zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

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
This commit is contained in:
delangel 2011-03-25 15:00:32 +00:00
parent 3383733379
commit c9283e6bc5
1 changed files with 1 additions and 11 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

10
java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
View File

@ -355,16 +355,6 @@ public class UnifiedGenotyperEngine {
// *** note that calculating strand bias involves overwriting data structures, so we do that last // *** note that calculating strand bias involves overwriting data structures, so we do that last
HashMap<String, Object> attributes = new HashMap<String, Object>(); HashMap<String, Object> attributes = new HashMap<String, Object>();
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 the site was downsampled, record that fact
if ( rawContext.hasPileupBeenDownsampled() ) if ( rawContext.hasPileupBeenDownsampled() )
attributes.put(VCFConstants.DOWNSAMPLED_KEY, true); attributes.put(VCFConstants.DOWNSAMPLED_KEY, true);