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Fixed bug where variants to phase were not being selected properly.

This commit is contained in:
Kiran V Garimella 2011-07-23 01:11:28 -04:00
parent 58eed20b83
commit 5521919cc9
1 changed files with 1 additions and 2 deletions
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3
public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmission.java
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@ -234,8 +234,7 @@ public class PhaseByTransmission extends RodWalker<Integer, Integer> {
finalGenotypes.add(father);
finalGenotypes.add(child);
if (mother.isCalled() && !father.isCalled() && !child.isCalled()) {
} else {
if (mother.isCalled() && father.isCalled() && child.isCalled()) {
ArrayList<Genotype> possibleMotherGenotypes = createAllThreeGenotypes(ref, alt, mother);
ArrayList<Genotype> possibleFatherGenotypes = createAllThreeGenotypes(ref, alt, father);
ArrayList<Genotype> possibleChildGenotypes = createAllThreeGenotypes(ref, alt, child);