@Test public void shouldPreserveSymbolicAlleleCase() { VCFFileReader reader = new VCFFileReader(new File(VariantBaseTest.variantTestDataRoot + "breakpoint.vcf"), false); VariantContext variant = reader.iterator().next(); reader.close(); // VCF v4.1 s1.4.5 // Tools processing VCF files are not required to preserve case in the allele String, except for // IDs, which are case sensitive. Assert.assertTrue(variant.getAlternateAllele(0).getDisplayString().contains("chr12")); }