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Back off experimental code that escaped last commit, not for general use yet

This commit is contained in:
Guillermo del Angel 2012-11-14 14:45:15 -05:00
parent 89bbe73a43
commit a68e6810c9
1 changed files with 3 additions and 2 deletions
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5
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
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@ -190,8 +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) // todo - uncomment if we want to also emit a null ref call (with no QUAL) if there's no evidence for REF and if EMIT_ALL_SITES is set
results.add(generateEmptyContext(tracker, refContext, null, rawContext)); // else if (UAC.OutputMode == OUTPUT_MODE.EMIT_ALL_SITES)
// results.add(generateEmptyContext(tracker, refContext, null, rawContext));
} }
} }