public static void addComplexGenotypesTest() { final List<Allele> allAlleles = Arrays.asList( Allele.create("A", true), Allele.create("C", false), Allele.create("G", false)); for (int nAlleles : Arrays.asList(2, 3)) { for (int highestPloidy : Arrays.asList(1, 2, 3)) { // site alleles final List<Allele> siteAlleles = allAlleles.subList(0, nAlleles); // possible alleles for genotypes final List<Allele> possibleGenotypeAlleles = new ArrayList<Allele>(siteAlleles); possibleGenotypeAlleles.add(Allele.NO_CALL); // there are n^ploidy possible genotypes final List<List<Allele>> possibleGenotypes = makeAllGenotypes(possibleGenotypeAlleles, highestPloidy); final int nPossibleGenotypes = possibleGenotypes.size(); VariantContextBuilder vb = new VariantContextBuilder("unittest", "1", 1, 1, siteAlleles); // first test -- create n copies of each genotype for (int i = 0; i < nPossibleGenotypes; i++) { final List<Genotype> samples = new ArrayList<Genotype>(3); samples.add(GenotypeBuilder.create("sample" + i, possibleGenotypes.get(i))); add(vb.genotypes(samples)); } // second test -- create one sample with each genotype { final List<Genotype> samples = new ArrayList<Genotype>(nPossibleGenotypes); for (int i = 0; i < nPossibleGenotypes; i++) { samples.add(GenotypeBuilder.create("sample" + i, possibleGenotypes.get(i))); } add(vb.genotypes(samples)); } // test mixed ploidy for (int i = 0; i < nPossibleGenotypes; i++) { for (int ploidy = 1; ploidy < highestPloidy; ploidy++) { final List<Genotype> samples = new ArrayList<Genotype>(highestPloidy); final List<Allele> genotype = possibleGenotypes.get(i).subList(0, ploidy); samples.add(GenotypeBuilder.create("sample" + i, genotype)); add(vb.genotypes(samples)); } } } } }
private static Genotype attr( final String name, final Allele ref, final String key, final Object... value) { if (value.length == 0) return GenotypeBuilder.create(name, Arrays.asList(ref, ref)); else { final Object toAdd = value.length == 1 ? value[0] : Arrays.asList(value); return new GenotypeBuilder(name, Arrays.asList(ref, ref)).attribute(key, toAdd).make(); } }
private static void addGenotypes(final VariantContext site) { // test ref/ref final Allele ref = site.getReference(); final Allele alt1 = site.getNAlleles() > 1 ? site.getAlternateAllele(0) : null; final Genotype homRef = GenotypeBuilder.create("homRef", Arrays.asList(ref, ref)); addGenotypeTests(site, homRef); if (alt1 != null) { final Genotype het = GenotypeBuilder.create("het", Arrays.asList(ref, alt1)); final Genotype homVar = GenotypeBuilder.create("homVar", Arrays.asList(alt1, alt1)); addGenotypeTests(site, homRef, het); addGenotypeTests(site, homRef, het, homVar); // test no GT at all addGenotypeTests( site, new GenotypeBuilder("noGT", new ArrayList<Allele>(0)).attribute("INT1", 10).make()); final List<Allele> noCall = Arrays.asList(Allele.NO_CALL, Allele.NO_CALL); // ploidy if (ENABLE_PLOIDY_TESTS) { addGenotypeTests( site, GenotypeBuilder.create("dip", Arrays.asList(ref, alt1)), GenotypeBuilder.create("hap", Arrays.asList(ref))); addGenotypeTests( site, GenotypeBuilder.create("noCall", noCall), GenotypeBuilder.create("dip", Arrays.asList(ref, alt1)), GenotypeBuilder.create("hap", Arrays.asList(ref))); addGenotypeTests( site, GenotypeBuilder.create("noCall", noCall), GenotypeBuilder.create("noCall2", noCall), GenotypeBuilder.create("dip", Arrays.asList(ref, alt1)), GenotypeBuilder.create("hap", Arrays.asList(ref))); addGenotypeTests( site, GenotypeBuilder.create("dip", Arrays.asList(ref, alt1)), GenotypeBuilder.create("tet", Arrays.asList(ref, alt1, alt1))); addGenotypeTests( site, GenotypeBuilder.create("noCall", noCall), GenotypeBuilder.create("dip", Arrays.asList(ref, alt1)), GenotypeBuilder.create("tet", Arrays.asList(ref, alt1, alt1))); addGenotypeTests( site, GenotypeBuilder.create("noCall", noCall), GenotypeBuilder.create("noCall2", noCall), GenotypeBuilder.create("dip", Arrays.asList(ref, alt1)), GenotypeBuilder.create("tet", Arrays.asList(ref, alt1, alt1))); addGenotypeTests( site, GenotypeBuilder.create("nocall", noCall), GenotypeBuilder.create("dip", Arrays.asList(ref, alt1)), GenotypeBuilder.create("tet", Arrays.asList(ref, alt1, alt1))); } // // // TESTING PHASE // // final Genotype gUnphased = new GenotypeBuilder("gUnphased", Arrays.asList(ref, alt1)).make(); final Genotype gPhased = new GenotypeBuilder("gPhased", Arrays.asList(ref, alt1)).phased(true).make(); final Genotype gPhased2 = new GenotypeBuilder("gPhased2", Arrays.asList(alt1, alt1)).phased(true).make(); final Genotype gPhased3 = new GenotypeBuilder("gPhased3", Arrays.asList(ref, ref)).phased(true).make(); final Genotype haploidNoPhase = new GenotypeBuilder("haploidNoPhase", Arrays.asList(ref)).make(); addGenotypeTests(site, gUnphased, gPhased); addGenotypeTests(site, gUnphased, gPhased2); addGenotypeTests(site, gUnphased, gPhased3); addGenotypeTests(site, gPhased, gPhased2); addGenotypeTests(site, gPhased, gPhased3); addGenotypeTests(site, gPhased2, gPhased3); addGenotypeTests(site, haploidNoPhase, gPhased); addGenotypeTests(site, haploidNoPhase, gPhased2); addGenotypeTests(site, haploidNoPhase, gPhased3); addGenotypeTests(site, haploidNoPhase, gPhased, gPhased2); addGenotypeTests(site, haploidNoPhase, gPhased, gPhased3); addGenotypeTests(site, haploidNoPhase, gPhased2, gPhased3); addGenotypeTests(site, haploidNoPhase, gPhased, gPhased2, gPhased3); final Genotype gUnphasedTet = new GenotypeBuilder("gUnphasedTet", Arrays.asList(ref, alt1, ref, alt1)).make(); final Genotype gPhasedTet = new GenotypeBuilder("gPhasedTet", Arrays.asList(ref, alt1, alt1, alt1)) .phased(true) .make(); addGenotypeTests(site, gUnphasedTet, gPhasedTet); } if (ENABLE_PL_TESTS) { if (site.getNAlleles() == 2) { // testing PLs addGenotypeTests( site, GenotypeBuilder.create("g1", Arrays.asList(ref, ref), new double[] {0, -1, -2}), GenotypeBuilder.create("g2", Arrays.asList(ref, ref), new double[] {0, -2, -3})); addGenotypeTests( site, GenotypeBuilder.create("g1", Arrays.asList(ref, ref), new double[] {-1, 0, -2}), GenotypeBuilder.create("g2", Arrays.asList(ref, ref), new double[] {0, -2, -3})); addGenotypeTests( site, GenotypeBuilder.create("g1", Arrays.asList(ref, ref), new double[] {-1, 0, -2}), GenotypeBuilder.create("g2", Arrays.asList(ref, ref), new double[] {0, -2000, -1000})); addGenotypeTests( site, // missing PLs GenotypeBuilder.create("g1", Arrays.asList(ref, ref), new double[] {-1, 0, -2}), GenotypeBuilder.create("g2", Arrays.asList(ref, ref))); } else if (site.getNAlleles() == 3) { // testing PLs addGenotypeTests( site, GenotypeBuilder.create( "g1", Arrays.asList(ref, ref), new double[] {0, -1, -2, -3, -4, -5}), GenotypeBuilder.create( "g2", Arrays.asList(ref, ref), new double[] {0, -2, -3, -4, -5, -6})); } } // test attributes addGenotypeTests(site, attr("g1", ref, "INT1", 1), attr("g2", ref, "INT1", 2)); addGenotypeTests(site, attr("g1", ref, "INT1", 1), attr("g2", ref, "INT1")); addGenotypeTests(site, attr("g1", ref, "INT3", 1, 2, 3), attr("g2", ref, "INT3", 4, 5, 6)); addGenotypeTests(site, attr("g1", ref, "INT3", 1, 2, 3), attr("g2", ref, "INT3")); addGenotypeTests( site, attr("g1", ref, "INT20", TWENTY_INTS), attr("g2", ref, "INT20", TWENTY_INTS)); if (ENABLE_VARARRAY_TESTS) { addGenotypeTests( site, attr("g1", ref, "INT.VAR", 1, 2, 3), attr("g2", ref, "INT.VAR", 4, 5), attr("g3", ref, "INT.VAR", 6)); addGenotypeTests( site, attr("g1", ref, "INT.VAR", 1, 2, 3), attr("g2", ref, "INT.VAR"), attr("g3", ref, "INT.VAR", 5)); } addGenotypeTests(site, attr("g1", ref, "FLOAT1", 1.0), attr("g2", ref, "FLOAT1", 2.0)); addGenotypeTests(site, attr("g1", ref, "FLOAT1", 1.0), attr("g2", ref, "FLOAT1")); addGenotypeTests( site, attr("g1", ref, "FLOAT3", 1.0, 2.0, 3.0), attr("g2", ref, "FLOAT3", 4.0, 5.0, 6.0)); addGenotypeTests(site, attr("g1", ref, "FLOAT3", 1.0, 2.0, 3.0), attr("g2", ref, "FLOAT3")); if (ENABLE_VARIABLE_LENGTH_GENOTYPE_STRING_TESTS) { // // // TESTING MULTIPLE SIZED LISTS IN THE GENOTYPE FIELD // // addGenotypeTests( site, attr("g1", ref, "GS", Arrays.asList("S1", "S2")), attr("g2", ref, "GS", Arrays.asList("S3", "S4"))); addGenotypeTests( site, // g1 is missing the string, and g2 is missing FLOAT1 attr("g1", ref, "FLOAT1", 1.0), attr("g2", ref, "GS", Arrays.asList("S3", "S4"))); // variable sized lists addGenotypeTests( site, attr("g1", ref, "GV", "S1"), attr("g2", ref, "GV", Arrays.asList("S3", "S4"))); addGenotypeTests( site, attr("g1", ref, "GV", Arrays.asList("S1", "S2")), attr("g2", ref, "GV", Arrays.asList("S3", "S4", "S5"))); addGenotypeTests( site, // missing value in varlist of string attr("g1", ref, "FLOAT1", 1.0), attr("g2", ref, "GV", Arrays.asList("S3", "S4", "S5"))); } // // // TESTING GENOTYPE FILTERS // // addGenotypeTests( site, new GenotypeBuilder("g1-x", Arrays.asList(ref, ref)).filters("X").make(), new GenotypeBuilder("g2-x", Arrays.asList(ref, ref)).filters("X").make()); addGenotypeTests( site, new GenotypeBuilder("g1-unft", Arrays.asList(ref, ref)).unfiltered().make(), new GenotypeBuilder("g2-x", Arrays.asList(ref, ref)).filters("X").make()); addGenotypeTests( site, new GenotypeBuilder("g1-unft", Arrays.asList(ref, ref)).unfiltered().make(), new GenotypeBuilder("g2-xy", Arrays.asList(ref, ref)).filters("X", "Y").make()); addGenotypeTests( site, new GenotypeBuilder("g1-unft", Arrays.asList(ref, ref)).unfiltered().make(), new GenotypeBuilder("g2-x", Arrays.asList(ref, ref)).filters("X").make(), new GenotypeBuilder("g3-xy", Arrays.asList(ref, ref)).filters("X", "Y").make()); }
private Genotype makeG(String sample, Allele a1, Allele a2) { return GenotypeBuilder.create(sample, Arrays.asList(a1, a2)); }