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Merged bug fix from Stable into Unstable

This commit is contained in:
Eric Banks 2012-04-23 10:30:30 -04:00
parent cd63bcb1b8 2761da975e
commit a733723439
1 changed files with 49 additions and 44 deletions
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93
public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmission.java
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@ -744,62 +744,67 @@ public class PhaseByTransmission extends RodWalker<HashMap<Byte,Integer>, HashMa
String mvfLine; String mvfLine;
if (tracker != null) { if (tracker == null)
VariantContext vc = tracker.getFirstValue(variantCollection.variants, context.getLocation()); return metricsCounters;
VariantContextBuilder builder = new VariantContextBuilder(vc);
GenotypesContext genotypesContext = GenotypesContext.copy(vc.getGenotypes()); final VariantContext vc = tracker.getFirstValue(variantCollection.variants, context.getLocation());
for (Sample sample : trios) { if (vc == null)
Genotype mother = vc.getGenotype(sample.getMaternalID()); return metricsCounters;
Genotype father = vc.getGenotype(sample.getPaternalID());
Genotype child = vc.getGenotype(sample.getID());
//Keep only trios and parent/child pairs final VariantContextBuilder builder = new VariantContextBuilder(vc);
if(mother == null && father == null || child == null)
continue;
ArrayList<Genotype> trioGenotypes = new ArrayList<Genotype>(3); final GenotypesContext genotypesContext = GenotypesContext.copy(vc.getGenotypes());
final int mvCount = phaseTrioGenotypes(vc.getReference(), vc.getAltAlleleWithHighestAlleleCount(), mother, father, child,trioGenotypes); for (Sample sample : trios) {
Genotype mother = vc.getGenotype(sample.getMaternalID());
Genotype father = vc.getGenotype(sample.getPaternalID());
Genotype child = vc.getGenotype(sample.getID());
Genotype phasedMother = trioGenotypes.get(0); //Keep only trios and parent/child pairs
Genotype phasedFather = trioGenotypes.get(1); if(mother == null && father == null || child == null)
Genotype phasedChild = trioGenotypes.get(2); continue;
//Fill the genotype map with the new genotypes and increment metrics counters ArrayList<Genotype> trioGenotypes = new ArrayList<Genotype>(3);
genotypesContext.replace(phasedChild); final int mvCount = phaseTrioGenotypes(vc.getReference(), vc.getAltAlleleWithHighestAlleleCount(), mother, father, child,trioGenotypes);
if(mother != null){
genotypesContext.replace(phasedMother); Genotype phasedMother = trioGenotypes.get(0);
if(father != null){ Genotype phasedFather = trioGenotypes.get(1);
genotypesContext.replace(phasedFather); Genotype phasedChild = trioGenotypes.get(2);
updateTrioMetricsCounters(phasedMother,phasedFather,phasedChild,mvCount,metricsCounters);
mvfLine = String.format("%s\t%d\t%s\t%s\t%s\t%s\t%s:%s:%s:%s\t%s:%s:%s:%s\t%s:%s:%s:%s",vc.getChr(),vc.getStart(),vc.getFilters(),vc.getAttribute(VCFConstants.ALLELE_COUNT_KEY),sample.toString(),phasedMother.getAttribute(TRANSMISSION_PROBABILITY_TAG_NAME),phasedMother.getGenotypeString(),phasedMother.getAttribute(VCFConstants.DEPTH_KEY),phasedMother.getAttribute("AD"),phasedMother.getLikelihoods().toString(),phasedFather.getGenotypeString(),phasedFather.getAttribute(VCFConstants.DEPTH_KEY),phasedFather.getAttribute("AD"),phasedFather.getLikelihoods().toString(),phasedChild.getGenotypeString(),phasedChild.getAttribute(VCFConstants.DEPTH_KEY),phasedChild.getAttribute("AD"),phasedChild.getLikelihoods().toString()); //Fill the genotype map with the new genotypes and increment metrics counters
if(!(phasedMother.getType()==mother.getType() && phasedFather.getType()==father.getType() && phasedChild.getType()==child.getType())) genotypesContext.replace(phasedChild);
metricsCounters.put(NUM_GENOTYPES_MODIFIED,metricsCounters.get(NUM_GENOTYPES_MODIFIED)+1); if(mother != null){
} genotypesContext.replace(phasedMother);
else{ if(father != null){
updatePairMetricsCounters(phasedMother,phasedChild,mvCount,metricsCounters); genotypesContext.replace(phasedFather);
if(!(phasedMother.getType()==mother.getType() && phasedChild.getType()==child.getType())) updateTrioMetricsCounters(phasedMother,phasedFather,phasedChild,mvCount,metricsCounters);
metricsCounters.put(NUM_GENOTYPES_MODIFIED,metricsCounters.get(NUM_GENOTYPES_MODIFIED)+1); mvfLine = String.format("%s\t%d\t%s\t%s\t%s\t%s\t%s:%s:%s:%s\t%s:%s:%s:%s\t%s:%s:%s:%s",vc.getChr(),vc.getStart(),vc.getFilters(),vc.getAttribute(VCFConstants.ALLELE_COUNT_KEY),sample.toString(),phasedMother.getAttribute(TRANSMISSION_PROBABILITY_TAG_NAME),phasedMother.getGenotypeString(),phasedMother.getAttribute(VCFConstants.DEPTH_KEY),phasedMother.getAttribute("AD"),phasedMother.getLikelihoods().toString(),phasedFather.getGenotypeString(),phasedFather.getAttribute(VCFConstants.DEPTH_KEY),phasedFather.getAttribute("AD"),phasedFather.getLikelihoods().toString(),phasedChild.getGenotypeString(),phasedChild.getAttribute(VCFConstants.DEPTH_KEY),phasedChild.getAttribute("AD"),phasedChild.getLikelihoods().toString());
mvfLine = String.format("%s\t%d\t%s\t%s\t%s\t%s\t%s:%s:%s:%s\t.:.:.:.\t%s:%s:%s:%s",vc.getChr(),vc.getStart(),vc.getFilters(),vc.getAttribute(VCFConstants.ALLELE_COUNT_KEY),sample.toString(),phasedMother.getAttribute(TRANSMISSION_PROBABILITY_TAG_NAME),phasedMother.getGenotypeString(),phasedMother.getAttribute(VCFConstants.DEPTH_KEY),phasedMother.getAttribute("AD"),phasedMother.getLikelihoods().toString(),phasedChild.getGenotypeString(),phasedChild.getAttribute(VCFConstants.DEPTH_KEY),phasedChild.getAttribute("AD"),phasedChild.getLikelihoods().toString()); if(!(phasedMother.getType()==mother.getType() && phasedFather.getType()==father.getType() && phasedChild.getType()==child.getType()))
} metricsCounters.put(NUM_GENOTYPES_MODIFIED,metricsCounters.get(NUM_GENOTYPES_MODIFIED)+1);
} }
else{ else{
genotypesContext.replace(phasedFather); updatePairMetricsCounters(phasedMother,phasedChild,mvCount,metricsCounters);
updatePairMetricsCounters(phasedFather,phasedChild,mvCount,metricsCounters); if(!(phasedMother.getType()==mother.getType() && phasedChild.getType()==child.getType()))
if(!(phasedFather.getType()==father.getType() && phasedChild.getType()==child.getType()))
metricsCounters.put(NUM_GENOTYPES_MODIFIED,metricsCounters.get(NUM_GENOTYPES_MODIFIED)+1); metricsCounters.put(NUM_GENOTYPES_MODIFIED,metricsCounters.get(NUM_GENOTYPES_MODIFIED)+1);
mvfLine = String.format("%s\t%d\t%s\t%s\t%s\t%s\t.:.:.:.\t%s:%s:%s:%s\t%s:%s:%s:%s",vc.getChr(),vc.getStart(),vc.getFilters(),vc.getAttribute(VCFConstants.ALLELE_COUNT_KEY),sample.toString(),phasedFather.getAttribute(TRANSMISSION_PROBABILITY_TAG_NAME),phasedFather.getGenotypeString(),phasedFather.getAttribute(VCFConstants.DEPTH_KEY),phasedFather.getAttribute("AD"),phasedFather.getLikelihoods().toString(),phasedChild.getGenotypeString(),phasedChild.getAttribute(VCFConstants.DEPTH_KEY),phasedChild.getAttribute("AD"),phasedChild.getLikelihoods().toString()); mvfLine = String.format("%s\t%d\t%s\t%s\t%s\t%s\t%s:%s:%s:%s\t.:.:.:.\t%s:%s:%s:%s",vc.getChr(),vc.getStart(),vc.getFilters(),vc.getAttribute(VCFConstants.ALLELE_COUNT_KEY),sample.toString(),phasedMother.getAttribute(TRANSMISSION_PROBABILITY_TAG_NAME),phasedMother.getGenotypeString(),phasedMother.getAttribute(VCFConstants.DEPTH_KEY),phasedMother.getAttribute("AD"),phasedMother.getLikelihoods().toString(),phasedChild.getGenotypeString(),phasedChild.getAttribute(VCFConstants.DEPTH_KEY),phasedChild.getAttribute("AD"),phasedChild.getLikelihoods().toString());
} }
}
//Report violation if set so else{
//TODO: ADAPT FOR PAIRS TOO!! genotypesContext.replace(phasedFather);
if(mvCount>0 && mvFile != null) updatePairMetricsCounters(phasedFather,phasedChild,mvCount,metricsCounters);
mvFile.println(mvfLine); if(!(phasedFather.getType()==father.getType() && phasedChild.getType()==child.getType()))
metricsCounters.put(NUM_GENOTYPES_MODIFIED,metricsCounters.get(NUM_GENOTYPES_MODIFIED)+1);
mvfLine = String.format("%s\t%d\t%s\t%s\t%s\t%s\t.:.:.:.\t%s:%s:%s:%s\t%s:%s:%s:%s",vc.getChr(),vc.getStart(),vc.getFilters(),vc.getAttribute(VCFConstants.ALLELE_COUNT_KEY),sample.toString(),phasedFather.getAttribute(TRANSMISSION_PROBABILITY_TAG_NAME),phasedFather.getGenotypeString(),phasedFather.getAttribute(VCFConstants.DEPTH_KEY),phasedFather.getAttribute("AD"),phasedFather.getLikelihoods().toString(),phasedChild.getGenotypeString(),phasedChild.getAttribute(VCFConstants.DEPTH_KEY),phasedChild.getAttribute("AD"),phasedChild.getLikelihoods().toString());
} }
builder.genotypes(genotypesContext); //Report violation if set so
vcfWriter.add(builder.make()); //TODO: ADAPT FOR PAIRS TOO!!
if(mvCount>0 && mvFile != null)
mvFile.println(mvfLine);
} }
builder.genotypes(genotypesContext);
vcfWriter.add(builder.make());
return metricsCounters; return metricsCounters;
} }