org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationTranscriptError 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.snpEffect.VariantEffect.ErrorWarningType;
import org.snpeff.util.Gpr;

/**
 * Test case where VCF entries hit a transcript that has errors
 *
 * @author pcingola
 */
public class TestCasesIntegrationTranscriptError extends TestCasesIntegrationBase {

	public TestCasesIntegrationTranscriptError() {
		super();
	}

	@Test
	public void test_01() {
		Gpr.debug("Test");
		String args[] = { "-classic", "testHg3763Chr20", path("short_codon_bug.vcf") };
		checkTranscriptError(args, ErrorWarningType.WARNING_TRANSCRIPT_INCOMPLETE);
	}

	@Test
	public void test_02() {
		Gpr.debug("Test");
		String args[] = { "-classic", "testHg3763Chr20", path("incorrect_ref.vcf") };
		checkTranscriptError(args, ErrorWarningType.WARNING_REF_DOES_NOT_MATCH_GENOME);
	}

}