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totally experimental UG feature, to be removed

This commit is contained in:
Guillermo del Angel 2012-10-30 13:57:54 -04:00
parent 92fa7e953a
commit c8e17a7adf
1 changed files with 3 additions and 0 deletions
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3
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
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@ -190,6 +190,9 @@ public class UnifiedGenotyperEngine {
final VariantContext vc = calculateLikelihoods(tracker, refContext, stratifiedContexts, AlignmentContextUtils.ReadOrientation.COMPLETE, null, true, model, perReadAlleleLikelihoodMap); final VariantContext vc = calculateLikelihoods(tracker, refContext, stratifiedContexts, AlignmentContextUtils.ReadOrientation.COMPLETE, null, true, model, perReadAlleleLikelihoodMap);
if ( vc != null ) if ( vc != null )
results.add(calculateGenotypes(tracker, refContext, rawContext, stratifiedContexts, vc, model, true, perReadAlleleLikelihoodMap)); results.add(calculateGenotypes(tracker, refContext, rawContext, stratifiedContexts, vc, model, true, perReadAlleleLikelihoodMap));
else if (UAC.OutputMode == OUTPUT_MODE.EMIT_ALL_SITES)
results.add(generateEmptyContext(tracker, refContext, null, rawContext));
} }
} }
} }