private static void makeSyntheticTests() { VariantContextBuilder rootBuilder = new VariantContextBuilder(); rootBuilder.source("test"); rootBuilder.loc("1", 10, 10); rootBuilder.alleles("A", "C"); rootBuilder.unfiltered(); ROOT = rootBuilder.make(); add(builder()); add(builder().alleles("A")); add(builder().alleles("A", "C", "T")); add(builder().alleles("A", "AC")); add(builder().alleles("A", "ACAGT")); add(builder().loc("1", 10, 11).alleles("AC", "A")); add(builder().loc("1", 10, 13).alleles("ACGT", "A")); // make sure filters work add(builder().unfiltered()); add(builder().passFilters()); add(builder().filters("FILTER1")); add(builder().filters("FILTER1", "FILTER2")); add(builder().log10PError(VariantContext.NO_LOG10_PERROR)); add(builder().log10PError(-1)); add(builder().log10PError(-1.234e6)); add(builder().noID()); add(builder().id("rsID12345")); add(builder().attribute("INT1", 1)); add(builder().attribute("INT1", 100)); add(builder().attribute("INT1", 1000)); add(builder().attribute("INT1", 100000)); add(builder().attribute("INT1", null)); add(builder().attribute("INT3", Arrays.asList(1, 2, 3))); add(builder().attribute("INT3", Arrays.asList(1000, 2000, 3000))); add(builder().attribute("INT3", Arrays.asList(100000, 200000, 300000))); add(builder().attribute("INT3", null)); add(builder().attribute("INT20", TWENTY_INTS)); add(builder().attribute("FLOAT1", 1.0)); add(builder().attribute("FLOAT1", 100.0)); add(builder().attribute("FLOAT1", 1000.0)); add(builder().attribute("FLOAT1", 100000.0)); add(builder().attribute("FLOAT1", null)); add(builder().attribute("FLOAT3", Arrays.asList(1.0, 2.0, 3.0))); add(builder().attribute("FLOAT3", Arrays.asList(1000.0, 2000.0, 3000.0))); add(builder().attribute("FLOAT3", Arrays.asList(100000.0, 200000.0, 300000.0))); add(builder().attribute("FLOAT3", null)); add(builder().attribute("FLAG", true)); // add(builder().attribute("FLAG", false)); // NOTE -- VCF doesn't allow false flags add(builder().attribute("STRING1", "s1")); add(builder().attribute("STRING1", null)); add(builder().attribute("STRING3", Arrays.asList("s1", "s2", "s3"))); add(builder().attribute("STRING3", null)); add( builder() .attribute( "STRING20", Arrays.asList( "s1", "s2", "s3", "s4", "s5", "s6", "s7", "s8", "s9", "s10", "s11", "s12", "s13", "s14", "s15", "s16", "s17", "s18", "s19", "s20"))); add(builder().attribute("VAR.INFO.STRING", "s1")); add(builder().attribute("VAR.INFO.STRING", Arrays.asList("s1", "s2"))); add(builder().attribute("VAR.INFO.STRING", Arrays.asList("s1", "s2", "s3"))); add(builder().attribute("VAR.INFO.STRING", null)); if (ENABLE_GENOTYPE_TESTS) { addGenotypesToTestData(); addComplexGenotypesTest(); } if (ENABLE_A_AND_G_TESTS) addGenotypesAndGTests(); if (ENABLE_SYMBOLIC_ALLELE_TESTS) addSymbolicAlleleTests(); }