public boolean containsSamples(final Collection<String> samples) { return getSampleNames().containsAll(samples); }
assertEqualsSet(gc.getSampleNames(), genotypeNames, "gc sample names vs. expected sample names"); Assert.assertTrue(ParsingUtils.isSorted(gc.getSampleNamesOrderedByName())); Assert.assertTrue(ParsingUtils.isSorted(gc.iterateInSampleNameOrder()));
public boolean containsSamples(final Collection<String> samples) { return getSampleNames().containsAll(samples); }
/** * @return the set of all sample names in this context, not ordered */ public Set<String> getSampleNames() { return getGenotypes().getSampleNames(); }
/** * @return the set of all sample names in this context, not ordered */ public Set<String> getSampleNames() { return getGenotypes().getSampleNames(); }
@Requires("samples != null") public boolean containsSamples(final Collection<String> samples) { return getSampleNames().containsAll(samples); }
/** * @return the set of all sample names in this context, not ordered */ public Set<String> getSampleNames() { return getGenotypes().getSampleNames(); }
public void calculateRawData(final VariantContext vc, final Map<String, PerReadAlleleLikelihoodMap> pralm, final ReducibleAnnotationData myData) { if( vc.getGenotypes().getSampleNames().size() != 1) throw new IllegalStateException("Calculating raw data for allele-specific rank sums requires variant context input with exactly one sample, as in a gVCF."); if(pralm == null) return; final Map<Allele, CompressedDataList<Integer>> perAlleleValues = myData.getAttributeMap(); for ( final PerReadAlleleLikelihoodMap likelihoodMap : pralm.values() ) { if ( likelihoodMap != null && !likelihoodMap.isEmpty() ) { fillQualsFromLikelihoodMap(vc.getGenotype(0).getAlleles(), vc.getStart(), likelihoodMap, perAlleleValues); } } }
Assert.assertTrue(sub.getGenotypes().getSampleNames().equals(expectedGC.getSampleNames()));