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Minor change: when tabulating concordance by AC, ignore sites with multiple segregating alleles in the population, at least for now 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4493 348d0f76-0448-11de-a6fe-93d51630548a
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chartl 2010-10-14 01:35:33 +00:00
parent 5034ca18dc
commit 4ac636e288
1 changed files with 2 additions and 2 deletions
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4
java/src/org/broadinstitute/sting/gatk/walkers/varianteval/GenotypeConcordance.java
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@ -297,8 +297,8 @@ public class GenotypeConcordance extends VariantEvaluator implements StandardEva
String interesting = null;
final boolean validationIsValidVC = isValidVC(validation);
final String evalAC = (eval != null && eval.hasAttribute(VCFConstants.ALLELE_COUNT_KEY) ) ? String.format("evalAC%s",eval.getAttributeAsString(VCFConstants.ALLELE_COUNT_KEY)) : null ;
final String validationAC = ( validationIsValidVC && validation.hasAttribute(VCFConstants.ALLELE_COUNT_KEY)) ? String.format("compAC%s",validation.getAttributeAsString(VCFConstants.ALLELE_COUNT_KEY)) : null;
final String evalAC = (eval != null && eval.getAlternateAlleles().size() == 1 && eval.hasAttribute(VCFConstants.ALLELE_COUNT_KEY) ) ? String.format("evalAC%s",eval.getAttributeAsString(VCFConstants.ALLELE_COUNT_KEY)) : null ;
final String validationAC = ( validationIsValidVC && validation.getAlternateAlleles().size() == 1 && validation.hasAttribute(VCFConstants.ALLELE_COUNT_KEY)) ? String.format("compAC%s",validation.getAttributeAsString(VCFConstants.ALLELE_COUNT_KEY)) : null;
// determine concordance for eval data
if (eval != null) {