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

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Variant annotation and effect prediction package.

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package org.snpeff.snpEffect.testCases.integration;

import org.junit.Test;
import org.snpeff.SnpEff;
import org.snpeff.util.Gpr;

/**
 * Invoke all integration test cases
 *
 * @author pcingola
 */
public class TestCasesIntegrationSnpEff extends IntegrationTest {

	@Test
	public void test_01() {
		Gpr.debug("Test");
		String expectedOutputFile = path("test.chr1.1line.out.classic.vcf");
		String args[] = { "eff", "-classic", "-noHgvs", "-noStats", "-noLog", "-noLof", "testHg3763Chr1", path("test.chr1.1line.vcf") };
		command(new SnpEff(args), expectedOutputFile);
	}

}