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Merge pull request #1338 from broadinstitute/db_issue_1291 

Fixed bug in dbSNP binding in VariantAnnotationEngine.  Closes issue #1291.
This commit is contained in:
David Benjamin 2016-04-21 20:21:08 -04:00
parent 44691f036b cfbf062f29
commit a43d2a7ed1
1 changed files with 1 additions and 1 deletions
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public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/VariantAnnotatorEngine.java
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@ -163,7 +163,7 @@ public class VariantAnnotatorEngine {
final Map<RodBinding<VariantContext>, String> overlapBindings = new LinkedHashMap<>(); final Map<RodBinding<VariantContext>, String> overlapBindings = new LinkedHashMap<>();
for ( final RodBinding<VariantContext> b : walker.getCompRodBindings()) for ( final RodBinding<VariantContext> b : walker.getCompRodBindings())
if ( b.isBound() ) overlapBindings.put(b, b.getName()); if ( b.isBound() ) overlapBindings.put(b, b.getName());
if ( dbSNPBinding != null && ! overlapBindings.keySet().contains(VCFConstants.DBSNP_KEY) ) if ( dbSNPBinding != null && ! overlapBindings.values().contains(VCFConstants.DBSNP_KEY) )
overlapBindings.put(dbSNPBinding, VCFConstants.DBSNP_KEY); // add overlap detection with DBSNP by default overlapBindings.put(dbSNPBinding, VCFConstants.DBSNP_KEY); // add overlap detection with DBSNP by default
variantOverlapAnnotator = new VariantOverlapAnnotator(dbSNPBinding, overlapBindings, engine.getGenomeLocParser()); variantOverlapAnnotator = new VariantOverlapAnnotator(dbSNPBinding, overlapBindings, engine.getGenomeLocParser());