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Fixed a bug that wrongly swapped the mother and father genotypes in case the child genotype missing.

This commit is contained in:
Laurent Francioli 2011-11-03 13:04:53 +01:00
parent 893787de53
commit 385a6abec1
1 changed files with 8 additions and 7 deletions
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15
public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmission.java
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@ -547,10 +547,15 @@ public class PhaseByTransmission extends RodWalker<HashMap<Byte,Integer>, HashMa
int parentsCalled = 0; int parentsCalled = 0;
Map<Genotype.Type,Double> firstParentLikelihoods; Map<Genotype.Type,Double> firstParentLikelihoods;
Map<Genotype.Type,Double> secondParentLikelihoods; Map<Genotype.Type,Double> secondParentLikelihoods;
ArrayList<Genotype.Type> bestFirstParentGenotype = new ArrayList<Genotype.Type>();
ArrayList<Genotype.Type> bestSecondParentGenotype = new ArrayList<Genotype.Type>();
ArrayList<Genotype.Type> bestChildGenotype = new ArrayList<Genotype.Type>();
Genotype.Type pairSecondParentGenotype = null; Genotype.Type pairSecondParentGenotype = null;
if(mother == null || !mother.isCalled()){ if(mother == null || !mother.isCalled()){
firstParentLikelihoods = getLikelihoodsAsMapSafeNull(father); firstParentLikelihoods = getLikelihoodsAsMapSafeNull(father);
secondParentLikelihoods = getLikelihoodsAsMapSafeNull(mother); secondParentLikelihoods = getLikelihoodsAsMapSafeNull(mother);
bestFirstParentGenotype.add(getTypeSafeNull(father));
bestSecondParentGenotype.add(getTypeSafeNull(mother));
pairSecondParentGenotype = mother == null ? Genotype.Type.UNAVAILABLE : mother.getType(); pairSecondParentGenotype = mother == null ? Genotype.Type.UNAVAILABLE : mother.getType();
if(father != null && father.isCalled()) if(father != null && father.isCalled())
parentsCalled = 1; parentsCalled = 1;
@ -558,6 +563,8 @@ public class PhaseByTransmission extends RodWalker<HashMap<Byte,Integer>, HashMa
else{ else{
firstParentLikelihoods = getLikelihoodsAsMapSafeNull(mother); firstParentLikelihoods = getLikelihoodsAsMapSafeNull(mother);
secondParentLikelihoods = getLikelihoodsAsMapSafeNull(father); secondParentLikelihoods = getLikelihoodsAsMapSafeNull(father);
bestFirstParentGenotype.add(getTypeSafeNull(mother));
bestSecondParentGenotype.add(getTypeSafeNull(father));
if(father == null || !father.isCalled()){ if(father == null || !father.isCalled()){
parentsCalled = 1; parentsCalled = 1;
pairSecondParentGenotype = father == null ? Genotype.Type.UNAVAILABLE : father.getType(); pairSecondParentGenotype = father == null ? Genotype.Type.UNAVAILABLE : father.getType();
@ -566,6 +573,7 @@ public class PhaseByTransmission extends RodWalker<HashMap<Byte,Integer>, HashMa
} }
} }
Map<Genotype.Type,Double> childLikelihoods = getLikelihoodsAsMapSafeNull(child); Map<Genotype.Type,Double> childLikelihoods = getLikelihoodsAsMapSafeNull(child);
bestChildGenotype.add(getTypeSafeNull(child));
//Prior vars //Prior vars
double bestConfigurationLikelihood = 0.0; double bestConfigurationLikelihood = 0.0;
@ -574,13 +582,6 @@ public class PhaseByTransmission extends RodWalker<HashMap<Byte,Integer>, HashMa
ArrayList<Integer> bestMVCount = new ArrayList<Integer>(); ArrayList<Integer> bestMVCount = new ArrayList<Integer>();
bestMVCount.add(0); bestMVCount.add(0);
ArrayList<Genotype.Type> bestFirstParentGenotype = new ArrayList<Genotype.Type>();
ArrayList<Genotype.Type> bestSecondParentGenotype = new ArrayList<Genotype.Type>();
ArrayList<Genotype.Type> bestChildGenotype = new ArrayList<Genotype.Type>();
bestFirstParentGenotype.add(getTypeSafeNull(mother));
bestSecondParentGenotype.add(getTypeSafeNull(father));
bestChildGenotype.add(getTypeSafeNull(child));
//Get the most likely combination //Get the most likely combination
//Only check for most likely combination if at least a parent and the child have genotypes //Only check for most likely combination if at least a parent and the child have genotypes
if(child.isCalled() && parentsCalled > 0){ if(child.isCalled() && parentsCalled > 0){