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Added subContextOfSamples to VariantContext 

-- This is a more convenient accesssor than subContextOfGenotypes, represents nearly all of the use cases of the former function, and potentially can be implemented more efficiently.
This commit is contained in:
Mark DePristo 2011-11-11 10:07:11 -05:00
parent e216e85465
commit ef9f8b5d46
3 changed files with 19 additions and 9 deletions
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2
public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/VariantEvalUtils.java
View File

@ -277,7 +277,7 @@ public class VariantEvalUtils {
* @return a new VariantContext with just the requested samples
*/
public VariantContext getSubsetOfVariantContext(VariantContext vc, Collection<String> sampleNames) {
VariantContext vcsub = vc.subContextFromGenotypes(vc.getGenotypes(sampleNames).values(), vc.getAlleles());
VariantContext vcsub = vc.subContextFromSamples(sampleNames, vc.getAlleles());
HashMap<String, Object> newAts = new HashMap<String, Object>(vcsub.getAttributes());

8
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
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@ -659,13 +659,7 @@ public class SelectVariants extends RodWalker<Integer, Integer> {
if ( samples == null || samples.isEmpty() )
return vc;
ArrayList<Genotype> genotypes = new ArrayList<Genotype>();
for ( Map.Entry<String, Genotype> genotypePair : vc.getGenotypes().entrySet() ) {
if ( samples.contains(genotypePair.getKey()) )
genotypes.add(genotypePair.getValue());
}
VariantContext sub = vc.subContextFromGenotypes(genotypes, vc.getAlleles());
VariantContext sub = vc.subContextFromSamples(samples);
// if we have fewer alternate alleles in the selected VC than in the original VC, we need to strip out the GL/PLs (because they are no longer accurate)
if ( vc.getAlleles().size() != sub.getAlleles().size() )

18
public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java
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@ -446,9 +446,25 @@ public class VariantContext implements Feature { // to enable tribble intergrati
* @return vc subcontext
*/
public VariantContext subContextFromGenotypes(Collection<Genotype> genotypes, Collection<Allele> alleles) {
return new VariantContext(getSource(), contig, start, stop, alleles, genotypes != null ? genotypeCollectionToMap(new TreeMap<String, Genotype>(), genotypes) : null, getNegLog10PError(), filtersWereApplied() ? getFilters() : null, getAttributes(), getReferenceBaseForIndel());
return new VariantContext(getSource(), contig, start, stop, alleles,
genotypes != null ? genotypeCollectionToMap(new TreeMap<String, Genotype>(), genotypes) : null,
getNegLog10PError(),
filtersWereApplied() ? getFilters() : null,
getAttributes(),
getReferenceBaseForIndel());
}
public VariantContext subContextFromSamples(Collection<String> sampleNames, Collection<Allele> alleles) {
return subContextFromGenotypes(getGenotypes(sampleNames).values(), alleles);
}
public VariantContext subContextFromSamples(Collection<String> sampleNames) {
return subContextFromGenotypes(getGenotypes(sampleNames).values());
}
public VariantContext subContextFromSample(String sampleName) {
return subContextFromGenotypes(getGenotype(sampleName));
}
/**
* helper routine for subcontext