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Proper use of builder. Previous conversion attempt was flawed

This commit is contained in:
Mark DePristo 2011-11-19 22:09:56 -05:00
parent 7d09c0064b
commit f392d330c3
1 changed files with 10 additions and 4 deletions
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14
public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java
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@ -1122,7 +1122,7 @@ public class ReadBackedPhasingWalker extends RodWalker<PhasingStatsAndOutput, Ph
private int start;
private int stop;
private Collection<Allele> alleles;
private GenotypesContext genotypes;
private Map<String,Genotype> genotypes;
private double log10PError;
private Set<String> filters;
private Map<String, Object> attributes;
@ -1135,15 +1135,21 @@ public class ReadBackedPhasingWalker extends RodWalker<PhasingStatsAndOutput, Ph
this.start = vc.getStart();
this.stop = vc.getEnd();
this.alleles = vc.getAlleles();
this.genotypes = GenotypesContext.copy(vc.getGenotypes()); // since vc.getGenotypes() is unmodifiable
this.genotypes = new HashMap<String, Genotype>();
for ( final Genotype g : vc.getGenotypes() ) {
this.genotypes.put(g.getSampleName(), g);
}
this.log10PError = vc.getLog10PError();
this.filters = vc.filtersWereApplied() ? vc.getFilters() : null;
this.attributes = new HashMap<String, Object>(vc.getAttributes());
}
public VariantContext toVariantContext() {
GenotypesContext gc = GenotypesContext.copy(this.genotypes.values());
return new VariantContextBuilder(name, contig, start, stop, alleles).id(id)
.genotypes(genotypes).log10PError(log10PError).filters(filters).attributes(attributes).make();
.genotypes(gc).log10PError(log10PError).filters(filters).attributes(attributes).make();
}
public GenomeLoc getLocation() {
@ -1155,7 +1161,7 @@ public class ReadBackedPhasingWalker extends RodWalker<PhasingStatsAndOutput, Ph
}
public void setGenotype(String sample, Genotype newGt) {
genotypes.add(newGt);
this.genotypes.put(sample, newGt);
}
public void setPhasingInconsistent() {