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Don't do genotype concordance on comp tracks without genotypes, even if they have an AC 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5321 348d0f76-0448-11de-a6fe-93d51630548a
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depristo 2011-02-25 21:11:50 +00:00
parent 15ce375787
commit 7ff8d23c64
1 changed files with 1 additions and 3 deletions
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4
java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/GenotypeConcordance.java
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@ -249,7 +249,7 @@ public class GenotypeConcordance extends VariantEvaluator {
String interesting = null; String interesting = null;
// sanity check that we at least have either eval or validation data // sanity check that we at least have either eval or validation data
if (eval == null && !isValidVC(validation)) { if ( (validation != null && !validation.hasGenotypes()) || eval == null && !isValidVC(validation)) {
return interesting; return interesting;
} }
@ -300,7 +300,6 @@ public class GenotypeConcordance extends VariantEvaluator {
} }
private String determineStats(final VariantContext eval, final VariantContext validation) { private String determineStats(final VariantContext eval, final VariantContext validation) {
String interesting = null; String interesting = null;
final boolean validationIsValidVC = isValidVC(validation); final boolean validationIsValidVC = isValidVC(validation);
@ -380,7 +379,6 @@ public class GenotypeConcordance extends VariantEvaluator {
} else { // multi sample calls } else { // multi sample calls
qualityScoreHistograms.incrValue( eval.getPhredScaledQual(), validation.isPolymorphic() ); qualityScoreHistograms.incrValue( eval.getPhredScaledQual(), validation.isPolymorphic() );
} }
} }
return interesting; return interesting;