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Fixed a bug in parent/child pairs reporting causing a crash in case the -mvf option was used and mother was not provided

This commit is contained in:
Laurent Francioli 2011-11-02 08:22:33 +01:00
parent b91a9c4711
commit 119ca7d742
1 changed files with 7 additions and 2 deletions
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9
public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmission.java
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@ -681,6 +681,7 @@ public class PhaseByTransmission extends RodWalker<HashMap<Byte,Integer>, HashMa
metricsCounters.put(NUM_PAIR_GENOTYPES_PHASED,0); metricsCounters.put(NUM_PAIR_GENOTYPES_PHASED,0);
metricsCounters.put(NUM_PAIR_HET_HET,0); metricsCounters.put(NUM_PAIR_HET_HET,0);
metricsCounters.put(NUM_PAIR_VIOLATIONS,0); metricsCounters.put(NUM_PAIR_VIOLATIONS,0);
String mvfLine = "";
if (tracker != null) { if (tracker != null) {
VariantContext vc = tracker.getFirstValue(variantCollection.variants, context.getLocation()); VariantContext vc = tracker.getFirstValue(variantCollection.variants, context.getLocation());
@ -712,19 +713,23 @@ public class PhaseByTransmission extends RodWalker<HashMap<Byte,Integer>, HashMa
if(father != null){ if(father != null){
genotypeMap.put(phasedFather.getSampleName(), phasedFather); genotypeMap.put(phasedFather.getSampleName(), phasedFather);
updateTrioMetricsCounters(phasedMother,phasedFather,phasedChild,isMV,metricsCounters); updateTrioMetricsCounters(phasedMother,phasedFather,phasedChild,isMV,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());
} }
else else{
updatePairMetricsCounters(phasedMother,phasedChild,isMV,metricsCounters); updatePairMetricsCounters(phasedMother,phasedChild,isMV,metricsCounters);
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());
}
} }
else{ else{
genotypeMap.put(phasedFather.getSampleName(),phasedFather); genotypeMap.put(phasedFather.getSampleName(),phasedFather);
updatePairMetricsCounters(phasedFather,phasedChild,isMV,metricsCounters); updatePairMetricsCounters(phasedFather,phasedChild,isMV,metricsCounters);
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());
} }
//Report violation if set so //Report violation if set so
//TODO: ADAPT FOR PAIRS TOO!! //TODO: ADAPT FOR PAIRS TOO!!
if(isMV && mvFile != null) if(isMV && mvFile != null)
mvFile.println(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())); mvFile.println(mvfLine);
} }