From 8e89ff170e283006a312c1a0dbd4bd07defe64a0 Mon Sep 17 00:00:00 2001
From: rpoplin <rpoplin@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Wed, 16 Mar 2011 03:06:03 +0000
Subject: [PATCH] Can't check substitution type of tri-allelic SNPs.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5451 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../walkers/variantrecalibration/ContrastiveRecalibrator.java   | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantrecalibration/ContrastiveRecalibrator.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantrecalibration/ContrastiveRecalibrator.java
index 6b4f59948..6bab10158 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantrecalibration/ContrastiveRecalibrator.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantrecalibration/ContrastiveRecalibrator.java
@@ -157,7 +157,7 @@ public class ContrastiveRecalibrator extends RodWalker<ExpandingArrayList<Varian
                 datum.annotations = dataManager.decodeAnnotations( ref.getGenomeLocParser(), vc, true ); //BUGBUG: when run with HierarchicalMicroScheduler this is non-deterministic because order of calls depends on load of machine
                 datum.pos = context.getLocation();
                 datum.originalQual = vc.getPhredScaledQual();
-                datum.isTransition = vc.isSNP() && ( VariantContextUtils.getSNPSubstitutionType(vc).compareTo(BaseUtils.BaseSubstitutionType.TRANSITION) == 0 );
+                datum.isTransition = vc.isSNP() && vc.isBiallelic() && ( VariantContextUtils.getSNPSubstitutionType(vc).compareTo(BaseUtils.BaseSubstitutionType.TRANSITION) == 0 );
                 dataManager.parseTrainingSets( tracker, ref, context, vc, datum, TRUST_ALL_POLYMORPHIC );
                 final double priorFactor = QualityUtils.qualToProb( datum.prior );
                 datum.prior = Math.log10( priorFactor ) - Math.log10( 1.0 - priorFactor );