From 3383733379bfbd0694a0111c20feff40ef27ba1b Mon Sep 17 00:00:00 2001 From: delangel Date: Fri, 25 Mar 2011 12:07:18 +0000 Subject: [PATCH] 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 --- .../gatk/walkers/annotator/VariantAnnotatorEngine.java | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java index 67ac390a3..beeaff20e 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java @@ -211,7 +211,12 @@ public class VariantAnnotatorEngine { private void annotateDBs(RefMetaDataTracker tracker, ReferenceContext ref, VariantContext vc, Map infoAnnotations) { for ( Map.Entry 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)) )