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

Go to download

Show more of this group Show more artifacts with this name
Show all versions of SnpEff Show documentation

Variant annotation and effect prediction package.

The newest version!

package org.snpeff.snpEffect.testCases.integration;

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

/**
 * Test case
 */
public class TestCasesIntegrationHgvsFrameShift extends TestCasesIntegrationBase {

	public TestCasesIntegrationHgvsFrameShift() {
		super();
	}

	/**
	 * Test HGVS.P in a synonymous frame shift
	 */
	@Test
	public void test_01_hgvs_frameshift() {
		Gpr.debug("Test");
		checkHgvs("testHg19Chr1", path("hgvs_frameshifts_syn_chr1.vcf"), 4);
	}

	/**
	 * Test HGVS.P in a synonymous frame shift
	 */
	@Test
	public void test_02_hgvs_frameshift() {
		Gpr.debug("Test");
		checkHgvs("testHg19Chr4", path("hgvs_frameshifts_syn_chr4.vcf"), 2);
	}

	/**
	 * Test HGVS.P in a synonymous frame shift
	 */
	@Test
	public void test_03_hgvs_frameshift() {
		Gpr.debug("Test");
		checkHgvs("testHg19Chr10", path("hgvs_frameshifts_syn_chr10.vcf"), 2);
	}

	/**
	 * Test HGVS.P in a synonymous frame shift
	 */
	@Test
	public void test_04_hgvs_frameshift() {
		Gpr.debug("Test");
		checkHgvs("testHg19Chr17", path("hgvs_frameshifts_syn_chr17.vcf"), 2);
	}

	/**
	 * Test HGVS.P in a synonymous frame shift
	 */
	@Test
	public void test_05_hgvs_frameshift() {
		Gpr.debug("Test");
		checkHgvs("testHg19Chr19", path("hgvs_frameshifts_syn_chr19.vcf"), 2);
	}

	/**
	 * Test HGVS frameshift at CDS end
	 */
	@Test
	public void test_06_hgvs_frameshift() {
		Gpr.debug("Test");
		checkHgvs("testHg3775Chr2", path("hgvs_frameshifts_cds_end.vcf"), 6);
	}

}