org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationInsEtc Maven / Gradle / Ivy

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Variant annotation and effect prediction package.

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package org.snpeff.snpEffect.testCases.integration;

import java.util.List;

import org.junit.Assert;
import org.junit.Test;
import org.snpeff.SnpEff;
import org.snpeff.snpEffect.commandLine.SnpEffCmdEff;
import org.snpeff.util.Gpr;
import org.snpeff.vcf.VcfEffect;
import org.snpeff.vcf.VcfEntry;

/**
 * Test random SNP changes
 *
 * @author pcingola
 */
public class TestCasesIntegrationInsEtc extends TestCasesIntegrationBase {

	/**
	 * Insertion on minus strand
	 */
	@Test
	public void test_01_InsOffByOne() {
		Gpr.debug("Test");
		String args[] = { "-classic", "-noHgvs", "testENST00000268124", path("ins_off_by_one.vcf") };

		SnpEff cmd = new SnpEff(args);
		SnpEffCmdEff snpeff = (SnpEffCmdEff) cmd.cmd();
		snpeff.setSupressOutput(!verbose);
		snpeff.setVerbose(verbose);

		List vcfEnties = snpeff.run(true);
		for (VcfEntry ve : vcfEnties) {

			// Get first effect (there should be only one)
			List veffs = ve.getVcfEffects();
			VcfEffect veff = veffs.get(0);

			Assert.assertEquals("Q53QQ", veff.getAa());
		}
	}

}