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Commenting out CMI pipeline test that wasn't meant to be in GATK repository (why was this merged??)

This commit is contained in:
Guillermo del Angel 2012-11-14 14:39:04 -05:00
parent 3771d074dc
commit 89bbe73a43
2 changed files with 7 additions and 3 deletions
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6
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java
View File

@ -277,8 +277,12 @@ public class VariantAnnotatorEngine {
if ( expression.fieldName.equals("ID") ) {
if ( vc.hasID() )
infoAnnotations.put(expression.fullName, vc.getID());
} else if (expression.fieldName.equals("ALT")) {
infoAnnotations.put(expression.fullName, vc.getAlternateAllele(0).getDisplayString());
} else if ( vc.hasAttribute(expression.fieldName) ) {
infoAnnotations.put(expression.fullName, vc.getAttribute(expression.fieldName));
infoAnnotations.put(expression.fullName, vc.getAttribute(expression.fieldName));
}
}
}

4
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
View File

@ -190,8 +190,8 @@ public class UnifiedGenotyperEngine {
final VariantContext vc = calculateLikelihoods(tracker, refContext, stratifiedContexts, AlignmentContextUtils.ReadOrientation.COMPLETE, null, true, model, perReadAlleleLikelihoodMap);
if ( vc != null )
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));
else if (UAC.OutputMode == OUTPUT_MODE.EMIT_ALL_SITES)
results.add(generateEmptyContext(tracker, refContext, null, rawContext));
}
}