diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/CallHLAWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/CallHLAWalker.java index 0d4349588..8466597f8 100644 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/CallHLAWalker.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/CallHLAWalker.java @@ -13,7 +13,7 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.LocusWalker; import org.broadinstitute.sting.gatk.walkers.genotyper.DiploidGenotype; import org.broadinstitute.sting.gatk.walkers.genotyper.GenotypeLikelihoods; -import org.broadinstitute.sting.gatk.walkers.genotyper.ThreeStateErrorGenotypeLikelihoods; +import org.broadinstitute.sting.gatk.walkers.genotyper.*; import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.Pair; @@ -228,7 +228,7 @@ public class CallHLAWalker extends LocusWalker>{ //Store confidence scores - this is a local hash that we use to get likelihood given a particular genotype Scores = new Hashtable(); for ( DiploidGenotype g : DiploidGenotype.values() ) { - Scores.put(g.toString(), gl.getLikelihood(g)); + Scores.put(g.toString(), G.getLikelihood(g)); } //Get likelihood score for homozygous ref: used to normalize likelihoood scores at 0.