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Corrected bug causing PhaseByTransmission to crash in case of new Genotype.Type

This commit is contained in:
Laurent Francioli 2011-11-16 09:33:13 +01:00
parent 1347beef40
commit 0dc3d20d58
1 changed files with 9 additions and 9 deletions
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18
public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmission.java
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@ -151,16 +151,16 @@ public class PhaseByTransmission extends RodWalker<HashMap<Byte,Integer>, HashMa
alleles.add(VAR); alleles.add(VAR);
alleles.add(VAR); alleles.add(VAR);
} }
else if(genotype == Genotype.Type.NO_CALL){
alleles.add(NO_CALL);
alleles.add(NO_CALL);
}
else{ else{
return null; return null;
} }
return alleles; return alleles;
} }
private boolean isPhasable(Genotype.Type genotype){
return genotype == Genotype.Type.HOM_REF || genotype == Genotype.Type.HET || genotype == Genotype.Type.HOM_VAR;
}
//Create a new Genotype based on information from a single individual //Create a new Genotype based on information from a single individual
//Homozygous genotypes will be set as phased, heterozygous won't be //Homozygous genotypes will be set as phased, heterozygous won't be
private void phaseSingleIndividualAlleles(Genotype.Type genotype, FamilyMember familyMember){ private void phaseSingleIndividualAlleles(Genotype.Type genotype, FamilyMember familyMember){
@ -271,21 +271,21 @@ public class PhaseByTransmission extends RodWalker<HashMap<Byte,Integer>, HashMa
public TrioPhase(Genotype.Type mother, Genotype.Type father, Genotype.Type child){ public TrioPhase(Genotype.Type mother, Genotype.Type father, Genotype.Type child){
//Take care of cases where one or more family members are no call //Take care of cases where one or more family members are no call
if(child == Genotype.Type.NO_CALL || child == Genotype.Type.UNAVAILABLE){ if(!isPhasable(child)){
phaseSingleIndividualAlleles(mother, FamilyMember.MOTHER); phaseSingleIndividualAlleles(mother, FamilyMember.MOTHER);
phaseSingleIndividualAlleles(father, FamilyMember.FATHER); phaseSingleIndividualAlleles(father, FamilyMember.FATHER);
phaseSingleIndividualAlleles(child, FamilyMember.CHILD); phaseSingleIndividualAlleles(child, FamilyMember.CHILD);
} }
else if(mother == Genotype.Type.NO_CALL || mother == Genotype.Type.UNAVAILABLE){ else if(!isPhasable(mother)){
phaseSingleIndividualAlleles(mother, FamilyMember.MOTHER); phaseSingleIndividualAlleles(mother, FamilyMember.MOTHER);
if(father == Genotype.Type.NO_CALL || father == Genotype.Type.UNAVAILABLE){ if(!isPhasable(father)){
phaseSingleIndividualAlleles(father, FamilyMember.FATHER); phaseSingleIndividualAlleles(father, FamilyMember.FATHER);
phaseSingleIndividualAlleles(child, FamilyMember.CHILD); phaseSingleIndividualAlleles(child, FamilyMember.CHILD);
} }
else else
phasePairAlleles(father, child, FamilyMember.FATHER); phasePairAlleles(father, child, FamilyMember.FATHER);
} }
else if(father == Genotype.Type.NO_CALL || father == Genotype.Type.UNAVAILABLE){ else if(!isPhasable(father)){
phasePairAlleles(mother, child, FamilyMember.MOTHER); phasePairAlleles(mother, child, FamilyMember.MOTHER);
phaseSingleIndividualAlleles(father, FamilyMember.FATHER); phaseSingleIndividualAlleles(father, FamilyMember.FATHER);
} }
@ -327,7 +327,7 @@ public class PhaseByTransmission extends RodWalker<HashMap<Byte,Integer>, HashMa
//Note that only cases where a null/missing/unavailable genotype was passed in the first place can lead to a null/missing/unavailable //Note that only cases where a null/missing/unavailable genotype was passed in the first place can lead to a null/missing/unavailable
//genotype so it is safe to return the original genotype in this case. //genotype so it is safe to return the original genotype in this case.
//In addition, if the phasing confidence is 0, then return the unphased, original genotypes. //In addition, if the phasing confidence is 0, then return the unphased, original genotypes.
if(phredScoreTransmission ==0 || genotype == null || !phasedGenotype.isAvailable() || phasedGenotype.isNoCall()) if(phredScoreTransmission ==0 || genotype == null || !isPhasable(genotype.getType()))
return genotype; return genotype;
//Add the transmission probability //Add the transmission probability