= List("ReadGroupCovariate", "QualityScoreCovariate", "CycleCovariate", "DinucCovariate")
+    this.covariate ++= List("ReadGroupCovariate", "QualityScoreCovariate", "CycleCovariate", "ContextCovariate")
     this.input_file :+= inBam
     this.out = outRecalFile
     this.analysisName = queueLogDir + outRecalFile + ".covariates"