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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1525 348d0f76-0448-11de-a6fe-93d51630548a

This commit is contained in:
sjia 2009-09-03 19:41:12 +00:00
parent 043c97eede
commit ee06c7f29f
1 changed files with 2 additions and 2 deletions
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4
java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/CallHLAWalker.java
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@ -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<Integer, Pair<Long, Long>>{
//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.