/** * Returns a map from sampleName -> Genotype for each sampleName in sampleNames. Returns a map * for consistency with the multi-get function. * * For testing convenience only * * @param sampleNames a unique list of sample names * @return subsetting genotypes context * @throws IllegalArgumentException if sampleName isn't bound to a genotype */ protected GenotypesContext getGenotypes(Collection<String> sampleNames) { return getGenotypes().subsetToSamples(new HashSet<String>(sampleNames)); }
/** * Returns a map from sampleName -> Genotype for each sampleName in sampleNames. Returns a map * for consistency with the multi-get function. * * For testing convenience only * * @param sampleNames a unique list of sample names * @return subsetting genotypes context * @throws IllegalArgumentException if sampleName isn't bound to a genotype */ protected GenotypesContext getGenotypes(Collection<String> sampleNames) { return getGenotypes().subsetToSamples(new HashSet<>(sampleNames)); }
/** * Returns a map from sampleName -> Genotype for each sampleName in sampleNames. Returns a map * for consistency with the multi-get function. * * For testing convenience only * * @param sampleNames a unique list of sample names * @return subsetting genotypes context * @throws IllegalArgumentException if sampleName isn't bound to a genotype */ protected GenotypesContext getGenotypes(Collection<String> sampleNames) { return getGenotypes().subsetToSamples(new HashSet<>(sampleNames)); }
public GenotypesContext getGenotypes(Set<String> sampleNames) { return getGenotypes().subsetToSamples(sampleNames); }
public GenotypesContext getGenotypes(Set<String> sampleNames) { return getGenotypes().subsetToSamples(sampleNames); }
public GenotypesContext getGenotypes(Set<String> sampleNames) { return getGenotypes().subsetToSamples(sampleNames); }
} else { VariantContextBuilder builder = new VariantContextBuilder(this); GenotypesContext newGenotypes = genotypes.subsetToSamples(sampleNames);
} else { VariantContextBuilder builder = new VariantContextBuilder(this); GenotypesContext newGenotypes = genotypes.subsetToSamples(sampleNames);
} else { VariantContextBuilder builder = new VariantContextBuilder(this); GenotypesContext newGenotypes = genotypes.subsetToSamples(sampleNames);
/** Makes a new VariantContext with only the desired samples. */ private static VariantContext subsetToSamplesWithOriginalAnnotations(final VariantContext ctx, final Set<String> samples) { final VariantContextBuilder builder = new VariantContextBuilder(ctx); final GenotypesContext newGenotypes = ctx.getGenotypes().subsetToSamples(samples); builder.alleles(ctx.getAlleles()); return builder.genotypes(newGenotypes).make(); } }
/** Makes a new VariantContext with only the desired samples. */ private static VariantContext subsetToSamplesWithOriginalAnnotations(final VariantContext ctx, final Set<String> samples) { final VariantContextBuilder builder = new VariantContextBuilder(ctx); final GenotypesContext newGenotypes = ctx.getGenotypes().subsetToSamples(samples); builder.alleles(ctx.getAlleles()); return builder.genotypes(newGenotypes).make(); } }
builder.genotypes(ctx.getGenotypes().subsetToSamples(CollectionUtil.makeSet(trio.MOTHER, trio.FATHER, trio.OFFSPRING))); builder.attribute(MENDELIAN_VIOLATION_KEY, type.name());
builder.genotypes(ctx.getGenotypes().subsetToSamples(CollectionUtil.makeSet(trio.MOTHER, trio.FATHER, trio.OFFSPRING))); builder.attribute(MENDELIAN_VIOLATION_KEY, type.name());