From c9283e6bc55877477d71a1585870221775106912 Mon Sep 17 00:00:00 2001 From: delangel Date: Fri, 25 Mar 2011 15:00:32 +0000 Subject: [PATCH] Refinement to previous commit: no need to duplicate code to annotate rsID since variantAnnotatorEngine is called from UG anyways. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5511 348d0f76-0448-11de-a6fe-93d51630548a --- .../walkers/genotyper/UnifiedGenotyperEngine.java | 12 +----------- 1 file changed, 1 insertion(+), 11 deletions(-) diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java index 17d2b7b29..4ec0e4358 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java @@ -355,16 +355,6 @@ public class UnifiedGenotyperEngine { // *** note that calculating strand bias involves overwriting data structures, so we do that last HashMap attributes = new HashMap(); - 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)); - - if ( rsID != null ) - attributes.put(VariantContext.ID_KEY, rsID); - // if the site was downsampled, record that fact if ( rawContext.hasPileupBeenDownsampled() ) attributes.put(VCFConstants.DOWNSAMPLED_KEY, true); @@ -734,4 +724,4 @@ public class UnifiedGenotyperEngine { return afcm; } -} \ No newline at end of file +}