package htsjdk.variant.vcf;
import java.io.File;
import htsjdk.variant.VariantBaseTest;
import htsjdk.variant.variantcontext.VariantContext;
import org.testng.Assert;
import org.testng.annotations.Test;
public class AbstractVCFCodecTest extends VariantBaseTest {
@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"));
}
}