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To address weird case with all hom-refs, but alt allele is present, skip AS_QD for all-ref sites and remove raw annotations whether or not they can be successfully finalized

This commit is contained in:
Laura Gauthier 2016-03-14 13:17:29 -04:00
parent 4efde50225
commit 31fc64f82c
2 changed files with 4 additions and 2 deletions
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2
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/AS_QualByDepth.java
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@ -172,6 +172,8 @@ public class AS_QualByDepth extends InfoFieldAnnotation implements ReducibleAnno
return null; return null;
final List<Integer> standardDepth = getAlleleDepths(genotypes); final List<Integer> standardDepth = getAlleleDepths(genotypes);
if (standardDepth == null) //all no-calls and homRefs
return null;
//Parse the VC's allele-specific qual values //Parse the VC's allele-specific qual values
List<Object> alleleQualObjList = vc.getAttributeAsList(GATKVCFConstants.AS_QUAL_KEY); List<Object> alleleQualObjList = vc.getAttributeAsList(GATKVCFConstants.AS_QUAL_KEY);

4
public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/VariantAnnotatorEngine.java
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@ -357,9 +357,9 @@ public class VariantAnnotatorEngine {
final Map<String, Object> annotationsFromCurrentType = currentASannotation.finalizeRawData(vc, originalVC); final Map<String, Object> annotationsFromCurrentType = currentASannotation.finalizeRawData(vc, originalVC);
if ( annotationsFromCurrentType != null ) { if ( annotationsFromCurrentType != null ) {
infoAnnotations.putAll(annotationsFromCurrentType); infoAnnotations.putAll(annotationsFromCurrentType);
//clean up raw annotation data after annotations are finalized
infoAnnotations.remove(currentASannotation.getRawKeyName());
} }
//clean up raw annotation data after annotations are finalized
infoAnnotations.remove(currentASannotation.getRawKeyName());
} }
// generate a new annotated VC // generate a new annotated VC