From 821bbfa9e0eb5a9d975277bfb011c6afcec6a673 Mon Sep 17 00:00:00 2001 From: Guillermo del Angel Date: Tue, 2 Aug 2011 13:17:20 -0400 Subject: [PATCH] Bug fixes and enhancements to run whole-genome indel VQSR, removed old chr20-only code and cleanup --- .../gatk/walkers/variantrecalibration/VariantDataManager.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java index 67d54a408..7426a7726 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java @@ -258,7 +258,7 @@ public class VariantDataManager { datum.consensusCount = 0; for( final TrainingSet trainingSet : trainingSets ) { - for( final VariantContext trainVC : tracker.getVariantContexts( ref, trainingSet.name, null, context.getLocation(), false, false ) ) { + for( final VariantContext trainVC : tracker.getVariantContexts( ref, trainingSet.name, null, context.getLocation(), true, false ) ) { if( trainVC != null && trainVC.isNotFiltered() && trainVC.isVariant() && ((evalVC.isSNP() && trainVC.isSNP()) || ((evalVC.isIndel()||evalVC.isMixed()) && (trainVC.isIndel()||trainVC.isMixed()))) && (TRUST_ALL_POLYMORPHIC || !trainVC.hasGenotypes() || trainVC.isPolymorphic()) ) {