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Fix to deal with multi-generational families being allowed if only one level (one 'trio', effectively) appears in the VCF

This commit is contained in:
Menachem Fromer 2013-05-06 15:47:27 -04:00
parent 86287dce76
commit c7dcc2b53b
1 changed files with 11 additions and 2 deletions
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13
protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmission.java
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@ -478,6 +478,16 @@ public class PhaseByTransmission extends RodWalker<HashMap<Byte,Integer>, HashMa
ArrayList<Sample> parents;
for(Map.Entry<String,Set<Sample>> familyEntry : families.entrySet()){
family = familyEntry.getValue();
// Since getFamilies(vcfSamples) above still returns parents of samples in the VCF even if those parents are not in the VCF, need to subset down here:
Set<Sample> familyMembersInVCF = new TreeSet<Sample>();
for(Sample familyMember : family){
if (vcfSamples.contains(familyMember.getID())) {
familyMembersInVCF.add(familyMember);
}
}
family = familyMembersInVCF;
if(family.size()<2 || family.size()>3){
logger.info(String.format("Caution: Family %s has %d members; At the moment Phase By Transmission only supports trios and parent/child pairs. Family skipped.",familyEntry.getKey(),family.size()));
}
@ -488,8 +498,7 @@ public class PhaseByTransmission extends RodWalker<HashMap<Byte,Integer>, HashMa
if(family.containsAll(parents))
this.trios.add(familyMember);
else
logger.info(String.format("Caution: Family %s skipped as it is not a trio nor a parent/child pair; At the moment Phase By Transmission only supports trios and parent/child pairs. Family skipped.",familyEntry.getKey()));
break;
logger.info(String.format("Caution: Child %s of family %s skipped as info is not provided as a complete trio nor a parent/child pair; At the moment Phase By Transmission only supports trios and parent/child pairs. Child skipped.", familyMember.getID(), familyEntry.getKey()));
}
}
}