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Same commit as previous one for VariantAnnotator. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5510 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
delangel 2011-03-25 12:07:18 +00:00
parent 8701dfe8d3
commit 3383733379
1 changed files with 6 additions and 1 deletions
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7
java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java
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@ -211,7 +211,12 @@ public class VariantAnnotatorEngine {
private void annotateDBs(RefMetaDataTracker tracker, ReferenceContext ref, VariantContext vc, Map<String, Object> infoAnnotations) {
for ( Map.Entry<String, String> dbSet : dbAnnotations.entrySet() ) {
if ( dbSet.getKey().equals(DbSNPHelper.STANDARD_DBSNP_TRACK_NAME) ) {
String rsID = DbSNPHelper.rsIDOfFirstRealSNP(tracker.getReferenceMetaData(DbSNPHelper.STANDARD_DBSNP_TRACK_NAME));
String rsID = null;
if (vc.isSNP())
rsID = DbSNPHelper.rsIDOfFirstRealSNP(tracker.getReferenceMetaData(DbSNPHelper.STANDARD_DBSNP_TRACK_NAME));
else if (vc.isIndel())
rsID = DbSNPHelper.rsIDOfFirstRealIndel(tracker.getReferenceMetaData(DbSNPHelper.STANDARD_DBSNP_TRACK_NAME));
infoAnnotations.put(VCFConstants.DBSNP_KEY, rsID == null ? false : true);
// annotate dbsnp id if available and not already there
if ( rsID != null && (!vc.hasID() || vc.getID().equals(VCFConstants.EMPTY_ID_FIELD)) )