private void validateGenotypes() { if ( this.genotypes == null ) throw new IllegalStateException("Genotypes is null"); for ( final Genotype g : this.genotypes ) { if ( g.isAvailable() ) { for ( Allele gAllele : g.getAlleles() ) { if ( ! hasAllele(gAllele) && gAllele.isCalled() ) throw new IllegalStateException("Allele in genotype " + gAllele + " not in the variant context " + alleles); } } } }
/** * helper routine for subcontext * @param genotypes genotypes * @return allele set */ private final Set<Allele> allelesOfGenotypes(Collection<Genotype> genotypes) { final Set<Allele> alleles = new HashSet<>(); boolean addedref = false; for ( final Genotype g : genotypes ) { for ( final Allele a : g.getAlleles() ) { addedref = addedref || a.isReference(); if ( a.isCalled() ) alleles.add(a); } } if ( ! addedref ) alleles.add(getReference()); return alleles; }
/** * helper routine for subcontext * @param genotypes genotypes * @return allele set */ private final Set<Allele> allelesOfGenotypes(Collection<Genotype> genotypes) { final Set<Allele> alleles = new HashSet<>(); boolean addedref = false; for ( final Genotype g : genotypes ) { for ( final Allele a : g.getAlleles() ) { addedref = addedref || a.isReference(); if ( a.isCalled() ) alleles.add(a); } } if ( ! addedref ) alleles.add(getReference()); return alleles; }
/** * helper routine for subcontext * @param genotypes genotypes * @return allele set */ private final Set<Allele> allelesOfGenotypes(Collection<Genotype> genotypes) { final Set<Allele> alleles = new HashSet<Allele>(); boolean addedref = false; for ( final Genotype g : genotypes ) { for ( final Allele a : g.getAlleles() ) { addedref = addedref || a.isReference(); if ( a.isCalled() ) alleles.add(a); } } if ( ! addedref ) alleles.add(getReference()); return alleles; }
private void validateGenotypes() { if ( this.genotypes == null ) throw new IllegalStateException("Genotypes is null"); for ( int i = 0; i < genotypes.size(); i++ ) { Genotype genotype = genotypes.get(i); if ( genotype.isAvailable() ) { final List<Allele> alleles = genotype.getAlleles(); for ( int j = 0, size = alleles.size(); j < size; j++ ) { final Allele gAllele = alleles.get(j); if ( ! hasAllele(gAllele) && gAllele.isCalled() ) throw new IllegalStateException("Allele in genotype " + gAllele + " not in the variant context " + alleles); } } } }
private void validateGenotypes() { if ( this.genotypes == null ) throw new IllegalStateException("Genotypes is null"); for ( int i = 0; i < genotypes.size(); i++ ) { Genotype genotype = genotypes.get(i); if ( genotype.isAvailable() ) { final List<Allele> alleles = genotype.getAlleles(); for ( int j = 0, size = alleles.size(); j < size; j++ ) { final Allele gAllele = alleles.get(j); if ( ! hasAllele(gAllele) && gAllele.isCalled() ) throw new IllegalStateException("Allele in genotype " + gAllele + " not in the variant context " + alleles); } } } }
@Test public void testCreatingNoCallAlleles() { Assert.assertTrue(NoCall.isNonReference()); Assert.assertFalse(NoCall.isReference()); Assert.assertFalse(NoCall.basesMatch(Allele.NO_CALL_STRING)); Assert.assertEquals(NoCall.length(), 0); Assert.assertTrue(NoCall.isNoCall()); Assert.assertFalse(NoCall.isCalled()); }
} else if (a.isCalled()) { final Allele newAllele; if (extraBaseCount > 0) {
if (allele.isCalled()) { String alleleString = allele.toString(); alleleCounts.putIfAbsent(alleleString, 0);
if (allele.isCalled()) { hasCalledAlleles = true; break;