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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
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rpoplin 2011-03-16 03:06:03 +00:00
parent 9c413fbc9e
commit 8e89ff170e
1 changed files with 1 additions and 1 deletions
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2
java/src/org/broadinstitute/sting/playground/gatk/walkers/variantrecalibration/ContrastiveRecalibrator.java
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@ -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 );