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PBT now uses getGenotypeLikelihoodString to avoid NPE when there are no PLs present

This commit is contained in:
Mark DePristo 2012-05-28 20:18:16 -04:00
parent 1818c29371
commit 7ce24a96f1
1 changed files with 13 additions and 3 deletions
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16
public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmission.java
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@ -795,7 +795,11 @@ public class PhaseByTransmission extends RodWalker<HashMap<Byte,Integer>, HashMa
if(father != null){ if(father != null){
genotypesContext.replace(phasedFather); genotypesContext.replace(phasedFather);
updateTrioMetricsCounters(phasedMother,phasedFather,phasedChild,mvCount,metricsCounters); 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()); 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.getLikelihoodsString(),
phasedFather.getGenotypeString(),phasedFather.getAttribute(VCFConstants.DEPTH_KEY),phasedFather.getAttribute("AD"),phasedFather.getLikelihoodsString(),
phasedChild.getGenotypeString(),phasedChild.getAttribute(VCFConstants.DEPTH_KEY),phasedChild.getAttribute("AD"),phasedChild.getLikelihoodsString());
if(!(phasedMother.getType()==mother.getType() && phasedFather.getType()==father.getType() && phasedChild.getType()==child.getType())) if(!(phasedMother.getType()==mother.getType() && 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);
} }
@ -803,7 +807,10 @@ public class PhaseByTransmission extends RodWalker<HashMap<Byte,Integer>, HashMa
updatePairMetricsCounters(phasedMother,phasedChild,mvCount,metricsCounters); updatePairMetricsCounters(phasedMother,phasedChild,mvCount,metricsCounters);
if(!(phasedMother.getType()==mother.getType() && phasedChild.getType()==child.getType())) if(!(phasedMother.getType()==mother.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%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()); 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.getLikelihoodsString(),
phasedChild.getGenotypeString(),phasedChild.getAttribute(VCFConstants.DEPTH_KEY),phasedChild.getAttribute("AD"),phasedChild.getLikelihoodsString());
} }
} }
else{ else{
@ -811,7 +818,10 @@ public class PhaseByTransmission extends RodWalker<HashMap<Byte,Integer>, HashMa
updatePairMetricsCounters(phasedFather,phasedChild,mvCount,metricsCounters); updatePairMetricsCounters(phasedFather,phasedChild,mvCount,metricsCounters);
if(!(phasedFather.getType()==father.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.:.:.:.\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.getLikelihoodsString(),
phasedChild.getGenotypeString(),phasedChild.getAttribute(VCFConstants.DEPTH_KEY),phasedChild.getAttribute("AD"),phasedChild.getLikelihoodsString());
} }
//Report violation if set so //Report violation if set so