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Forgot to commit code i relied upon 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3503 348d0f76-0448-11de-a6fe-93d51630548a
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chartl 2010-06-08 21:01:35 +00:00
parent 736098b58d
commit 5ed2818ffb
1 changed files with 4 additions and 0 deletions
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4
java/src/org/broadinstitute/sting/gatk/walkers/varianteval/MendelianViolationEvaluator.java
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@ -157,6 +157,10 @@ public class MendelianViolationEvaluator extends VariantEvaluator {
return isViolation(vc, momG.getAlleles(), dadG.getAlleles(), childG.getAlleles()); return isViolation(vc, momG.getAlleles(), dadG.getAlleles(), childG.getAlleles());
} }
public static boolean isViolation(VariantContext vc, TrioStructure trio ) {
return isViolation(vc, vc.getGenotype(trio.mom), vc.getGenotype(trio.dad), vc.getGenotype(trio.child) );
}
public static boolean isViolation(VariantContext vc, List<Allele> momA, List<Allele> dadA, List<Allele> childA) { public static boolean isViolation(VariantContext vc, List<Allele> momA, List<Allele> dadA, List<Allele> childA) {
//VariantContext momVC = vc.subContextFromGenotypes(momG); //VariantContext momVC = vc.subContextFromGenotypes(momG);
//VariantContext dadVC = vc.subContextFromGenotypes(dadG); //VariantContext dadVC = vc.subContextFromGenotypes(dadG);