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Added reporting of the number of genotypes updated.

This commit is contained in:
Laurent Francioli 2011-11-08 15:15:51 +01:00
parent 385a6abec1
commit 571c724cfd
1 changed files with 16 additions and 1 deletions
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17
public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmission.java
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@ -113,6 +113,7 @@ public class PhaseByTransmission extends RodWalker<HashMap<Byte,Integer>, HashMa
private final Byte NUM_PAIR_GENOTYPES_PHASED = 7;
private final Byte NUM_PAIR_HET_HET = 8;
private final Byte NUM_PAIR_VIOLATIONS = 9;
private final Byte NUM_GENOTYPES_MODIFIED = 11;
//Random number generator
private Random rand = new Random();
@ -742,6 +743,8 @@ public class PhaseByTransmission extends RodWalker<HashMap<Byte,Integer>, HashMa
metricsCounters.put(NUM_PAIR_HET_HET,0);
metricsCounters.put(NUM_PAIR_VIOLATIONS,0);
metricsCounters.put(NUM_TRIO_DOUBLE_VIOLATIONS,0);
metricsCounters.put(NUM_GENOTYPES_MODIFIED,0);
String mvfLine;
if (tracker != null) {
@ -775,15 +778,21 @@ public class PhaseByTransmission extends RodWalker<HashMap<Byte,Integer>, HashMa
genotypeMap.put(phasedFather.getSampleName(), phasedFather);
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());
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{
updatePairMetricsCounters(phasedMother,phasedChild,mvCount,metricsCounters);
if(!(phasedMother.getType()==mother.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%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{
genotypeMap.put(phasedFather.getSampleName(),phasedFather);
updatePairMetricsCounters(phasedFather,phasedChild,mvCount,metricsCounters);
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());
}
@ -820,7 +829,9 @@ public class PhaseByTransmission extends RodWalker<HashMap<Byte,Integer>, HashMa
metricsCounters.put(NUM_PAIR_GENOTYPES_PHASED,0);
metricsCounters.put(NUM_PAIR_HET_HET,0);
metricsCounters.put(NUM_PAIR_VIOLATIONS,0);
metricsCounters.put(NUM_TRIO_DOUBLE_VIOLATIONS,0);
metricsCounters.put(NUM_TRIO_DOUBLE_VIOLATIONS,0);
metricsCounters.put(NUM_GENOTYPES_MODIFIED,0);
return metricsCounters;
}
@ -844,6 +855,8 @@ public class PhaseByTransmission extends RodWalker<HashMap<Byte,Integer>, HashMa
sum.put(NUM_PAIR_HET_HET,value.get(NUM_PAIR_HET_HET)+sum.get(NUM_PAIR_HET_HET));
sum.put(NUM_PAIR_VIOLATIONS,value.get(NUM_PAIR_VIOLATIONS)+sum.get(NUM_PAIR_VIOLATIONS));
sum.put(NUM_TRIO_DOUBLE_VIOLATIONS,value.get(NUM_TRIO_DOUBLE_VIOLATIONS)+sum.get(NUM_TRIO_DOUBLE_VIOLATIONS));
sum.put(NUM_GENOTYPES_MODIFIED,value.get(NUM_GENOTYPES_MODIFIED)+sum.get(NUM_GENOTYPES_MODIFIED));
return sum;
}
@ -865,5 +878,7 @@ public class PhaseByTransmission extends RodWalker<HashMap<Byte,Integer>, HashMa
logger.info("Number of pair-genotypes phased: " + result.get(NUM_PAIR_GENOTYPES_PHASED));
logger.info("Number of resulting Het/Het pairs: " + result.get(NUM_PAIR_HET_HET));
logger.info("Number of remaining mendelian violations in pairs: " + result.get(NUM_PAIR_VIOLATIONS));
logger.info("Number of genotypes updated: " + result.get(NUM_GENOTYPES_MODIFIED));
}
}