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More complete fix to previous commit 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4571 348d0f76-0448-11de-a6fe-93d51630548a
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ebanks 2010-10-25 20:47:37 +00:00
parent 67a776d53c
commit 071799453c
1 changed files with 14 additions and 11 deletions
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25
java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java
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@ -671,17 +671,20 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> {
VariantContext vc = contexts.size() == 1 ? contexts.iterator().next() : null;
if ( vc != null && SAMPLES_LIST.size() > 0 && vc.hasGenotypes(SAMPLES_LIST) ) {
//if ( ! name.equals("eval") ) logger.info(String.format("subsetting VC %s", vc));
vc = vc.subContextFromGenotypes(vc.getGenotypes(SAMPLES_LIST).values());
HashMap<String,Object> newAts = new HashMap<String,Object>(vc.getAttributes());
VariantContextUtils.calculateChromosomeCounts(vc,newAts,true);
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) && !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)));
}
if ( SAMPLES_LIST.size() > 0 && vc != null ) {
boolean hasGenotypes = vc.hasGenotypes(SAMPLES_LIST);
if ( hasGenotypes ) {
//if ( ! name.equals("eval") ) logger.info(String.format("subsetting VC %s", vc));
vc = vc.subContextFromGenotypes(vc.getGenotypes(SAMPLES_LIST).values());
HashMap<String,Object> newAts = new HashMap<String,Object>(vc.getAttributes());
VariantContextUtils.calculateChromosomeCounts(vc,newAts,true);
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 ( !hasGenotypes && !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)));
}
}
map.put(name, allowExcludes && excludeComp(vc) ? null : vc);
}