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Fix for the case of the truth VCF file having multiple SNPs at the same locus. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4567 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
rpoplin 2010-10-25 15:04:50 +00:00
parent 16c64558b4
commit da64183854
2 changed files with 8 additions and 4 deletions
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6
java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/GenerateVariantClustersWalker.java
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@ -186,8 +186,10 @@ public class GenerateVariantClustersWalker extends RodWalker<ExpandingArrayList<
variantDatum.qual = vc.getPhredScaledQual();
final DbSNPFeature dbsnp = DbSNPHelper.getFirstRealSNP(tracker.getReferenceMetaData(DbSNPHelper.STANDARD_DBSNP_TRACK_NAME));
final VariantContext vcHapMap = tracker.getVariantContext(ref, "hapmap", null, context.getLocation(), false);
final VariantContext vc1KG = tracker.getVariantContext(ref, "1kg", null, context.getLocation(), false);
final Collection<VariantContext> vcsHapMap = tracker.getVariantContexts(ref, "hapmap", null, context.getLocation(), false, true);
final Collection<VariantContext> vcs1KG = tracker.getVariantContexts(ref, "1kg", null, context.getLocation(), false, true);
final VariantContext vcHapMap = ( vcsHapMap.size() != 0 ? vcsHapMap.iterator().next() : null );
final VariantContext vc1KG = ( vcs1KG.size() != 0 ? vcs1KG.iterator().next() : null );
variantDatum.isKnown = ( dbsnp != null );
variantDatum.weight = WEIGHT_NOVELS;

6
java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
View File

@ -226,8 +226,10 @@ public class VariantRecalibrator extends RodWalker<ExpandingArrayList<VariantDat
variantDatum.isTransition = VariantContextUtils.getSNPSubstitutionType(vc).compareTo(BaseUtils.BaseSubstitutionType.TRANSITION) == 0;
final DbSNPFeature dbsnp = DbSNPHelper.getFirstRealSNP(tracker.getReferenceMetaData(DbSNPHelper.STANDARD_DBSNP_TRACK_NAME));
final VariantContext vcHapMap = tracker.getVariantContext(ref, "hapmap", null, context.getLocation(), false);
final VariantContext vc1KG = tracker.getVariantContext(ref, "1kg", null, context.getLocation(), false);
final Collection<VariantContext> vcsHapMap = tracker.getVariantContexts(ref, "hapmap", null, context.getLocation(), false, true);
final Collection<VariantContext> vcs1KG = tracker.getVariantContexts(ref, "1kg", null, context.getLocation(), false, true);
final VariantContext vcHapMap = ( vcsHapMap.size() != 0 ? vcsHapMap.iterator().next() : null );
final VariantContext vc1KG = ( vcs1KG.size() != 0 ? vcs1KG.iterator().next() : null );
variantDatum.isKnown = ( dbsnp != null );
double knownPrior_qScore = PRIOR_NOVELS;