4ff8225d787bbb96cfd472a186068a4d01e66802,public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextUnitTest.java,VariantContextUnitTest,testVCromGenotypes,#,425
Before Change
Genotype g5 = new Genotype("--", Arrays.asList(del, del), 10);
VariantContext vc = new VariantContext("test", snpLoc,snpLocStart, snpLocStop , alleles, Arrays.asList(g1,g2,g3,g4,g5));
VariantContext vc12 = vc.subContextFromGenotypes(Arrays.asList(g1,g2));
VariantContext vc1 = vc.subContextFromGenotypes(Arrays.asList(g1));
VariantContext vc23 = vc.subContextFromGenotypes(Arrays.asList(g2, g3));
VariantContext vc4 = vc.subContextFromGenotypes(Arrays.asList(g4));
VariantContext vc14 = vc.subContextFromGenotypes(Arrays.asList(g1, g4));
VariantContext vc5 = vc.subContextFromGenotypes(Arrays.asList(g5));
After Change
public void testVCromGenotypes() {
List<Allele> alleles = Arrays.asList(Aref, T, del);
Genotype g1 = new Genotype("AA", Arrays.asList(Aref, Aref), 10);
Genotype g2 = new Genotype("AT", Arrays.asList(Aref, T), 10);
Genotype g3 = new Genotype("TT", Arrays.asList(T, T), 10);
Genotype g4 = new Genotype("..", Arrays.asList(Allele.NO_CALL, Allele.NO_CALL), 10);
Genotype g5 = new Genotype("--", Arrays.asList(del, del), 10);
VariantContext vc = new VariantContext("test", snpLoc,snpLocStart, snpLocStop , alleles, Arrays.asList(g1,g2,g3,g4,g5));
VariantContext vc12 = vc.subContextFromSamples(new HashSet<String>(Arrays.asList(g1.getSampleName(),g2.getSampleName())));
VariantContext vc1 = vc.subContextFromSamples(new HashSet<String>(Arrays.asList(g1.getSampleName())));
VariantContext vc23 = vc.subContextFromSamples(new HashSet<String>(Arrays.asList(g2.getSampleName(), g3.getSampleName())));
VariantContext vc4 = vc.subContextFromSamples(new HashSet<String>(Arrays.asList(g4.getSampleName())));
VariantContext vc14 = vc.subContextFromSamples(new HashSet<String>(Arrays.asList(g1.getSampleName(), g4.getSampleName())));
VariantContext vc5 = vc.subContextFromSamples(new HashSet<String>(Arrays.asList(g5.getSampleName())));
Assert.assertTrue(vc12.isPolymorphic());