From 3566ad21461f297f28ebdf9beab8de043e75af3a Mon Sep 17 00:00:00 2001 From: chartl Date: Thu, 21 Oct 2010 17:37:45 +0000 Subject: [PATCH] Wrong if statement. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4544 348d0f76-0448-11de-a6fe-93d51630548a --- .../sting/gatk/walkers/varianteval/VariantEvalWalker.java | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java index ff1fbde4e..a100cab59 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java @@ -672,7 +672,7 @@ public class VariantEvalWalker extends RodWalker { VariantContext vc = contexts.size() == 1 ? contexts.iterator().next() : null; - if ( vc != null && vc.hasGenotypes(SAMPLES_LIST) && SAMPLES_LIST.size() > 0 && !name.equals("dbsnp") ) { + if ( vc != null && vc.hasGenotypes(SAMPLES_LIST) && SAMPLES_LIST.size() > 0 ) { //if ( ! name.equals("eval") ) logger.info(String.format("subsetting VC %s", vc)); vc = vc.subContextFromGenotypes(vc.getGenotypes(SAMPLES_LIST).values()); HashMap newAts = new HashMap(vc.getAttributes()); @@ -680,7 +680,7 @@ public class VariantEvalWalker extends RodWalker { vc = VariantContext.modifyAttributes(vc,newAts); logger.debug(String.format("VC %s subset to %s AC%n",vc.getName(),vc.getAttributeAsString(VCFConstants.ALLELE_COUNT_KEY))); //if ( ! name.equals("eval") ) logger.info(String.format(" => VC %s", vc)); - } else if ( vc != null && ! vc.hasGenotypes(SAMPLES_LIST) ) { + } else if ( vc != null && ! vc.hasGenotypes(SAMPLES_LIST) && !name.equals("dbsnp") ) { throw new UserException(String.format("Genotypes for the variant context %s do not contain all the provided samples %s",vc.getName(), getMissingSamples(SAMPLES_LIST,vc))); }