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Major bugfix for per sample VariantEval 

-- per sample stratification was not being calculated correctly.  The alt allele was always remaining, even if the genotype of the sample was hom-ref.  Although conceptually fine, this breaks the assumptions of all of the eval modules, so per sample stratifications actually included all variants for everything.  Eric is going to fix the system in general, so this commit may break the build.
This commit is contained in:
Mark DePristo 2011-09-07 12:18:11 -04:00
parent d5641cfac5
commit a1920397e8
1 changed files with 1 additions and 1 deletions
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public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/VariantEvalUtils.java
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@ -277,7 +277,7 @@ public class VariantEvalUtils {
* @return a new VariantContext with just the requested samples
*/
public VariantContext getSubsetOfVariantContext(VariantContext vc, Collection<String> sampleNames) {
VariantContext vcsub = vc.subContextFromGenotypes(vc.getGenotypes(sampleNames).values(), vc.getAlleles());
VariantContext vcsub = vc.subContextFromGenotypes(vc.getGenotypes(sampleNames).values());
HashMap<String, Object> newAts = new HashMap<String, Object>(vcsub.getAttributes());