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UnifiedGenotyperEngine.calculateGenotypes() is not only used in UG but in other walkers - vc attributes shouldn't be inherited by default or it may cause undefined behaviour in those walkers, so only inherit attributes from input vc in case of UG calling this function

This commit is contained in:
Guillermo del Angel 2012-06-29 23:51:52 -04:00
parent 14274c43d9
commit f631be8d80
1 changed files with 20 additions and 3 deletions
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23
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
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@ -188,7 +188,7 @@ public class UnifiedGenotyperEngine {
else { else {
final VariantContext vc = calculateLikelihoods(tracker, refContext, stratifiedContexts, AlignmentContextUtils.ReadOrientation.COMPLETE, null, true, model); final VariantContext vc = calculateLikelihoods(tracker, refContext, stratifiedContexts, AlignmentContextUtils.ReadOrientation.COMPLETE, null, true, model);
if ( vc != null ) if ( vc != null )
results.add(calculateGenotypes(tracker, refContext, rawContext, stratifiedContexts, vc, model)); results.add(calculateGenotypes(tracker, refContext, rawContext, stratifiedContexts, vc, model, true));
} }
} }
} }
@ -309,6 +309,22 @@ public class UnifiedGenotyperEngine {
} }
public VariantCallContext calculateGenotypes(RefMetaDataTracker tracker, ReferenceContext refContext, AlignmentContext rawContext, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc, final GenotypeLikelihoodsCalculationModel.Model model) { public VariantCallContext calculateGenotypes(RefMetaDataTracker tracker, ReferenceContext refContext, AlignmentContext rawContext, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc, final GenotypeLikelihoodsCalculationModel.Model model) {
return calculateGenotypes(tracker, refContext, rawContext, stratifiedContexts, vc, model, false);
}
/**
* Main entry function to calculate genotypes of a given VC with corresponding GL's
* @param tracker Tracker
* @param refContext Reference context
* @param rawContext Raw context
* @param stratifiedContexts Stratified alignment contexts
* @param vc Input VC
* @param model GL calculation model
* @param inheritAttributesFromInputVC Output VC will contain attributes inherited from input vc
* @return VC with assigned genotypes
*/
public VariantCallContext calculateGenotypes(RefMetaDataTracker tracker, ReferenceContext refContext, AlignmentContext rawContext, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc, final GenotypeLikelihoodsCalculationModel.Model model,
final boolean inheritAttributesFromInputVC) {
boolean limitedContext = tracker == null || refContext == null || rawContext == null || stratifiedContexts == null; boolean limitedContext = tracker == null || refContext == null || rawContext == null || stratifiedContexts == null;
@ -408,8 +424,9 @@ public class UnifiedGenotyperEngine {
// *** note that calculating strand bias involves overwriting data structures, so we do that last // *** note that calculating strand bias involves overwriting data structures, so we do that last
final HashMap<String, Object> attributes = new HashMap<String, Object>(); final HashMap<String, Object> attributes = new HashMap<String, Object>();
// inherit attributed from input vc // inherit attributed from input vc if requested
attributes.putAll(vc.getAttributes()); if (inheritAttributesFromInputVC)
attributes.putAll(vc.getAttributes());
// if the site was downsampled, record that fact // if the site was downsampled, record that fact
if ( !limitedContext && rawContext.hasPileupBeenDownsampled() ) if ( !limitedContext && rawContext.hasPileupBeenDownsampled() )
attributes.put(VCFConstants.DOWNSAMPLED_KEY, true); attributes.put(VCFConstants.DOWNSAMPLED_KEY, true);