From 05ad6ecf72391a782c3f4f5331837fc7af102d97 Mon Sep 17 00:00:00 2001
From: rpoplin <rpoplin@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Mon, 11 Apr 2011 18:27:47 +0000
Subject: [PATCH] bug fix in MDCP

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5613 348d0f76-0448-11de-a6fe-93d51630548a
---
 scala/qscript/core/MethodsDevelopmentCallingPipeline.scala | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/scala/qscript/core/MethodsDevelopmentCallingPipeline.scala b/scala/qscript/core/MethodsDevelopmentCallingPipeline.scala
index 8947d3589..fe31b6bf2 100755
--- a/scala/qscript/core/MethodsDevelopmentCallingPipeline.scala
+++ b/scala/qscript/core/MethodsDevelopmentCallingPipeline.scala
@@ -209,6 +209,7 @@ class MethodsDevelopmentCallingPipeline extends QScript {
     if (qscript.deletions >= 0)
       this.max_deletion_fraction = qscript.deletions
     this.out = t.rawVCF
+    this.glm = org.broadinstitute.sting.gatk.walkers.genotyper.GenotypeLikelihoodsCalculationModel.Model.SNP
     this.baq = if (noBAQ) {org.broadinstitute.sting.utils.baq.BAQ.CalculationMode.OFF} else {org.broadinstitute.sting.utils.baq.BAQ.CalculationMode.CALCULATE_AS_NECESSARY}
     this.analysisName = t.name + "_UGs"
     this.jobName =  queueLogDir + t.name + ".snpcall"
@@ -217,7 +218,7 @@ class MethodsDevelopmentCallingPipeline extends QScript {
   // 1b.) Call Indels with UG
   class indelCall (t: Target) extends GenotyperBase(t) {
     this.out = t.rawIndelVCF
-    this.glm = org.broadinstitute.sting.gatk.walkers.genotyper.GenotypeLikelihoodsCalculationModel.Model.DINDEL
+    this.glm = org.broadinstitute.sting.gatk.walkers.genotyper.GenotypeLikelihoodsCalculationModel.Model.INDEL
     this.baq = org.broadinstitute.sting.utils.baq.BAQ.CalculationMode.OFF
     this.analysisName = t.name + "_UGi"
     this.jobName =  queueLogDir + t.name + ".indelcall"