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Refactoring a few useful routines for detecting mendelian violations 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3043 348d0f76-0448-11de-a6fe-93d51630548a
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depristo 2010-03-19 13:19:01 +00:00
parent 56092a0fc2
commit 7b17bcd0af
1 changed files with 7 additions and 2 deletions
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9
java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval2/MendelianViolationEvaluator.java
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@ -139,11 +139,16 @@ public class MendelianViolationEvaluator extends VariantEvaluator {
} }
public static boolean isViolation(VariantContext vc, Genotype momG, Genotype dadG, Genotype childG ) { public static boolean isViolation(VariantContext vc, Genotype momG, Genotype dadG, Genotype childG ) {
return isViolation(vc, momG.getAlleles(), dadG.getAlleles(), childG.getAlleles());
}
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);
int i = 0; int i = 0;
for ( Allele momAllele : momG.getAlleles() ) { Genotype childG = new Genotype("kidG", childA);
for ( Allele dadAllele : dadG.getAlleles() ) { for ( Allele momAllele : momA ) {
for ( Allele dadAllele : dadA ) {
if ( momAllele.isCalled() && dadAllele.isCalled() ) { if ( momAllele.isCalled() && dadAllele.isCalled() ) {
Genotype possibleChild = new Genotype("possibleGenotype" + i, Arrays.asList(momAllele, dadAllele)); Genotype possibleChild = new Genotype("possibleGenotype" + i, Arrays.asList(momAllele, dadAllele));
if ( childG.sameGenotype(possibleChild, false) ) { if ( childG.sameGenotype(possibleChild, false) ) {