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Must check whether there's a normal vs. extended pileup before asking for it.

This commit is contained in:
Eric Banks 2011-11-02 20:45:24 -04:00
parent e1edd6bd12
commit 52b16bf739
2 changed files with 2 additions and 2 deletions
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2
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthOfCoverage.java
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@ -41,7 +41,7 @@ public class DepthOfCoverage extends InfoFieldAnnotation implements StandardAnno
int depth = 0; int depth = 0;
for ( Map.Entry<String, AlignmentContext> sample : stratifiedContexts.entrySet() ) for ( Map.Entry<String, AlignmentContext> sample : stratifiedContexts.entrySet() )
depth += sample.getValue().getBasePileup().depthOfCoverage(); depth += sample.getValue().hasBasePileup() ? sample.getValue().getBasePileup().depthOfCoverage() : sample.getValue().getExtendedEventPileup().depthOfCoverage();
Map<String, Object> map = new HashMap<String, Object>(); Map<String, Object> map = new HashMap<String, Object>();
map.put(getKeyNames().get(0), String.format("%d", depth)); map.put(getKeyNames().get(0), String.format("%d", depth));
return map; return map;

2
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/QualByDepth.java
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@ -43,7 +43,7 @@ public class QualByDepth extends InfoFieldAnnotation implements StandardAnnotati
if ( context == null ) if ( context == null )
continue; continue;
depth += context.getBasePileup().depthOfCoverage(); depth += context.hasBasePileup() ? context.getBasePileup().depthOfCoverage() : context.getExtendedEventPileup().depthOfCoverage();
} }
if ( depth == 0 ) if ( depth == 0 )